Caught Our Notice: Doesn’t anyone do a literature review any more?

Via Wikimedia

Titles: (1) Whole-Genome De Novo Sequencing of the Lignin-Degrading Wood Rot Fungus Phanerochaete chrysosporium (ATCC 20696)

(2) Structure revision of aspergicin by the crystal structure of aspergicine, a co-occurring isomer produced by co-culture of two mangrove epiphytic fungi

What Caught Our Attention: Two articles by different groups of authors recently suffered from the same (fatal) flaw: A poor literature review. The article, “Whole-Genome De Novo Sequencing of the Lignin-Degrading Wood Rot Fungus Phanerochaete chrysosporium (ATCC 20696),” claimed to have sequenced a strain already sequenced in 2004 and published in a well-cited article.  According to Clarivate Analytics’ Web of Science, the 2004 article was cited 474 times before the now-retracted article was published. And that 2004 article appeared in a highly-cited journal, Nature Biotechnology.

The article, “Structure revision of aspergicin by the crystal structure of aspergicine, a co-occurring isomer produced by co-culture of two mangrove epiphytic fungi” claimed to have determined the crystal structure of aspergicine, which had already been reported in 2008 in the Journal of Organic Chemistry. Although the 2008 article was only cited 37 times, the Journal of Organic Chemistry, like Nature Biotechnology, is also a highly cited journal.

Both seem like a good reminder to check — and then re-check — that you’ve done a proper literature review.

Journal: 1) Genome Announcements, 2) Journal of Organic Chemistry

Authors: 1) Chang-Young Hong, Su-Yeon Lee, Sun-Hwa Ryu, Sung-Suk Lee, Myungkil Kim

2) Feng Zhu, Jie-sen Li, Wu-cheng Xie, Jun-jun Shi, Feng Xu, Zhao-feng Song, Yi-lu Liu

Affiliations: 1) National Institute of Forest Science, South Korea 2) Foshan University, China

The Notices:

Whole-Genome De Novo Sequencing of the Lignin-Degrading Wood Rot Fungus Phanerochaete chrysosporium (ATCC 20696):

The publisher hereby retracts this manuscript. After the manuscript was published, it came to our attention that the sequence of the same strain was previously reported (1). We apologize to the readers of Genome Announcements and regret any inconvenience this causes.

(1)Martinez D, Larrondo LF, Putnam N, Sollewijn Gelpke MD, Huang K, Chapman J, Helfenbein KG, Ramaiya P, Detter JC, Larimer F, Coutinho PM, Henrissat B, Berka R, Cullen D, Rokhsar D. 2004. Genome sequence of the lignocellulose degrading fungus Phanerochaete chrysosporium strain RP78. Nat Biotechnol 22:695–700. 10.1038/nbt967.

Structure revision of aspergicin by the crystal structure of aspergicine, a co-occurring isomer produced by co-culture of two mangrove epiphytic fungi:

Subsequent to publication it has been determined that the crystal structure of aspergicine was previously reported as Circumdatin B in the following article:

Ryuhei Ookura, Keijiro Kito, Takshi Ooi, Michio Namikoshi & Takenori Kusumi, ‘Structure Revision of Circumdatins A and B, Benzodiazepine Alkaloids Producted by Marine Fungus Aspergillus ostianus, by X-ray Crystallography, Journal of Organic Chemistry, 73 (11), 4252 – 4247, DOI: 10.1021/jo800348d

Date of Articles:  1) August 2017  2) March 2017

Times Cited, according to Clarivate Analytics’ Web of Science:  1) Journal not indexed 2) Once

Date of Notices: 1) November 16, 2017  2) January 8, 2018

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12 thoughts on “Caught Our Notice: Doesn’t anyone do a literature review any more?”

  1. In a way it is nice to see findings reproduced, as a lot of scientific results are never even attempted to be reproduced, since no one wants to publish “old” news.

  2. I’m a librarian. People definitely don’t do literature reviews. Or when they do, they call it a systematic review even when it isn’t.

  3. I’ve been reading this blog for years but haven’t commented until now – is this title a play on Kanye West’s “Do anybody make real sh!t anymore?”? A good Kayne West reference is basically the only thing that ever gets me to unlurk.

    Also, as a librarian I’m 100% with Amanda. I can’t even count the number of times I’ve screamed NARRATIVE REVIEWS ARE NOT SYSTEMATIC REVIEWS into the void.

  4. Retraction seems completely unwarranted. The papers still present sound results, even if they are not novel. In the genome case, having two sequences could provide an insight into the genetic diversity within the strain; there may have been novel insights presented in the analysis and discussion. In the crystal structure case, another structure may give a better, more robust, picture of the protein’s structure. A correction or editorial notice would certainly be in order, but not a retraction.

    Also, this is a major failure not of lab management (the article seems to assume they embarked on these major projects without looking at the literature–but I think maybe they were actually scooped and just slow to publish) but of peer reviewers, who should know there were already prominent papers showing these results and suggested citing and comparing the new results with the old papers.

  5. re: the retraction in (1), hasn’t sequencing and assembling technology improved a lot since 2004, and in particular could the new data be of better quality? (otoh, just googling–not even google scholaring–for “Phanerochaete chrysosporium genome” comes up with plenty of hits)

  6. I am with Nahhf. It was a waste of time and effort to triplicate the job, but should not have been retracted, unless it was plagiarism (which could have easily been checked). Apart from the reasons mentioned by Nahhf and Jake it would allow to inspect and compare the quality and reproducibility of this kind of work. I hope the papers can be un-retracted again.

  7. I also don’t see why a study that replicates previous work should be retracted – in other fields people are worrying the inability to publish replications, and poorly supported results standing because of this – except that in an ideal world they would have cited the previous work, and discussed any differences in the results within the discussion section of the paper. I can see a case for a correction being arguable in these instances.

  8. Yes, it is precious that a result was reproduced. However, the author were not aware of the existing result, which leaves us readers a mixed feeling: Did they plagiarize the previous research, or just overlook it? After all, it is difficult to exclude the former possibility because one feature of plagiarism is that “I steal your idea, whether it was published or not, and represent it as my innovation”. I think the decisions of retraction were based on this reasoning.

    It is really a waste to retract such reproducible results. These retractions seem a punishment to the authors. In fact, both sides of authors and editorial offices did not do their good job to find out such duplications without citing the existing data in the same journals. So, such retraction should also be regarded as a punishment to the journals/editorial teams. The only difference is, a retraction has immediate impacts on the authors, but the cost for the jourmal/editor is almost indirect and small.

    One question is left: Could this couple of papers have escaped such death sentences if they were published on the other journals?

  9. This is a case when corrections were warranted, not retractions. Yes, the authors earned some embarrassment for lax literature reviews, but if the underlying experimental work was sound, this is a blow to the reproducible science effort. These incidents do not reflect well upon the American Society of Microbiology or Taylor and Francis.
    Another excellent post from the RW staff.

  10. In the case of the natural products, it points out a little-recognized problem in the field with nomenclature. Using scientific names is not practical leading to unwieldy names, but each group just invents a name and slaps it on to a molecule making it difficult to trace. There seems to be little effort to adopt names other groups have used and expand in the series even when it is recognized that the structures bear strong resemblances.

    I agree that the papers should not be retracted, but corrected to acknowledge that it is not novel and add a citation to the original work.

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