Debunking Denialism

Defending science against the forces of irrationality.

Extensive Plagiarism Found in Yeastbook Initiative

Plagiarism in Genetics Journal

Scientific misconduct occurs when a scientist fabricates or falsifies data, plagiarizes previous writing or other questionable research practices. These behaviors damage science in many ways, from contributing to flawed decisions on the efficacy of treatments to hurting the credibility of the scientific community in the eyes of the public. Therefore, exposing scientific misconduct is extremely important in order to safeguard the accuracy of scientific data and credibility for scientific projects. Debunking Denialism was recently provided with evidence from a reader that the renowned scientific journal Genetics published a paper in their Yeastbook Initiative that contains several large paragraphs that were plagiarized from a previous publication by the two authors and one additional colleague. Because scientific integrity is so incredibly vital, this evidence is posted here in full.

Genetics is the journal of the Genetics Society of American and their Yeastbook project is intended as a “comprehensive compendium of reviews that presents the current state of knowledge of the molecular biology, cellular biology, and genetics of the yeast Saccharomyces cerevisiae” (Hinnebusch and Johnston, 2011), which is one of the most important model organisms in all of biology. The Yeastbook review paper in question, which concerns the molecular biology of budding yest nucleus, is Taddei and Gasser (2012). The original review paper that it plagiarizes is Taddei, Schober and Gasser (2010) published in Cold Spring Harbor Perspectives in Biology. This article presents a few of the more egregious examples that could be found in Taddei and Gasser (2012) with the corresponding sections from Taddei, Schober and Gasser (2010).

Section on the nuclear envelope / nuclear pore complex

The first example of plagiarism comes from the first paragraph in the section “Nuclear envelope and nuclear pore complex” in Taddei and Gasser (2012). This is pretty much word-for-word identical to the corresponding paragraph in the “Nuclear Envelope Associated Proteins and the Nuclear Pore Complex” section from Taddei, Schober and Gasser (2010).

Taddei and Gasser (2012) Taddei, Schober and Gasser (2010)
Trafficking between the nucleoplasm and the cytoplasm occurs through ∼200 NPCs, which enable the free diffusion of small molecules as well as the regulated transport of macromolecules by the importin machinery (Alber et al. 2007; D’Angelo and Hetzer 2008; Aitchison and Rout 2012). Intriguingly, NPCs provide a platform for messenger RNA (mRNA) transcription and quality control, as well as its export, [...] Trafficking between the nucleoplasm and the cytoplasm occurs through approximately 200 nuclear pore complexes (NPCs), which allow the free diffusion of small molecules, whereas regulating the transport of macromolecules. NPCs also provide a platform for mRNA transcription and quality control, as well as its export.

The plagiarism is pretty lazy and not exactly subtle. In this section, “approximately” was change to “~” and NPCs was written out instead of using the abbreviation. A similar thing happened with messenger RNA. The second example occurs a few sentences later:

Taddei and Gasser (2012) Taddei, Schober and Gasser (2010)
They form a doughnut-shaped structure with an eightfold symmetry around a central channel, with flexible protein filaments emanating from the core into both the cytoplasm and the nucleoplasm. These provide binding sites for the transport of proteins, mRNA, and chromatin. A detailed map for the relative position of each nucleoporin was calculated on the basis of multiple molecular, biochemical, and structural data revealing a strongly modular structure (Alber et al. 2007). Each pore is a doughnut-shaped structure with eightfold symmetry around a central channel. Flexible protein filaments emanate from the core into both the cytoplasm and nucleoplasm, providing binding sites for both transport proteins and chromatin. A detailed map for the relative position of each nucleoporin was calculated based on multiple molecular, biochemical, and structural data revealing a strongly modular structure (Alber et al. 2007).

Instead of using a full stop, Taddei and Gasser (2012) decided to use a comma and then put together two sentences, effectively getting them a failing grade in creative scientific writing. The first example in this section looks like this:

Taddei and Gasser (2012) Taddei, Schober and Gasser (2010)
Of particular interest are the integral proteins of the INM (Lusk et al. 2007), including Doa10, a RING domain containing proteins that targets nuclear proteins for degradation; Mps3, a member of the SUN (Sad1, UNC-84) family that is a shared component of the INM and the SPB (Jaspersen et al. 2002); and helix–extension–helix-1 and -2 (Heh1 and Heh2) (M. C. King et al. 2006; Fridkin et al. 2009), which are orthologs of the mammalian lamin-associated protein MAN1 Of particular interest are the integral proteins of the inner nuclear membrane (INM) (Lusk et al. 2007) including: Doa10, a RING domain containing protein that targets nuclear proteins for degradation, Mps3, a member of the SUN (Sad1, UNC-84) family that is a shared component of the INM and of the spindle pole body (SPB; Jaspersen et al. 2002), and Helix–extension–helix-1 and -2 (Src1 or Heh1 and Heh2) (King et al. 2006), which are orthologs of the mammalian lamin associated protein MAN1.

It is intriguing that the text is not completely identical. For instance, notice that a semicolon has been removed before Doa10 in the 2012 paper compared with the 2010 one. So it is clear that they started with the 2010 text and ever so slightly modified it. Strange that the modifications are so small though, almost like they did it so that the text “looks better” instead of trying to hide the plagiarism.

Section on chromatin dynamics

More plagiarism can be found in the section on chromatin dynamics.

Taddei and Gasser (2012) Taddei, Schober and Gasser (2010)
Rapid time-lapse imaging led to the distinction of at least two types of motion in yeast: small random movements (0.5 µm in a 10.5-sec interval) (Heun et al. 2001b). Rapid time-lapse imaging led to the distinction of at least two types of motion in yeast: small random movements (0.5 µm in a 10.5 s interval) (Heun et al. 2001).

In this case, they gave up making minor changes and just used the entire sentences outright. A few paragraphs later, the authors return to their strategy of slightly modifying their text.

Taddei and Gasser (2012) Taddei, Schober and Gasser (2010)
In almost every eukaryotic nucleus, the most prominent subnuclear compartment is the nucleolus. In budding yeast, the nucleolus is a crescent-shaped structure occupying roughly one-third of the nuclear volume, abutting the NE and lying opposite the SPB (Yang et al. 1989; Bystricky et al. 2005). This compartment can be considered as a factory dedicated to ribosome biogenesis. Its morphology is strongly influenced by the cell growth rate, probably as a result of adapting the rate of ribosome production to the needs of the cell (Oakes et al. 1993; Powers and Walter 1999). The most evident subnuclear compartment is the nucleolus, a crescent-shaped structure abutting the nuclear envelope and occupying roughly one third of the nucleus opposite the spindle pole body (Yang et al. 1989; Bystricky et al. 2005). This subcompartment is the site of RNA pol I-mediated rDNA transcription and ribosome subunit assembly and can be seen as a factory dedicated to ribosome biogenesis. Its morphology is strongly influenced by the cell growth rate, probably as a result of adapting the rate of ribosome production to the needs of the cell (Oakes et al. 1993; Powers and Walter, 1999).

Section on nuclear compartmentation

Plagiarism does not just occur in the main body of the text, but also the figure texts (figure 4 in both papers).

Taddei and Gasser (2012) Taddei, Schober and Gasser (2010)
Parallel mechanisms lead to yeast telomere attachment at the nuclear envelope. At different stages of the cell cycle, the telomere-associated proteins mediate different contacts with INM components. Sir4-PAD domain binds the Esc1 C terminus, as well as Yku80 and Mps3. Yku80 binds telomerase, which also associates with Mps3 in S phase through Est1. There is an unidentified anchor for yeast Ku in G1 phase that is neither Esc1 nor Mps3 dependent. Parallel mechanisms lead to yeast telomere attachment at the nuclear envelope. At different stages of the cell cycle the telomere associated proteins mediate different contacts with inner nuclear membrane components. The Sir4-PAD domain binds the Esc1 C terminus, as well as yKu80 and Mps3. yKu80 binds telomerase, which also associates with Mps3 in S phase through Est1. There is an unidentified anchor for yKu in G1 phase that is neither Esc1- nor Mps3-dependent.

This was surprising, seeing how researchers often look at figures to get a feel for the content of a paper. Although there are more examples of plagiarism to be found in paper, the cases discussed above is sufficient to drive the central point home.

This most likely not a case of accidental plagiarism. There are several paragraphs are almost word-for-word identical, except in a few places where an abbreviation has been replaced by the full word, or a full stop being replaced by a comma. It is interesting to note that the abstract and the first introduction section is completely re-written. Maybe Taddei and Gasser (2012) started writing a fresh review, but then ran out of time? Another, more malevolent interpretation is that those sections worked as a shield to prevent the causal reader from noticing the plagiarism. After all, most scientists read the abstract and maybe scans the paper quickly to find out if the material is relevant for their own research project. Spotting this kind of plagiarism requires a more detailed reading of the paper. After all, the editors and reviewers of a renowned journal like Genetics did not catch it before publication or during the two years since the Yeastbook paper got published. Some might say that this is just self-plagiarism and thus not a big deal, but remember that there is a third author on the original paper as well.

There are many questions that remain unanswered. Why did the editor or reviewers at the journal not discover this? Why was the third author of the original paper (Schober) not on the Yeastbook review? Did this person discover the plagiarism and opted out? Now that this story has been broken, will the journal do anything about it?

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6 responses to “Extensive Plagiarism Found in Yeastbook Initiative

  1. Skeptek August 3, 2014 at 14:38

    It seems that the authors either didn’t think anyone would care, or that it somehow doesn’t matter that they’ve duplicated previous writings. It couldn’t be that they didn’t think anyone would notice – could it? Very strange.

    BTW…
    When you write “renounced scientific journal Genetics”, do you mean “renowned”? Otherwise, I can’t tell what you mean.

    The phrase is “ever so slightly”, not “every so slightly”.

    No offense, but proof-reading is a virtue that I truly wish you would embrace. These little errors are very common on this blog, quite distracting to the reader, and take away from the otherwise excellent quality of your work.

  2. Criticaldragon1177 August 4, 2014 at 02:59

    Emil Karlsson,

    The people who perpetrated this ought to be ashamed of themselves.

    • Emil Karlsson August 4, 2014 at 08:32

      They might be able to get out of trouble by arguing that it was merely self-plagiarism, but there is a third author on the original paper so it wouldn’t be as simple.

  3. Erin Branscome August 11, 2014 at 19:29

    I’m sorry if this is a stupid question, but why is it such a big deal if they plagiarized themselves? It’s lazy, sure, but it’s not like they stole someone else’s work…why is it considered fraud?

    • Emil Karlsson August 11, 2014 at 20:35

      First, the original paper had three authors, so it is technically plagiarism above and beyond mere self-plagiarism. Second, all forms of plagiarism goes against core research ethical principles. Third, it can often be a copyright issue if the original paper is published in a non-open access journal.

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