The World's Biggest Scientific Journal Suspended From PubMed: What Went Wrong?

Summary

The presenter argues that the suspension of Scientific Reports from new PubMed indexing is a serious warning about the journal’s quality control. The National Library of Medicine is reviewing the journal’s status. Articles already indexed remain in PubMed, but newly published papers are not being added while the review is underway.

To illustrate his concerns, the presenter examines papers published in Scientific Reports and points to what he describes as signs of image manipulation, fabrication, or inadequate review. His examples span several fields:

• Duplicated or reused images: In studies of cancer cells, mouse tissues, tumors, plants, nanoparticles, bacteria, shrimp, and rock formations, he highlights image regions that appear identical or overlapping despite being presented as different samples or experimental conditions.
• Possible image editing: He points to apparent copy-and-paste boundaries, repeated image fragments, and scribbles or other unexplained marks in figures.
• Questionable scientific content: Examples include a network diagram with no gene labels, implausible UV spectra, a screenshot that appears to include browser tabs and the Windows taskbar, and a diagram depicting a bacterial cell with mitochondria.
• Concerns about data and methods: He questions whether a small Kaggle dataset of 30 records could support the claims made for a proposed strabismus diagnostic system. He also describes alleged fabricated “comet analyses” and nonsensical AI-generated scientific diagrams.

The presenter says editorial responses have been inconsistent. Some papers were corrected, retracted, or withdrawn, while others remained unchanged or received corrections that he considers unclear or incomplete. He also describes reporting concerns to the journal and says that, in several cases, he saw no meaningful action for an extended period.

How the presenter assesses the papers

The presenter describes several methods he uses to examine the papers:

• Inspect figures for images that are supposed to represent different samples or conditions.
• Crop, align, rotate, mirror, or adjust the brightness and contrast of image regions to compare them.
• Look for matching fragments, repeated patterns, editing boundaries, or other signs that images may have been reused or altered.
• Check whether figures and diagrams are interpretable and scientifically plausible.
• Compare images across papers and journals, and examine cited datasets to assess whether they seem adequate for the study’s claims.

These checks are presented as the presenter’s analysis and allegations, not as independent verification of every case.

Broader criticism and implications

The presenter argues that many of the problems he describes are conspicuous enough that competent reviewers or editors should have noticed them. He criticizes Scientific Reports for what he sees as reactive and inconsistent post-publication oversight, including not proactively tracking concerns raised on PubPeer. He says the burden often falls on outsiders to report problems one by one.

He also contrasts these examples with the journal’s public claims about rigorous peer review and high-quality research. The video notes that a 2024 open letter raised concerns about the journal, and that the presenter later reviewed its 2025 output and continued to identify papers he considered problematic. He does not claim these criticisms caused the PubMed suspension, but argues that the journal had been warned about quality concerns.

Finally, the presenter describes Scientific Reports as a major revenue source for Springer Nature, citing its high article-processing charge and large publication volume. He questions whether authors will continue submitting if the journal loses indexing or reputation, and suggests that the PubMed review could pressure the journal to change its practices.

Speakers and sources featured

• Speaker: The video’s presenter, Sholto David.
• Named reporting, commentary, and oversight sources: Retraction Watch; the U.S. National Library of Medicine and PubMed/Medline; Dorothy Bishop’s blog and the open letter published there; Chris Graff of Springer Nature, quoted via Chemistry World; PubPeer; and Smut Clyde’s For Better Science blog.
• Other sources and venues discussed: Kaggle; Bluesky; Scientific Reports and Springer Nature; and comparison journals including Nano Letters, Frontiers, Plants (MDPI), and BMC Complementary Medicine and Therapies.
• The video also discusses papers by research teams associated with institutions including the University of Pennsylvania and Stanford. These researchers are presented as authors of the papers, not as speakers in the video.