Following the Lindau elogy there is a new Südhof paper in Neuroscience.
The biggest issue? Undisclosed self-interest. Südhof opens by admitting his own lab is under PubPeer scrutiny, then analyzes PubPeer as if providing neutral commentary. This is never adequately acknowledged as the primary driver of the piece. His attack on PubPeer commentors for income-dependent bias applies with greater force to himself.
The “income” claim misrepresents PubPeer’s structure. The assertion that PubPeer’s key proponents base their livelihood on comment success conflates a handful of individuals with the platform as a whole. PubPeer is a registered non-profit. The overwhelming majority of commentors are anonymous volunteers – I know only of a few exceptions Bik/Patreon, David/Dana Farber or Oransky/service fees. The characterization implies a structural commercial incentive that does not exist institutionally. Verdict – clearly wrong.
The Occam’s razor argument is logically invalid. He argues: if you wanted to fake a Western blot, you’d just load fake samples rather than manipulate images – therefore image manipulation is less likely. This is not my empirical experience: Image manipulation happens to rescue weak signals, fix failed loading controls, save time. The existence of an allegedly simpler path to fraud does not preclude the actual path taken. Applied consistently, this reasoning exculpates most detected fraud by construction.
“Minor issues with no bearing on main findings” is asserted without evidence. He repeats the Lindau argument as if established. The opposite is frequently documented: duplicated Western blots in result-critical panels, reused patient data across trials presented as independent cohorts, fabricated dose-response curves. No data are provided on PubPeer’s false positive rate, proportion of retractions later shown unjustified, or what fraction of flagged issues were peripheral vs. central to conclusions. Verdict – not a scientific argument
The proposed alternatives? Just a return control to the same failed system? eLife comments, Nature “Matters Arising”, and BioRxiv comments require formal authorship and pass through editorial gatekeeping by the same journals that sat on integrity concerns for years before PubPeer forced action. The history of that institutional failure is the reason PubPeer exists, and it goes entirely unaddressed.
Where Südhof is right. The description of the author-journal power imbalance is accurate and underappreciated. Journals recruit reviewers for free, make unilateral acceptance and retraction decisions, collect open-access fees, and provide authors no due process. A paper can be retracted without the authors having any formal right of appeal. COPE guidelines nominally govern this process but confer authority on journals, not authors.
(with AI support)