PubPeer – a website to comment on scientific papers

If you are interested in scientific integrity, you will probably know PubPeer, a website where you can leave anonymous or signed comments on scientific papers.

PubPeer was launched in late 2012 by neuroscientist Brendon Stell and brothers Richard and George Smith, with Boris Barbour and Gabor Brasnjo acting as advisers. At the start, the founders and advisers were anonymous, but they revealed their identity in 2015.

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Human Photosynthesis

Unfortunately, several angry Twitter users pointed out it was insensitive of me and irrelevant to mention the country where the Human Photosynthesis Study Center scientists are located. I am confused about this, but I do not want to be insensitive. It appears it is OK to mention most countries but not certain others. I will just try to continue to be an equal-opportunity science integrity detective.

Yesterday, Twitter user @Arroboso pointed out research on “Human Photosynthesis” through this tweet.

Of course I was curious. Last time I checked, humans are not capable of photosynthesis. Instead, I learned that humans are heterotrophs, organisms that rely on eating other organism to get their energy from.

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Three diets, three papers, one retraction, and lots of concerns

Note: this post is not an allegation of misconduct. I do not have any strong feelings about low- or high-carb diets.

This post tells the tale of three paper. Paper #1 was retracted, republished as paper #2, and republished a second time as paper #3. Let’s take a look at what happened. Based on an original Twitter thread on Twitter and on ThreadReaderApp.

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Falsification: The Andrew Wakefield case

The Andrew Wakefield case

One of the best-known examples of data falsification is a study described in a 1998 Lancet paper with Dr. Andrew Wakefield as the lead author. In this paper, 12 children with autism and chronic enterocolitis were described, and these symptoms started immediately after MMR (Measles / Mumps / Rubella) vaccination in 8 of these children.

However, a 2004 investigation by Sunday Times reporter Brian Deer revealed concerning issues with patient recruitment and undisclosed financial conflicts of interest.

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Falsification: Haruko Obokata case

STAP treatment papers

Haruko Obokata was a researcher and laboratory head at the Japanese Riken Center for Developmental Biology. In 2014, she published 2 Nature papers (here and here) in which she described an acid treatment to turn somatic cells (mouse blood cells) into pluripotent stem cells, a method that she named “stimulus-triggered acquisition of pluripotency” or STAP.

Hours after publication, serious doubts about the validity of the paper were raised on Paul Knoepfler’s blog and PubPeer. Soon, people noticed similarities between photos in the Nature papers and those found in Obokata’s PhD thesis, in which these photos represented different experiments than those described in the Nature papers. In addition, no one was able to reproduce the STAP treatment, which just sounded too simple to be true.

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SkeptiCalCon 2019

A warm welcome on a warm day. Photo: Elisabeth Bik.

Sunday June 9, 2019, I attended the 10th SkeptiCalCon, a 1-day conference on science and skepticism. The event was sponsored by the Bay Area Skeptics (BAS) and the Sacramento Area Skeptics (SAS).

BAS and SAS remain focused on what (Carl) Sagan called “extraordinary claims” (which require “extraordinary evidence,” as his adage reminds us) but we also seek to improve the general public understanding of science and critical thinking. Scientific skepticism is independent of other movements which sometime also claim the term “skeptic.” Scientific skepticism can be embraced by all, whether religious or non-religious, trained in science or new to the scientific method, or anyone interested in better understanding truth and reality.

From the SkeptiCalCon website. Source:

The event was held in the Hyatt Regency hotel next to San Francisco International Airport. It was an unusually hot day and temperatures got pretty toasty in the Garden Pavilion. But it was a great conference.

The conference was held in the Garden Pavilion at the Hyatt Regency near SFO airport, just South of San Francisco. Photo: Elisabeth Bik.

Here is a summary of all the talks and activities. You can also read about it on Twitter using the hashtags #SkeptiCalCon or #SkeptiCal2019.

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False affiliations and fake authors

In this blog post I will talk about scientific papers that use false affiliations or fake authors.

What is an affiliation?

In scientific papers, the “affiliation” is the institute that each author belongs to. It is usually listed below the author names, as the “department, university” of the institute each authors worked at during the time that the study was conducted.

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The Sexpert papers

This blog post is not intended to be an allegation of misconduct. I am just wondering about unclear affiliations, findings, and ethics approval. Be aware that this post contains links to articles about sexual activities and suicide. These links are intended for mature audiences only and might contain sensitive material that is NSFW.

A Gizmodo article by Jennings Brown, published in March 2019, describes the curious case of The Fake Sex Doctor Who Conned the Media Into Publicizing His Bizarre Research on Suicide, Butt-Fisting, and Bestiality.

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World Conference on Research Integrity

The 6h World Conference on Research Integrity is currently happening in Hong Kong. You can follow all the tweets using the hashtag #WCRI2019. Thanks to many nice people who are live-tweeting from the conference, all of us who could not be there can still follow the conference from a distance.

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Surfing the water-DNA waves

A post about another “peer reviewed” paper published by World Scientific publishers (not included in any predatory publisher list that I could find). Based on this Twitter thread.

This paper is written by the same first author on the pregnancy/virus model from my previous post, a cardiology doctor from Rome. According to his website he “graduated with honors in Medicine and Surgery from the University of Rome “La Sapienza” and is now publishing under the affiliation of the Guglielmo Marconi University in Rome. 

The paper was published in the International Journal of Geometric Methods in Modern Physics – which seem to have a consistent problem with the quality of their peer review.

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