There's something I find slightly odd about Extended Data Fig. 2g. Most of the rightmost (4th) lane seems to be darker than the immediately adjacent background. The issue is just discernible with the naked eye, but I've adjusted levels and contrast to highlight it in this image:



Intuitively, I would have expected any signal simply to add to the background and therefore to increase the overall intensity. There are other variations in background of similar magnitude across the image (darker towards the bottom left), but the change at the edge of the 4th lane is rather sharp and well aligned with the lane.

#65

You mean this one, right?

Extended Data Fig. 2g, lane 2 and lane 3 are too similar.



This can happen? Any idea?

Two regions in Extended Data Fig. 2g seem to display very little noise. This can be seen in this processed version, in which a 'sharpen' operation slightly increases the noise and equalises the background, followed by a shadowing operation. The absence of noise gives a flat grey appearance.

#80

These are the images of different color channels. Compare red and green.

It is worth linking to a detailed discussion of the FACS experimental design posted by Jun Seita on Paul Knoepfler's blog:

http://www.ipscell.com/2014/03/guest-post-by-dr-jun-seita-a-simple-proposal-to-make-stap-protocols-clearer/

#122

His commentary is convoluted and not premised on much which would actually be helpful. The comments section of that blog allude to the faults.

#109

There is newspaper coverage of the Riken panel's news conference regarding their "final report" e.g.

http://www.japantimes.co.jp/news/2014/04/01/national/high-profile-stem-cell-papers-contain-fraudulent-parts-riken/

The report is not yet available in English at Riken.

There are apparently two clear examples of image manipulation that are tantamount to falsification. In the news coverage it is not stated which, though they appear to be gels.

It is not clear if the papers will be retracted. Obokata objects to the findings.

If the Riken report is available in Japanese if would be of interest to have an English translation posted. Or even a summary of the key points.

Before a press conference on the final report of investigation committee about STAP papers, RIKEN replaced the interim report of the investigation released on 15 Mar with a new version which deleted large parts of gel images on 31 Mar WITHOUT ANY NOTIFICATION, just a day before the press conference.

See pp.9-10: large parts of Gel 1 / Gel 2 images were deleted.

Original version on 15 Mar

http://web.archive.org/web/20140314222554/www.riken.jp/~/media/riken/pr/topics/2014/20130314_1/document-5.pdf

New version on 31 Mar
http://www.riken.jp/~/media/riken/pr/topics/2014/20130314_1/document-5.pdf

In the press conference on 1 Apr, the committee explained Obokata requested to delete the large parts of Gel 1 / Gel 2 as mentioned above because they were "unpublished data".

But some experts argue that Gel 1 seems to be an original version of a gel image in their application to international patent, Fig. 20.

http://patentscope.wipo.int/search/en/detail.jsf;jsessionid=D69EB75A5D6EF3620894BE3F2E2716BB.wapp2nA?docId=WO2013163296&recNum=1&tab=Drawings&maxRec=&office=&prevFilter=&sortOption=&queryString=

The Science piece about the retraction is quite interesting. The gel splice that was commented early on had been spotted by a referee at Science (who then rejected the MS).

http://www.sciencemag.org/content/344/6189/1215.full (sub required.)

https://research.bwhanesthesia.org/research-groups/cterm/stap-cell-protocol
Albeit the paper has been retracted, Prof. Vacanti opened a revised protocol for generating STAP cells. What's going on?

After carefully analyzing the partially "censored" Nature reviewer comments letter to Obokata in April 2013,
http://news.sciencemag.org/sites/default/files/NATURE%20REVIEWS.pdf

it appears that at that time, the editor in charge of communicating the editorial decision and reviewer's response might have been Francesca Cesari, Chief Biological Science Editor (see text comparisons and partially uncensored top "F" and side "a" in signature).


This partial evidence is supported by the fact that the same editor would later communicate the decision to reject Dr. Kenneth Ka-Ho Lee's unsuccessful attempt at "creating" STAP cells.
https://www.researchgate.net/publication/259984904_Stimulus-triggered_fate_conversion_of_somatic_cells_into_pluripotency/reviews/103

Regardless of who the editor(s) responsible to accept both STAP papers might be, the scientific community would gain in better understanding how these papers ended up being accepted in December 2013 despite serious concerns from reviewers in April 2013 (that were, for the most part, unanswered in the final version).

Mistakes by editor(s) can happen, but it can only be professionally acceptable if those editor(s) come clean with the scientific community as to what happened and provide solutions to prevent those mistakes, instead of pretending there is nothing they could have done to prevent such a debacle (which is what we are currently stuck with unfortunately):
http://www.nature.com/news/stap-retracted-1.15488

The big question is whether the referees ever saw and gave an opinion on the revised version of the manuscript. I know journals like Nature tend to review the impact more than the science, but to proceed to an editorial acceptance in the face of such initial reports would be truly shocking. Is it possible that a second round of reports have simply not yet come to light?

#130

That's the key question indeed! What happened in those 8 months? Did the authors address reviewers' criticism? It doesn't seem likely looking at what was eventually published. Did the editors choose new reviewers, who then gave positive comments? A rather weird editorial policy.
Did the editors sent the re-submitted paper to reviewers at all?
What we know is that in those 8 months someone at Nature became so confident in the study that even a related piece by an authoritative scientist (Austin Smith) was published: http://www.nature.com/nature/journal/v505/n7485/full/505622a.html
As pointed out above in a previous comment, Nature's editorial lied when writing that "editors and referees could not have detected the fatal faults in this work". This could be one of the first example of an editorial on two retracted papers to be retracted!

#115

In the recently published BCA in Nature (Konno et al E4 | NATURE | VOL 525 | 24 SEPTEMBER 2015), the authors demonstrate that intestine and pancreas tissue was GFP-negative from the host!

Demonstrations that STAP cells weren’t made have now been published by Nature in two BCA (brief communications arising) critiques.

http://www.nature.com/news/failed-replications-put-stap-stem-cell-claims-to-rest-1.18412

It is interesting that Nature will publish matters arising articles after the relevant paper is retracted, but not before. Does this policy only apply to stem cell papers?

Jacob Hanna tweets that social media was irrelevant to the STAP discovery process. Also that PubPeer used this opportunity for self-promotion. While it is likely the case that STAP was, for many researchers, their first introduction to PubPeer, I have no recollection that PubPeer went on a promotional binge. It is not of much import either way but we are scientists and should be factual so, in that regard, is there or is there not evidence of PubPeer self-promotion during the STAP scandal? Here is an image of the tweeting



The image was captured from this link

https://storify.com/cells_nnm/social-media-reaction-on-2-stap-refutation-papers-

#134

What is surprising is Dr. Hanna is an author in a new Nature paper, "Failure to replicate the STAP phenomenon" http://www.nature.com/nature/journal/v525/n7570/full/nature15513.html

OK, why is that a Nature publication, and why did we need this now? It's not a breakthrough or advance, people have established this. Dr. Lee was rejected from the very same journal, and already published it (F1000): http://www.ipscell.com/2014/05/perspectives-on-lee-lab-f1000-paper-that-stap-cell-method-does-not-work/

This seems like unethical favoritism by the journal, yet again on the same topic.

"is there or is there not evidence of PubPeer self-promotion during the STAP scandal?"

There was a blog post: http://blog.pubpeer.com/?p=117

#136

So there was - and still is. But is blogging on your own site self-promotion? My understanding of self-promotion is that this requires reaching out to those not already in the know (or who do know but have lost interest). Was there a press release, an email spam campaign, a cunningly engineered twitter storm?

#136

In the opinion of many, yes. It is ok to disagree.

#136

I do not think what was described above qualifies in any useful way. So I think it would be more convincing if you provided an example or explained. A useful definition of self-promotion should not be one that is inherent in the basic function of the website, i.e., a blog post, and links to the discussion. It would be distinct self-promotion if the major purpose of the discussion and dissemination of it were for the purpose of attention without other merits to the coverage, rather than it just being a hot topic covered in a normal manner. Without such, it is analogous to calling a publication in a real journal self-promotion. Technically all publications are, but it is generally not much of a stinging accusation.