[M T]

MT, sorry I was incorrect in stating the Cell paper with the most egregious problem was only two authors. It was the 1999 Cell paper on which he was a senior author.

Here is the figure-

The level of detail in the alteration also appeared to be intentional, she added. Some image manipulations in other Tessier-Lavigne papers are duplications, meaning the same western blot is used to represent different results, and researchers could conceivably use the same image twice by mistake. “If they had reused the same blot, you could argue negative blots all look the same, we just grabbed the wrong blot,” said Bik. In this figure, though, parts of a single western blot have been copied and appear multiple times.

https://www.statnews.com/2022/11/30/stan...ed-images/

As I mentioned earlier Bik did work at Stanford previously. There is no public knowledge I'm aware of that points to any axe to grind, and it seems strange to make that the thrust of a defense for MTL. It's not like MTL is the only or first person Bik has identified as authoring an article with manipulated figures.

First off, I am not setting out to defend MTL.  I have no reason to defend or attack him. AFAIK, he's had no direct impact on me.  I will say that I respect the fact that he is the Stanford President -- he likely has done something well.

I still haven't seen you quote anything from PubPeer, so I'll keep referring to it since that seems where most such issues are raised & considered, rather than news sources.  For that 1999 paper, concerns were raised on PubPeer in 2015.    Cell magazine has published (Dec. 2022) a statement that in 2015, these issues were considered by Cell and the decision was to take no action.  A portion of that statement reads

We decided, based on information available, to take no further action because in 1999 we did not have policies prohibiting the unmarked splicing of images

This is about image 3A in the paper.  Just to clarify to others, the image linked above was not the image from the paper, but the image edited by Bik (and I believe reproduced in a news article).  Indeed, in PubPeer, Bix has a newer version of her version of image 3A.  The concerns acknowledged by Cell is that some areas are duplicated in this image, which is not mentioned as something they noticed in 2015.  Cell does not indicate whether the authors were among those that brought the concerns to Cell's attention. Stanford sources indicate that MTL did contact Cell.

Here is the image as I see it in my web browser from the original paper on the Cell website.
https://i.ibb.co/hCPLtSb/MTL1999-3-A-web.png
The areas in question look almost pure white.  That doesn't mean that they weren't manipulated somehow, but that the end result was basically white.

Ok, maybe the web display isn't good enough to show what's going on.  I downloaded the PDF version, zoomed it to 200% and again took a screen shot.
https://i.ibb.co/hV7fCmS/MTL1999-3-A-pdfx2.png
Still almost pure white.

Ok, let's try downloading the powerpoint and zooming it to 300% and again take a screen dump.
https://i.ibb.co/6vSc4T9/MTL1999-3-A-pptx3.png
Aha, I can spot some noise in the pure white.

Why aren't we seeing what was in the Bix version of this image?  I suspect software was used to dramatically increase the contrast to bring out patterns in the lower order bits of the colors.

If this particular image is your concern, all I can say is "Big deal".   The person that created this should not have duplicated virtually pure white areas and pasted it over virtually pure white areas.  But, I can see how a person might not realize that overlaying one white area with another white area might be a big No-No and cause someone to consider it to be fraud.   For the purposes of science, it shouldn't have been done.  It *could* hide something nefarious, but what could possibly be in that column that would invalidate the results?

As for anyone other than the person that prepared/manipulated the image files to go into the paper, I can't see anyone, coauthor or reviewer, possibly spotting that manipulation by eyeball, especially if they expect the regions to be nearly purely white.   Even in 2015, the commenters did not notice the duplication in this figure.

Was there duplication of regions?  If I trust Bix to be honest and the software not to be broken, then probably there was.  Does it invalidate the results?  Personally I think not, but I'll leave it to Cell and that community.  Is this duplication fraudulent?  Flatly, no.

Do I think Bix is making a mountain out of a mole hill?  Yes. Bix's first post is 7 years after the previous comments. Somehow these immediately wound up as news articles rather than hashing the issues out technically.


[In case someone in the future can detect it, I had to go through and get rid of all the doubled & quadrupled lines that MyBB puts in when you edit/preview a post, at least with my browser & OS. I wouldn't want someone saying I fraudulently altered the whitespace (sorry, for the questionable technical term) ;-]

[M T]

MT, sorry I was incorrect in stating the Cell paper with the most egregious problem was only two authors. It was the 1999 Cell paper on which he was a senior author.

Here is the figure-

The level of detail in the alteration also appeared to be intentional, she added. Some image manipulations in other Tessier-Lavigne papers are duplications, meaning the same western blot is used to represent different results, and researchers could conceivably use the same image twice by mistake. “If they had reused the same blot, you could argue negative blots all look the same, we just grabbed the wrong blot,” said Bik. In this figure, though, parts of a single western blot have been copied and appear multiple times.

https://www.statnews.com/2022/11/30/stan...ed-images/

As I mentioned earlier Bik did work at Stanford previously. There is no public knowledge I'm aware of that points to any axe to grind, and it seems strange to make that the thrust of a defense for MTL. It's not like MTL is the only or first person Bik has identified as authoring an article with manipulated figures.

First off, I am not setting out to defend MTL.  I have no reason to defend or attack him. AFAIK, he's had no direct impact on me.  I will say that I respect the fact that he is the Stanford President -- he likely has done something well.

I still haven't seen you quote anything from PubPeer, so I'll keep referring to it since that seems where most such issues are raised & considered, rather than news sources.  For that 1999 paper, concerns were raised on PubPeer in 2015.    Cell magazine has published (Dec. 2022) a statement that in 2015, these issues were considered by Cell and the decision was to take no action.  A portion of that statement reads

We decided, based on information available, to take no further action because in 1999 we did not have policies prohibiting the unmarked splicing of images

This is about image 3A in the paper.  Just to clarify to others, the image linked above was not the image from the paper, but the image edited by Bik (and I believe reproduced in a news article).  Indeed, in PubPeer, Bix has a newer version of her version of image 3A.  The concerns acknowledged by Cell is that some areas are duplicated in this image, which is not mentioned as something they noticed in 2015.  Cell does not indicate whether the authors were among those that brought the concerns to Cell's attention. Stanford sources indicate that MTL did contact Cell.

Here is the image as I see it in my web browser from the original paper on the Cell website.
https://i.ibb.co/hCPLtSb/MTL1999-3-A-web.png
The areas in question look almost pure white.  That doesn't mean that they weren't manipulated somehow, but that the end result was basically white.

Ok, maybe the web display isn't good enough to show what's going on.  I downloaded the PDF version, zoomed it to 200% and again took a screen shot.
https://i.ibb.co/hV7fCmS/MTL1999-3-A-pdfx2.png
Still almost pure white.

Ok, let's try downloading the powerpoint and zooming it to 300% and again take a screen dump.
https://i.ibb.co/6vSc4T9/MTL1999-3-A-pptx3.png
Aha, I can spot some noise in the pure white.

Why aren't we seeing what was in the Bix version of this image?  I suspect software was used to dramatically increase the contrast to bring out patterns in the lower order bits of the colors.

If this particular image is your concern, all I can say is "Big deal".   The person that created this should not have duplicated virtually pure white areas and pasted it over virtually pure white areas.  But, I can see how a person might not realize that overlaying one white area with another white area might be a big No-No and cause someone to consider it to be fraud.   For the purposes of science, it shouldn't have been done.  It *could* hide something nefarious, but what could possibly be in that column that would invalidate the results?

As for anyone other than the person that prepared/manipulated the image files to go into the paper, I can't see anyone, coauthor or reviewer, possibly spotting that manipulation by eyeball, especially if they expect the regions to be nearly purely white.   Even in 2015, the commenters did not notice the duplication in this figure.

Was there duplication of regions?  If I trust Bix to be honest and the software not to be broken, then probably there was.  Does it invalidate the results?  Personally I think not, but I'll leave it to Cell and that community.  Is this duplication fraudulent?  Flatly, no.

Do I think Bix is making a mountain out of a mole hill?  Yes. Bix's first post is 7 years after the previous comments. Somehow these immediately wound up as news articles rather than hashing the issues out technically.


[In case someone in the future can detect it, I had to go through and get rid of all the doubled & quadrupled lines that MyBB puts in when you edit/preview a post, at least with my browser & OS. I wouldn't want someone saying I fraudulently altered the whitespace (sorry, for the questionable technical term) ;-]