On 2017 Jun 09, M Mangan commented:

There has now been an EFSA review of the paper, with an eye towards regulatory aspects in the EU. They describe the work as incomplete and with "severe shortcomings".

http://onlinelibrary.wiley.com/doi/10.2903/sp.efsa.2017.EN-1249/abstract

On 2017 Jan 03, M Mangan commented:

There have now been some really good summaries of issues with this work.

Is GM corn really different to non-GM corn? http://sciblogs.co.nz/code-for-life/2016/12/31/gm-corn-really-different-non-gm-corn/

What are isogenic lines and why should they be used to study GE traits? http://themadvirologist.blogspot.com/2017/01/what-is-isogenic-line-and-why-should-it.html

Another: http://biobeef.faculty.ucdavis.edu/2017/01/03/i_would_appreciate_your_comments/

On 2016 Dec 22, M Mangan commented:

The top fold change showed in this paper turns out to be a plant pathogen protein, that might have been affecting the maize. http://www.uniprot.org/uniprot/W7LNM5

If that is the case, it may demonstrate the power of -omics in revealing that the claims of differences have to be evaluated very carefully. They may not be what the authors claim they are.

We await some explanation of this large difference between samples from the authors.

Edit to add: The author Mesnage asked me to post questions at the journal site, but is not coming over to answer them. Maybe the authors will find them here, so I'll also add them here as well.

There's a lot of nonsense drama below now, but I want to hear from the authors (Robin Mesnage asked me to post here, but I can't see if he's responding):

1. What is your explanation for the fact that top fold-change proteins in your data set are fungal proteins (and it's a known maize pathogen)?

2. Are you aware that fungal contamination could result in similar changes in regards to the pathway changes that you describe? Did you consider this at all? Why didn't you address this in your paper?

3. If you wish to dismiss your own top reported proteins, how can you stand by the importance of the fold-change claims you are making about other proteins?

Thanks for your guidance on this. It's very perplexing.

On 2016 Dec 22, M Mangan commented:

The top fold change showed in this paper turns out to be a plant pathogen protein, that might have been affecting the maize. http://www.uniprot.org/uniprot/W7LNM5

If that is the case, it may demonstrate the power of -omics in revealing that the claims of differences have to be evaluated very carefully. They may not be what the authors claim they are.

We await some explanation of this large difference between samples from the authors.

Edit to add: The author Mesnage asked me to post questions at the journal site, but is not coming over to answer them. Maybe the authors will find them here, so I'll also add them here as well.

There's a lot of nonsense drama below now, but I want to hear from the authors (Robin Mesnage asked me to post here, but I can't see if he's responding):

1. What is your explanation for the fact that top fold-change proteins in your data set are fungal proteins (and it's a known maize pathogen)?

2. Are you aware that fungal contamination could result in similar changes in regards to the pathway changes that you describe? Did you consider this at all? Why didn't you address this in your paper?

3. If you wish to dismiss your own top reported proteins, how can you stand by the importance of the fold-change claims you are making about other proteins?

Thanks for your guidance on this. It's very perplexing.

On 2017 Jan 03, M Mangan commented:

There have now been some really good summaries of issues with this work.

Is GM corn really different to non-GM corn? http://sciblogs.co.nz/code-for-life/2016/12/31/gm-corn-really-different-non-gm-corn/

What are isogenic lines and why should they be used to study GE traits? http://themadvirologist.blogspot.com/2017/01/what-is-isogenic-line-and-why-should-it.html

Another: http://biobeef.faculty.ucdavis.edu/2017/01/03/i_would_appreciate_your_comments/

On 2017 Jun 09, M Mangan commented:

There has now been an EFSA review of the paper, with an eye towards regulatory aspects in the EU. They describe the work as incomplete and with "severe shortcomings".

http://onlinelibrary.wiley.com/doi/10.2903/sp.efsa.2017.EN-1249/abstract