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closeResults of this study challenged in Mol. Cell. Proteomics
Posted by Apis_mellifera on 19 Jan 2011 at 00:08 GMT
I have just written a point-by-point technical response to this work that can be found at Mol. Cell. Proteomics: http://www.mcponline.org/
Leonard Foster
RE: Results of this study challenged in Mol. Cell. Proteomics
jdevans replied to Apis_mellifera on 20 Jan 2011 at 17:45 GMT
Thanks for the clear analysis, Leonard. Knowing the authors, in my opinion this was an honest mistake caused by querying a much reduced database, and thereby falling into the well known trap of False Discovery.
Your results are supported by the associated Army report (now available by email request to CBRN@conus.army.mil for ECBC publication TR-814). This longer document includes the Query database (as Appendix A). As you infer in your reanalysis, this database was composed of honey bee viral RNA's, and (mostly) IIV-6 peptides from the moth, along with a small set of Nosema protein-coding genes and some oddities (including one nematode protein and the vasa protein of a Brazilian stingless bee, which were subsequently 'found' in sampled U.S. bees). You make a good case that, had the peptidic spectra been used to query a database inclusive of honey bee proteins, the results would be quite different.
Even if, as seems more likely, a new virus was not found in this study, the raw peptidic data are presumably sound and would likely be a treasure for those wishing to mine for bee proteins or other microbes. Also the bioassays involving moth IIV with and without Nosema are solid and give credence to interactive effects among viruses and fungi.
Jay Evans
RE: RE: Results of this study challenged in Mol. Cell. Proteomics
jdevans replied to jdevans on 24 Jan 2011 at 21:01 GMT
Thank you much for the reply Dr. Bromenshenk,
I agree there will be more discoveries in the raw data, hints of which were given by Dr. Wick at the recent National Beekeeping meeting (from human skin cells to gonnorhea and thermophiles along with the known bee microbes). As requested by several scientists at that meeting, releasing these data as RAW or DTA files seems like the best thing to do if you wish to give this study 'legs' whether the iridovirus story holds up or not. I'll repeat that such data would be a treasure when it is available to the public (and key if you address the challenges in Dr. Foster's peer-reviewed MCP article).
Until then, your high-profile PlosOne paper argues for discovery and quantitative results which now appear to be based upon peptidic searches against a quite small database (Appendix A in Army report TR-814). Could you please confirm that the results in this paper (specifically Tables 1-3 and Figs 1 and 2) reflect queries of Appendix A in TR-814, or were they against a more complete database?
All the best and thanks for the dialogue,
Jay
RE: Results of this study challenged in Mol. Cell. Proteomics
beeresearch replied to Apis_mellifera on 21 Jan 2011 at 20:07 GMT
The US Army proteomics team is preparing their point by point response to Drs Evans and Foster. We will ask the journal that posted Foster's comments to post the Army's response to his critique.
We note that an Excel spreadsheet of the results used in our paper was provided to the editors of PloS ONE and to Drs. Evans and Foster, as well as the Army's Technical Report which now has been approved for clearance and has been printed.
These documents include only the data used in the analysis for the PLoS ONE paper, not the entire data set. We did see bee proteins and peptides, hundreds of plant pathogens, and an assortment of other insect and mammalian pathogens, such as one might expect to find when mice invade a colony. We are working on additional papers related to these discoveries and that part of the data set.
RE: RE: Results of this study challenged in Mol. Cell. Proteomics
jdevans replied to beeresearch on 31 Jan 2011 at 21:13 GMT
Thank you much for the reply Dr. Bromenshenk,
I agree there will be more discoveries in the raw data, hints of which were given by Dr. Wick at the recent National Beekeeping meeting (from human skin cells to gonnorhea and thermophiles along with the known bee microbes). As requested by several scientists at that meeting, releasing these data as RAW or DTA files seems like the best thing to do if you wish to give this study 'legs' whether the iridovirus story holds up or not. I'll repeat that such data would be a treasure when it is available to the public (and key if you address the challenges in Dr. Foster's peer-reviewed MCP article).
Until then, your high-profile PlosOne paper argues for discovery and quantitative results which now appear to be based upon peptidic searches against a quite small database (Appendix A in Army report TR-814). Could you please confirm that the results in this paper (specifically Tables 1-3 and Figs 1 and 2) reflect queries of Appendix A in TR-814, or were they against a more complete database?
All the best and thanks for the dialogue,
Jay