Welcome to my personal web site
Letter to Nature - censored?
Following Nature's recent Damascene conversion, I sent the following letter, asking it to be considered for publication:
"Your editorial announcing measures to reduce irreproducibility is a welcome, if long overdue acknowledgement of the inadequate reporting of experimental detail in much of the peer-reviewed literature. However, your final sentence that exhorts “others to take note of … our initiatives, and do whatever they can to improve research reproducibility” is an obvious attempt to deflect attention away from the active disregard high impact factor journals such as Nature have shown in the past for this issue.
One area of particular concern has been the quantification of nucleic acids by real-time quantitative PCR (qPCR) and reverse transcription (RT)-qPCR, probably to-day’s most widely used molecular techniques. Their seeming simplicity and reliability is gainsaid by their actual complexity and inconsistency; in practice, this means that the biological relevance of many published qPCR-based results is open to question, with reported differences caused by technical, rather than actual variability. How do we know results are suspect? It is not credible to report a 1.5-fold difference in mRNA levels normalised against a single, unvalidated reference as significant. It is not possible to assess the validity of a comparison of mRNA levels in multiple samples when there is no information about its purity or integrity. It is not feasible to compare mRNA levels based on unknown PCR efficiencies.
These issues that have caused many of us to spend the last decade spelling out the inexcusable lack of transparency especially prevalent in high impact factor journals and stimulated the publication of the minimum information for the publication of quantitative realtime PCR experiments (MIQE) guidelines, aimed at encouraging better experimental practice. The problem we now face is rather serious: Thousands of publications that report suspect data are populating and corrupting the peer-reviewed scientific literature. Let us hope that this belated acknowledgment by Nature will lead to researchers remembering the main reason for publishing, namely allowing their peers to reproduce their results, if so desired".
I received the following reply:
"Thank you for your Correspondence submission, which we regret we are unable to publish. Pressure on our limited space is severe, so we can offer to publish only a very few of the many submissions we receive.
However, we would like to draw your attention to our online commenting facility in case you would be prepared to post your letter there instead. In which case, please go to the original article on our website (http://www.nature.com/nature/archive/index.html) and enter your message in the box provided beneath it".
When I tried to do this, I received the following email:
"This account has been banned from commenting due to posting of comments classified as inappropriate or other violations of our Terms of Service".
"Your editorial announcing measures to reduce irreproducibility is a welcome, if long overdue acknowledgement of the inadequate reporting of experimental detail in much of the peer-reviewed literature. However, your final sentence that exhorts “others to take note of … our initiatives, and do whatever they can to improve research reproducibility” is an obvious attempt to deflect attention away from the active disregard high impact factor journals such as Nature have shown in the past for this issue.
One area of particular concern has been the quantification of nucleic acids by real-time quantitative PCR (qPCR) and reverse transcription (RT)-qPCR, probably to-day’s most widely used molecular techniques. Their seeming simplicity and reliability is gainsaid by their actual complexity and inconsistency; in practice, this means that the biological relevance of many published qPCR-based results is open to question, with reported differences caused by technical, rather than actual variability. How do we know results are suspect? It is not credible to report a 1.5-fold difference in mRNA levels normalised against a single, unvalidated reference as significant. It is not possible to assess the validity of a comparison of mRNA levels in multiple samples when there is no information about its purity or integrity. It is not feasible to compare mRNA levels based on unknown PCR efficiencies.
These issues that have caused many of us to spend the last decade spelling out the inexcusable lack of transparency especially prevalent in high impact factor journals and stimulated the publication of the minimum information for the publication of quantitative realtime PCR experiments (MIQE) guidelines, aimed at encouraging better experimental practice. The problem we now face is rather serious: Thousands of publications that report suspect data are populating and corrupting the peer-reviewed scientific literature. Let us hope that this belated acknowledgment by Nature will lead to researchers remembering the main reason for publishing, namely allowing their peers to reproduce their results, if so desired".
I received the following reply:
"Thank you for your Correspondence submission, which we regret we are unable to publish. Pressure on our limited space is severe, so we can offer to publish only a very few of the many submissions we receive.
However, we would like to draw your attention to our online commenting facility in case you would be prepared to post your letter there instead. In which case, please go to the original article on our website (http://www.nature.com/nature/archive/index.html) and enter your message in the box provided beneath it".
When I tried to do this, I received the following email:
"This account has been banned from commenting due to posting of comments classified as inappropriate or other violations of our Terms of Service".