Retraction

Research integrity: the experience of a doubting Thomas

The sensational "reactome array" paper published in Science in 2009 was investigated in Spain by the Ethics Committee of Consejo Superior de Investigaciones Cientificas (CSIC) after Science issued an editorial expression of concern. The paper was retracted in 2010 because of "skepticism" due to "errors" in chemistry. The "errors" were so profound that many readers expressed doubt that they were really errors, but part of an elaborate hoax. I conducted a forensic analysis of mass spectrometry data in the paper's Supporting Online Material (SOM) and was able to prove that thousands of data values were in fact fabricated. The SOM contains signatures of improper extensive spreadsheet manipulations of incorrect atomic and molecular mass values as well as impossibly repetitive deviations of found molecular mass values from their expected values. No evidence of real mass spectrometry data was detected. Both CSIC and Science have been content to retract the paper without acknowledging the fabrications or assigning responsibility for them. Neither CSIC nor Science has expressed interest in having an independent investigation determining how the paper came to be written, reviewed and published. Their weak response to this episode is a daunting signal that there is an impending crisis in research integrity and science journalism.

Dealing with scientific integrity issues: the Spanish experience

Integrity has been an important matter of concern for the scientific community as it affects the basis of its activities. Most countries having a significant scientific activity have dealt with this problem by different means, including drafting specific legal or soft law regulations and the appointment of stable or ad hoc committees that take care of these questions. This has also been the case in Spain. After the period of transition between dictatorship to a democratic regime, and, particularly, after the entrance in the European Union, scientific activity has increased in the country. As it could be expected, problems of misconduct have appeared and different institutions have been dealing with these matters. One of the best examples is that of Consejo Superior de Investigaciones Cientificas (CSIC), the largest institution devoted to scientific research belonging to the Spanish Government. The experience of the CSIC’s Ethics Committee in dealing with conflicts related to scientific practices is discussed here.

Learning from our GWAS mistakes: from experimental design to scientific method

Many public and private genome-wide association studies that we have analyzed include flaws in design, with avoidable confounding appearing as a norm rather than the exception. Rather than recognizing flawed research design and addressing that, a category of quality-control statistical methods has arisen to treat only the symptoms. Reflecting more deeply, we examine elements of current genomic research in light of the traditional scientific method and find that hypotheses are often detached from data collection, experimental design, and causal theories. Association studies independent of causal theories, along with multiple testing errors, too often drive health care and public policy decisions. In an era of large-scale biological research, we ask questions about the role of statistical analyses in advancing coherent theories of diseases and their mechanisms. We advocate for reinterpretation of the scientific method in the context of large-scale data analysis opportunities and for renewed appreciation of falsifiable hypotheses, so that we can learn more from our best mistakes.