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Biomedical researchers should declare their assumptions.

Recently, the Editor-in-Chief of Science asked its reviewers and editors to identify papers submitted to the journal that demonstrate excellence in transparency and instill confidence in the results (McNutt 2014). This was done in response to issues with irreproducibility (primarily) in preclinical studies. There may be other ways scientific papers can be made more transparent and reliable. Sometimes very solid, or at least well-intentioned, scientific reports contain assumptions which, if false, severely weaken the work. Assumptions are facts taken for granted, and in an argument, assumptions must be allowed as true for that particular argument to advance. Calling assumptions into question is a legitimate way to undermine a claim or simply deepen our understanding of the issue; however, if assumptions are never identified (declared), then spurious claims sometimes may be advanced as fact. One example of this occurred in a 1978 paper in Nature that is frequently quoted concerning cultural evidence of dog domestication. That letter reported a human skeleton found in a grave in what is now Israel with its hand resting on the chest of a puppy skeleton (Davis and Valla 1978) and the authors interpreted this as evidence of affection between the human and the dog. They said, "The puppy, unique among Natufian burials, offers proof that an affectionate rather than gastronomic relationship existed between it and the buried person." Offers proof? Several assumptions are actually necessary to draw this conclusion which were not identified in the paper: 1) that the puppy was purposely buried with the human, 2) that the hand was intentionally placed on the puppy, and 3) that this placement meant affection or familiarity between the two. Any one of these assumptions could have been false. In our opinion, readers of scientific and/or biomedical papers would benefit from a brief textbox or section at the beginning of each paper wherein underlying assumptions are disclosed. Mathematicians know all too well the dangers of hidden assumptions. There is perhaps no other discipline that can so readily prerequisite the importance of clearly stating all relevant assumptions. The counterpart in mathematics of hypothesis-driven experimentation and conclusion is the statement of proposition (or theorem) with a corresponding proof using formal logic. In this paradigm, the current setting (or global assumptions) and assumptions related to the problem at hand are carefully crafted and explicitly listed. From these assumptions and previously established results, the desired result may be deduced through an application of formal logic (proof by induction is an exception). Making a false assumption, either explicitly or implicitly, will always lead to erroneous results. Thus, it is a common practice in mathematics papers to a priori list all of assumptions regarding the proposition to be stated and proved (Lee 2010). "Perhaps biologists should do the same."

REFERENCES

Davis, S. J. M., and F. R. Valla. 1978. Evidence for domestication of the dog 12,000 years ago in the Natufian of Israel.

Nature 276: 608-610.

Lee, K. P. 2010. A guide to writing mathematics. http://www.cs.ucdavis.edu/~amenta/w10/writingman.pdf McNutt, M. 2014. Reproducibility. Science (Editorial) 343: 229.

Jerome Goddard (1) and Jerome Goddard II (2)

(1) Department of Biochemistry, Molecular Biology, Entomology, and Plant Pathology, Mississippi State University, Mississippi State, MS 39762

(2) Department of Mathematics and Science, Auburn University Montgomery, Montgomery, AL 36117

E-mail: jgoddard@entomology.msstate.edu
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Title Annotation:COMMENT
Author:Goddard, Jerome; Goddard, Jerome, II
Publication:Journal of the Mississippi Academy of Sciences
Geographic Code:1U6MS
Date:Jul 1, 2015
Words:553
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