While it is not deliberate, much of today's biomedical research contains logical and technical flaws, showing a need for corrective action

Abstract

Biomedical research has advanced swiftly in recent decades, largely due to progress in biotechnology. However, this rapid spread of new, and not always-fully understood, technology has also created a lot of false or irreproducible data and artifacts, which sometimes have led to erroneous conclusions. When describing various scientific issues, scientists have developed a habit of saying “on one hand… but on the other hand…”, because discrepant data and conclusions have become omnipresent. One reason for this problematic situation is that we are not always thoughtful enough in study design, and sometimes lack enough philosophical contemplation. Another major reason is that we are too rushed in introducing new technology into our research without assimilating technical details. In this essay, we provide examples in different research realms to justify our points. To help readers test their own weaknesses, we raise questions on technical details of RNA reverse transcription, polymerase chain reactions, western blotting and immunohistochemical staining, as these methods are basic and are the base for other modern biotechnologies. Hopefully, after contemplation and reflection on these questions, readers will agree that we indeed know too little about these basic techniques, especially about the artifacts they may create, and thus many conclusions drawn from the studies using those ever-more-sophisticated techniques may be even more problematic.

Evidence for immortality and autonomy in animal cancer models is often not provided, which causes confusion on key issues of cancer biology

“…This "coercion hypothesis" (Fig. 5), proposed by us a few years ago [720] and recently [47,303,466] on the essence of animal models of carcinogenesis, deserves experimental testing.…”

“…The genes mediating the two or three genetic hits described above remain unknown. One of the reasons is that we have been encountering a logical plight for decades regarding our research strategies and approaches, as repeatedly pointed out by us before [47,296,720,762]: the results from the approaches we used, such as genetic engineering, can only tell us that certain manipulations or alterations, like concomitant overexpression of the c-myc and a k-ras mutant, and the ensuing cascades of molecular changes, can eventually cause neoplastic transformation or tumor formation. However, we still do not know whether cells in humans or in untreated animals really do spontaneously develop to neoplasms because of the abnormalities of these genes and via these cascades of molecular changes.…”

“…Starting about 40 years ago, molecular biologists, many lacking strict training and clinical experience in surgical pathology or oncology, have gradually replaced medical doctors and traditional biologists to now dominate the fraternity of carcinogenesis research [46,47], thus moving "experimental cancer research" into a new phase. In this latest incarnation, molecular biologists have established numerous genetically manipulated animal models of carcinogenesis and in vitro systems of neoplastic transformation of normal cells which have led us to deeper mechanisms of how genes regulate behaviors of normal and neoplastic cells.…”

ACTB and GAPDH proteins appear at multiple positions of SDS-PAGE and may not be suitable for serving as reference genes for the protein level determination in such techniques as Western blotting

“…This is technically feasible since different isoforms having the same antigen-sequence may manifest different conformations inside the antibody-producing animal, making B lymphocytes produce some antibodies that recognize only one isoform but not the others. As we have discussed before [36,42], this compromise between the researchers and the antibody suppliers actually leads to a biased, somewhat misleading, result. Many published WB results that have only a single band detected may be due to this compromise, although there certainly are many cases in which the gene of interest does indeed produce only a single protein form in the given cell types at the given situation.…”

Spontaneous Cancers, But Not Many Induced Ones in Animals, Resemble Semi-New Organisms that Possess a Unique Programmed Cell Death Mode Different from Apoptosis, Senescent Death, Necrosis and Stress-Induced Cell Death

“…The tumors so induced manifest malignant morphology and even behaviors, and thus are pathologically diagnosed as cancers. However, once the tumor inducer has been withdrawn, many of the tumors will hastily disappear via regression of the tumor cells; the tumors can be sustained in the absence of the inducer only until a very advanced stage 63,64. This phenomenon, although rarely mentioned in the literature of recent years, was already documented in the German literature by Fischer in 1906 (B. Fischer, Münch.…”