Research Hypothesis: A Brief History, Central Role in Scientific Inquiry, and Characteristics

Document Type : Editorial

Authors

1 Endocrine Physiology Research Center, Research Institute for Endocrine Molecular Biology, Research Institute for Endocrine Sciences, Shahid Beheshti University of Medical Sciences, Tehran, Iran

2 Obesity Research Center, Research Institute for Metabolic and Obesity Disorders, Research Institute for Endocrine Sciences, Shahid Beheshti University of Medical Sciences, Tehran, Iran

3 Department of Molecular, Cellular, and Biomedical Sciences, Sophie Davis School of Biomedical Education, City University of New York School of Medicine, New York, NY 10031, USA

4 Micronutrient Research Center, Research Institute for Endocrine Disorders, Research Institute for Endocrine Sciences, Shahid Beheshti University of Medical Sciences, Tehran, Iran

10.34172/ahj.1623

Abstract

Background: A well-constructed hypothesis is central to scientific knowledge, guiding the research process from a problem to its potential solution. This paper aims to provide a brief history of the scientific hypothesis, emphasize its central role in hypothesis-driven research, and outline the characteristics of a well-formulated scientific hypothesis.
Methods: We conducted a narrative review of philosophical and scientific literature to examine the evolution of hypothesis formulation within the hypothetico-deductive (HD) framework, with emphasis on Karl Popper’s principles of falsifiability and deduction.
Findings: The HD method remains the cornerstone of scientific inquiry, with hypothesis formulation serving as a critical link between theory and empirical testing. The 5E rule, which is a framework that defines an effective research hypothesis as Explicit, Evidence-based, Ex-ante, Explanatory, and Empirically testable, ensures that hypotheses are clear, relevant, and actionable within scientific investigation.
Conclusion: Despite its importance, hypothesis formulation is often underemphasized in modern biomedical research, where many struggle to construct well-defined, testable hypotheses.

Highlights

Zahra Bahadoran(google scholar)(pubmed)

Keywords


  1. Bahadoran Z, Mirmiran P, Ghasemi A. Biomedical research: the research problem matters. Addict Health. 2025;17(1):1542. doi: 10.34172/ahj.1542.
  2. Hattiangadi JN. The structure of problems, (part I). Philos Soc Sci. 1978;8(4):345-65. doi: 10.1177/004839317800800402.
  3. Bahadoran Z, Mirmiran P, Kashfi K, Ghasemi A. Biomedical research: formulating a well-built and worth-answering research question. Addict Health. 2025;17(1):1564. doi: 10.34172/ahj.1564.
  4. McGaghie WC, Bordage G, Shea JA. Problem statement, conceptual framework, and research question. Acad Med. 2001;76(9):923-4.
  5. Glass DJ, Hall N. A brief history of the hypothesis. Cell. 2008;134(3):378-81. doi: 10.1016/j.cell.2008.07.033.
  6. Glass DJ. A critique of the hypothesis, and a defense of the question, as a framework for experimentation. Clin Chem. 2010;56(7):1080-5. doi: 10.1373/clinchem.2010.144477.
  7. Ayala FJ. Darwin and the scientific method. Proc Natl Acad Sci U S A. 2009;106(Suppl 1):10033-9. doi: 10.1073/ pnas.0901404106.
  8. Mahootian F, Eastman TE. Complementary frameworks of scientific inquiry: hypothetico-deductive, hypothetico-inductive, and observational-inductive. World Futures. 2009;65(1):61-75. doi: 10.1080/02604020701845624.
  9. Elliott KC, Cheruvelil KS, Montgomery GM, Soranno PA. Conceptions of good science in our data-rich world. Bioscience. 2016;66(10):880-9. doi: 10.1093/biosci/biw115.
  10. O’Malley MA, Elliott KC, Burian RM. From genetic to genomic regulation: iterativity in microRNA research. Stud Hist Philos Biol Biomed Sci. 2010;41(4):407-17. doi: 10.1016/j. shpsc.2010.10.011.
  11. Willis LD. Formulating the research question and framing the hypothesis. Respir Care. 2023;68(8):1180-5. doi: 10.4187/ respcare.10975.
  12. Lund T. Research problems and hypotheses in empirical research. Scand J Educ Res. 2022;66(7):1183-93. doi: 10.1080/00313831.2021.1982765.
  13. Parathasarathy S, Samantaray A, Jain D. A well-formulated research question: the foundation stone of good research. Indian J Anaesth. 2023;67(4):326-7. doi: 10.4103/ija. ija_226_23.
  14. Polit DF, Beck CT. Nursing Research: Principles and Methods. Lippincott Williams & Wilkins; 2004.
  15. Bulajic A, Stamatovic M, Cvetanovic S. The importance of defining the hypothesis in scientific research. Int J Educ Admin Pol Stud. 2012;4(8):170-6. doi: 10.5897/ijeaps12.009.
  16. Denscombe M. Research Proposals: A Practical Guide. 2nd ed. McGraw-Hill Education; 2020.
  17. Mentis MT. Hypothetico-deductive and inductive approaches in ecology. Funct Ecol. 1988;2(1):5-14. doi: 10.2307/2389454.
  18. Betts MG, Hadley AS, Frey DW, Frey SJ, Gannon D, Harris SH, et al. When are hypotheses useful in ecology and evolution? Ecol Evol. 2021;11(11):5762-76. doi: 10.1002/ece3.7365.
  19. Toledo AH, Flikkema R, Toledo-Pereyra LH. Developing the research hypothesis. J Invest Surg. 2011;24(5):191-4. doi: 10.3109/08941939.2011.609449.
  20. Nenty HJ. Writing a quantitative research thesis. Int J Educ Sci. 2009;1(1):19-32.
  21. Kalinichenko L, Kovalev D, Kovaleva D, Malkov O. Methods and tools for hypothesis-driven research support: a survey. Informatics and its Applications. 2015;9(1):28-54. doi: 10.14357/19922264150104.
  22. Thompson WH, Skau S. On the scope of scientific hypotheses. R Soc Open Sci. 2023;10(8):230607. doi: 10.1098/ rsos.230607.
  23. Turner DP, Deng H, Houle TT. Statistical hypothesis testing: overview and application. Headache. 2020;60(2):302-8. doi: 10.1111/head.13706.
  24. Lawal Y, Ayi OJ, Idoko AI. A study of common errors in hypothesis formulation and testing among university students in social and management sciences. J Adv Res Multidiscip Stud. 2024;4(2):48-60. doi: 10.52589/jarms-d3yi4x5c.
  25. Wulff JN, Sajons GB, Pogrebna G, Lonati S, Bastardoz N, Banks GC, et al. Common methodological mistakes. Leadersh Q. 2023;34(1):101677. doi: 10.1016/j.leaqua.2023.101677.
  26. Gabbi C, Sauer RM. Grantsmanship writing tips: background, hypothesis and aims. Eur J Intern Med. 2019;61:25-8. doi: 10.1016/j.ejim.2019.02.002.
  27. Jeong JS, Kwon YJ. Definition of scientific hypothesis: a generalization or a causal explanation? J Korean Assoc Sci Educ. 2006;26(5):637-45. doi: 10.14697/jkase.2006.26.5.637.
  28. Supino PG. The research hypothesis: role and construction. In: Supino PG, Borer JS, eds. Principles of Research Methodology: A Guide for Clinical Investigators. New York: Springer; 2012. p. 31-53. doi: 10.1007/978-1-4614-3360-6_3.
  29. Ormrod RF. Evidence and proof: scientific and legal. Med Sci Law. 1972;12(1):9-20. doi: 10.1177/002580247201200104.
  30. Bhagyamma G, Wasiq MR. Exploring hypotheses in scientific inquiry: challenges, formulation, and testing. VBCL Law Rev. 2023(8):87-106.
  31. Lipowski EE. Developing great research questions. Am J Health Syst Pharm. 2008;65(17):1667-70. doi: 10.2146/ajhp070276.
  32. Tully MP. Research: articulating questions, generating hypotheses, and choosing study designs. Can J Hosp Pharm. 2014;67(1):31-4. doi: 10.4212/cjhp.v67i1.1320.
  33. Fraenkel JR, Wallen NE, Hyun HH. How to Design and Evaluate Research in Education. 11th ed. New York: McGraw- Hill Education; 2023.
  34. Wolff J, Krebs C. Hypothesis testing and the scientific method revisited. Curr Zool. 2008;54(2):383-6.
  35. Bains W. How to write up a hypothesis: the good, the bad and the ugly. Med Hypotheses. 2005;64(4):665-8. doi: 10.1016/j. mehy.2004.10.003.
  36. Barroga E, Matanguihan GJ. A practical guide to writing quantitative and qualitative research questions and hypotheses in scholarly articles. J Korean Med Sci. 2022;37(16):e121. doi: 10.3346/jkms.2022.37.e121.
  37. Fudge DS. Fifty years of J. R. Platt’s strong inference. J Exp Biol. 2014;217(Pt 8):1202-4. doi: 10.1242/jeb.104976.
  38. Laudan L. Science and Hypothesis: Historical Essays on Scientific Methodology. Springer; 1981.
  39. Erren TC. The quest for questions--on the logical force of science. Med Hypotheses. 2004;62(4):635-40. doi: 10.1016/j.mehy.2003.10.022.
  40. Hopayian K. Why medicine still needs a scientific foundation: restating the hypotheticodeductive model - part two. Br J Gen Pract. 2004;54(502):402-3.
  41. Willis BH, Beebee H, Lasserson DS. Philosophy of science and the diagnostic process. Fam Pract. 2013;30(5):501-5. doi: 10.1093/fampra/cmt031.
  42. Cassan E. “A new logic”: bacon’s Novum organum. Perspect Sci. 2021;29(3):255-74. doi: 10.1162/posc_a_00368.
  43. Mulligan L. Robert Hooke and certain knowledge. Seventeenth Century. 1992;7(2):151-69. doi: 10.1080/0268117x.1992.10555341.
  44. Voit EO. Perspective: dimensions of the scientific method. PLoS Comput Biol. 2019;15(9):e1007279. doi: 10.1371/ journal.pcbi.1007279.
  45. Kell DB, Oliver SG. Here is the evidence, now what is the hypothesis? The complementary roles of inductive and hypothesis-driven science in the post-genomic era. Bioessays. 2004;26(1):99-105. doi: 10.1002/bies.10385.
  46. Coccia M, Benati I. Comparative models of inquiry. In: Farazmand A, ed. Global Encyclopedia of Public Administration, Public Policy, and Governance. Heidelberg: Springer International Publishing; 2022. p. 2112-8.
  47. Weinberg R. Point: hypotheses first. Nature. 2010;464(7289):678. doi: 10.1038/464678a.
  48. Woolhouse RS. The Empiricists. Bodmer W, Butler C, Evans R, eds. Oxford: Oxford University Press; 1988.
  49. Allen JF. Bioinformatics and discovery: induction beckons again. Bioessays. 2001;23(1):104-7. doi: 10.1002/1521- 1878(200101)23:1 < 104::Aid-bies1013 > 3.0.Co;2-2.
  50. Ayala FJ. On the scientific method, its practice and pitfalls. Hist Philos Life Sci. 1994;16(2):205-40.
  51. Ghasemi A, Mirmiran P, Kashfi K, Bahadoran Z. Scientific publishing in biomedicine: a brief history of scientific journals. Int J Endocrinol Metab. 2023;21(1):e131812. doi: 10.5812/ ijem-131812.
  52. Blystone RV, Blodgett K. WWW: the scientific method. CBE Life Sci Educ. 2006;5(1):7-11. doi: 10.1187/cbe.05-12-0134.
  53. Stone P. Deciding upon and refining a research question. Palliat Med. 2002;16(3):265-7. doi: 10.1191/0269216302pm562xx.
  54. Emmert-Streib F. Severe testing with high-dimensional omics data for enhancing biomedical scientific discovery. NPJ Syst Biol Appl. 2022;8(1):40. doi: 10.1038/s41540-022-00251-8.
  55. Lawson AE. The generality of hypothetico-deductive reasoning: making scientific thinking explicit. Am Biol Teach. 2000;62(7):482-95. doi: 10.2307/4450956.
  56. Johnson PD, Besselsen DG. Practical aspects of experimental design in animal research. ILAR J. 2002;43(4):202-6. doi: 10.1093/ilar.43.4.202.
  57. Cramer M, Hölldobler S, Ragni M. When Are Humans Reasoning with Modus Tollens? Proceedings of the Annual Meeting of the Cognitive Science Society; 2021.
  58. Ri YS. Modus ponens and modus tollens: their validity/ invalidity in natural language arguments. Stud Log Gramm Rhetor. 2017;50(1):253-67. doi: 10.1515/slgr-2017-0028.
  59. Ade-Ali FA. Logical Positivist Conception of Knowledge and the Verification Principle: A Reflection. Am Int J Soc Sci. 2014;3(6):118-23.
  60. Gillies D. Philosophy of Science in the Twentieth Century: Four Central Themes. Wiley; 1993.
  61. Sidebotham D, Barlow CJ, Martin J, Jones PM. Interpreting frequentist hypothesis tests: insights from Bayesian inference. Can J Anaesth. 2023;70(10):1560-75. doi: 10.1007/s12630- 023-02557-5.
  62. Salsburg D. The Lady Tasting Tea: How Statistics Revolutionized Science in the Twentieth Century. New York: W. H. Freeman and Company; 2001.
  63. Farrugia P, Petrisor BA, Farrokhyar F, Bhandari M. Practical tips for surgical research: Research questions, hypotheses and objectives. Can J Surg. 2010;53(4):278-81.
  64. Green SB. Hypothesis testing in clinical trials. Hematol Oncol Clin North Am. 2000;14(4):785-95. doi: 10.1016/s0889- 8588(05)70311-7.
  65. Ialongo C. Understanding the effect size and its measures. Biochem Med (Zagreb). 2016;26(2):150-63. doi: 10.11613/ bm.2016.015.
  66. Browner WS, Newman TB, Cummings SR, Hulley SB. Getting ready to estimate sample size: hypotheses and underlying principles. In: Hulley SB, Cummings SR, Browner WS, Grady DG, Newman TB, eds. Designing Clinical Research. 4th ed. China: Lippincott Williams & Wilkins; 2013. p. 43-54.
  67. Bordage G, Dawson B. Experimental study design and grant writing in eight steps and 28 questions. Med Educ. 2003;37(4):376-85. doi: 10.1046/j.1365-2923.2003.01468.x.
  68. Kantorovich A. Philosophy of science: from justification to explanation. Br J Philos Sci. 1988;39(4):469-94. doi: 10.1093/ bjps/39.4.469.
  69. Brian Haynes R. Forming research questions. J Clin Epidemiol. 2006;59(9):881-6. doi: 10.1016/j.jclinepi.2006.06.006.
  70. Batty LM, Lording T, Ek ET. How to get started: from idea to research question. In: Musahl V, Karlsson J, Hirschmann MT, Ayeni OR, Marx RG, Koh JL, et al, eds. Basic Methods Handbook for Clinical Orthopaedic Research: A Practical Guide and Case Based Research Approach. Berlin: Springer; 2019. p. 57-63. doi: 10.1007/978-3-662-58254-1_7.
  71. Rubin M. When does HARKing hurt? Identifying when different types of undisclosed post hoc hypothesizing harm scientific progress. Rev Gen Psychol. 2017;21(4):308-20. doi: 10.1037/gpr0000128.
  72. Evers J. The Texas sharpshooter fallacy. Hum Reprod. 2017;32(7):1363. doi: 10.1093/humrep/dex103.
  73. Gasparyan AY, Ayvazyan L, Mukanova U, Yessirkepov M, Kitas GD. Scientific hypotheses: writing, promoting, and predicting implications. J Korean Med Sci. 2019;34(45):e300. doi: 10.3346/jkms.2019.34.e300.
  74. Horrobin DF. Ideas in biomedical science: reasons for the foundation of Medical Hypotheses. Med Hypotheses. 1976;2(1):29-30. doi: 10.1016/s0306-9877(76)80020-5.
  75. Hulley SB, Newman TB, Cummings SR. Getting started: the anatomy and physiology of clinical research. In: Hulley SB, Cummings SR, Browner WS, Grady DG, Newman TB, eds. Designing Clinical Research. 4th ed. China: Lippincott Williams & Wilkins; 2013. p. 2-13.
  76. Rüegg C, Tissot JD, Farmer P, Mariotti A. Omics meets hypothesis-driven research. Partnership for innovative discoveries in vascular biology and angiogenesis. Thromb Haemost. 2008;100(5):738-46.
  77. Kitsios GD, Zintzaras E. Genome-wide association studies: hypothesis-”free” or “engaged”? Transl Res. 2009;154(4):161- 4. doi: 10.1016/j.trsl.2009.07.001.
  78. Hunter DJ, Altshuler D, Rader DJ. From Darwin’s finches to canaries in the coal mine--mining the genome for new biology. N Engl J Med. 2008;358(26):2760-3. doi: 10.1056/ NEJMp0804318.
  79. Pearson TA, Manolio TA. How to interpret a genome-wide association study. JAMA. 2008;299(11):1335-44. doi: 10.1001/jama.299.11.1335.
  80. Jorgensen TJ, Ruczinski I, Kessing B, Smith MW, Shugart YY, Alberg AJ. Hypothesis-driven candidate gene association studies: practical design and analytical considerations. Am J Epidemiol. 2009;170(8):986-93. doi: 10.1093/aje/kwp242.
  81. Platt JR. Strong inference: certain systematic methods of scientific thinking may produce much more rapid progress than others. Science. 1964;146(3642):347-53. doi: 10.1126/ science.146.3642.347.
  82. Chamberlin TC. The method of multiple working hypotheses. Science. 1890;15(366):92-6. doi: 10.1126/science.ns- 15.366.92.
  83. Lundberg JO, Gladwin MT, Weitzberg E. Strategies to increase nitric oxide signalling in cardiovascular disease. Nat Rev Drug Discov. 2015;14(9):623-41. doi: 10.1038/nrd4623.
  84. Follmann M, Griebenow N, Hahn MG, Hartung I, Mais FJ, Mittendorf J, et al. The chemistry and biology of soluble guanylate cyclase stimulators and activators. Angew Chem Int Ed Engl. 2013;52(36):9442-62. doi: 10.1002/anie.201302588.