A scientific controversy may be a fundamental disagreement among scientists about the validity of a major theory, a secondary scientific controversy, i.e., "scientists disagreeing about a less central aspect of a scientific idea."
True scientific controversy ... is healthy and involves disagreements over how data should be interpreted, over which ideas are best supported by the available evidence, and over which ideas are worth investigating further.
Anne E. Egger said, "Controversies cause progress in science by encouraging research on the topic in question."
List of scientific controversies
- Animal cognition - Can animals learn human language? If so, how much?
- "Scientists have long debated whether any other species can develop the ability to learn human language."
- Race and intelligence
- ADHD - see Attention-deficit hyperactivity disorder controversies
- Biopsychiatry controversy
- Labeling theory
- The atomic theory in 19th century chemistry
- String theory
- Pfiesteria shumwayae - toxicity and life cycle
- The existence of mantle plumes
- Abraham–Minkowski controversy, a physics debate concerning electromagnetic momentum within dielectric media.
- Standard Model of cosmology
- Drake equation, several terms in the equation are largely or entirely based on conjecture
- Extraterrestrial life
- the relationship between tropical storms and global warming 
- Arsenic in DNA
- Cold fusion
- Food irradiation
- HPV immunization
- McMullin, E., 1987, Scientific controversy and its termination, in Jr., H.T.E., and Caplan, A.L., eds., Scientific controversies: Case studies in resolution and closure of disputes in science and technology: Cambridge, Cambridge University Press.
- Alex, a Parrot Who Had a Way With Words, Dies - New York Times