While these assumptions make up the premise for using the Scientific Method, we have to keep in mind that there is such a phenomenon as the Placebo Effect,in which people preceive feeling better after receiving what they thought was treatment.

Also, not everything in Nature follows a linear cause and effect trajectory. Think of tornadoes. Scientists use "fuzzy logic" to explain what does not fit a linear model.

And, sometimes it is impossible to discover the cause of things that happen. Technology may help in this instance, just like the microscope helped to explain the existence of bacteria as the cause of many diseases in the 1800s.