Darwin's friend Thomas Henry Huxley called the scientific method "organized common sense" or "simply common sense at its best," which is almost completely true. There is no established list of steps or rules in the scientific method, but certain features are universally recognized by scientists, some of which are presented here.

Science investigates only physical causation and occurrences. This does not mean that scientists believe only in physical processes. Many scientists are religious people. However, scientists do not introduce non-physical causation into scientific explanations or investigation. Scientists recognize that science is one way of knowing--a very powerful and successful way, but not the only way. As paleontologist Stephen Jay Gould frequently pointed out, science has been extremely successful at explaining how the world works and how it evolved but is not always very useful in helping to generate values and ethics. It is just not designed to do that. Perhaps it may have been said best by the astronomer Galileo: Science tells humans "how the heavens go, not how to go to Heaven." Scholars may use the scientific method to investigate the reliability of religious texts, or the mental basis of religious experience, but usually do not presume to use science as a basis for their religious experiences. Therefore, most scientists dismiss the recent intelligent design challenges to evolutionary science because the Intelligent Designer, admitted by everyone to be a supreme supernatural being, cannot "itself" be investigated scientifically. Belief in a supreme spiritual being is, as it has always been, a legitimate human activity, but it is not science. In this way, as in many others listed below, the scientific method is useful only because of its limitations. If science tries to be everything, it will end up being nothing. If no physical explanation is possible, the scientist concludes that he or she does not have a scientific explanation--even if he or she privately believes a religious explanation.

Some scholars have attempted to bring ethical and religious concepts into a unified field of scientific knowledge, an approach that Wilson calls consilience. At the present time, however, this concept has not gained universal acceptance.

Science investigates only repeatable occurrences. This is the principal reason that science is limited to physical processes and data. Miracles happen only once; or, if they happen more than once, they cannot be counted on to happen on any investigable schedule. Some creationists claim that creation science is scientific in the same sense that forensic science is scientific. The occurrences of murder are unique and unpredictable, but forensic science can investigate them. However, this reasoning is invalid. Forensic science is based upon facts and processes that are well understood from many repeated observations: regarding rates of bodily decomposition, symptoms of trauma, the physics of footprints, etc. No such database exists for the results of miracles. . .

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