The biological definition of evolution refers to changes in the gene pool of a population from generation to generation by such processes as mutation, natural selection, and genetic drift.  As such there is not a flaw in terms of “definition” because these changes can be observed. The flaws with relation to evolution occur when these observations of genetic change are applied to infer support for larger theoretical assumptions that lack the support provided by rigorous application of the scientific method. The debate regarding the theory is often cloaked in religious, cultural and political overtones that may lead to emotional, irrational and fallacious arguments on both sides.
In the first case, evolution is often used as an explanation for the origin of life. This is a fallacious and flawed application. Evolution is described by some as the “cornerstone of modern biology.”  If this is true then it must agree with Louis Pasteur’s law of biogenesis that “all life [is] from life”  In the history of earth no life has ever been observed arising from non-living matter. Thus, presenting evolutionary theory as the answer to the origin of life fails the test of scientific method since the suggested “scientific” theory is not reproducible science. It therefore a flawed application of the observable science to present evolution as a scientific explanation for the origin of life.
In the second case, evolution is often used as an explanation of all forms of life emerging from a single ancestor. This is described as the theory of universal common descent.  This introduces an important distinction between the concepts of micro evolution and macro evolution. Micro evolution is observable science. The famous example is the English moth, Biston betularia, which is found in light and dark coloration as controlled by a single gene. Over a period of 50 years, beginning in 1848, it was observed that the population of dark moths grew from 2% of the population to 95% of the population due to the presence of soot in the environment at the beginning of the England’s industrial revolution.  Lighter colored moths that were more visible to birds were eaten more. This is a simple observable example of natural selection. While natural selection and micro evolution can be studied directly, macro evolution cannot.  It is a result of “inferring” process from observed patterns. Macro evolution is a theoretical explanation of evolution from simple to more complex organisms. This is a critical distinction. Observable micro evolution is a result of natural selection and is the result of the loss of genetic information. Observable mutation is the result of mistakes in the genetic copying process and again results in the loss of genetic information. The observed processes of evolution do not provide scientific basis for the introduction of “new” genetic information to the existing genetic code to allow for “evolution” from simple to more complex forms. Thus, presenting evolutionary theory as “scientific” explanation for universal common descent is a fallacious application of observed science because it fails the simple test of explaining where the new genetic information for complex systems comes from. It does not come from copying errors or natural selection because these evolutionary processes result in the loss of genetic information.
Rigorous application of the scientific method is based on gathering observable, empirical, measurable evidence that is then subjected to the principles of reasoning.  The results must be objective and documented so they can be verified and reproduced. Unfortunately the study of evolution and many of its appended theories has become polemical rather than objective. The arguments of proponents on both sides of the debate are more accurately arguments about presuppositions. It is clear that evolution as an acutely scientific endeavor does explain changes in the gene pool from generation to generation. It is however a flawed application of the observed science to assert these processes provide satisfactory scientific explanation for the origin of life or universal common descent.
Heading: What is evolution?
Heading: Evidence for Common Descent and Macro evolution