Is our world autonomous or its existence requires another level of reality that acts in the background to bring about the phenomena? This is an intriguing question that has not been settled by science since the time that the Eleatic philosophers challenged the autonomy of the world 2,500 years ago. If our world is not autonomous, then there are significant implications regarding every aspect of our lives, including our science and religion. Non-autonomy would further imply that life did not emerge by chance but there is an underline intelligence that governs its creation and evolution. In essence, the possibility of a non-autonomous world directly challenges the consistency of modern evolution theory. The intelligent design vs. evolution debate is probably the most controversial one of our times. Beyond Intelligent Design approaches the notorious intelligent design doctrine from a novel perspective based on the virtual reality hypothesis and in a way that allows falsification through experimentation. Obscured facts regarding the foundations of classical but also of modern science are presented that challenge the autonomy of this world. The shaky foundations of modern science warrant the investigation of alternatives, such as theories that deny the autonomy of this world and corroborate the hypothesis of intelligent interaction, which in turn indirectly supports the intelligent design hypothesis. Beyond Intelligent Design takes the reader on a journey in time and space that starts in Elea, at around 550 BC. Elea was a small ancient Greek colony in the south of Italy. It is where the strongest blow to common scientific wisdom was ever delivered by a group of poets and philosophers against efforts to understand the world through observation, experimentation and inductive reasoning. Then, the book proceeds to reconcile the Eleatic arguments with the ideas expressed by Cartesian philosophers of the 17th century, discusses how Descartes, Newton and Leibniz dealt with them and then presents some of the foundational weaknesses of the most successful modern scientific theories, special relativity and quantum mechanics. Beyond Intelligent Design does not attempt to provide direct support to the intelligent design hypothesis but instead argues that science must not exclude alternatives theories, such as those that challenge the autonomy of this world, because such autonomy is not evident. More importantly, the book asserts that alternative theories about the emergence of the world and human life should be part of the educational curriculum because they can provide a balance to the cultivation of human values.