1. A method for operating a human-made thinking system, comprising the step of: (a) establishing a knowledge structure comprising a file organizing mechanism, and more than one element files including identifying information and knowledge information; wherein the identifying information identifies the elements, wherein the knowledge information includes knowledge about the elements, wherein the knowledge is information related to at least one direct links of the elements with other elements of the knowledge structure; (b) establishing a process structure comprising at least one process file, and establish a system log; (c) establishing an executing system comprising an internal control mechanism, and at least one thinking mode; wherein the internal control mechanism includes at least one internal control rule, and at least one structure rule; wherein the thinking mode includes at least one corresponding thinking rule; (d) running the executing system wherein the internal control mechanism can operate constantly, wherein the thinking mode can be activated according to the internal control rules of internal control mechanism; wherein according to the thinking rule, direct link between a first existing element and a second existing element can be used to establish new direct links between the first existing element and at least one existing element with direct link with the second existing element; wherein according to the thinking rule, process files can be used to establish new direct links between the existing elements.