So now the issue seems to be duplicate content for the clearlyexplained.com website. If the site is to be a better reference website it basically should use wikipedia as the base. The question is really does it matter? search engines might penalise the site but does that matter? It may or may not. It's really hard to tell.
Some sites may not get penalised if the format is 'optimised' for other display systems. But the clearlyexplained.com website is really attempting to make for a better user experience when reading an article. It does include the traditional culture, nature & technology subdivisions within a topic. take for example DNA
DNA ClearlyExplained.Com currently sits as http://clearlyexplained.com/nature/life/dna
but if it gets converted to http://clearlyexplained.com/DNA would simplify the access and use of the information.