Are there any gaps in Darwin's Theory of Natural Selection/Evolution?

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An article and news clip published by ABC News defines one very specific gap which exists in Charles Darwin's Theory of Natural Selection and Evolution. According to the article, Darwin himself questioned his theory based upon one thing: flowers. Given that it only took 45 million years for 400,000 different species of flowers to cover the earth. Given this "incredibly short period of time," flowers "seemed to mock natural selection."

An article from National Geographic states that George, the "last of his kind," was not exactly that. In fact, DNA which matches George (a Galapagos turtle) has been found in at least nine other turtles. Essentially, this proves that these turtles share some of their DNA and characteristics with the last of "their" kind, George.

Finally, an article in Smithsonian Magazine defines the greatest gaps in Darwin's theories. According to the article, "Three fields in particular—geology, genetics and paleoanthropology—illustrate both the gaps in Darwin's own knowledge and the power of his ideas." Therefore, as new scientific information is discovered, Darwin's theories can be found to have "gaps." 

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