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What does the reflexive/personnel pronoun refer to?

“There is an irony in all this. Xenophobia has probably existed for as long as people have. But racist attitudes were reinforced in the 19th century by an enthusiasm for physical anthropology and eugenics. The former attempted to classify human beings on the basis of visible characteristics, such as skin colour, head shape and facial features, that are genetically inherited. If this had been a neutral analysis, it would have been unexceptional. But often it was not neutral. It not only classified, but ranked. White-skinned Europeans put themselves at the top—and black-skinned Africans at the bottom. Add eugenics to that mix and the result was toxic.

“The 3MAG project will not, alone, overthrow the legacy of these misadventures and the prejudices they reinforced. The thinking that gave rise to them is still too deeply ingrained in too many minds for it to do that by itself—even, probably, for it to come close.” [from The Economist]

I tried to analyze this sentence.

1.S+V+O: The thinking is ingrained in minds
2. I can see the phrase “too…to”; “The thinking is too …to do that by itself”;

The thinking is too …for it todo that by itself;
The thinking is even too…for it to come close.

But I can’t figure out what does “The thinking”, “them”, “that”, “itself”refers to. Therefore I don’t understand the sentence. Could anyone help explain it?

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