"Trouble is" is an idiomatic was of saying "The problem with [something] is that ______________." Example: We want to get married. Trouble is, she's still married to her first husband." "The thinking is wrong -- profoundly so": "so" refers back to "wrong," so this means "The thinking is not just wrong, it is profound [very, deeply, fundamentally] wrong." Other examples of similar structures: "They hated each other -- profoundly so" or "They loved each other -- deeply so". "In each case, so refers back to what was said before about hate or love. ". . . , if we are to believe X." This structure is used to say something is the case, but only if X is true. You can use this structure if you do not know, or don't want to say, that X is true. Examples: "The stock market is going to crash next year, if we are to believe what some economists are saying." "North Korea is going to launch another missile next week, if we are to believe the reports on the North Korean news."

This is definitely a confusing sentence. It might make more sense this way: If we are to believe the body of evidence from the cognitive science then the thinking is profoundly wrong. The author is stating that the science proves the thinking referenced is wrong.

这语法是最简单不过的了，很明显， the thinking is wrong - profoundly so 在语法里叫插入语。主句是Trouble is if we are to believe a growing body of evidence from the cognitive science. 问题在于我们是否要去相信越来越多来源于认知科学方面的证据。 主句是一个条件状语从句，if在这里当是否讲，不是如果的意思！ 你多做做GRE阅读题就可以锻炼出来了，这简直就是小儿科了。