David Brooks, from the New York Times is a very perceptive observer and commentator on culture, including knowledge of contemporary brain and mind science. On October 20, 2011 (http://www.nytimes.com/2011/10/21/opinion/brooks-who-you-are.html?_r=1&ref=davidbrooks) he wrote:
"We are players in a game we don't understand. Most of our own thinking is below awareness. Fifty years ago, people may have assumed we are captains of our own ships, but, in fact, our behavior is often aroused by context in ways we can't see. Our biases frequently cause us to want the wrong things. Our perceptions and memories are slippery, especially about our own mental states. Our free will is bounded. We have much less control over ourselves than we thought."
In this article, discussing the work of Nobel laureate, Daniel Kahneman, and his late colleague, Amos Tversky, he implicitly differentiates the cognitive unconscious from the dynamic unconscious. In other words there two kinds of mental activities which go on outside of our awareness: mental activities, such as ordinary memory, which can occur without the influence of emotions (cognitive unconscious) and mental activities, such any forgetting something ordinary as a result of an emotional conflict despite normal brain activity (the dynamic unconscious). For example, you are at a party at your boss's house and forget his name as you introduce him to your spouse, without being aware that you are still angry at him because he berated you the week before.
Psychoanalysts since Sigmund Freud have known that emotions affect cognitions without the person being aware of the mechanism.
In 1901, in his classic, "The Psychopathology of Everyday Life," Freud discussed how forgetting may not just be a simple mistake, but may be motivated by emotional conflict. In the example of the man at the party, he very likely was not aware of his tremendous anger but could not directly express that anger because he was afraid that he would further antagonize his boss. Instead he effaced his boss' existence for the moment by forgetting the boss' name and could deny his hostility towards the boss by joking at his own stupidity for forgetting the name because he was "nervous."
There is no question that contemporary cognitive neuroscientists such as Kahneman and Tversky have systematically demonstrated "that the flaws [of human cognition, such as memory or decision making] are not just in the passions but in the machinery of cognition." Yet, we not only understand via the methods of psychoanalysis that passions DO affect cognitions, but modern cognitive neuroscientists have demonstrated neural interconnections between the areas of the brain that are actively prominent during cognition (prefrontal cortex) and the areas of the brain that are active during emotional arousal (the limbic system, such as the amygdala).
Whenever we have to make decisions as to how to act we always perform an unconscious mental compromise between our judgments and our emotions. This compromise has been demonstrated many times by cognitive neuroscientist Drew Westen and his colleagues. For example, these scientists found that in the Clinton-Lewinsky scandal, someone's emotional response to the scandal (whether they thought Clinton was right or wrong) "could account for 85 out of 100 subjects' inferences about the meaning of "high crimes and misdemeanors" in the U.S. Constitution, regardless of whether subjects had ever read either newspaper accounts or the Constitution."
During the contested 2000 election between George W. Bush and Al Gore, Westen and his colleagues found that people's emotional beliefs about the candidates affected their consideration whether one method of counting ballots (manual versus machine) was more valid than the other.
We should not be surprised at these results: When emotions are strong, our cognitive functions will be profoundly affected. And, thus, much too often the problem is not just in the "machinery of cognition" because, in the brain, the machinery of cognition and the machinery of emotions are always interconnected.