Interesting way you put it...
Many secularist believe the "conscience" is a construct of our mind to deal with things like morals, ethics, good and evil, rather than an attribute of our creator who gave us a soul...
There are some “constructs”. Constructs are things we create to describe something that we did not. Much like the knowledge of good and evil.
Oh, and “In other words, the brain may be channeling what some people call the soul, rather than responsible for creating it” is a quote from the article, though I am flattered that you thought I said it.
How do they explain its being at odds with our nature?
We know things to be right and wrong even though we fight against it with all our desire. This ineffectual denial is the very basis of leftism and their hatred of God, especially the Christian God.