Colette, I'm glad you received several responses on your intriguing post.
Personally, the way I read the paper in question and, in particular, the conclusion "We found cognitive deficits previously described .... etc" is a thought-provoking reminder that it's helpful from time to time to question our assumptions and beliefs. The idea that childhood adversities and toxic stress "cause" cognitive and affective adaptations that can be measured in anatomy, physiology and behavior has not only intuitive appeal, but has considerable empirical evidence from animal and human research. In addition, there is mounting research suggesting mechanisms underlying such causal effect, such as gene x environment interactions, epigenetic changes, and chronic low-grade inflammation. Many of us, myself included, take this array of ideas and beliefs as scientific facts. Also, again myself included, many of us have an emotional or irrational stake at these ideas and beliefs being truthful.
So it seems disconcerting and even anxiety-provoking when a study comes along that makes us question those beliefs. All in all and in the absence of multiple replications, I take Danese's work with a grain of salt. Meanwhile, I continue my research, clinical work and education believing that there is a complex, recursive web of cause-effect relationships among adverse environments, the developing brain, resilience-promoting resources and idiosyncratic vulnerabilities associated with long-lasting physiological and behavioral adaptations, many of which in time can be considered maladaptive. Without forgetting that this web of relationships is immersed in a "soup" of social and structural determinants of health.
Best of luck with your thesis!
Andres