Alexander responded to these criticisms on Alex Tsakiris' Skeptiko podcast.
Specifically Alexander responded to Harris:
"Isolated preservation of cortical regions might have explained some elements of my experience, but certainly not the overall odyssey of rich experiential tapestry. The severity of my meningitis and its refractoriness to therapy for a week should have eliminated all but the most rudimentary of conscious experiences: peripheral white blood cell [WBC] count over 27,000 per mm3, 31 percent bands with toxic granulations, CSF WBC count over 4,300 per mm3, CSF glucose down to 1.0 mg/dl (normally 60-80, may drop down to ~ 20 in severe meningitis), CSF protein 1,340 mg/dl, diffuse meningeal involvement and widespread blurring of the gray-white junction, diffuse edema, with associated brain abnormalities revealed on my enhanced CT scan, and neurological exams showing severe alterations in cortical function (from posturing to no response to noxious stimuli, florid papilledema, and dysfunction of extraocular motility [no doll's eyes, pupils fixed], indicative of brainstem damage). Going from symptom onset to coma within 3 hours is a very dire prognostic sign, conferring 90% mortality at the very beginning, which only worsened over the week. No physician who knows anything about meningitis will just “blow off” the fact that I was deathly ill in every sense of the word, and that my neocortex was absolutely hammered. Anyone who simply concludes that “since I did so well I could not have been that sick” is begging the question, and knows nothing whatsoever about severe bacterial meningitis."
In a second blog article in response to the Skeptiko podcast, Harris seems not to have read Alexander's comments on Skeptiko—nor Alexander's book—very carefully, stating "I find that my original criticism of Alexander’s thinking can stand without revision" and further stating:
"[Alexander] doesn’t understand what would constitute compelling evidence of cortical inactivity. The proof he offers is either fallacious (CT scans do not detect brain activity) or irrelevant (it does not matter, even slightly, that his form of meningitis was “astronomically rare”)—and no combination of fallacy and irrelevancy adds up to sound science. The impediment to taking Alexander’s claims seriously can be simply stated: There is absolutely no reason to believe that his cerebral cortex was inactive at the time he had his experience of the afterlife. The fact that Alexander thinks he has demonstrated otherwise—by continually emphasizing how sick he was, the infrequency of E. coli meningitis, and the ugliness of his initial CT scan—suggests a deliberate disregard of the most plausible interpretation of his experience. It is far more likely that some of his cortex was functioning, despite the profundity of his illness...."
Specifically, Harris did not address the "diffuse meningeal involvement and widespread blurring of the gray-white junction, diffuse edema, with associated brain abnormalities" nor the neurological exams all of which indicate severe damage to the cortex and brainstem.
Alexander examined nine neuroscientific hypotheses that might explain his experience, including the hypothesis that some isolated cortical networks may have been functioning. That explanation would not explain the robust, richly interactive nature of his recollections.
Harris points to the fact that Alexander remembered his NDE "suggests that the cortical and subcortical structures necessary for memory formation were active at the time". Harris dismisses the possibility that memory as a function of consciousness may also be—as Alexander contends—independent of the brain. If the memories are stored outside Alexander's brain, they are "presumably somewhere between Lynchburg, Virginia, and heaven".
Finally, Harris completely misreads Alexander's account of coming to recognize that the beautiful girl on the butterfly wing was his deceased sister Betsy, whom he had never met because he had been adopted. Harris characterizes this as "wishful thinking" and "self-deception leading to a distortion of memory":
"While in his coma, he saw a beautiful girl riding beside him on the wing of a butterfly. We learn in his book that he developed his recollection of this experience over a period of months—writing, thinking about it, and mining it for new details. It would be hard to think of a better way to engineer a distortion of memory."
If Harris had read a little more carefully, he would have realized that Alexander's memories were vivid at the time he regained consciousness and that he wrote down every detail of his journeys in the six weeks after his recovery. The memories were "right there, crisp and clear". Then four months after his recovery, he received the photograph of his deceased sister.
"She looked so strangely, hauntingly familiar. But of course, she would look that way. We were blood relations and shared more DNA than any other people on the planet...."
The next morning, after reading a story about a child NDEr who met her deceased brother but wasn't aware she had a brother, Alexander recognized that his deceased sister was the beautiful girl on the butterfly wing.