Trudy Rueda’s lawyer asked Barnes to review Noah Whitmer’s brain scans before her trial. Barnes wasn’t able to testify because of a scheduling conflict, but he says the scans indicate that the baby had a thrombosis — a blood clot within a blood vessel. The prosecution’s doctors saw the thrombosis, too, but they claimed it was a result of abuse. To Barnes, the clotting suggested infant stroke, which can be triggered by an infection. He says the fact that Noah was not taking a bottle or napping normally in the days before he was hospitalized suggests that his condition could have been subtly deteriorating during that time. “It’s a very striking pattern,” Barnes says of the thrombosis. “The baby not eating well may reflect the process which starts this. Usually, it’s not a process that happens acutely and the baby crashes. It can start relatively slowly.”

Barnes also testified at Audrey Edmunds’s hearing challenging her conviction. He said that it was difficult to know for sure what had happened to Natalie Beard based on her scans; at the time of her death, hospitals were using CT scans, rather than also using M.R.I.’s, which provide more detail. But he did say that he saw the possibility of a thrombosis.

To a degree, some of the alternative explanations from defense-side doctors are accepted in the child-abuse field. A 2009 textbook that Cindy Christian co-edited includes a discussion of diseases and accidental injuries that can mimic the effects of abusive head trauma. Leventhal, the Yale pediatrician, told me about an unusual case involving an accidental fall. “A child who was sitting in a highchair and put his feet up on the table in front of him and rocked himself backward,” Leventhal said. “When the child was taken to the hospital, the ophthalmologist said, ‘This is shaken baby,’ because of the massive retinal bleeding. Luckily, there were seven people playing cards in the room when the baby fell.” Leventhal continued, “The subdural hematoma continued to bleed, and it turned out he had a previous bleeding disorder, a clotting problem.”

Leventhal and others in the child-abuse field emphasize that such hemorrhaging as a result of a fall is very rare. In order for doctors to determine what caused an injury, they begin with a list of alternatives, ruling out the ones that don’t match a patient’s symptoms until they arrive at a diagnosis, with a reasonable degree of medical certainty. But defense-side doctors like Barnes say that in a criminal case, physicians should be more careful about testing their assumptions, and they should give the possibility of an alternative explanation — a stroke, say, caused by an infection — more weight.

It’s on this question of probable causes that the doctors who testify in these cases split. Prosecution-side experts rely on a set of studies that indicate that when children have subdural bleeding and extensive retinal hemorrhaging, they are far more likely to have been abused than injured in any other way. In a 2010 paper in Pediatrics, Christian and the pediatric ophthalmologist Alex Levin concluded that the evidence supporting the “diagnostic specificity” of “severe” retinal hemorrhaging has significantly increased. “Some children have such severe retinal hemorrhaging that it is much more likely to be from abusive head trauma,” Christian told me. She testified to this at Rueda’s trial, because Noah Whitmer had severe retinal hemorrhaging. Levin similarly called Natalie Beard’s retinal bleeding “textbook severe” when he testified for the prosecution at Audrey Edmunds’s 2007 hearing. When the prosecutor asked him how significant these findings were for diagnosing shaken-baby syndrome, Levin answered: “Very important. We really don’t have any other cause for this particular kind of hemorrhaging and retinal findings.”

Defense experts, however, criticize the methodology of these studies. And even taken at face value, they say, the studies show that severe retinal hemorrhaging is far more common in abuse cases, not that it’s never found in any other circumstance. At the 2010 meeting of the American Academy of Forensic Sciences, the Canadian forensic pathologist Evan Matshes presented the results of a study, under peer review, of 123 autopsies performed on infants in Miami-Dade County who died under natural or accidental circumstances, or from homicides. Of the children with retinal hemorrhages, 53 percent died from accidental or natural causes, and 47 percent died as a result of homicide. Severe retinal hemorrhages were identified in some of the children in the accident group. Although the children in the homicide group were more likely to have severe retinal hemorrhages than the other groups, this finding could be explained by factors other than abuse, according to Matshes. The children in the homicide group had isolated head injuries and were more likely to be resuscitated for a period of time, he says. In the aftermath, they were more likely to develop brain swelling and bleeding disorders that may explain the severe retinal hemorrhaging. Matshes puts his conclusions like this, “It is simply incorrect to state that severe retinal hemorrhaging is diagnostic of abuse or shaking.” He is now working on a study that looks at whether infants with subdural and retinal hemorrhaging might in fact have neck injuries, which could indicate shaking, that go undetected, because doctors haven’t looked in the right place for them. Matshes and his team are conducting autopsies of the entire cervical spinal column, which is not usually dissected in shaken-baby cases. The goal is to determine whether injuries there could explain how shaking can cause brain damage or death — and whether this additional diagnostic tool might one day help distinguish which babies have in fact been abused, and which have subdural and retinal bleeding from other causes.

Underlying the clash over the medical research on shaken-baby syndrome is another one about human nature. How likely is an adult with no history of wrongdoing to do terrible harm to a child by violently shaking it? To pediatricians like Leventhal and Christian, the sad answer, born of experience, is that such a lapse is all too possible. When I described Trudy Rueda’s case to Leventhal, he told me about cases in which he had met and liked a parent or caregiver who ended up confessing to harming a child. Was there truly no indication that the adult in question was capable of such an act? The doctors who treat abused children insisted that sometimes, there isn’t. They described disturbing confessions, like one that made headlines in Florida last year after a 22-year-old mother told the police that she had shaken her 3-month-old baby and perhaps caused him to hit his head, because he wouldn’t stop crying while she was playing FarmVille. Leventhal cites a 2010 study that included 29 people who confessed in the French courts to shaking infants and who described the abuse as extremely violent.