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For four years now, Robert J. Wilkes has insisted he did not hurt his infant son the night baby Gabriel fell suddenly and fatally ill.

A jury didn’t buy it. Wilkes was sentenced to 40 years in prison for killing the 3 1/2 -month-old boy in what a prosecutor called “a violent and repetitive and rageful act.”

Now the Montana Innocence Project is appealing Wilkes’ conviction, saying his public defender was ineffective and that new evidence shows Gabriel suffered from a rare and commonly fatal liver disorder.

“There can be no greater tragedy in this world than the untimely death of an infant. Nothing can be done to bring Gabriel back to his family,” it wrote in the appeal filed last week in Missoula County District Court.

“But just as surely, Robert Wilkes was unjustly convicted of a terrible crime. That wrong can now be righted.”

Wilkes had won custody of his son not long before the incident on Oct. 4, 2008. He told law enforcement officers and attorneys the same story: A neighbor baby-sat Gabriel that day, and Wilkes chatted with her and fed the baby a bottle when he picked Gabriel up. He went home and put Gabriel on the floor to rest. But when he checked him a few minutes later, the baby was vomiting from his nose and mouth. Wilkes couldn’t find his cellphone, and ran with Gabriel back to the neighbor’s so that she could call 9-1-1.

The limp, unresponsive baby first was taken to Community Medical Center and then to a hospital in Spokane, where he eventually was removed from life support.

Two years later, the jury convicted Wilkes and Missoula County District Judge Ed McLean sentenced him to 40 years, with 10 conditionally deferred.

The prosecution had sought life.

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Although Deputy Missoula County Attorney Suzy Boylan avoided the term shaken baby syndrome at Wilkes’ trial, the case revolved around the contention that Wilkes must have hurt his child.

After all, the baby sitter had seen Gabriel drink a bottle with no problem minutes earlier. Something must have happened after Wilkes left her home, the argument went. Dr. Rich Kaplan testified that Gabriel had three sets of injuries consistent with abusive head trauma.

But Kaplan, a certified child abuse pediatrician from Minnesota, also cautioned during the trial that the science of shaken babies is far from clear.

Boylan told the Missoulian after the trial that in 11 years, she’d only seen two or three shaken baby cases that could be charged.

Boylan did not return a call seeking comment about the appeal.

According to the Innocence Project’s appeal, “over the past decade, opposition to SBS (shaken baby syndrome) has grown from a trickle to a virtual avalanche.”

The Innocence Project works on behalf of people who it feels were wrongfully convicted.

The Innocence Project’s appeal includes exhibits from experts who reviewed Gabriel’s medical records and came to different conclusions from Kaplan’s.

Gabriel suffered from a rare liver disease called neonatal hemochromatosis. Those symptoms could have explained some of Gabriel’s injuries, according to Peter J. Stephens, a North Carolina forensic pathologist.

“The failure to present a balanced view of current medical information by the defense, coupled with the prosecution’s reliance on medical dogma that is rapidly being superseded, resulted in a miscarriage of justice,” Stephens wrote.

Gabriel also had a chronic subdural (beneath the skin) hemorrhage likely caused by a mildly traumatic birth, wrote Dr. Joseph M. Scheller, a pediatric neurologist Maryland.

“Infants who suffer from cerebral venous sinus thrombosis are often mistaken for victims of abusive head injury. This unfortunately was the case with Gabriel, he did not suffer abuse; he died from a rare but real medical condition,” Scheller wrote.

Because of that new evidence, and also because public defender Scott Spencer didn’t seek adequate expert testimony on Wilkes’ behalf, the Montana Innocence Project made the appeal. In fact its lone expert, forensic pathologist Dr. Thomas Bennett of Billings corroborated the state’s theory, according to the appeal.

Nor did Spencer appeal Wilkes’ conviction – the only time in Montana in the last decade, as far as the Innocence Project could determine, that a homicide case hasn’t been appealed.

Around the country, several convictions based on shaken baby syndrome have been overturned, said Montana Innocence Project executive director Jessie McQuillan.

She said she’d like to see Wilkes’ case added to the national conversation on the issue.

Reporter Gwen Florio can be reached at 523-5268, gwen.florio@missoulian.com, or @CopsAndCourts.

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