Emberly McLean-Bernard, born six weeks premature in rural Mississippi, weighed less than five pounds when doctors sent her home. She did not cry and barely ate, her mother said, and not two days elapsed before she began to gasp for breath. Jocelyn McLean rushed her daughter to the nearest emergency room, but the baby was already turning blue.

The medical team went straight to code blue, pumping air into the baby’s lungs, trying to force an IV line into Emberly’s neck and scalp, prodding her with a rectal thermometer — but her vital signs kept failing. After four hours, they gave up.

A state medical examiner concluded that the death had not occurred because of a medical problem, but had been a homicide, the result of “blunt force injuries with signs of strangulation.”

Ms. McLean, a 29-year-old Black mother with two other small children, was charged with capital murder.

Ms. McLean was stunned. The emergency room doctor who had tried to save the baby was shocked. But Dr. Joye Carter, a forensic pathologist tapped by the defense to review the case, saw an all-too-familiar pattern: a medical examiner who made a ruling without talking to the doctor or even examining the hospital records. Supervisors who signed off on his decision. A criminal justice system that all too often sends Black people to prison on evidence that might not have convicted someone else. In court, Ms. McLean and her lawyer recalled, Ms. McLean was called a “monster.”

She spent more than a year in jail before Dr. Carter’s autopsy review forced the state medical examiner and prosecutor to acknowledge that the baby’s injuries could be explained by the desperate attempts to save her that night.

“I’m thankful that this woman didn’t murder her child,” Steven Jubera, the assistant district attorney in Tallahatchie County, said in an interview after the charges were dismissed. “But the flip side of it is, ‘My God, I’ve had a woman locked up.’”

The nation’s death investigation system, a patchwork of medical examiners, freelance experts and elected coroners who may have no medical training, is responsible for examining suspicious and unexplained deaths. Wrapped in a mantle of scientific authority, its practitioners translate the complexities of disease, decomposition, toxicology and physics into simple categories like accident, homicide or death by natural causes, setting in motion the legal system’s gravest cases and wielding tremendous influence over juries.

Yet these experts are far from infallible. As forensic science of all kinds faces scrutiny about its reliability, with blood splatter patterns, hair matching and even fingerprints no longer regarded as the irrefutable evidence they once were, the science of death has been roiled over the past year with questions about whether the work of medical examiners is affected by racial bias, preconceived expectations and the powerful influence of law enforcement.

A study published last year by the Journal of Forensic Sciences found evidence of cognitive bias when 133 forensic scientists were presented with identical medical evidence in hypothetical cases involving child deaths. The deaths were more likely to be ruled an accident if the child was white and the caregiver was a grandmother; they were more frequently ruled a homicide when the child was Black and being cared for by the mother’s boyfriend.

The study, whose authors included Dr. Carter, touched on the very essence of the simmering debate over forensic pathology. It showed, its authors said, that judgments that ought to be based on science can become clouded by prejudice when medical examiners allow their findings to be affected by information that is not medically relevant. But many leaders in the field insist that medical examiners are obligated to consider the totality of the case before them — including statistics showing that boyfriends are more likely than blood relatives to commit child abuse.

The new research was met by an explosive backlash. The National Association of Medical Examiners complained that the study had been poorly designed and improperly conducted. One association member filed an ethics complaint against Dr. Carter and the three other forensic pathologists listed as authors, claiming that the paper would do “incalculable damage to our profession.”

One of the authors suggested retracting the paper simply to end the controversy. “I can’t even sleep at night because of all the hate and vitriol that I’ve received,” he wrote in an email shared with The Times. In frustration, Dr. Carter, who had spent years trying to expand racial representation in the profession, resigned as head of the organization’s diversity committee.

Recent cases like the death of George Floyd in Minneapolis — where some experts contended that the prolonged weight of police officers on Mr. Floyd was not the cause of his death — have catapulted the debate over bias into the public arena.

Dr. Andrew Baker, the chief medical examiner in Minneapolis, who would go on to perform the official autopsy in the Floyd case, acknowledged in an address to the American Academy of Forensic Sciences in 2015 that “egregious failures of the system have led to tragic consequences for innocent defendants.”

But he attributed the failings to bad apples in the profession, not a failure to implement safeguards against error. “Overt failings — such as incompetence, dishonesty, fraud and corruption — do not constitute cognitive bias,” he said.

Dan Simon, a professor of law and psychology who served for six years on the federal committee charged with creating better forensic standards, said medical examiners have been uniquely resistant to adopting reforms. “They stand out in their recalcitrance,” he said. “And it’s a serious problem.”

Critics say that a reluctance to admit the possibility of bias, combined with a lack of diversity in the profession and a traditionally cozy relationship with law enforcement, can increase the chances of racial disparities when medical examiners err. A string of Black and Latino defendants have been freed in recent years, some from death row, after the autopsy findings that had helped convict them were disproved.

In one California case, Vicente Benavides spent 25 years on death row on charges of raping and sodomizing his girlfriend’s 21-month-old daughter so brutally that it killed her. Mr. Benavides was released in 2018 after experts said the cause of death presented at trial was anatomically impossible.

Before getting involved in the case of Emberly’s death in Mississippi, Dr. Carter had spent much of her career taking on the issue of racial bias in the forensics profession.

She attended medical school at Howard University, which was then the only historically Black school with a pathology residency, and in 1992 became the first Black woman to lead a medical examiner’s office, in Washington. She realized that there was virtually no pipeline to train and recruit nonwhites in her profession even though more than half of homicide victims in the country are Black.

Later on, she heard absurd claims from fellow medical examiners, including that Black people were impervious to pain and that bruises cannot be detected on dark skin. She came to believe that a lack of cross-cultural training was causing mistakes with large consequences.

Some of those ramifications became apparent during her forensic pathology residency, in the 1980s, when she was the only Black pathologist in the office of the medical examiner in Miami.

A string of poor Black women were turning up dead in dismal settings — cheap hotels, abandoned buildings, open fields. Though the women were found in similar poses, the deputy medical examiner believed their deaths had been triggered by a combination of cocaine use and voluntary sex. Nearly all were classified as drug-induced accidents.

Dr. Carter pushed back. The victim she examined had a severe crack habit, but Dr. Carter declined to call the death an accident.

She was right — after a public outcry, the autopsies were reviewed; injuries were found that had been overlooked or dismissed, and the deaths were all reclassified as homicides. A man with prior rape convictions became the prime suspect in 32 killings over nearly a decade. He died before he could be brought to trial.

Over the years, the most commonly cited source of bias in forensic pathology has been law enforcement influence, in part because in some places police detectives are routinely present during autopsies.

In the Mississippi case, it may have been the other way around: The prosecutor, Mr. Jubera, said there was no suspicion of foul play in Emberly’s death until the pathologist called it a homicide. That left, he said, only one suspect: her mother.

For months after Emberly’s death, Jocelyn McLean called the county coroner and the state medical examiner’s office looking for an explanation of why her daughter had died, worried that she had missed a warning sign, or that the hospital had released the baby too soon.

She got no answers. The medical examiner’s office had a massive backlog that was forcing families, the police and courts across the state to wait lengthy periods for autopsy reports.

But unlike in many jurisdictions, Mississippi’s medical examiners were board-certified forensic pathologists working in a state-of-the-art lab. Still, 15 months ticked by before the local prosecutor was notified by the pathologist on the case, Dr. J. Brent Davis, that the death was a homicide.

Ms. McLean, who was living near Atlanta and had been visiting Mississippi when she went into labor, saw the first sign of trouble in December 2017, when she received a Facebook message from a caseworker at the Georgia Division of Family and Children Services warning that if Ms. McLean’s two living children were not seen by the agency within 48 hours, they would be removed from her custody.

During the subsequent visit, the caseworker disclosed that state authorities in Mississippi had concluded that Emberly had been a victim of child abuse. “I was like, ain’t no way. Ain’t no way that could have happened,” Ms. McLean said. “She was in my custody the whole time.”

Emberly’s siblings, who were then toddlers, were forced to strip naked for an exam and were removed from Ms. McLean’s custody for almost a year.

Her first chance to see the autopsy report came in early 2019, when she agreed to sit down with Mississippi homicide investigators to give a voluntary statement.

During that interview, one of the investigators claimed that a tear in Emberly’s rectum could have been caused only by sexual abuse.

Ms. McLean responded in a tone of subdued disbelief: “Are you saying she was raped?”

As she began to grasp what the investigators were implying, she twice asked to take a lie-detector test. None was administered.

The prosecutor, Mr. Jubera, said he ultimately disregarded the medical examiner’s findings of potential sexual abuse, saying that they “didn’t make sense in this scenario.” But he did not question the homicide ruling. “I have to rely on my experts,” he said.

He theorized that Ms. McLean, upset by relationship problems with Emberly’s father, had killed the baby in a “postpartum snap.”

Three years after Emberly’s death, Ms. McLean was indicted on a charge of capital murder.

She remained in jail for almost a year, telling her children over video visits that she was working at a new job. When the pandemic delayed her trial, a judge allowed her release on a $250,000 bond and a $350-a-month ankle monitor.

Her court-appointed lawyer, Tara Lang, was troubled by the case. Mississippi has the country’s highest infant mortality rate, and the baby had been released from the neonatal ward before she began to gain weight.

Dr. Rodney Baine, the doctor who had tried to save Emberly’s life, told Ms. Lang that the baby showed no signs of injury when she arrived at the hospital but was simply very vulnerable and very sick.

He reiterated that contention in an interview with The Times. “It’s just A.O.G.,” Dr. Baine said. “Act of God.”

Ms. McLean found herself wondering if the medical examiner would have looked at the death of a white child differently. “I’m a Black mother,” she said. “He just knew, off rip — she killed her baby.”

Her lawyer was introduced to a medical expert she was told might be able to help: Dr. Carter.

“When I looked at the autopsy, I had already read the medical records,” Dr. Carter, 65, said. “So then I was like, ‘What? This doesn’t make any sense. This makes no sense at all.’”

The medical examiner’s report, she wrote in a memo, did not mention several alternative explanations for the baby’s condition: a post-mortem test for a virus that came back positive, thermometer probes that could have caused the rectal tear, multiple attempts to find a vein that left bruising and puncture wounds in her head and neck.

“It was clear immediately to me that the doctor hadn’t reviewed the medical records,” Dr. Carter said.

It is not clear why Dr. Davis did not have the records in his case file or insist on getting them.

“I’ve done I don’t know how many autopsies — the first thing you look at is the emergency room records,” said Dr. Baine, the emergency room physician who had tried to save Emberly.

The Tallahatchie County coroner, Ginger Meriwether, did not return calls for comment. Dr. Davis, who conducted the examination, and the supervisors who approved it also declined to comment.

“This is the kind of case that chills you to the bone,” Dr. Carter said.

In October, more than five years after Emberly died, Jocelyn McLean’s capital murder trial was finally set to begin.

Her lawyer, Ms. Lang, had been raising serious questions about the case for more than a year, sending the prosecutor first the missing medical records, then Dr. Carter’s review of the autopsy report.

Mr. Jubera had in turn sent them to the state medical examiner’s office and to Dr. Davis, who was by then working in Utah.

Months went by with no response. So Ms. Lang prepared to confront Dr. Davis on the witness stand about how he had reached his conclusions.

Just days before trial, Dr. Davis abruptly changed his mind. The death was not a homicide after all, he wrote in a memo to Mr. Jubera. The baby’s injuries were “consistent with lifesaving efforts” and, in the genital area, diaper rash.

Dr. Davis wrote that the revision was prompted by a review of the hospital records, which he said he had not seen before. Without them, he said, there had been “no other explanation” for the injuries. The charges were dropped.

The Innocence Project has filed a civil rights lawsuit against the medical examiners involved, saying that a “grossly inadequate and reckless investigation” had deliberately ignored evidence that weighed in Ms. McLean’s favor.

On the eve of her trial, Ms. McLean had made arrangements for her children to be cared for while she was in Mississippi, and had even planned a good-luck dinner with her co-workers at McDonald’s, where she is an assistant manager.

Instead, she found herself seated in the back corner of a library in Douglasville, Ga., speaking to a reporter.

She was relieved that the case had been dropped, she said, but for her the real turning point had come many months before, when her lawyer called with the news that Dr. Carter had recognized that no one had killed her baby.

“It was a type of relief,” she said, “that somebody believed me.”

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