In 2011 Tarek Mehanna, a young Muslim man from Massachusetts, was convicted of giving material support to terrorists. His “crime” was translating readily available Arabic-language texts—an activity that many constitutional experts defended as protected by the First Amendment. The decision highlights a broader trend in federal courts, as judges weigh political and popular pressure to be tough on terrorism against bedrock constitutional protections. As part of a research team from Human Rights Watch and Columbia Law School’s Human Rights Institute, I have helped examine 494 terrorism cases prosecuted by the Department of Justice. The team’s 2014 report concludes that anti-Muslim bias affected the judgment of courts under both the Bush and Obama administrations, regardless of the judge’s political leanings. This system is likely to confront an even more grievous test when faced with President Donald Trump, and Attorney General Jeff Sessions, who have each used anti-Muslim rhetoric in personal and political statements.

Judges recognize the particular weightiness of terrorism cases. In 2012 the highest court of the state of New York considered the case of accused gang member Edgar Morales, who had been convicted under a state terrorism statute passed following the attacks of September 11. The statute defines terrorism as an offense committed “with the intent to intimidate or coerce a civilian population.” Morales was accused of firing a weapon into a Mexican American neighborhood during an episode of gang-related violence. The Bronx district attorney charged Morales with terrorism on the grounds that he intended to intimidate residents of that neighborhood. Following a guilty verdict delivered by the jury, Morales became a convicted terrorist.

The aura of terrorism spills over from court into the entire criminal justice pipeline, from pretrial treatment to sentencing and confinement.

On appeal of the terrorism charge, Judge Victoria Graffeo clarified that terrorism means something specific in the public consciousness. By framing criminal acts as terrorism, “the People . . . were permitted to introduce otherwise inadmissible evidence that unduly prejudiced the jury’s ability to fairly adjudicate [Morales’s] guilt or innocence,” she wrote. “Without the aura of terrorism looming over the case, the activities of defendant’s associates in other contexts would have been largely, if not entirely, inadmissible.” Judge Graffeo concluded that the “spillover effect” of this aura prejudicially influenced the jury’s findings. Because the evidence submitted with respect to the terrorism charge made it impossible to rule fairly on the other charges, Edgar Morales got a new trial.

The effects of exposure to the aura of terrorism are not limited to court procedures, though. They spill over into the entire criminal justice pipeline, from pretrial conditions and treatment to post-trial sentencing and confinement.

Before a trial even starts, the pall of terrorism affects the conditions under which a judge agrees to confine a defendant. Most of the cases we examine in our report saw individuals thrown into pre-trial solitary confinement. Syed Fahad Hashmi, accused of storing rain socks and ponchos for an al Qaeda–affiliated acquaintance, was held in solitary confinement for more than three years before trial. Much of that time was imposed as administrative segregation pursuant to Special Administrative Measures (SAMs)—purportedly for the security of the prison, not for any disciplinary infraction.

SAMs impose severe restrictions on a prisoner’s communication with family and friends, other prisoners, and can even require that attorney–client communications be monitored. Defense attorneys in several cases told us that SAMs compromised their ability to fairly represent their clients. The UN special rapporteur on torture said Hashmi’s pretrial conditions amounted to a violation of the UN Convention Against Torture. Under such conditions, enforced for indefinite periods where uncertainty adds to anguish, Hashmi became one of many accused who eventually plead to criminal charges in exchange for certainty and relief. In Hashmi’s case, those charges included terrorism, and he is not alone.

• • •

At trial federal prosecutors are often allowed to introduce bogeyman evidence in terrorism cases. Juries are regularly overwhelmed by evidence that would otherwise have been thrown out by a judge under the Federal Rules of Evidence. Those decisions are discretionary, though, and rarely overturned.

In case after case, judges abdicated their responsibility to balance the relevance of evidence against its potential for prejudice.

Pete Seda, the founder of an Islamic Charity in Oregon, was prosecuted for tax fraud in a case that included no terrorism charges. Prosecutors repeatedly reminded the jury that they were not trying to prove Seda was connected to terrorism. Still, the trial judge permitted the government to frequently refer to a “mujahideen” leader, whom the defendant did not know, as part of a tangential network described by an expert witness. He allowed evidence of this leader’s relationship to Osama bin Laden, despite its irrelevance to the underlying case. The prosecution referred to the concept of jihad thirty-two times over the course of the trial without linking it to tax evasion. The judge allowed the government to present a violent video to the jury, because a still image of the video was found on a computer Seda may have once accessed. The government filed six separate motions to restrict Seda’s access to classified evidence, even though the prosecutors admitted that the evidence would help Seda defend himself. All six motions were granted. Pete Seda was, of course, convicted.

In Mehanna’s case, one of the issues raised on appeal was a deluge of images and videos, mostly retrieved as cached files from Mehanna’s personal computer: they included twenty-eight images of the World Trade Center in flames and thirty-three video clips depicting terrorist attacks and their aftermath. The trial court allowed the prosecution to refer to Osama bin Laden eighteen times before the close of trial even though they never claimed a connection between Mehanna and bin Laden. The effect, if not the purpose of the evidence, was to terrify the jury into associating Mehanna with well-known Muslim terrorists.

Under the weight of this prejudice, a jury’s decision to convict someone such as Mehanna makes more sense. No one—neither the judge, nor the prosecutor, nor the jury—wants to be responsible for letting loose a terrorist. Such patterns of risk aversion in the incremental application of the law are common. In case after case that we reviewed, judges abdicated their responsibility to balance the relevance of evidence against its potential for prejudice. Moreover, in some of these cases, judges gave short shrift to otherwise serious constitutional and human rights concerns that were raised by the defense.

For example, in the case of Omar Abu Ali, a Virginia man charged with material support, prosecutors were permitted to submit a videotaped confession elicited by Saudi authorities, which Abu Ali said was obtained through torture. Meanwhile the trial judge forbade the defense to submit U.S. State Department reports documenting torture in Saudi Arabia—including evidence of the torture of two UK nationals in prison at the same time as Abu Ali. Similarly, in the case of Muhammad Salah, a confession elicited in Israeli custody, which Salah claimed was the product of torture, was admitted through an anonymous Israeli intelligence official at trial. At the government’s request, and over defendant’s objection, judges have permitted anonymous witnesses in several other cases, against the settled constitutional right for a defendant to directly confront his or her accusers. Judges have also granted the government’s request to keep jury members’ names anonymous, out of a supposed concern for their safety. The effect of that anonymity inevitably spills into their decision-making.

No one—neither the judge, nor the prosecutor, nor the jury—wants to be responsible for letting loose a terrorist.

Even at the sentencing phase—and even in cases where courts have expressed frustration with the government’s conduct—judges are still affected by the pressures I have described. Consider, for example, the case of the Newburgh Four, in which an FBI informant ensnared four men in a plot to attack an Air Force base with Stinger missiles. The FBI produced the plot, the means, and the fake missiles. At sentencing District Judge Colleen McMahon expressed her dismay: “I believe beyond a shadow of a doubt that there would have been no crime here except the government instigated it, planned it and brought it to fruition.” Still, the Judge both upheld the jury’s conviction, and imposed a sentencing enhancement based on the weapons involved in the plot, the Stinger missiles that the government agent introduced. Instead of deviating downward, the judge sentenced each of the four men to twenty-five years in prison.

• • •

Under presidents Bush and Obama, federal courts failed to check the executive’s quest to amass terrorism-related convictions. At best, many federal judges used their discretion in favor of the government’s War on Terror; at worst, they went out of their way to accommodate the government’s requests. This pattern of judicial abdication is even more frightening now, in the era of an overtly Islamophobic White House.

For how long will the aura of terrorism cloud our judgment? Each president has asked the American public for the benefit of the doubt while he fights the War on Terror. Americans have, for the most part, indulged that request with a mix of fear and institutional respect. The judiciary has similarly fallen in line, forgoing their solemn responsibility to coolheaded impartiality. But when the executive abuses the public’s trust by lying or obscuring the truth, the responsibility falls heaviest on the judiciary to hold the executive to account. That responsibility has never been more important.