AP / The Lowell Sun & Robin Young

Boston Marathon bombing suspects, from left, Tamerlan and Dzhokhar Tsarnaev.

Tamerlan Tsarnaev landed on America's terrorist watch list in 2011. Tamerlan's younger brother, Dzhokhar, now charged in the Boston Marathon bombing case, seems not to have made the list.

Ultimately, Tamerlan's inclusion on the watch list did not lead investigators to detect the April 15 bomb plot that killed three and wounded at least 260 – prompting inevitable questions about why not, and whether "dots" of intelligence and information that could have been connected were not.

America's terrorist watch list is all about connecting dots – and it is certain to be a focal point for future congressional hearings pegged to the Boston case. A key part of the vast counter-terrorism net cast by the federal government after the 9/11 attacks, the watch list is actually at least nine lists drawn from a single government database. Criteria for determining who gets "nominated" for inclusion in that database – and, then, who actually makes it onto an agency's specific list – are tightly guarded secrets.

CSMonitor quiz: How much do you know about terrorism?

What does seem clear, however, is that the spigot opened wide in the past three years, leading to torrential growth in the core terrorism database. Whether those extra mounds of data give investigators a more accurate view of the universe of terrorists, or whether they have the unintended effect of making prospective terrorists harder to find and the dots harder to connect, is a matter of hot debate – and one that the Boston bombing case may well intensify.

"There's absolutely no question that they're just choking on the volume of information, both classified and unclassified, that's going into the system," says Dakota Rudesill, a visiting professor at Georgetown University Law Center who served, during President Obama's first term, as special assistant in the policy, plans, and requirements directorate of the Office of the Director of National Intelligence, which includes the National Counterterrorism Center. "You're taking on this immense challenge with all this data – like finding a particular needle in a haystack of needles."

US officials bridle at inferences that the system is overwhelmed.

"Certainly, the volume has grown, and the list has grown for a number of reasons," says a US counterterrorism official who spoke on background because he is not permitted to speak on the record. "The intelligence is better; the value of sharing information is seen as better by the agencies involved. The watch list is created specifically to be one of the big dot-connectors in the counterterrorism effort – it's among the most sophisticated systems the government has – and it's proven itself to be effective."

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The making of the watch lists

Like a giant digital vacuum, the Terrorist Identities Datamart Environment (TIDE), a highly classified database maintained by the National Counterterrorism Center in McLean, Va., each day sweeps up thousands of names, aliases, birth dates, and other potential terrorist tidbits – known as "derogatory information" – and tries to match them with hundreds of thousands of names, faces, and identifying biometric data also sent in by the Central Intelligence Agency, the State Department, the Federal Bureau of Investigation, and other US agencies.

"TIDE is the granddaddy repository – not a watch list itself, but it feeds the lists," says Mark Randol, a specialist on domestic intelligence and counterterrorism formerly with the Congressional Research Service (CRS). "The whole deal with a watch list is that you need a place where the objective is to see if you can identify, and stop, people you think are terrorists from just coming into the US and disappearing into the woodwork to plot attacks."

As of December, TIDE contained the names of 875,000 individuals (not including aliases), the counterterrorism center reports. Each day, TIDE sends a river of new names to the Terrorism Screening Center, run by the FBI. The screening center combines TIDE's names with those on the FBI's own domestic terrorism list to create the Terrorism Screening Database (TSDB) – America's master terrorist watch list.

Both TIDE and the TSDB have been expanding fast. TIDE grew from 740,000 names in 2011 to 875,000 in 2012 – an 18 percent jump. The TSDB, for its part, jumped 23 percent from 423,000 individuals in May 2010 to 520,000 in October 2012, according to the CRS and the Terrorism Screening Center.

What happens to the identifying information about a known or suspected terrorist after it is put onto the master terrorism list? The FBI's screening center sends that information to four US agencies with primary responsibility for straining out would-be terrorists, which then add it to their own unclassified watch lists.

State Department. Its Consular Lookout and Support System (CLASS) screens passport and visa applicants.

Department of Homeland Security (DHS). It uses the Traveler Enforcement Compliance System (TECS), which flows into the Interagency Border Inspection System and the Automated Targeting System – lists used by the US Customs and Border Protection for border and port security.

FBI. Its National Crime Information Center list is disseminated as a tool for police departments across the United States. The bureau also has its own Guardian database (different from the TSDB), and Tamerlan Tsarnaev was reportedly on it.

Transportation Security Administration. The TSA, part of the DHS, keeps three air-passenger screening lists – "no fly," "selectee," and "secure flight." The no-fly list is one of the most exclusive watch lists, winnowed to those tagged as possible terrorists who are to be blocked from getting on a US-bound flight. The selectee list signals that an air traveler requires extra screening but being on that list does not necessarily prevent that person from boarding. Both lists have about 20,000 names, the Terrorism Screening Center reports. The secure flight list allows expedited boarding for passengers whose prescreened personal information is compared with watch list data.

Actions that lead to a person being nominated to TIDE as a "known or suspected" terrorist include engaging in terrorist activity, preparing or planning an attack, gathering information on targets, raising funds for attacks, and soliciting membership in a terrorist organization. Less-obvious criteria remain cloaked in secrecy, including nominations that come from foreign intelligence agencies. In 2009, the FBI's own inspector general noted some dissatisfaction with the process, saying the bureau "failed to nominate known or suspected terrorists in 15 percent of the cases we reviewed."

Getting off the list has been problematic, too. The inspector general criticized the FBI for being "untimely in its removal of the subjects" from the watch list in 72 percent of cases reviewed. Travelers who are often delayed at airports are not usually on a watch list; rather, their names and personal information are similar to that of someone who is. In 2012, at least 14,000 records were deleted from TIDE or terrorist watch lists after it was determined that the people no longer met the criteria for inclusion, the counterterrorism center says. US residents make up about 1 percent of TSDB listings.

But civil liberties experts are not satisfied.

"We still don't have access to the information we need to allow us to evaluate how well it's working or how many [who should not be on the list] have been able to get off," says Sharon Bradford Franklin, senior counsel at The Constitution Project, a Washington-based civil liberties group.

How Tsarnaev made the watch list

In March 2011, the FBI interviewed Tsarnaev after Russian intelligence services warned that he had become radicalized. By June, the FBI concluded a basic "assessment" without adding derogatory data to his file, The Washington Post reported. His name, however, did remain in the FBI's Guardian database – an internal watch list.

In September, the Russians again sent up a flare about Tsarnaev's radicalization, this time to the CIA. By year's end, his name had been added to TIDE and the TSDB watch list, the Post reported.

Three days before Tsarnaev left for southern Russia, his name popped up in the TECS system. It is not clear why the rising number of red flags – including his travel to a part of Russia where Islamic radicals are active and his online postings of jihadist videos – did not set off alarm bells. Some analysts say they believe that some important details simply didn't make it into the database.

"If they get the Russian tip, and they were also aware of [the] fact he was visiting Russia and jihadist websites, then I'm not altogether convinced the FBI would have said they found nothing on him," Mr. Randol says. "The fact they didn't see a problem means to me they were not aware of these details."

The near miss that changed watch-listing

AFP - Getty Images file

Umar Farouk Abdulmutallab set off a bomb in his underwear aboard a Detroit-bound airliner on Christmas Day 2009. A month before his father had warned U.S. authorities. Abdulmutallab's name was added to TIDE -- but didn't make it onto the watch list.

Connecting dots so that clues are not left floating in a sea of data was a top goal after the near-miss Christmas Day bombing attempt in 2009. Nigerian national Umar Farouk Abdulmutallab famously tried to blow up a Detroit-bound airplane using plastic explosives hidden in his underwear.

On Nov. 18, 2009, Mr. Abdulmutallab's own father reported his son's radicalization to US Embassy officials in Nigeria. A week later, the son's name was added to TIDE, but not to the watch list – in part because the source of the derogatory information was not included, weakening it. Five weeks later, Abdulmutallab tried to blow up the plane.

Afterward, President Obama ordered a review to determine why Abdulmutallab's name had not appeared on the master watch list. Later in 2010, the nominating criteria changed, with the result that more names and data flowed into TIDE and the TSDB. One measure of the increase: The number of US citizens and lawful permanent residents on the no-fly list more than doubled, the Government Accountability Office (GAO) found in a 2012 study of watch list changes.

Even before the changes, concern was evident within the intelligence community about the huge amount of data being funneled into TIDE. Back in March 2010, Russell Travers, then deputy director of information sharing and knowledge development at the National Counterterrorism Center, told a Senate panel that the inflow of 10,000 names a day to TIDE had required some adjustments. Among them was the advent of special "pursuit teams" of analysts to explore threads, threats, and loose ends that would help "connect the dots," he said, acknowledging that the step was "an experiment."

The 2012 GAO report likewise noted concern among "nominating agencies" about their abilities to process so much information – especially after the changes that followed the underwear bombing attempt. It noted that "agencies are ... pursuing staffing, technology, and other solutions to address challenges in processing the volumes of information."

A notable watch list success

U.s. Marshals Service / AP file

Faisal Shahzad, shown in a U.S. Marshal's Service mugshot, got on an airplane for Pakistan after the attempt to set off a car bomb in New York's Times Square. A watch list flagged him, and authorities arrested him on the jet.

Despite the fire hose of incoming information, the US saw some success in apprehending terrorism suspects. After someone tried to set off a car bomb in New York's Times Square on May 1, 2010, investigators traced the crime to Pakistani-American Faisal Shahzad – and added his name to the no-fly list at 12:30 p.m. on May 3. Later that evening, Mr. Shahzad was indeed attempting to make his getaway to Pakistan. Minutes before his flight was to depart, authorities spotted his name during a final check.

"What used to happen in days now happens in minutes or seconds," the US counterterrorism official says of recent watch list updating and technology upgrades. "The Times Square bomber actually got on the plane thinking he was getting away. But we have a real-time transactional interface with the Customs and Border Patrol. They screened the passenger manifest, arrested him, and took him off the plane."

Today, says the US counterterrorism official, the backlog of information has been eliminated and analytical resources are adequate. The number of names on the TSDB fluctuates, but during the past year appears to have "leveled off" at about a half million, he says.

Unconnected 'dots' in Tsarnaev case?

Questions remain, however, about the government's handling of Tsarnaev during the year leading up to the Boston bombings. Some wonder why he was not a candidate for extra scrutiny by a pursuit team or by the FBI. Others ask why federal authorities did not inform local police of the warnings about Tsarnaev's possible radicalization, so they could possibly keep an eye out.

Were there dots that, if connected, would have led to closer FBI scrutiny and prevention of the Boston Marathon bombings? If so, did data overload play a role?

"No, actually more data makes it more effective," insists the counterterrorism official. "The more derogatory information in there, the better able the system is to screen, and the better the whole system works."

But data overload is likely to be raised in future hearings on Capitol Hill, some say.

"I hope the Boston case will lead to a new revision of the watch list, to see whether we are adding just too much information on people so that it leads to a needle-in-the-haystack problem," Randol says.

"Right now, it isn't clear that there are plans in place to review the effectiveness of the watch list or whether the level of misidentification is growing because the haystacks are getting too big."

This report, "Terrorist watch lists: Are they working as they should?," first appeared on CSMonitor.com.

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In the fall of 2011, a key Boston police counterterror intelligence unit -- funded with millions of dollars in U.S. homeland security grants -- was closely monitoring anti-Wall Street demonstrations, including tracking the Facebook pages and websites of the protesters and writing reports on the potential impact on "commercial and financial sector assets" in downtown areas, according to internal police documents.

The police monitoring of the activities of Occupy Boston -- an off-shoot of the Occupy Wall Street protests that swept the country in 2011 -- came during a period after the U.S. government received the second of two warnings from the Russian government about the radical Islamic ties of alleged Boston Marathon bomber Tamerlan Tsarnaev.

Boston Police Commissioner Ed Davis told a congressional panel Thursday that his department was never alerted by any federal agency to the information about Tsarnaev, but added that it was "hard to say" whether it would have made any difference in preventing the bombing. FBI  officials have insisted that the intelligence about Tsarnaev was vague and uncorroborated and that their own assessment at the time produced no "derogatory" information that justified opening a full-scale investigation.

But the internal Boston police documents, recently obtained by a civil liberties group, could raise fresh questions about the role of Homeland Security-funded "fusion centers" like the Boston Regional Intelligence Center, or BRIC, which conducted the monitoring. The Boston unit  is one of 72 such units set up to collect, analyze and share intelligence about potential terror threats. While  Homeland Security Secretary Janet Napolitano has called the units “one of the centerpieces” of the nation’s counterterrorism efforts, congressional critics have questioned their effectiveness and accused them in some cases of writing "useless" reports that infringed on civil liberties.

“They  were monitoring completely lawful activities,” said Mara Verheyden-Hilliard, executive director of the Partnership for Civil Justice, a civil liberties group that recently obtained the documents on the BRIC’s monitoring of Occupy Boston under the Freedom of Information Act. She said the BRIC monitoring was an example of the “vast expenditure of government money” to collect intelligence on activities unrelated to terrorism, in violation of First Amendment rights.

A Boston police spokeswoman said the department has changed its reporting procedures since the monitoring of the protests and emphasized that the BRIC is “about a lot more than terrorism.”

A Homeland Security official declined comment, saying the BRIC, like other fusion centers, was “locally owned and operated.” But the official noted that, just five days before the marathon bombing, the BRIC did produce an assessment for the event that, while concluding there was “no specific” or “credible” threat information, advised that “officials should be aware of a range of potential terrorist threats, from scattered unsophisticated attacks to dispersal of chemical or biological agents.” The assessment also identified the marathon finish line — where the bombing took place — as well as Fenway Park as “an area of increased vulnerability.”

The internal police documents about the activities of the BRIC show that on Sept. 30, 2011 — just two days after the second Russian warning about Tsarnaev was sent to the CIA — the Boston police unit was focused on an upcoming “Take Back Boston Rally” planned for the city’s Dewey Square.

“Approximately 100 people are listed as attending the Take Back Boston Rally on the event’s Facebook page and Occupy Boston organziers are encouraging people to attend it as well,” reads one BRIC report written by a U.S. homeland security official on Sept. 30, 2011. “The BRIC has received information that approximately 700 people will participate in the Take Back Boston march, with approximately 100 people staying to camp out as part of Occupy Boston.”

A follow-up report, three days days later, tracked the number of protesters, noting that “the size of the camp in Dewey Square has steadily grown over the weekend” and that “according to the group’s website” the demonstrators were planning two marches, including one to a “local media station, very likely to be Fox News Boston on Beacon Hill.”

Verheyden-Hilliard, whose group obtained the documents, said it was not surprising that the BRIC would be reporting such information since later documents appear to show Homeland Security officials requesting such data. In one “Daily Intelligence Briefing,” dated Oct. 21, 2011, the “Threat Management Division” of Homeland Security’s Federal Protective Service outlines a “template for creating the daily intelligence brief for your region” and then cites a “list of events we want to request” that officials submit “for daily briefing information.” Among the categories, in addition to reporting on domestic terrorist acts and “significant criminal activity” is one called “Peaceful Activist Demonstrations.”

NBC News

Boston Police Commissioner Ed Davis testifies Thursday before a House committee on the marathon bombings.

In his testimony Thursday, Commissioner Davis acknowledged to a House committee that his department, which runs the BRIC, was never provided any of the intelligence from the FBI and CIA that Tsarnaev, a resident of Cambridge, had been twice flagged by the Russians as an Islamic radical with ties to “underground” groups in that country.

“We were not aware of the two brothers,” Davis said in response to questioning by Rep. Mike McCaul of Texas, chairman of the House Homeland Security Committee. “We were not aware of Tamerlan’s activities.”

Davis acknowledged that police counterterrorism detectives were assigned to an FBI Joint Terrorism Task Force (JTTF) -- a separate unit from the Homeland Security fusion centers that serves as the government's primary investigative arm for probing terror threats. An FBI agent at the Boston JTTF conducted an “assessment” of Tsarnaev in 2011 after the first warning about his ties was sent by Russia’s FSB intelligence service. The assessment found no “derogatory” information about Tsarnaev that justified conducting a formal investigation. Later information about Tsarnaev included a second Russian warning to the CIA on Sept. 28, 2011.

But while Boston police had access to the JTTF’s classified database, Davis said that his own officers assigned to the task force were never  specifically alerted to any the information about Tsarnaev. “They tell me they received no word about that individual prior to the bombing.”

FBI spokesman Jason Pack said Thursday that state and local members of the JTTF are “responsible for maintaining awareness of possible threats” in their areas and could have performed “customized key word searches” of the FBI database that would have yielded the information about Tsarnaev.

NBC News researcher Taylor Sears contributed to this report.

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NEW YORK -- Federal prosecutors on Thursday revealed charges that accuse a Tunisian man who had lived in Canada with applying for a visa "to remain in the United States to facilitate an act of terrorism." 

The charges name Ahmed Abassi, a native of Tunisia who had been living in Canada.  Prosecutors say he came to New York in mid-March. 

Federal investigators say he met with the men involved in a plot -- first revealed in mid-April -- to attack an Amtrak passenger train from New York to Toronto.  They say the plotters discussed blowing up a bridge at Niagara Falls to cause the train to plunge into the gorge below. 

Canadian authorities announced in mid-April that the plot had been stopped. They disclosed then that they had arrested two men -- Chaieb Esseghaier of Montreal, a 30-year-old Tunisian graduate student who is reported to have guerrilla warfare training and is described as the ringleader, and Raed Jaser of Toronto, 35, a school bus driver.

Frank Gunn / AP

Chiheb Esseghaier, one of two suspects arrested last week in Canada in connection with the alleged terror plot to derail a passenger train near the U.S.-Canada border, arrives at Buttonville Airport outside Toronto on April 23.

Federal prosecutors from the Southern District of New York said Thursday that Abassi was arrested 17 days ago. The fact that word of his arrest was withheld indicates he was likely providing some information about the plot to investigators. 

He is charged with fraudulently applying for a work visa "in order to remain in the United States to facilitate an act of international terrorism," according to a statement from the Justice Department. 

Authorities in Canada said in April that an al Qaeda facilitator in Iran had worked with Esseghaier, and also that the train they intended to target was an Amtrak train originating in New York's Penn Station. 

"Esseghaier was simply a bad guy, and dangerous. This guy was purely evil," said one investigator, and had scientific training and the technical ability to make chemical bombs. 

Law enforcement officials say Esseghaier met Abassi during a trip to New York. But they say the meeting did not go well.  Abassi, they say, thought he should be the person in charge. As a result of the failure to get along, Abassi did not have a role in the derailment plot. Authorities did not spell out any further the basis for the visa fraud charge beyond saying it was to facilitate an “act of terror.” 

The FBI has covertly monitored the activities of the two Canadian men, their contact with overseas Al Qaeda facilitators and others, and their possible connection to others who could be linked to the plot. 

"What Mr. Abassi didn't know was that one of his associates, privy to the details of the plan, was an undercover FBI agent," said George Venizelos, the FBI Assistant Director in Charge of the New York office. 

The yearlong covert investigation involved electronic and physical surveillance. Authorities emphasize, however, that this was no sting operation.  It was, they say, a significant terror plot, once which failed to get more notice because of the Boston Marathon bombings. 

CTV News via Reuters

Raed Jaser is seen arriving at court in the back of a police car in Toronto on April 23.

Esseghaier and Jaser made their initial court appearances in Canada in April. They are charged with conspiracy to commit murder, conspiracy to interfere with transportation and participating in terrorist group activities. Esseghaier told the court that the Criminal Code of Canada “is not a holy book” and did not apply to him.

Richard Esposito is senior executive producer of the NBC News investigative unit; Jonathan Dienst is WNBC chief investigative reporter and NBC News contributing correspondent in New York City; Pete Williams is NBC News justice correspondent.

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The family of the Boston Marathon bombing suspect killed in a shootout with police can’t find a place to bury him, even as his body is being prepared for just that purpose.

An uncle of suspect Tamerlan Tsarnaev arrived in Worcester, Mass., on Sunday to “prepare the body” of his nephew for burial.

Ruslan Tsarni, of Mongomery Village, Md., came to the city about 40 miles west of Boston with three other men, who were not family members,  and met with the director of the Graham Putnam & Mahoney Funeral Parlors.

The men who joined Tsarni were planning "religious washings" in accordance with Muslim burial rites on 26-year-old Tamerlan Tsarnaev’s body, the funeral director Peter Stefan said.

Stefan said he and the family have been unable to find a cemetery in Massachusetts willing to take the body. Still, though he’s had "no offers" of a cemetery, he expects the suspect will be buried in the state.

"We have to bury this guy,” Stefan told reporters in an impromptu news conference Sunday. "Whatever it is, whoever he is, in this country, we bury people. I don't care who it is. That's what I do.”

A small number of demonstrators had protested at the funeral home over the weekend, holding signs and chanting "USA!" One sign read: "Do not bury him on U.S. soil."

According to The Associated Press, several people drove by the funeral home Sunday and yelled, including one man who shouted, "Throw him off a boat like Osama bin Laden!"

Apparently in response to those protests, Stefan remarked, "I can't separate sins from sinners. I can't pick and choose. This is what we do."

For his part, the uncle said that Cambridge, Mass., was Tsarnaev’s home, not the southern Russian republics of his roots.

“He lived in America, he grew up here,” Tsarni said. “Any contemplations that his body should be taken to his home country, they cannot believe. His home country was indeed Cambridge, Massachusetts.”

Stefan said he is planning to ask the city of Cambridge to provide a burial plot, and if Cambridge turns him down, he will seek help from state officials.

Shortly after Tamerlan and his 19-year-old brother Dzhokhar were identified as suspects in the bombings that killed three and injured more than 200, Tsarni said the brothers may have been motivated by shame and hatred.

“Being losers, hatred to those who were able to settle themselves,” Tsarni said at the time.

Dzhokhar, 19, remains in a prison hospital while he awaits legal proceedings on federal terrorism charges. He could face the death penalty.

NBC News' Alexandra Moe and The Associated Press contributed to this report.

Related:

• DNA on Boston bomb does not match suspect's wife, investigators say
• Boston suspects had plotted July 4 attack, investigators say
• What motivated bombing suspects? 'Being losers,' uncle says

Mark Lennihan / AP file

Visitors look over the waterfalls at the National September 11 Memorial and Museum on Feb. 25 in New York.

NEW YORK -- Faced with hefty operating costs, the foundation building the 9/11 museum at the World Trade Center has decided to charge an admission fee of $20 to $25 when the site opens next year.

The exact cost of the mandatory fee has not yet been decided.

Entry to the memorial plaza with its twin reflecting pools will still be free.

The decision to charge for the underground museum housing relics of the Sept. 11, 2001, terror attacks has been greeted with dismay by some relatives of 9/11 victims.

"People are coming to pay their respects and for different reasons," said Janice Testa of Valley Stream, whose firefighter brother Henry Miller Jr. died at the twin towers. "It shouldn't be a place where you go and see works of art. It should more be like a memorial place like a church that there's no entry fee."

Testa was visiting the memorial Saturday with relatives from Florida.

The memorial plaza opened in 2011 on the 10th anniversary of the terror attacks, but disputes over funding have pushed the museum's opening back to spring 2014.

With the cost of operating the memorial and museum projected to be $60 million a year, the memorial foundation voted at its board meeting last week to charge a mandatory admission fee for the museum.

"This is something that is going to be important and is going to be worth the expenditure," Joseph Daniels, president of the National September 11 Memorial and Museum, said Saturday.

Daniels said the museum will be free during certain hours every week and will offer student and senior discounts.

Foundation officials had considered an optional donation but rejected the idea.

"We decided that it's more fiscally prudent to have a straight ticket charge," Daniels said.

Debra Burlingame, a foundation board member whose brother was the pilot of one of the hijacked planes, said the trade center site is expensive to build on and to protect.

"The World Trade Center site remains a target of interest among terrorists, so the security has to be robust and relentless," Burlingame said in a phone interview. "There's a big price tag on that.

"Would we like to be able to say this is free? Absolutely," Burlingame added. But she called it "irresponsible to hope that year after year we have donations that will cover an expense like security."

Some visitors to the memorial were divided about charging admission to the museum.

Retired school psychologist Valerie Cericola of Lavalette, N.J., said the entry fee sounded fair.

"You need to keep it open, you need to keep it running," she said. "It's an expense."

But Jennifer Reyes, a friend of Cericola's daughter who was born on Sept. 11, 2001, said the museum should ask for an optional donation.

"I think a donation like $10 would be good," Jennifer said.

AP radio correspondent Julie Walker contributed to this report. 

Related: Images of the World Trade Center site from PhotoBlog

A badly wounded but awake Dzhokhar Tsarnaev showed little signs of fear or remorse during his hospital room court hearing earlier this week and his heart monitor didn’t register a blip when he was told he was facing the death penalty in the Boston Marathon bombing case, according to a source familiar with the events inside the hospital room when he was read his rights.

Tsarnaev’s face was splotched and swollen, his left hand was bandaged, and he was unable to talk during the brief court hearing presided over by U.S. Judge Marianne Bowler on Monday afternoon.

The surviving bombing suspect mouthed rather than said the word “no” when asked if he could afford a lawyer and nodded in the affirmative when asked if he understood his rights.

But Tsarnaev appeared to fully follow the proceeding, the source said. The most telling moment, the source said, came early on when, after Tsarnaev was informed of the two charges against him, the judge asked prosecutor William Weinreb to spell out the possible penalties he was facing.

“Your honor, the maximum penalty is death,” Weinreb said, according to a public transcript of the proceeding.

Tsarnaev showed no reaction — nor did his heart monitor register any change, the source said. “There was no blip at all,” said the source.

But heart monitors don’t always register emotional responses — and there is no way to tell what impact medications Tsarmaev may have been given had, according to medical experts.

There have also been conflicting reports about Tsarnaev’s mental state in the days after his capture. “Over the weekend, he’s in and out of lucidity,” Rep. Mike Rogers, chairman of the House Intelligence Committee, said on MSNBC’s “Andrea Mitchell” show on Thursday. “He’s got — he’s on medication, he’s talking, but he’s not talking, he’s unconscious, he’s going for medical procedures.”

But those present at the bedside court hearing were convinced that Tsarnaev was fully cognizant of the circumstances he was facing, the source said. Judge Bowler agreed. “I find the defendant is alert, mentally competent and lucid,” she said, according to the transcript. “He is aware of the nature of the proceedings.”

Handout / FBI via Reuters

Dzhokhar Tsarnaev, 19, has been charged in the Boston Marathon bombing.

The court proceeding erupted as a source of controversy Thursday when Rogers charged that Judge Bowler had interfered with FBI questioning of Tsarnaev – and that the Justice Department failed to object — when she ordered that Tsarnaev be read his rights on Monday, a day after he was charged in a then-sealed complaint at 6:47 p.m. Sunday.

FBI agents were questioning Tsarnaev — and getting his responses in writing — under a “public safety exception” that allows agents to obtain information from criminal suspects for 48 hours without reading them their constitutional rights informing them they have the right to remain silent and a right to a lawyer. The information that agents got — including the disclosure Thursday that Tsarnaev and his brother had talked about driving to Times Square to set off more bombs — came during those sessions over the weekend.

But Rogers said Thursday that FBI agents “weren’t quite finished with him” when Bowler directed that the court hearing take place that Monday. “To have the court affirmatively push their way in, is — A) I think it's wrong, and B) we should have given the FBI the time that they needed.” Justice Department officials “have a lot of explaining to do.”

Bowler, asked by NBC News about Rogers’ charges in her federal courtroom in Boston Thursday, replied: “The court does not comment.”

A  federal law enforcement official disputed Rogers’ account, telling NBC News that FBI agents had already left the hospital room and wrapped up their questioning before the court hearing took place mid-day Monday. In a statement emailed to reporters Thursday, Justice Department spokesman Dean Boyd said that, after the criminal complaint was filed, the rules of criminal procedure required the judge to advice the defendant of his rights. 

“The prosecutors and FBI agents in Boston were advised of the scheduled initial appearance in advance of its occurrence,” he said. 

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