In the days since our first blog post about the Osama bin Laden DNA identification, we've seen plenty of questions--and a little new information--on how the match was performed. We rounded up the latest news on the science behind the identification and got some expert insight from Robin Cotton, Associate Professor and Director of the Biomedical Forensic Sciences Program at Boston University.

• Where was the lab work done? We don't know exactly, but Cotton points out that it is not at all unusual for DNA analysts and other forensic scientists to be working in Afghanistan and Iraq. For instance, this want ad for a "DNA Analyst wishing to be apart of a dynamic team to work in deployed forensic laboratories in Iraq and/or Afghanistan" was posted to the American Academy of Forensic Sciences job board just last month. A quick look at the preferred skills for the job--"Experience with the following: ABI 3130xl (or 3100), Identifiler, Yfiler, and/or Minifiler chemistries, ABI 7500 (or 7000), ABI GeneMapper ID software, and/or the EZ 1 robot"--suggests some of the equipment that could have been used in this case.
  
  Contrary to the television-CSI-induced assumption that DNA matches require enormous, gleaming laboratories, said Cotton, the Bin Laden DNA identification could have been performed in a mobile lab unit about the size of a trailer. "The equipment that you see doesn't take up a lot of space, it doesn't require extraordinary kinds of electrical power," said Cotton. "It requires a clean place--you couldn't do it outdoors in the sand--but it wouldn't be hard to have what you needed," provided it "has the physical design to prevent contamination."


• Bin Laden's half-sister's brain? Everyone from the New York Times to yours truly has called up Massachusetts General Hospital hoping for a confirmation of the report, first carried on ABC News, that an MGH-held DNA sample from Obama Bin Laden's half-sister's brain had been used to clinch the DNA match. However, the hospital was not able to confirm the story, saying in a statement that its "policy is to not release patient information to law enforcement agencies without a subpoena or similar order, and that after a reasonable inquiry it could find no indication that it had received a subpoena regarding DNA for a relative of Osama bin Laden.''


• So whose DNA did they use? We don't know exactly, though officials have said that the analysis involved samples from multiple different relatives. The more, the better, explained Cotton--especially if the samples came from half-siblings. Scientists expect full siblings to share, on average, 50% of their short tandem repeats (STR), sequences of "junk DNA" that are a standard for forensic identification, though the match for a particular STR region could be zero, half, or 100%. Things get murkier with half-siblings. "You would have to have a collection of half-siblings" to make a solid identification, said Cotton. In the case of half-brothers who shared a father, explained Cotton, researchers could also use Y-chromosome analysis. But the "virtually 100-percent" confidence level claimed by the government would be difficult to obtain using half-siblings alone. A sample from one of Bin Laden's children, some of whom are believed to have been in the Abbottabad compound when Bin Laden was killed, could produce a match at a higher confidence level. But, added Cotton, until officials tell us more about the sources of the samples, we can only guess at precisely how they arrived at the match.


• It's not all about DNA By examining photos of the body believed to be Bin Laden's against existing Bin Laden photos, intelligence officials said, they "were able to determine with 95-percent certainty that the body was Osama bin Laden." We don't know exactly how the match was made (you're probably getting used to hearing that by now) but Spencer Ackerman at Wired's Danger Room speculated that a handheld biometric device called the SEEK (Secure Electronic Enrollment Kit) II could have done the job. According to Ackerman, the four-pound device "takes iris scans, fingerprints and facial scans and ports them back to an FBI database in West Virginia in seconds." The SEEK II can "talk" to the FBI database wirelessly or by linking up with a local computer, and it can also be preloaded with its own on-board biometric database.

The mystery of Air France Flight 447, the Airbus A330 that crashed into the Atlantic Ocean on June 1, 2009, may soon be solved. After a two-year, multi-million-dollar search, the plane's two "black boxes" have been discovered and brought to the surface. The flight data recorder, which archives measurements like altitude and airspeed from the plane's instruments, was recovered Sunday. Then, on Monday, the cockpit voice recorder was raised from the water.

The flight data recorder, in a photo provided by the BEA. Photo: Johann PESCHEL/BEA/ECPAD

NOVA reconstructed the doomed flight's final moments in Crash of Flight 447, which premiered in February. Combing weather data, radio transmissions, wreckage analysis, and flight simulations, our experts pieced together a scenario in which Flight 447 unknowingly flew into a 250-mile-wide thunderstorm. That storm may have been carrying droplets of super-cooled water that froze on contact with the plane's speed-sensing pitot tubes, producing faulty airspeed data that set off a cascade of failures and ultimately caused the plane to stall out and, when the pilots could not regain control, crash. But without the black boxes, we could never know whether this scenario was absolutely true, or very plausible historical fiction.

We went back to some of the experts who helped us reconstruct the conditions of the crash to get their views on what the discovery of the black boxes means--and whether we will finally be able to close the book on this mystery.

"I must say that the recovery of both the FDR (Flight Data Recorder) and CVR (Cockpit Voice Recorder) memories in the AF447 circumstances is a great achievement," said Tony Cable, a former investigator with the UK Air Accidents Investigation Branch. The task took a lot of tenacity and "a fair element of luck."

"Standard procedure after recovering a recorder from underwater is to store and transport it while immersed in fresh water, in order to minimize corrosion and salt crystal and mud deposition," said Cable. Once stabilized, the recorders will be transported aboard a French Navy ship to Paris for analysis. The journey will take a little over a week.

From there, an initial readout from the devices, which amounts to "replaying the flight" from takeoff to landing, should be available with 24 hours, said Captain John Cox, a veteran pilot now working as an air safety consultant. Captain Martin Alder, an Airbus training pilot, said that the recorder data can be replayed graphically, "not unlike watching Microsoft Flight Sim in the external view." Experts from Airbus, Air France, and France's investigation agency, the BEA, will work in two teams to pore through the data from each memory device. A complete analysis of the thousands of parameters archived by the flight data recorder will take several weeks.

Of course, added Alder, "It all depends on the data retrieved being usable or accessible." The flight data recorder was separated from its protective housing, causing some to question whether its data would be readable. "I'm very hopeful that there will be usable data in both recorders," said Cox, based on BEA photos which show the condition of the devices. The recorder data are stored on digital chips designed to survive immersion in deep water. "I have been pretty surprised at the impact and overheat abuse that memory chips will put up with and remain viable," said Cable.

When we heard that Osama Bin Laden had been positively identified using DNA, we wanted to know: How did they do that so quickly?

"Forensic DNA testing can be done very quickly--in a few hours," says George Church, Professor of Genetics at Harvard Medical School and Director of the Center for Computational Genetics. (Church also heads up the Personal Genome Project, which we covered on NOVA scienceNOW back in 2008.) "Typically the protocol is PCR"--that's polymerase chain reaction, a technique for making multiple copies of a piece of DNA--"from tiny amounts of sample, followed by gel separation of DNA size variants." These "size variants," which are DNA chunks of different lengths, together create a unique "fingerprint" that can be used to identify an individual.

For a blow-by-blow account of how this all could be accomplished in under five hours, check out Christie Wilcox's excellent guest blog at Scientific American.

One recent report suggested that the purported Osama Bin Laden sample was verified against tissue from his sister, which (according to the report) had been held at Massachusetts General Hospital (MGH) after her death in Boston last year. MGH has not yet been able to confirm any piece of that story. However, Church points out, "It had been known for years that samples of a Bin Laden relative's DNA were available."

The downside of PCR, says Church, is that it is vulnerable to contamination. "One (unlikely) way that this can go wrong is if someone accidentally or intentionally contaminates the sample with overwhelming amounts of another DNA sample."

For more on DNA and its use in forensic identification, check out this primer from the Human Genome Project.