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How do you ID a dead Osama?

The views expressed are those of the author and are not necessarily those of Scientific American.

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Osama bin Laden is dead. At least, that’s what we’ve been told, and I tend to believe such things.

But how do they know it’s him? Well, they have the visual evidence and the body, for one. But to be certain it’s not a look-alike, the U.S. government has taken a step above and beyond to make sure they’ve got who they think they have: DNA analysis.

Now, I’m not entirely sure what DNA analysis has been done, but I can say this for certain—whatever method they used could be completed in a matter of hours given a lab ready to go and focused solely on this. Using commonplace PCR methods—which, for the record, is what I use in my lab every day—Bin Laden could easily be ID’d faster than you’d think. Heck, I can get DNA from a fish and turn it into sequences or genotypes in 24 hours, so I think the US government can work faster than me when time is of the essence. Allow me to explain how they could do it so quickly.

Step 1. Extract DNA

If they’ve got his body, then they’ve got enough DNA to run a billion or two genetic tests. It takes extremely little DNA to run genetic tests – on the order of single cells. So having even a 1 mm square piece of flesh would provide more DNA than they would even have use for. Extraction takes very little time. All you need to do it place the cells/tissue in some kind of solution that will break up the cell’s membranes, thus liberating the DNA from the nucleus without damaging the DNA too much. There are hundreds of extraction kits and protocols. I don’t know what the gov’t extraction policy is, but the Arkansas State Crime Lab just uses sodium hydroxide and hydrochloric acid to extract DNA from their samples (which, btw, is how I get DNA from my fish samples, too). For example, this is their protocol for buccal punches (a.k.a. cheek tissue):

1. Place 52 μl of 0.01 M NAOH in each well with 2.0 mm of tissue.

2. Incubate samples at 65°C for 10 minutes.

3. Add 10 μl of 0.1 M Tris HCl (pH 7.3).

4. Mix.

5. Let stand for 5 minutes.

6. Samples are now ready for amplification


TOTAL TIME: 15 min

Step 2: Amplify Identifying DNA Sequences

Once you have DNA, you’re ready to ID your suspect. While there have been a few methods used in the past, the onset of Polymerase Chain Reaction, or PCR technology, has made looking at parts of a genome pretty darn quick and easy.

The namesake of PCR, polymerase, is a very special enzyme that cells use to duplicate DNA. Polymerases are found in all creatures because we all must, at some point, have cells divide to grow and reproduce. When our cells divide, we have to make two copies of our genome—one for each new cell. To do this, our cells unwind the DNA, spread apart the two matching strands, then use each as templates to make two new strands. Polymerases are the enzymes that actually do that—they attach to single strands of DNA and grab matching nucleotides to create the other half of the strand.

PCR was invented in the 1980s and takes advantage of how our DNA reacts to temperature. At lower temperatures, like in our bodies, DNA sticks to it’s complementary half and forms a tight helix. But as you turn up the heat, our DNA denatures—that is, it unwinds and each half of the helix separates. We can’t use our own cell’s polymerases for PCR because they can’t stand that kind of heat. Instead, we’ve borrowed an enzyme from a particularly heat-tolerant bacteria to do the job for us.

PCR uses multiple cycles of heating and cooling to create thousands to millions of copies of a single piece of DNA. But how do we copy just what we want? Well, it turns out that polymerases need a little help getting started. They require a short sequence of RNA to tell them where to attach, called a primer. Because we can design this primer to match any unique sequence in the genome, we can target where the polymerase will attach, and voila. You’ve just picked your little chunk of genome to amplify over and over and over again. The total process doesn’t take all that long – you heat it up for a bit, run it through a set of temperature cycles, and then you’re good to go. The Arkansas protocol, for example, takes just about two and a half hours.

In the case of DNA fingerprinting, a set of very special genome regions called Short Tandem Repeats (or STRs) are used. These are non-coding sections that vary a lot between people. To be certain of ID, 13 separate regions, called loci, are compared between people. The chance that two people who are not twins would be the exact same across all 13 different loci is approximately 1 in 575 trillion.

The best part of PCR is that you can attach things to those primers to make the new DNA really easy to find. For example, the AmpFlSTR® Identifiler™ PCR Amplification Kit used by Arkansas has the primers for 15 different STR loci all tagged with fluorescent dyes. That means once you’re done with the PCR, you’re just a hop skip and a jump away from a full genetic ID.

TOTAL TIME: 3 hours, tops.

Step 3: Genotyping

Once you have your DNA amplified, you need to find out what it looks like. In the case of STRs, you’re looking for how many repeats are in each DNA chunk. In other words, you’re looking to see how long they are. Because they’re each flagged with a fluorescent dye, the sequence in and of itself doesn’t matter, just the size. Some people just run this out on a gel, which is what we see in our classic TV fingerprinting:

But nowadays, more and more labs are shifting to genotyping analysis with the help of automated machines. Determining the size of fluorescent labeled DNA sequences is the job of specialized machines like the ABI 3130xl Genetic Analyzer. It can take a sample of DNA and tell you how much DNA you have at what sizes in what colors. The output looks something like this:

The pattern of peaks are the person’s "DNA Fingerprint". All you gotta do then is line them up with the peaks of your target person, and it’s either a match or it’s not.

TOTAL TIME: 1 hour, maybe less.

So how long did it take to get Bin Laden’s fingerprint? Well, with the three steps here, just under 5 hours. And for all I know, the FBI has a faster way of doing it—I wouldn’t exactly be shocked. That, and some are reporting he actually died last week sometime, and they’ve been waiting for the DNA confirmation—which also, frankly, wouldn’t shock me.

Of course, to ID Bin Laden in this way, they would have to have some Bin Laden DNA lying around to compare it to. I don’t know if they had some from some inside source, or not. What they do have is brain tissue from Bin Laden’s sister, who died in the US. They can compare his genetic signature to hers and determine if they are related — which is as close as you can get to guaranteeing it’s Bin Laden without a sample of his actual DNA from prior to his death.

About the Author: Christie Wilcox is a science writer who moonlights as PhD student in Cell and Molecular Biology at the University of Hawaii at Manoa. Follow Christie on her blog, Observations of a Nerd, or on Facebook or Twitter.

The views expressed are those of the author and are not necessarily those of Scientific American.

Comments 32 Comments

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  1. 1. David N'Gog 1:01 pm 05/2/2011

    Let us not politicize this. The hunt for Osama and his capture has been orchestrated for years by leaders of different parties. (and the lead that led to him has been followed for longer than Obama has been in the white-house).

    Let’s just be happy he has been caught. I’ve no doubt they can provide ample ID in the time given. I’m surprised they let him die (if they did). Surely he’d be more valuable dead in one of the convenient overseas CIA "constitution-free" prison camps our country runs than dead and dumped in the ocean.

    Even dead- I wonder what sort of information could have been retrieved from studying his body- ample study could have perhaps shown where he had been- what stressed he had been exposed to.

    Perhaps compounds from explosives (if he had been hands on). Maybe his overall health could tell us something.

    I’m more interested not in evidence he is who he is- but evidence that we really have dumped the body in the sea.

    Seems a waste of a storehouse of much information.

    Link to this
  2. 2. Kotababy 1:20 pm 05/2/2011

    It is not Obama that caught him! It is special services…They have been tracking him for years…has nothing to do with Obama. We held Hussain’s body for 11days…why did they conviently dispose of Osama’s body so quickly. As far as I can see, this is all based on hear say without any proof.

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  3. 3. justanobody 1:21 pm 05/2/2011

    Look, JamesDavis, I don’t really care for Bush, but your argument is odd. Unless you can point me to specific Obama policies that lead to bin Laden’s death, then your argument holds no water. Equally, we can’t credit Bush either. This man (bin Laden) attacked us, we retaliated,and it has take us this long to get him. Bush wasn’t on the battle field and neither was Obama.

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  4. 4. Marcello09 1:47 pm 05/2/2011

    Now *this* is science! And it’s an enjoyable read, too. Sure, it’s based on recent political events, but the meat and potatoes are all science. This is why I read Scientific American. Please, give us more articles like this, and less of the agenda-driven political quackery that has been rearing it’s ugly head a bit too often on this website.

    Nice work, Ms. Wilcox!

    Link to this
  5. 5. rodestar99 1:56 pm 05/2/2011

    Yeah you are right…the only achievement greater than
    Obama killing Osama is when Al Gore invented the internet
    I wonder if he snuck up behind and got him with an ice
    pick or maybe he used a garote. Maybe we will find out
    when he releases his memoirs.

    Link to this
  6. 6. justanobody 2:03 pm 05/2/2011

    I agree with your comment, Marcello09. This was an excellent article.

    Link to this
  7. 7. AdrianaH 2:41 pm 05/2/2011

    Excellent article Christie! I’ve worked with DNA throughout my professional career and I find your article extremely clear; I’m sure lay people will find it very readable.
    One question: how do you get any lab work done when you live in Hawaii? :-)

    Link to this
  8. 8. Soccerdad 3:28 pm 05/2/2011

    I oppose nearly everything Obama stands for. However, I give him credit for pursuing OSBL and for having the guts to carry out this mission. But without W’s secret prisons and enhanced interrogation, this day may never have come to pass.

    Link to this
  9. 9. JamesSavik 3:31 pm 05/2/2011

    It’s a lot easier than all of that. Osama bin Laden will be the corpse that even the buzzards won’t touch.

    Link to this
  10. 10. EyesWideOpen 5:20 pm 05/2/2011

    Hopefully and presumably the U.S. government documented the deceased Osama through a combination of DNA evidence, video, credible eye-witnesses, and other forensic techniques (i.e. maintaining a critical body part in chemical storage). Why?

    Because an Osama lookalike could rise on video and claim he traded a skin sample (for DNA testing) for his release! If this happens and the U.S. has all its ducks in a row so to speak, they can demolish any imposter’s claim he valiantly negotiated his release from "the big Satan" in exchange for agreeing to disappear forever. If the U.S. cannot counter such a diabolical imposter, can you imagine the political implications? It could lead to war in the Middle East.

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  11. 11. RuffusMD 5:49 pm 05/2/2011

    Interesting that they can do DNA typing on a aircraft carrier in the ocean. And in less than 6 hours ?

    Link to this
  12. 12. jbo83 8:46 pm 05/2/2011

    Wouldn’t you know some idiot with a soccer ball for a head just couldn’t pass up the opportunity to give all the credit to the administration of the airhead, GWB, whose sleuths couldn’t find Osama for almost a decade with the assistance of every major intelligence agency in the world. Maybe bouncing Soccer Ball Head off the wall of one of GWB’s secret torture chambers for a few days would rearrange his brain matter so it could learn to think. Take pity on the guy’s kid. He has to grow up without a real dad, only a soccer ball.

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  13. 13. syhprum1 5:41 am 05/3/2011

    May I take ‘Soccerdad’ you are in favour of torture (for other people) if it serves american political ends

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  14. 14. Soccerdad 8:34 am 05/3/2011

    Not America’s "political ends" but rather our national security interests. And not "torture" which includes irreversable physical harm, but fear and extreme physical discomfort – you bet. So that’s a yes with qualifiers.

    Link to this
  15. 15. spamless 10:45 am 05/3/2011

    Thanks for the interesting article. Regarding a DNA base against which to compare, doesn’t Bin Laden have something on the order of 30 brothers and half-brothers? So just finding the corpse to have been a member of the family is not in and of itself conclusive.

    Link to this
  16. 16. Rrags 11:29 am 05/3/2011

    Well, from what I understand from the media no country wanted his remains including Saudi Arabia. I think disposing the body in Sea is the best as there would have been a shrine for him. And Saddam Hussein was the Head of a country and was handed over to the Government for a trial may be a mock trial. Osama was a no body. We all hope we are hearing the truth.

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  17. 17. Rrags 11:31 am 05/3/2011

    Oh !!!! Excellent Article. Not many would even know the process of DNA.

    Link to this
  18. 18. prakashvm 11:41 am 05/3/2011

    Yes. The process of extraction is understood.
    But what do you compare this with?
    Do you have a sample to compare with and how genuine is that sample?

    Link to this
  19. 19. Desert Navy 1:41 pm 05/3/2011

    Christie, This is just a timely, readable, easily understood article. I am sincerely reminded of Dr. Asimov’s non-fiction writings; factual, first-hand experience, an obvious intent to convey knowledge as opposed to opinion, a modicum of humor, and no pandering to a personal political agenda.


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  20. 20. rockfalls3 4:05 pm 05/3/2011

    I was thinking the same thing: would they normally have
    a device to perform PCR on the USS Carl Vinson (or any other ship in the area)?
    There must have been some other method that was used to
    decode at least a portion of the DNA. It’s reasonable to
    assume that rather than distribute DNA samples of
    assorted bin Laden family members to all ships in the
    area, they either distributed DNA results or made it
    possible to send the Osama results to a central location
    (back in the States?) that could compare the new sample
    with any old ones and produce a probability of a match.
    The alternative is that the sample used for DNA matching
    was airlifted off the ship and flown elsewhere, to an
    undisclosed location that had the equipment to perform
    the PCR work.

    Link to this
  21. 21. Markle 12:05 am 05/4/2011

    The planning for this started months ago. The Seals have been training for almost as long in a custom built exact replica of the compound. They probably had the carrier and all other assets in place somewhere in this timeframe.

    Link to this
  22. 22. SinJin7 2:55 pm 05/4/2011

    Good day.

    I am a Project Administrator for a DNA testing group on a retail level. From what I understand of this section of the science, we cannot confirm paternity/relationship within 13 loci of str testing. We use the standard TMRCA, and to confirm with certainty, we ask that 68 loci are tested. Beyond that, we also confirm in conjunction, using a snp test. Even at 13 loci, there is a great possibility of inconsistency in results as we have witnessed in our project. The element of time is usually longer than a month because of the demand/resources. However, most paternity labs claim a turnaround time of results in a best case scenario 2 days.

    Can you further explain how these differences are counter to what you claim?

    Thank you.

    Link to this
  23. 23. George Vth 3:29 pm 05/4/2011

    I am disturbed that conservative comments reveal a hate of Obama more than Osama, their main concern is that Obama not be credited with with his death.

    Link to this
  24. 24. jackpol 5:40 pm 05/4/2011

    Do we really need proof that he is dead? Isn’t it logical that if bin Laden really were still alive he would be trumpeting that news to the world? Or maybe he’s waiting to arise on the third day!

    Link to this
  25. 25. ConcernedCitizen 3:31 am 05/5/2011

    You shoot a video and show the world.

    Link to this
  26. 26. dmachugh 8:39 am 05/5/2011

    Very nice summary Christie.
    At the risk of being pedantic, the oligonucleotide primers used for PCR are synthetic DNA not RNA.
    Also, with regard to the number of genetic markers used – this was only a preliminary screen, which could easily be done in a couple of hours. I assume OBL’s samples will be subjected to much higher resolution single nucleotide polymorphism (SNP) chip array analyses; For example, the latest human SNP chip array has ~2.4 million genetic markers – I would imagine that every scrap of biological evidence collected at the scene will also be genotyped using these methods (stamps on envelopes, old cigarette butts etc). This will give investigators a powerful database of genetic information on potential suspects and will allow them to determine complex familial relationships among individuals who may have been present in the complex and elsewhere.

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  27. 27. SinJin7 11:18 am 05/5/2011

    This is an insightful post, thank you. It has been said that the comparison is being made with the sister, of course we know that women do not carry the Y-Chromosome. This for myself, begs the question of how they are going to prove paternal relationship. No SNP or STR is possible in this case and can only prove maternal relationship within a specific timeframe, using TMRCA.

    What else can they do that I am missing?

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  28. 28. HowardB 5:46 pm 05/5/2011

    Well it certainly is good news, especially after two terms where Bush couldn’t get him.

    However I think the administration is making a key strategic error here. They are buying into the whole conspiracy theory world by getting sucked into the ID issue. They should have simply stated that they killed Bin Laden, that they are 100% satisfied it is him and that is an end to it. No photos, no DNA, nothing. If people question it, let them. Close the door.

    It will become clear over time that he is not appearing in his bulletins and time will move on.

    By getting sucked into the ID issue it is creating a monster that will never be sated.

    Link to this
  29. 29. TheMadApe 11:23 pm 05/5/2011

    How do you take a tissue sample from Osama, extract the DNA, prepare the DNA for assay, test the DNA, curate the raw DNA sequence data, assemble the reads or QC the genotype, compare the tested DNA to a reference, and make a positive identity determination all within 12 hours- let alone transport the tissue samples all the places they’d need to have gone in order to get this done.

    Either you are naive or part of the coverup!

    Link to this
  30. 30. pfgetty 8:29 pm 05/6/2011

    This is from an article by Michael Ruppert:

    Let’s start with what I consider the most-obvious proof that the Obama administration is lying. It comes from a world-class microbiologist who allowed me to use this quote on condition of anonymity. The simple proof of his accuracy is to just ask any microbiologist experienced in DNA sequencing about his statement. There are tens of thousands of them around the world.

    Here is what he wrote me:

    I am a molecular biologist and I’ve built a lucrative career in human genetics. I have run one of the world’s largest and most productive DNA genotyping facilities and now I am helping to build the global market for clinical whole human genome sequencing for the world’s largest human genome sequencing facility. I have worked with the absolute best genome scientists from the military, academia, medicine, and industry from around the world. I know DNA. And, one thing I know about DNA is that you cannot, repeat CANNOT: take a tissue sample from a shot-in-the-noggin-dead-guy in a north central Pakistan special forces op, extract the DNA, prepare the DNA for assay, test the DNA, curate the raw DNA sequence data, assemble the reads or QC the genotype, compare the tested DNA to a reference, and make a positive identity determination…. all in 12 hours- let alone transport the tissue samples all the places they’d need to have gone in order to get this done.

    Some might try to argue that ruggedized, field ready kits could test a DNA sample- which is true if one is attempting to determine the CLASS of a bacteria. It is not true if one is trying to determine the specific identity of an individual. Any way you slice it, the real work would require days, and I find it unlikely (although not impossible) that an aircraft carrier would have a laboratory outfitted for this kind of work… it is not the Starship Enterprise out there.

    So, maybe they did get Osama. But there is no f**king way they had any genetic proof of it by the time they dumped the body over the side. What is it that we are not supposed to see with all this distraction? I think the French call it “legerdemain”.

    Link to this
  31. 31. Phatgrower 3:31 pm 05/7/2011

    If you can do all this analysis in 24 hours, why don’t you tackle morg. disease? I’ve got the fibers, and so do many of my friends,
    If you look at a patient for just one hour, you won’t believe the stuff you’ll find. Come take a look and get some genetic analysis of myself and these fibers. Just cuz you may think it’s not real, doesn’t mean you shouldn’t at least look and see…

    Link to this
  32. 32. Phatgrower 3:37 pm 05/7/2011

    Yea, that’s what we know. Maybe they can do it in 1 minute with state-of-the-art biochips. But 6 hours is still unreal.

    Link to this

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