Observations of a Nerd

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-a-like, the government has taken steps 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 let me 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.

Comments

  1. #1 Taupo
    May 1, 2011

    To be precise, it would be Bin Laden’s half sister DNA from Brain Tissue we would be talking about. Awesome Observations, btw!

  2. #2 Soren
    May 1, 2011

    cool

    I wondered if it was possible to do it this fast.

    Here in Denmark the forensics use some seriously outdated methods, the turnaround time for DNA evidence is measured in months.

    In a recent high profile case they rushed it and had an answer in just 2 weeks

  3. #3 Leslie
    May 1, 2011

    I love that Osama was killed exactly 8 years to the day from when BUSH made his “Mission Accomplished” speech .. so I am sticking to it happening on May 1st and dismissing conspiracy rumors re happened a week ago … :)

    BTW .. you are so cool

  4. #4 don
    May 1, 2011

    must do this now to check if he’s the osama we need.

  5. #5 Lucia Malla
    May 1, 2011

    I once remember seeing a Roche salesman bragging about a PCR machine they developed for the military that could do PCRs in the field, with barely almost no prep. This would cut the time to confirm an ID even more.

  6. #6 Jay DeSoto
    May 2, 2011

    Sure, of course they could, but did they? Or is Obamma just lying to us again?!

  7. #7 Scicurious
    May 2, 2011

    So glad you wrote this up! Was thinking of doing something like it myself. :)

  8. #8 Jay DeSoto
    May 2, 2011

    By the way, what time did the individual in question die(time at the location of his death, or Mecca, or whatever) in order to have him buried in accordence with Muslim burial requirements. I mean how long did they have to work with if something went wrong?

  9. #9 Alex
    May 2, 2011

    My understanding is that Osama had pretty severe kidney problems and needed regular dialysis, it wouldn’t surprise me if his DNA had been acquired from hospitals that performed this.
    Excellent article!

  10. #10 IanW
    May 2, 2011

    Trust you to get a great science article out of it. I miss this at Sci blogs.

  11. #11 David/Abel
    May 2, 2011

    Very nice, Christie. My guess about the time lag is that they 1) needed to find a secure lab to do the analysis and, perhaps more relevant, 2) needed to have the sister’s DNA in the same lab.

    In this case, travel time was probably the rate-limiting step.

  12. #12 Wikked Intent
    May 2, 2011

    Osama was identified from “familial” DNA samples that were taken from his own family members.

  13. #13 Greg Laden
    May 2, 2011

    Throwing your sample into the ocean is not recommended.

  14. #14 Iddo
    May 2, 2011

    Nice writeup Christie. Here is what the lab techs may look like: http://is.gd/LUo4ny

  15. #15 Steven Coon
    May 2, 2011

    Pesonally I am glad they got him.
    Hopefully this is not a ruse!

  16. #16 Juville Dario-Becker
    May 2, 2011

    This is very, very timely.Thanks for simplifying the concepts for my students.

  17. #17 Robert Stass
    May 2, 2011

    Great blog Christie. This is spot on for my next biology exam here in the UK (although I doubt they’ll ask me about it in quite this context :P) Very helpful :)
    Can I have your life please? It looks awesome
    @robstass

  18. #18 Dave
    May 2, 2011

    I’m also a grad student in a bio lab with all the necessary equipment, but unrelated to this type of work. Do you have an idea of primer sequences for the loci that generate a nice visual pattern like that could be run out on a gel? I realize there are companies that do this sort of thing for high-priced art, but the equipment is all around me and I’d love to give it a shot. Thanks.

  19. #19 MonkeeRench
    May 2, 2011

    Excellent explanation Christie, IMHO. Surely do wish you were my biology teacher 55 years ago, instead of one of the athletic coaches (but who did a surprisingly good job sparking interest in science).

    Could you do your 3-hour-tops DNA analysis in a helicopter ride, say with a Roche-field-kit, or would it have to wait until landing, say at an airbase near Kabul? I seriously doubt it was done in Abbottadad, where any preliminary decision was probably based on the digital face recognition analysis (surely more adaptable to combat conditions).

    Best regards,
    Lou

  20. #20 Mike Olson
    May 2, 2011

    Nice explanation. But, once you i.d. a dead Osama, what do you do with the body? I suppose you could put the head on pike as a warning to other Osamas. But, once that warning is out there we wouldn’t want to create a shrine. Cremation with ashes spread across an ocean? Dumped into space from a shuttle? How about dumped into a NYC toilet and flushed into the NYC sewer system? Personally having thousands of fundamentalists fanatics with deadly intent upon their mind praying to a sewer field seems like a great ironic justice.

  21. #21 amit soni
    May 2, 2011

    i have a very simple question if their were 7 sadams then why only one osama also osama without his security force and if he was caught then why he was shooted till death is he had commited suicied ? Also how can one country allow other millitary to do so without permission and also they carried body of osama and his family also with just 1 km his military head quart

  22. #22 amit soni
    May 2, 2011

    In this technology world osama cannot die easily he may be living a safe life in america only i think v must watch film FACEOFF.and by the way last query why saddam was caught live and osama not also where is his body do you know scientist keep brains for test like inestine brain. So frriends dont worry its just my brains query. i dont want v all to be scared but think different then your brain will say my query only.

  23. #23 amit soni
    May 2, 2011

    this news are not clear also it shows a bunch of doubts like why so hurry in osama funeral time between mission ,death,dna,and funeral is so small if an earthquake come anywhere in world we may come to know in minute then why why this mission silently cleared out.

  24. #24 amit soni
    May 2, 2011

    its unclear and untrustful’ answer for death of osama we have to wait for right answer time will show a clear picture.

  25. #25 amit soni
    May 2, 2011

    watch film swordfish it will clear death theory properly then answer me is osama a dead man.

  26. #26 Mike Lisieski
    May 2, 2011

    @Dave:

    You could talk to Paul Vanouse (http://visualstudies.buffalo.edu/people/vanouse/artwork.html) – he’s a prof. at my university who uses DNA gels in his art.

    @amit

    lol. Thanks for the laugh.

    @Christie

    Great post.

  27. #27 Jack
    May 2, 2011

    Thank you so much for this- I am an artist who loves science and I will check back with you and see your blog again!

    Thanks again!

  28. #28 Hodor
    May 3, 2011

    @2: Having to wait months for a DNA analysis probably isn’t caused by outdated methods, but most likely by forensics labs simply being overworked because there has been an increasing emphasis on forensic evidence (including DNA) in criminal trials in recent years. Even without modern automated methods (except for maybe a thermocycler), the actual PCR and electrophoresis shouldn’t take more than a few days.
    With Bin Laden, which is as high-profile as it can possibly get, the analysis was obviously prioritized over everything else. Chances are the people planning the operation had already set up a field lab and flown in CIA forensics people for the specific purpose of confirming Bin Laden’s death as quickly as possible.

  29. #29 Garnetstar
    May 3, 2011

    The comparison sample of bin Laden’s own DNA was no doubt acquired from a champagne glass used during a Bush dinner party.

  30. #30 Sean Boyd
    May 3, 2011

    A nice explanation of how such a process can be quickly performed. Thank you for taking the time to do so.

  31. #31 Grey
    May 3, 2011

    “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. ”

    Great to know you are so difficult to shock. I would have thought the idea that the US Government has presented a completely fantasy account of Osama bin Laden’s death and have been sitting on his death for several weeks would be fairly shocking if you believe in transparency and democracy.

    I have no complaints about the 4 hour time scale, but having a genotyping lab on the Carl Vinson or in Bagram – no one seems to know here – is more surprising.
    But I am sure it won’t surprise the unshockable Dr Wilcox

  32. #32 Misterio Vida
    May 4, 2011

    well… even if there are technologies available for on-site DNA testing, i dont think commandos carry these in their bags…and lets assume there is a state-0f-the-art lab in bagram (afghanistan and not virignia)i wonder how come they got the brain tissue from osama’s sister so quickly all the way from USA? and why the haste in burying your sample? no postmortem and nothing? but still nice blog having a lot of information on DNA fingerprinting..keep it up…

  33. #33 Mike Crichton
    May 4, 2011

    Misterio Vida :
    i wonder how come they got the brain tissue from osama’s sister so quickly all the way from USA?

    They’re had the sample from his sister for almost a year, I assumed they sequenced it a long time ago. That done, they just needed to email the saved results to wherever they were testing Osama’s DNA, and hey presto!

    and why the haste in burying your sample?

    The standard answer is that they had to get rid of his body quickly so that his followers didn’t demand it back and punctuate that demand with terrorist attacks. Doing so in an unknown location prevented his tomb from becoming a shrine.

    Personally, I would be extremely shocked if they didn’t take another tissue sample and freeze it before dumping him, though. Technically, the DNA test didn’t prove that it was _him_, just that it was a sibling of his sister. As he was the only known sibling who wasn’t already accounted for, it’s probably the correct assumption, but we’d need more samples from other relatives to be absolutely certain. But in any case, if by some freakish coincidence it wasn’t him, I’m sure we’ll hear about it soon enough.

  34. #34 Tuya
    May 4, 2011

    I am actually surprised how fast they buried him. Didn’t they want to bring him to U.S and study his brain activity, etc? It just was hard to believe it when I heard.

  35. #35 Leo
    May 5, 2011

    Great article. And a SCIAM article is already 1/2 a Nobel..

    Well done.

  36. #36 Alex
    May 5, 2011

    Tuya, I’m gonna go out on a limb here and say it’s probably difficult to study brain activity in a corpse.

    Well written article Christie; unfortunately, any discussion of Bin Laden these days seems to bring the lunatics and conspiracy theories out en-masse. Maybe you could do a follow-up on critical thinking :)

  37. #37 Misterio Vida
    May 10, 2011

    Mike Crichton

    the organization of osama, al-qaeda claims to be wahabi muslims who are against the shrines so there was no question of his tomb becoming a shrine.

    and where are international law and justice and ethics?
    the same arguments were used by Hitler and mussolini and all other dicatators but when it comes to USA and obama and bush then there is nothing wrong with committing war crimes… if the CIA was so much confident then they should have a fair trial and let the world see that justice and law prevails in the USA irrespective of the accused…

    i don’t think any court in the world even the most incompetent would be willing to accept such an evidence as the CIA had the DNA samples of OSAMA and now they claim they took DNA from the dead osama and compare them and found it to be a match? who would believe it? instead of victory, this undue haste will remain a stigma for the american people in the time to come…

  38. #38 Misterio Vida
    May 10, 2011

    Alex

    what you expected when some article is written about osama?
    there are good people in this world doing bad things and there are bad people doing good things and then there are bad people doing bad things… but science should be above all bias and prejudice… and when one think objectively the first question which comes to mind is: who made osama? and the answer will be CIA and USA. the next question should be how can a man on a dialysis machine survive in the mountains of tora bora under the showers of Daisy cutters and B52? and the answer can be either he was not in tora bora or he was killed. then the next question can be: where was his body for all those year? and the answer could be simple. on ice.
    when there is no proof then conspiracy theories are bound to pop up. that is why we were thinking that the CIA made an undue haste in burial of the body. and with that, buried the truth forever.

  39. #39 Alex
    May 12, 2011

    “what you expected when some article is written about osama?”

    I expect crazy people to pop out of the woodwork.

  40. #40 Alex
    May 14, 2011

    Alex

    so you don’t want any scientific and logical discussion? okay then celebrate the shoddy evidence and cia justice as american victory..this is why forefathers of america fought their wars? george washington and thomas jefferson would be cringing on this…

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