Twenty-five years ago the process of identifying someone by typing their DNA was extremely difficult and time consuming. It was not done on a large scale.
Fast-forward to today, where we are told that the military and the CIA were able to genotype Osama bin Laden's DNA and identify him with 99.9% certainty in less than 12 hours.
How is this possible? Following is a primer on the current state of DNA forensic technology that answers this question and raises others.
First, however, full disclosure: I am no fan of President Obama's policies, particularly his decision to extend tax cuts for the wealthy and his willingness to buy into Republican frames by focus on the deficit. That being said, I am perfectly willing to give him total and full credit for planning and authorizing a gutsy military operation if he can prove it was bin Laden, both because that would be the right thing to do, and because I think it can get us out of Afghanistan (see below). Second, particularly in light of Benazir Bhutto's statement in November 2007and because I believe the War on Terror was ginned up by the military establishment to increase military spending for reasons of empire building (and BTW thereby create thousands of new Republican voters), I will believe that Osama bin Laden was killed when I see some evidence, and will not just trust the word of various CIA and military officials. Finally, even if bin Laden is not dead, I do believe we can and should use the "Witch is Dead" theme to extract our country from the Oz-like PermaWar footing we have been on for the last decade (more on this later).
This diary will attempt to explain how military and CIA officials could genotype bin Laden's DNA within hours after he was killed and do so with such a high level of certainty that they could bury bin Laden at sea so that no further testing was needed (or possible).
A Brief History of Forensic DNA Genotyping for Identification
As you many of you in our reality-based community know, Watson and Crick correctly predicted the structure of the DNA molecule in 1953. For this prediction and their empirical confirmation of it, they were awarded the Nobel Prize in 1962.
In 1982, relying on seminal work by a Pakistani/Indian scientist named H. Gobind Khorana, a surfer and scientist named Kary Mullis invented the polymerase chain reaction, or PCR. This enabled the scaling of DNA analysis in that sequences of DNA could be amplified (or replicated) in high volumes.
Later in the 80s, two forms of forensic DNA genotyping for identification in criminal investigations were introduced. The first was called "RFLP" or Restriction Fragment Length Polymorphism, and the second was "VNTR" or Variable Number Tandem Repeatanalysis.
In 1989, forensic DNA genotyping became popularized in a book by Joseph Wambaugh called The Blooding.
Court Challenges to DNA Forensic Genotyping for Identification
Both RFLP and VNTR testing were gradually introduced in both state and later, federal courts in the United States. Initially, there was little opposition, but soon a groundswell of opposition developed because DNA testing as practiced at that time was both difficult to justify from a population genetics standpoint, and was prone to cross-contamination.
With regard to population genetics, the problem was that only a small number of sites, or alleles, on the suspect's or victim's DNA were being probed. This reduced the power of the technology as a means to identify the individual.
With regard to cross-contamination, the problem was that in some cases forensic laboratory workers did not use proper procedures to analyze the DNA sequences, resulting in contamination of the samples that produce false positives, i.e. matches that were incorrect. In other cases, some forensic laboratory directors actually committed crimes by knowingly mixing DNA from the suspect with DNA found at the crime scene in order to obtain convictions for the prosecution.
These resulted in court challenges to the use of DNA forensic technology to convict criminals.
VNTR Technology Improves - STR becomes gold standard
Meanwhile, the technology continued to improve, and in the early to mid-1990s another type of forensic DNA technology called STR, or Short Tandem Repeat analysis emerged. STR analysis enabled scientists to test a larger number of sequences in order to increase the power and confidence of the results.
Today STR analysis is the standard and as part of that analysis, 13 sequences or loci are tested for each sample that will be used for identification in the United States.
However, these sequences and loci are only sufficient under certain circumstances, for instance when an individual is being matched to a sample at a crime scene.
In cases of paternity or lineage where the individuals who are being matched may be half-sisters or distant relatives, the number of loci may need to be increased.
Questions About The Timing and Processing of STR Analysis on bin Laden's Sample for Identification, and About The Population Genetics Underlying the "Match"
STR analysis can be conducted quickly but must be done in a laboratory setting with a large machine that is optimized to conduct such analysis in large batches. In the case of bin Laden, there are many such machines available at major research universities, and the military presumably also has the technology available in its forensic typing operation near Denver, CO. The CIA probably also has its own machine or access to a machine near Washington, DC.
However, this means that the sample must have been extracted from bin Laden's body and then flown from Pakistan to the United States processing facility. This is a trip of up to several hours by plane. Then the samples must be prepped and processed and the analysis completed.
In addition, to ensure that a match is reliably identified, courts require that a chain of custody from the time the initial sample is collected until it reaches the testing facility (or courtroom).
Finally, here we have significant uncertainty over who exactly was used to "match" bin Laden's DNA. If it was a half-sister or other distant relative, the number of loci used to call a match must be increased to provide reliable identification.
Here are at least three relevant questions the media should be asking:
1. How, exactly, the sample was processed and where and by whom was the analysis performed?
2. Since cross-contamination is a significant risk in DNA forensic technology, what steps were taken during collection to ensure that blood spatters did not contaminate the sample and that custody was preserved with integrity on the trip from Pakistan to the testing facility?
3. Why was bin Laden's body buried at sea where no one could find it before positive forensic DNA identification was made?
4. From whom, exactly, were referent samples taken for analysis?
All in all, from death and sample collection to final results, if we assume the testing was performed stateside, I think one must conclude that the entire process must have taken more than 12 hours.
That, combined with the issue of population genetics regarding bin Laden's half-sister has quite rightly now led the NY Time to publish their piece linked above about DNA analysis. These are interesting questions, and they should be answered.
Updated by maxschell at Tue May 03, 2011 at 01:13 PM PDT
Semiot's comment below quite lucidly states that if we accept that Obama is rational, then bin Laden must be dead. As Zedaker also notes, it is likely the CIA/military kept tissue samples. Given these two points, it should not be a problem to provide DNA evidence that the man killed on Sunday and buried at sea was bin Laden. And it can be proven without the need for gory pics.