Update on OBL DNA test: More speculation that a lab was standing by to prepare and analyze DNA samples using new technology capable of providing a rapid result.

Typical lab-based DNA matching tests like this can take up to 14 days; they’re painstaking and need to be repeated several times to ensure the sample’s not contaminated from any other DNA sources. But that’s not necessarily the only way to do these tests: late in 2010, a University of Arizona team presented research on a machine that can do the analysis in just two hours in a largely automated way. It’s possible that knowing they were engaged on a mission to capture bin Laden, U.S. forces arranged for access to a machine like this to be on quick alert — probably for flying blood, cheek cells, and other samples taken from the body to the lab for expedited analysis.

Update: I just remembered that some time ago it was conjectured that OBL had Marfan’s syndrome, a rare disease of the connective tissue. Victims typically have gaunt features, long limbs and long slim fingers. It was thought that President Lincoln may have had Marfan’s syndrome. If OBL did have the disease, then the DNA screen could have easily been expanded to include a screen for the mutations in the fibrillin-1 (FBN1) gene known to cause the disease, and in turn used as additional prior evidence for calculating the probability of the dead man’s identity.

Undoubtedly you’ve read by now one or more reports that the man killed in Pakistan was, with 99.9% certainty, Osama bin Laden (OBL). You do not have to be a conspiracy nut or deeply skeptical of any government claim to be critical of this particular claim. I happen to believe the man killed was very likely OBL, a claim importantly different than the one stated – 99.9% certain. Reading people’s comments to the various news reports, many appear confused or incredulous over a couple things:

1. If the government did not already have a DNA sample from OBL, what did they compare the sample from the dead man to?

Most likely his (putative) sister [1,2]. The most common DNA test to perform in this situation is one which compares specific portions of the nuclear DNA extracted from the samples, portions called “short tandem repeats” (STR). Without going into detail, the more related two people are the more similar their STRs will be. Comparing the STRs from the dead man’s sample to the STRs of the (putative) sister would allow one to make a claim of the likelihood of kinship of the two people, but not a claim of x% certainty of identity of the dead man. That’s different:

The key distinction, Thompson says, is that the results speak to the probability of a relationship between the two people, not the actual identity of the dead man. “If the DNA test compared the profile of the man shot in Pakistan with bin Laden’s family members,” Thompson says, “the results could properly be presented only as a likelihood ratio, stating the relative likelihood of observing the particular markers found in the dead man if he were, say, the father or brother of a known bin Laden family member, than if he were a randomly chosen individual.”

2. A DNA test could not have been performed this rapidly – in less than 24 hours of the killing the government had made its claim of 99.9% certainty of identification.

I don’t doubt the test could have been performed this quickly. Preparing a sample for that type of test and performing it (see PCR) could be accomplished in under 24 hours in a competent lab equipped with a modern sequence analyzer. It seems to me reasonable that the lab would have needed to be told in advance to get ready in order to complete it this quickly, but that is by no means impossible or even unlikely. After all, this operation had been planned for some time.

Expanding a bit on point #1: One can convert transform a likelihood ratio into a probability. Statisticians especially regard the two measures as technically different. In order to do this you need to quantify other prior evidence of identity and/or relationship. For example, comparing a photograph of the dead man to a previously obtained photograph of OBL could be one basis for such a prior probability, something clearly the Seals who did the killing could have done. Another possibility is that the lab also compared mitochondrial DNA (mtDNA, different from nuclear DNA) from the dead man and the putative sister. Since 100% of everyone’s mtDNA is inherited solely from their mother, then if the mtDNA from sister and dead man matched that too could be used as prior evidence. As could a Y-chromosome comparison between the dead man and a (putative) son; evidently OBL had many. The reports I read did not provide the details of the actual tests performed.

Performing all this analysis in such a short period of time would be very challenging, and necessary to achieve a statistical estimate of %certainty of identity, which is why I am dubious of this specific claim. But given the tests which were most likely performed in this short period of time, I can easily believe the man killed was very likely OBL.

Update: Inter-sample contamination is also a concern when performing DNA tests, but I am not so cynical as to think that this was a problem in this case.

One advantage of using the WordPress software is the companion app available for smart phones, the Android app in our case. It’s a tight little app, useful for creating, editing or deleting posts, and it provides most all the features of comment moderation available in the main application. When a new comment arrives I’m notified within minutes (you can set the app to scan the blog every n minutes or hours). If it’s spam, one touch flags it as spam and updates the blog instantly, no matter where in the world I happen to be. Not that I’m a member of the jet set. That’s not what the “Air” in Airedale means.

No tiara or horse drawn coach. No cheer from a royalty-enthralled throng. Still, every bit a fairytale from start to present. Just look at ’em.

Spring has paid ransom to winter. Life unfolds, water unfreezes; everything that winter had done is undone. Soon brown will yield to green and all will have been paid in full.  The snow is gone, the sun beams sixteen hours daily, the streams are swelling and somewhere in deep ocean water the salmon are stirring. Here at home, in the middle of our yard, a scar emerges as a reminder of winter’s dig to repair the septic break. Several of our  trees were pruned courtesy of a famished, winter moose undaunted by our six foot fence. What doesn’t kill you makes you stronger.

Easter weekend the uprights tootled down to Soldotna, AK to spend a few days with friends at their house on the Kenai River. Yes, that Kenai River, where men are men and salmon are frightened. No salmon yet but they’ll show up. In the meantime, Mom stepped down to the River’s edge (in Master’s shoes) and dispersed several chunks of freezer-burned salmon onto the ice left stubbornly clinging to the shore. Scamper back up to the house and wait inside for the eagles to swoop down and take the salmon away. Across the river moose congregated and ate what they could find, then bedded down at night to rest so they could wake refreshed and start all over again the next day. A word of caution to you moose: when the salmon return so will the bears.

Yours truly with the wind in his hair. Cook Inlet looms in the distance. We never tire of this. Under ten minutes from our house.

A sobering point of view of the future from Arnold Kling [1].

The two unavoidable facts of life. The misery of this head ‘n chest cold I’ve suffered the last few days had me wondering if the former was nigh. So I set myself to the other unavoidable fact. I discovered I did a very poor job of tax planning this year. Ordinarily we could rely on a tax refund, a few hundred bucks, sometimes more. This year – spank! The amount we owe to the feds should be enough to pay for our own warhead – our names etched lightly on the tip of the ordnance: “Courtesy of the Nibbe family. Enjoy!” A sturdy expression of participatory democracy, a direct connection between the means and the end. In that spirit I have suggested that the 1040 include check boxes for the taxpayer to indicate where (or where not) she wants her tax dollars spent. Like the United Way does. My guess is that this would put an end to The War on Drugs lickety-split. And I imagine a great deal of other government profligacy as well. Instead, we have no idea, or more correctly no direct say, in how our tax dollars are spent. Supposedly, all the money is placed in a big pot of munificence to be later doled out by benevolent-minded folks who swore to protect and serve TheAmericanPeople^®. I’m sure that happens to a limited extent. Increasingly, much of it now goes to pay interest on a debt incurred by having to borrow to pay for ever more profligacy past promises and obligations. Before too much longer we (my bride & I) will, ourselves, become obligations.

One consolation of the first inevitable fact of life is that it brings a merciful end to the second.

Wow. Just wow.

Five years to begin growing do-it-yourself eyes in humans seems overly optimistic, but thousands of blind people and others with deteriorating retinal function surely hope not.

So I just Shazam‘d myself singing – with great verisimilitude I thought – Moonshadow by Cat Stevens. While seated in our car in the Costco parking lot.

Shazam returned: “Sorry, we couldn’t find a match for this music.“

Which is not to say it was bad music. Merely that Shazam has not yet captured to its database the Acapella silk of my voice performing Moonshadow.

Still, a stunning application for $4.99, or better yet free if you happened over to Amazon this morning as I did. A promotion for the opening of their app store for Android.

According to one of the creators of Shazam, the software relies on a database of >8 million songs, each of which has been decomposed into multiple numeric, digital signatures.

I haven’t seen it produce a false positive yet.

While out walking on a mountain trail we all were treated to a beautiful view of the western mountains eclipsed by a superior mirage – the Fata Morgana. The eyes don’t know any better, they report to the brain what they see – a flat,  unbroken, snow-covered plateau stretching far to the north and south. Your brain pauses, searches memory. Confusion renders. Wait, last time we were here there were soaring, jagged peaks over there? A breach of trust occurs. The brain says, Eyes, I am downgrading your sensory trust level. Your report does not accord with what I have stored in memory. A dispute erupts. The optic nerve blames it on the retina who, it claims, improperly fixed the light waves (photons) in the first place. No, the retina reacts, my fixation was not improper, your transduction of what I sent you is faulty! In the meantime – we’re talking quantum time here – the brain quickly defers to the other four senses desperate for accurate reports on what’s going on, out there, in reality.

The following day, the dispute resolved, we were all out again on another trail when suddenly we came upon a Lynx! It was clearly undaunted by our presence, hunting a squeaky squirrel that had sought safety in the high branches of a tree. While Mom secured Lucy and me, Master alertly removed his phone from his pocket and walked slowly toward the Lynx.

Love his poetry. Spare and gut-felt.

Godspeed, John.

Years ago a friend gifted me a broadside he had done on John’s work. I framed it; it now hangs on my office wall.

Poem of the Forgotten

I came to this place,
a young man green and lonely.

Well quit of the world,
I framed a house of moss and timber,
called it a home,
and sat in the warm evenings
singing to myself as a man sings
when he knows there is no one to hear.

I made my bed under the shadow
of leaves, and awoke
in the first snow of autumn,
filled with silence.

– John Haines