Rod's Alter Ego

A friend of mine who lives in New Hampshire is flying to Portland, Oregon tomorrow to meet his father in-law. Together they will ride their bikes to the other Portland. The one in Maine that is. Four thousand miles. They figure it’ll take them 9-10 weeks. They’re blogging the adventure here. They’re soliciting donations for two charities; leave a comment if you’d care know which ones.

Weather here in Alaska has moderated a bit. Cooler today, but sunny and pleasant. We dug up the trees that were ravaged by the Moose this past winter and replaced two of them with Mayday trees. We placed them (we hope) sufficiently far enough away from the fence so as not to tempt moose to lean over and eat them, or worse, crash through the fence again and ravage them. We had the area in the backyard where the septic was repaired this winter re-graded and seeded. Already there is a soft, dense green whisker emerging. In a few weeks we’ll be mowing. Just in time for my parents visit! They will be here the first two weeks of July. Last time my father was here was close to twenty years ago.

In the meantime me and the misses missus celebrated our 5th wedding anniversary. Like it was yesterday. Pictured here at her boss’s wedding this past Saturday in Big Lake, AK.

If summer sunshine is a zero sum game, then…  well, let’s not talk about that, or you know what will happen. An outstanding day! In fact, the entire past week or more has been outstanding, weather-wise. Bluesky and 70+ degrees today, Memorial Day – meaning it’s not yet June in Alaska. Mentioning this only threatens to bring the roof down. So I’ll shut up now.

A picture or three.

The sun and bluesky started days ago and it made us all kind of giddy, including my wife:

The mountain trails are clear and ready. Couldn’t resist a ride to the top of the “Bee” trails, and down again. Near the top, ready to descend Yellow Jacket. Anchorage looms in the distance:

Today on the road bikes, heading toward Girdwood, 35 miles south of Anchorage. Wife shows off:

Rocking the final climb, on the way back home. My steed in the foreground:

Part Terrier, of course.

A big fat Pfft to that rapture nonsense. We’re still here. Nevermind that. Next we’ll hear that some who were formerly among us no longer are. Conclusion: Gone in the Rapture! Uh huh. The old evidence from absence trick. Until weeks later when one or more of them is spotted incoherent and stumbling about in someone’s backyard. Then it will be spun as evidence of a sign – “They’ve been returned to us to foretell the next rapture!” And this time you all better believe it.

Where are the scientists eager to find “the gene” for this gullible behavior. Are these people hard-wired to be gullible? In which case we, qua disbelievers, should substitute sympathy for ridicule. Or: Does holding silly beliefs actually improve an individual’s evolutionary fitness. Perhaps believers have more and fitter children? The  questions suggest a straightforward experiment to begin. Gather up a few thousand of the gullible and a similar number of disbelievers. Take a buccal swab from each and send it to 23andMe. They perform the genome wide association study (GWAS). Identify polymorphisms statistically significant for the gullibility phenotype. Results are summarized and published in a high-impact journal; cc CNN.

Done.

Okay…

So we are recently back from Seattle where I attended a provocative conference on systems biology and the future of translational medicine.

It wasn’t all work. And speaking of enraptured: We found the Dahlia Lounge

A friend remarked that the photo belies my wife’s real age. Me not so much. He was right of course.

Our colons – my bride’s ‘n mine – appeared almost unused, judging from the pictures. Which I won’t share with you, you’ll have to take our word for it. The stuff they’ve seen digested in fifty one years. My God.

We were both put on the ten year followup plan.

As the Versed tickled my GABA_A receptors, my last malformed sentence to the gastro-guy must’ve sounded like Mr. Bill under the broiler.

In recovery, still somewhat mush-mouthed,  I asked when I could expect the doctor to come by and share the results with me. “He was just here, Mr. Nibbe,” said the nurse.

Well, yes, of course he was… just here. I thought. At least I think I thought.

Well aware of the half-life of Versed the nurse wasn’t the least bit concerned by my brain fart, and reminded me to expect more than the average number of  usual farts in the next hour or so.

“It’s not gas,” she reassured me. “Merely medical air. Don’t resist expelling it.”

I lost four pounds prepping for the procedure. I now have the same revulsion for Jello and chicken broth as I did for Peach Schnapps in high school.

The evening  after the procedure, when solid food was once again indicated, I put back on two of the four pounds.

Moral: never, ever, take mastication for granted.

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].