Oh, Sweet Solids

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 GABAA 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 Post

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.

99.9% Certainty It Was OBL – Really?

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.

Yeah, Have A Nice Day

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

I don’t think of the long-term budget fight as being between Democrats and Republicans or between rich and poor. I look at it as a fight between people with funded retirements and unfunded retirements.

If I have saved enough to support my lifestyle in retirement, then I have a funded retirement. If my neighbor who teaches in public school wants to support a similar lifestyle based on her pension, then she has a retirement that is somewhat unfunded. That is, as of now, her pension plan has only about fifty cents for every dollar of promised benefits.

Social Security and Medicare also are unfunded. Their “trust funds” consist of government bonds. If I took care of my own retirement the same way, the drawer where I keep statements from mutual funds that I own would instead be filled with IOU’s from myself. More important, the actuarial shortfall in Social Security and Medicare, like that in my neighbor’s pension plan, is very large.

Down the road, someone is going to get the shaft. It could be my neighbor, it could be me, or it could be both of us. That is, people who are relying on the unfunded systems–public sector pensions, Social Security, and Medicare–might find their benefits cut. Or people who are relying on personal savings could wind up having those savings taxed away in order to address the shortfalls in the public systems. Or all of us could have our savings eroded by inflation, from which we may not be able to protect ourselves.

Have a nice day.

1. Hat Tip Instapundit

Death & Taxes

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.

Sing To Me

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.

R.I.P. John Haines

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

Voices

A perfectly miserable day. Bluesky. Nary a breeze. A prescient 38 degrees.

I say prescient because can there be any doubt that Spring is nigh!

Spirit-filled, I lifted the Santa Cruz off the J-hooks, re-aired the tires, oiled the chain and set out on this year’s debut ride. In an ordinary year I would have been out riding several times by now, but this year I didn’t bother to put studded tires on the bike, in part because I’ve been too damn preoccupied. Besides, today riding on slightly under-inflated knobbies was all that was required, most everywhere the trail surface was  tacky and sticky. I pedaled a brisk 8-10 miles through Anchorage’s southern neighborhoods. The familiarity felt good. Like a walk in the mountains with the dogs a bike ride centers me. Introspection comes easy and it’s not unusual that I find myself talking to myself. The beauty of this symmetry is you always win an argument should one arise, the tragedy being you always lose.

As I pedaled about I thought about our science and where to take it next. Sometimes an idea will come to me and I feel an urgency to write it down lest I forget, but then I think, if it’s an idea of merit I won’t forget it. I should know better by now. When I was in the lab conducting experiments I never got into the useful habit of quickly committing important results or findings to my lab notes, I would leave that for the end of the day, but inevitably I would occasionally forget things. Why do we sometimes ignore our own good advice? ‘Tis a mystery.

Who’s Lying?

I was recently made aware of an article that appeared at Forbes.com, titled:

The Wisconsin Lie Exposed – Taxpayers Actually Contribute Nothing To Public Employee Pensions

How can this be? For those public employees whose only source of wages is a paycheck from the state, all their compensation comes from the taxpayers. So what’s  going on?

The author bases his claim on something written by another person at Tax.com (url provided), who argued that Scott Walker, by saying that state workers should contribute more toward their pension and medical benefits was “casting the impression” that state workers presently don’t pay anything toward their pension plan, and that the contribution is actually an additional “gift” from the taxpayers. This author went on to say that state worker’s pensions are really funded by money that is part of the employees overall compensation package, negotiated by the union that represents them in collective bargaining. Hence, he says, employees’ pensions are really funded entirely by their own compensation, and taxpayers contribute nothing.

The Forbes author picked up on this and concluded that Wisconsin taxpayers were lied to by Scott Walker.  But I don’t think anyone in Wisconsin is really confused about where a public employee’s compensation comes from, or what Scott Walker meant by contribute more. Many commenters to the Forbes article certainly weren’t confused.

The point here isn’t to argue for Dems or Repubs or Tea Party or any of that. The point is honesty in reporting. In a supposed attempt to expose a lie, the author arguably committed one. At the very least he presented a straw man argument, although his replies to certain commenters indicates he doesn’t understand why.