Red Slayers

Flies meticulously tied with generations old wisdom. The fly rod balanced, perfect, well-worn but ready. Alone, you weave your way along the bank of a serene stream. A warm breeze ripples the water. Your secret hole cuddles a cut bank. The philosophical arc of the line; your first cast. The fly lights on the water, disappears in a sun glinted eddy. Drift. You wait, expectant. All is calm. Until, that first strike!

The quintessential fishing experience, right? Not ours! Instead, we – my bride and I – donned our chest waders, put on our slop boots, slogged along a muddy bank at low tide, stepped into the icy, silty water of the Kasilof river where it empties into Cook Inlet, shouldered our way into position among countless other netters, and noisily awaited the push of red (sockeye) salmon.


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For an hour or more all we did is sift water. We felt foolish, outwitted by the fish. Because you can’t see them run, the water is too murky. Someone standing next to me claimed he felt one bump into his leg. And I thought, “Maybe they’re swimming upstream behind us!” Clever suckers. Nutty Alaskan kids running barefoot through the surf. It was a mystery how they avoided turning blue.

But the weather was fabulous!

Mount Redoubt Volcano looms in the distance.

Dip netting is a uniquely Alaskan experience, as only Alaskans are legally allowed to dip net for personal use catch, which is 25 per person, and an additional 10 for each household member, none of whom need be present to fish for themselves. My bride and I fished the evening high tide, spent a sleepless night camped on the beach, thanks to the all night partiers camped next to us, and then I trundled out of the tent early (3 am!) and fished the morning high tide. We came home with ten in the cooler, just like these:

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When you consider we had to clean, fillet, vacuum seal and freeze these bad boys (actually, 3 were female) ourselves… well, it was a blessing we didn’t get more. Should last us through winter.

Next year, as Arnold says, “We’ll be back.”

So Long Sol

Behold: His ‘n Her Copper River red salmon fillets. Lightly brushed with evo and dusted with Johnny’s seasoning salt. Mine with a sprinkle of tarragon, hers without. Hot grill ~12 minutes.

They account for not even a smidgen of the total commercial harvest this year from the Copper River. And this one made it past the gauntlet of commercial nets, thinking it was on its way to reproductive success, only to be thwarted by a sport fisher further upstream.

We are over the solstice hump; the sun set ~30 seconds earlier than yesterday. And still you could tee off at 8 pm and easily get in 18 holes. I am famous infamous among friends for the reminder each year that the days are getting shorter. This year I made the announcement on a friend’s backyard deck during the first hour of one of our frequent soirees. Under bluesky and beaming sunlight, and having just emptied the bottle of Tempranillo Reserve (2004) I had brought, the annual indiscretion went almost unnoticed, receiving only a mild scolding from the person who heard it. Good food, friends, and wine can compensate for a number of bad behaviors. All were present in abundance that evening.

Desert Nostalgia

Reading around the web today got me to thinking about creative writing. How much I used to enjoy it. Here’s a quiet essay I wrote about fourteen years ago that got some nice comments, and was even selected for publication in a University anthology. One person commented that it read like a prayer. After all these years it still gives me goosebumps to read it.

On Detecting Good Genes

One of my pet peeves is the oft repeated claim that the basis for one’s affection for another person is rooted in a desire for their genes. Something traceable to our “Caveman” days.

An example of this claim I read recently was made by someone talking about the Wiener affair. She explained – feebly I thought – why women should not pick attractive husbands. Excusing women (and men) for how they are “wired” to pick a mate she said this (bold emphasis mine):

But who can blame her? She, like so many women — and men — pick a mate based on pretty predictable factors, dating back to caveman days when all we were trying to do was survive and keep our species going, according to physical anthropologist and Why Him? Why Her? author Helen Fisher, who has been studying human courtship for decades. We’re drawn to guys like Weiner because they have good genes we can pass on to our kids. The downside is that we take a huge risk on whether he’s going to be sexually faithful to us.

There’s so many problems with the claim it’s difficult to know where to begin my criticism. First of all, men and women are not drawn to each other based on an affection for genotype; if anything they are drawn to each other based on phenotype, i.e. broadly on the features and behaviors the other exhibits. It is not possible to know simply by assessing somebody’s phenotype whether they have good genes or bad genes. One reason is that for the vast majority of human phenotypes, even those we might want our children to inherit, we have no idea what genes are involved. Take intelligence for instance. Undoubtedly, there is a genetic basis that explains some variability in intellectual ability. Although we don’t know what that genetic basis is precisely, we do know that environment and learning play a huge role in outcome. So if your goal is to have smart children, then you are as likely, or maybe more likely, to get them if you raise them in a learning environment similar to the environment other smart people experienced in their formative years, than by trying to identify a mate with “good” genes. Again, for the simple reason that we don’t know what genes code for intelligence, even if one somehow could detect “good” genes.

For the record, I share the belief of many systems biologists who think intelligence, like other complex phenotypes, can not be explained by the activity of one or a few gene products.

Another basis for my criticism is that, even if you believe that phenotypes (traits) are directly encoded by the genes, you would still fail to detect the “infidelity” gene(s) in Weiner because he is deliberately keeping that behavior secret from potential mates. I’m certain his wife was unaware of those “bad genes” when she married him. Had she been able to detect the “infidelity gene” in Weiner, and wanted to save her son (or daughter) from inheriting this perfidy, presumably she would not have married Weiner. Just as a person who, assuming their primary concern was the quality of their children, would hesitate to marry another person if they knew that person had a bad gene that might recombine during meiosis with their own bad copy to cause a debilitating disease in their child.  This is the basis for certain Mendelian disorders in children, caused by inheriting a bad (recessive) gene from both parents, nether of whom is affected. The biggest reason many of these diseases are not prevented in children is not because we don’t know the bad gene(s) involved, sometimes we do, but precisely because, contrary to what the author of the article claimed, we can’t detect by observation if a person has “good” genes or “bad” genes.

I think the reason people continue to repeat this silliness – generally, that what we do as humans is explained by our genes and our desire to mate with someone with “good” genes – owes to their being duped by an increasing number of books and pop science articles related to evolutionary biology, many of which greatly oversimplify human biology in order to account for what we do or why we do it. These people don’t understand the actual science, or the corresponding limitations of our present knowledge.

UPDATE: In the event you are skeptical that any scientist would take the idea that there is a human gene for infidelity seriously: here you go.

Summer Breeze

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.

Another Alaskan For Global Warming

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:

Ridicule or Sympathy?

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.

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.