Landis: the odd thing about the test results

On NPR a specialist in doping described Landis results differently from the news stories. This is typical of what we're reading:

KRT Wire | 07/27/2006 | Landis denies cheating, admits Tour win will be questioned

...The test conducted at France's anti-doping laboratory in Chatenay-Malabry turned up high levels of testosterone, which medical experts say can increase stamina in the short run.

According to a statement posted on the Web site of Phonak, a cycling union official informed Landis' team that the rider's sample revealed 'an unusual level of testosterone/epitestosterone' when he was tested July 20.

The story on NPR was that his free testosterone was not in fact elevated. The epitestosterone was very low, so the ratio was elevated to about 11. Anything above 6 is out of the accepted range, so a value of 11 is extreme.

I was hoping someone on medlogs would do a more clinical analysis, but so far the press reports are just repeating the elevated testosterone line. I admit I'm harboring the faint hope it's something innocent, but I'm also curious about what would mess up the ratio. An effect of another banned substance? It's been too long since I knew my endocrinology ...

Shrillblog: The History of the Shrill

DeLong writes The History of the Shrill. Made me look back to the first post. I think I joined on the 2nd post. Been reading every since.

Damn, I'm going to have to pay the NYT so I can read Krugman again ...

The most important MS Office preferences

SIVACRACY.NET: MS Office Upgrade, With Important New Features. I loved the one about "same ... default attributes". There are so many I could add that are MS Word specific. Maybe 'Destroy document after every third style applied ...'.

DeLong's top 20

DeLong lists the twenty blogs he reads most frequently. I'll check out the few I don't know.

Hijacked by the right, a scientist disembarks

A few years back a real scientist published a well respected paper noting some cooling trends in parts of Antarctica. The author became an unwitting recruit of the arational right - including performance artists like Crichton and Coulter. He chose the New York Times as his exit from the madness. My favorite line is emphasized ...

Cold, Hard Facts - New York Times

... Our results have been misused as “evidence” against global warming by Michael Crichton in his novel “State of Fear” and by Ann Coulter in her latest book, “Godless: The Church of Liberalism.” Search my name on the Web, and you will find pages of links to everything from climate discussion groups to Senate policy committee documents — all citing my 2002 study as reason to doubt that the earth is warming. One recent Web column even put words in my mouth. I have never said that “the unexpected colder climate in Antarctica may possibly be signaling a lessening of the current global warming cycle.” I have never thought such a thing either.

Our study did find that 58 percent of Antarctica cooled from 1966 to 2000. But during that period, the rest of the continent was warming. And climate models created since our paper was published have suggested a link between the lack of significant warming in Antarctica and the ozone hole over that continent. These models, conspicuously missing from the warming-skeptic literature, suggest that as the ozone hole heals — thanks to worldwide bans on ozone-destroying chemicals — all of Antarctica is likely to warm with the rest of the planet. An inconvenient truth?

Also missing from the skeptics’ arguments is the debate over our conclusions. Another group of researchers who took a different approach found no clear cooling trend in Antarctica. We still stand by our results for the period we analyzed, but unbiased reporting would acknowledge differences of scientific opinion.

The disappointing thing is that we are even debating the direction of climate change on this globally important continent. And it may not end until we have more weather stations on Antarctica and longer-term data that demonstrate a clear trend.

In the meantime, I would like to remove my name from the list of scientists who dispute global warming. I know my coauthors would as well.

Never even thought. That is pretty definite.

There's still important science to be done about what's happening over antarctica, and there's work to be done to improve climate models and better characterize all the contributors to global warming and climate change.

There's also important social science research to be done on the nature of irrationality in the American right ....

I didn't miss his slightly strained pitch for more monitoring stations in Antarctica. I'm sure that's a good thing on the merits, but it also reflects a scientist's love for his domain of study ...

Partitioning Iraq: 2003, 2006 and Leo Strauss

Sometime between 2002 and 2003, I noted two things:

• Rumsfeld is probably not a blithering idiot
• His methods in Iraq were manifestly not consistent with his stated aims

Therefore his stated aims were not his true aims. So what where (are?) his true aims?

In August of 2003 I wrote (emphasis is new below, I corrected some spelling errors too):

Bush's mishandling of the UN and Turkey, and the failure of the neoCons to listen to listen rationally to the CIA and the State Department, has really put the US behind the 8 ball. On the other hand, I don't think things are hopeless, and I'm pretty sure the UN alone won't be able to patch things up; if the US/UK leave Iraq the country will be partitioned. (I suspect Rumsfeld's strategy was always to partition Iraq between the Turks/Kurds/Iran and Kuwait, leaving a central Sunni portion without oil revenue.)

Partitioning Iraq, and surrendering the southern portion (less the oil?) to Iran now is now a commonly proposed desperate solution. No surprises there, except I thought this would come up more last year.

Why did Rumsfeld decide to partition Iraq? That’s very speculative, even by my standards. It probably has something to with Turkey — everything does in the middle east.

It may also be that this was his second choice. Perhaps given sufficient troops, allies and resources he would have aligned his methods with his stated aims. He knew from the moment Turkey dropped out, however, that the resources weren’t there. Instead he aligned his true aims with his resources but fed the original aims to the masses. A Straussian solution.

Why all the Flash based documentation? It's about languages ...

I’ve been a bit annoyed by all the Flash based software documentation I come across. I like the speed, convenience and portability of reading. I couldn’t figure out why these small demos were taking over the world…

Until I visited the BlogJet site (my Windows blogging client, alas, there’s nothing this good on the OS X side) and noticed the developers were Russian. Then I tried the Flash demo and learned something important quickly.

A lot of my favourite applications are developed by small companies with few or no employees who can write good English language documentation. It’s far cheaper and easier for these companies to illustrate key issues using a compact and fast Flash demo.

Reading and typing were very important when I was growing up. They’ll probably still be important 10 years from now … On the other hand —– 40 years from now? Who can say. Besides, not everyone thinks in words…

 

The real estate bust and the effect of mortgage statements on consumer spending

I think I can confirm this NYT impression for the Twin Cities metro area, and also suggest a reason why it may have a quicker than expected impact on consumer spending ...

Sales Slow for Homes New and Old - New York Times

Adding it all together, a variety of experts now say, the housing industry appears to be moving from a boom to something that is starting to look a lot like a bust.

We bought and sold at the height of the boom. We couldn't wait any longer. Since we traded up I expected we'd end up with a short to longer term 5-7% loss (meaning I thought we overpaid by 10% but about half that was covered by our prior home sale). Our tough.

What I didn't expect was to have this explicitly stated in our mortgage statement.

Background first. Back when home prices were climbing, our bank began putting a number on the monthly mortgage statement reflecting the increase in equity. It was a very deliberate, and somewhat evil, move to make people feel wealthier. More wealth, more borrowing, more bank revenues. Except it also means more risk, since the rising numbers were illusory.

Economists have talked about this risky 'wealth effect' of the housing bubble, but they don't often talk about how that 'wealth effect' is mediated. In our case the bank was very explicitly communicating the 'wealth effect'.

That worked well for lenders when housing prices were going up, but for some odd reason our bank didn't turn off this number when prices started falling. So we now see a negative number -- roughly in line with my expectations.

So our bank is now explicitly communicating the opposite of the wealth effect --the poverty effect. Anyone who looks at their mortgage statement, especially those who enjoyed seeing the older rising numbers, are now seeing the falling numbers.

This direct and explicit communication may accelerate the consumer response to falling housing prices. The old delays will likely compress, resulting in a faster contraction. I wonder if the Fed is expecting this ...

Interoperability, standards, and the evolution of the codon

Standards are a big deal in healthcare IT (my industry). Standards for the building blocks of knowledge, standards for the way knowledge is assembled, standards so that software can act on knowledge and exchange knowledge between systems.

It is surprisingly hard to make the case for these standards. They have an up front cost, particularly early on. If you've got something that works, why change? The strongest argument is from economics -- even if it's tough to adopt a standard, eventually network effects will mandate its use and time will address the defects. (The hard part, of course, is knowing what the real standard will be ...) The future cost may be much higher than near term adaptation ...

Now we have a possible supporting argument from the history of life on earth. Standards adoption by proto-life was important to intra-organismal interoperability ...

The Loom : In the Beginning Was Linux?:

... Scientists have long debated how the same genetic code wound up in all living things. Why twenty amino acids? Why three nucleotides? One possibility was that it was just a "frozen accident." Another has been that it evolved in an ancient lineage and provided an evolutionary edge against others with different codes. ...

...Evolution gradually produced more precise genetic codes, Woese and his colleagues argue, but different communities of microbes evolved different codes. In each community, a shared code made it easier for microbes to share genes. If you plug a gene into an organism with a radically different code, it will produce a radically different protein--mostly likely one that is useless as well. It's like grabbing a piece of software and trying to run it on the wrong operating system.

The more microbes used the same genetic code, the bigger the pool of genes they could all take advantage of. Those shared innovations benefited the entire community as it competed with communities with other genetic codes. Imagine microbes colonizing some bizarre new ecological niche--a seep of petroleum, for example, or undersea volcanic chambers. The microbes that can take advantage of more innovations will outcompete the ones that belong to the smaller community. This advantage would also drive the evolution of different genetic codes to be more like one another, because communities of microbes would get access to even more innovations.

Over time, the benefits of a big innovation pool wiped out the original diversity of rare codes, replacing it with one universal language. Only later did life begin to lose its communal nature and begin to evolve into separate lineages that we see now as the tree of life. While those lineages produced things as different as humans and bacteria, they all share the same genetic code that evolved during that communal age.

Great analysis, but a better analogy would have been file formats and software, not operating systems and software (ok, so the distinction is blurry). Government lawyers made the same mistake in the Microsoft monopoly trial and the judge made the same mistake during the penalty phase. Data formats are far more important than software. Our software/os/interpreters are quite different from those of viruses and bacteria, but the data formats persist. Microsoft should have been forced to surrender control over their data formats -- and forget about their software.

In that regard evolution has something to teach open source movements, which historically have paid far too much attention to software and not enough attention to data. Health informatics understood this twenty years ago, and now fights over file formats with state governments indicates others are catching on ...

ID - nucleosomes and DNA control

Another example of icomprehensibly baroque and bizarre "design":

Scientists Say They’ve Found a Code Beyond Genetics in DNA - New York Times

... Having the sequence of units in DNA determine the placement of nucleosomes would explain a puzzling feature of transcription factors, the proteins that activate genes. The transcription factors recognize short sequences of DNA, about six to eight units in length, which lie just in front of the gene to be transcribed.

But these short sequences occur so often in the DNA that the transcription factors, it seemed, must often bind to the wrong ones. Dr. Segal, a computational biologist, believes that the wrong sites are in fact inaccessible because they lie in the part of the DNA wrapped around a nucleosome. The transcription factors can only see sites in the naked DNA that lies between two nucleosomes.

It's described a kind of statistical code, not directly deterministic, but on average the right places get bound. I suspect it's another variant of meaning being embedded in topology as well as sequence. Only a madman would design such a bizarre system of encoding information, yet it is incomprehensibly robust ...

Fritos flavor twists: exhibit A in the American Obesity epidemic

My wife showed me a small bag of FRITOS FLAVOR TWISTS™ Honey BBQ Flavored Corn Chips. These are the sort of thing horrible parents like us sometimes allow their poorly served children to have. This itty bitty snack sized bag contains "4 servings".

Four. 4.

Why did FritoLay corporation decide to call this a "four serving bag"? Maybe it's because one serving has 160 calories and 15% of the fat RDA. So the typical snack sized bag priced at 99 cents, has 640 calories and 60% of the fat RDA.

In other words, one bag has about half the calories the average adult needs in a day.

I used to think the tobacco companies were all alone in the pit of corporate damnation. Philip Morris, meet FritoLay.

Domesticating rats, domesticating humans

Soviet-era geneticists showed they could domesticate foxes and rats in a human lifetime. The tame animals show white spots in their fur, smaller skulls and floppy rounded ears. Now researchers are trying to figure out which genes were selected for. The same genes might have been responsible for the domestication of humans ...

Nice Rats, Nasty Rats: Maybe It’s All in the Genes - New York Times

...Richard Wrangham, a primatologist at Harvard, has proposed that people are a domesticated form of ape, the domestication having been self-administered as human societies penalized or ostracized individuals who were too aggressive.

Dr. Paabo said that if Mr. Albert identified the genes responsible for domestication in rats, “we would also look at those genes in humans and apes to see if they might be involved in human evolution.”

Human self-domestication, if it occurred, would probably not have exactly the same genetic basis as tameness in animals. But Mr. Albert said that if he could pinpoint the genetic difference between the tame and ferocious rats, he would compare the chimp genome and the human genome to see if they showed a similar difference.

One possibility is that a handful of genes — perhaps even just one — underlie all the changes seen in domestication. A structure in the embryo of all vertebrates, known as the neural crest, is the source of cells that constitute much of the face, skull and pigment cells, and many parts of the peripheral nervous system and endocrine system. If the genes in the neural crest cells were delayed just a little in coming into action, a whole range of tissues could be affected, including the maturation of the adrenal glands that underlies the first fear response of young animals, Dr. Fitch has written.

Could a single gene that affects the timing of neural crest cell development underlie the whole phenomenon of animal and human domestication? “There would be one happy science Ph.D. student if that were true,” Mr. Albert said.

Of course the domestication of humans might have occurred long before homo sapiens, perhaps in homo erectus. Or maybe it's just ongoing. There may be a tension between domestication and sexual selection behaviors; it would be easy to imagine domestication varying over the course of human history ...

Update 7/26: I didn't give enough thought to the key concept here -- how quickly this transition occurs. Eight generations for the foxes. That's not an eyeblink, it's an instantaneous flip/flop on evolutionary time scales. This wild/tame behavior smells like some kind of evolved "switch mechanism" -- the organism can range from 'viscious' to 'tame' very quickly depending on environmental changes. I think there may even be evidence of this in baboon troupes that have been isolated by rivers and the like. I wonder if this is unique to mammals or if it's seen in birds and other social animals. (Ants, perhaps?)

With this kind of responsiveness isolated groups of humans and pre-humans might have gone back and forth many times over the past million years or so, depending on the local environment. We know the level of violence in medieval times was shocking by today's standards, and we know from gene frequency studies that human evolution can act on surprisingly short time scales. Wouldn't it be interesting if anglo-saxon of 2006 were genetically more domesticated than the anglo-saxon of 1000 ACE?

Using the futures market to predict the efficacy of clinical claims to cure Alzheimer's

The BBC today headlined a claim that  Daily pill to 'cure Alzheimer's'. In mice, of course.

Now there is some justification for the interest in PBT2. It's similar to a medication that's been approved in humans, and they've done some preliminary testing for toxicity in humans. On the other hand, we can cure tons of stuff in mice, and we don't really know the relationship between amyloid and dementia.

In some amounts amyloid seems to help protect the brain from injury, so if you reduce the amyloid you might be enabling another injurious process. (Of course we know of many human disorders where the body overreacts to injury, such that the response is 'worse than the disease'. Amyloid deposition could fall into that category.)

There are a zillion reasons this might not go anywhere. On the other hand, the economic impact of slowing dementia onset is enormous. Many more people would work into their 60s and 70s. (A large number of Americans stop work in their 50s, and numbers are even higher elsewhere.) The social security problems would diminish greatly as would medicare costs (dementia is a slow and costly killer).

So one way to judge how real this is would be to look for movement in the 30 year bond rates and related markets … If one really thought this would work, there would be some interesting speculative opportunities …

Ten decluttering tips

From a web site devoted to ... decluttering. Lord, talk about narrowcasting. Great Tips however. I think my wife might go for this one.

Smoking is good for the earth, bicycling is bad

Before I tell you the story, think about the title. Why would that be true?
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It's the longevity, of course (NYT).Incredibly, a witty fellow has earned great fame by pointing out that since bicycling is associated with longevity, bicycles are bad for the environment. Hmm. Sounds obvious, and conversely, smoking is good.

I suspect the tricky part of the paper was showing that whatever one saves on the bicycle, is more than made up in more years of using electricity and consuming stuff. The caveat is that if bicycling is somewhat dangerous, and I wonder if he took the increased trauma risk into full account.

It's a funny story, but the bicyclist author has a serious point to make. Whatever lifestyle changes we make, they can be swamped by increasing lifespan. If gas prices rise we drive less and walk more, using less gas but living longer and thus using more energy ...