Friday, February 25, 2011

Shame of the Smithsonian

Shame on us ...

The billionaire Koch brothers’ war against Obama : The New Yorker

... The David H. Koch Hall of Human Origins, at the Smithsonian’s National Museum of Natural History, is a multimedia exploration of the theory that mankind evolved in response to climate change. At the main entrance, viewers are confronted with a giant graph charting the Earth’s temperature over the past ten million years, which notes that it is far cooler now than it was ten thousand years ago. Overhead, the text reads, ‘HUMANS EVOLVED IN RESPONSE TO A CHANGING WORLD.’ The message, as amplified by the exhibit’s Web site, is that ‘key human adaptations evolved in response to environmental instability.’ Only at the end of the exhibit, under the headline ‘OUR SURVIVAL CHALLENGE,’ is it noted that levels of carbon dioxide are higher now than they have ever been, and that they are projected to increase dramatically in the next century. No cause is given for this development; no mention is made of any possible role played by fossil fuels. The exhibit makes it seem part of a natural continuum. The accompanying text says, ‘During the period in which humans evolved, Earth’s temperature and the amount of carbon dioxide in the atmosphere fluctuated together.’ An interactive game in the exhibit suggests that humans will continue to adapt to climate change in the future. People may build ‘underground cities,’ developing ‘short, compact bodies’ or ‘curved spines,’ so that ‘moving around in tight spaces will be no problem.’

The Koch brothers are immensely wealthy bankers of the Republican War on Reason. In addition to funding attacks on health care reform, government of all forms, and environmental regulations, they fund a variety of organizations designed to block CO2 regulation.

That's a bad, but the behavior of the Smithsonian is much worse. Omissions speak loudly.

UnReason: The Republican War on Reason

Gay marriage is a done deal. That culture battle is done. We lost the gun wars, but we won on Gay rights.

So now peace has broken out across the land, and all Americans are respectfully negotiating to a common end, recognizing that we do have fundamentally different thoughts on what the strong owe the weak.

Cough. No, of course not. The latest battle in the Culture Wars is the Republican War On Reason. This time it's not merely a War on Science, it's a War on Reason in all forms. The GOP has become the UnReason party, where agnatology is a shibboleth (emphases mine) ...

... agnotology, the study of culturally-induced ignorance or doubt. Agnotology is not, primarily, the study of ignorance in the ordinary sense of the term. So, for example, someone who shares the beliefs of their community, unaware that those beliefs might be subject to challenge, might be ignorant as a result of their cultural situation, but they are not subject to culturally-induced ignorance in the agnotological sense.

But this kind of ignorance is not at issue in the case of birtherism...

Rather, birtherism is a shibboleth, that is, an affirmation that marks the speaker as a member of their community or tribe...

This worship of UnReason was strong in the Bush years, when a "senior Bush advisor" (Cheney? Rumsfeld?) disparaged the "reality based community" ...

... guys like me were 'in what we call the reality-based community,' which he defined as people who 'believe that solutions emerge from your judicious study of discernible reality.' I nodded and murmured something about enlightenment principles and empiricism. He cut me off. 'That's not the way the world really works anymore,' he continued. 'We're an empire now, and when we act, we create our own reality. And while you're studying that reality -- judiciously, as you will -- we'll act again, creating other new realities, which you can study too, and that's how things will sort out. We're history's actors . . . and you, all of you, will be left to just study what we do.'

Obama brought us back in into the world of the rational, but the UnReasoners didn't go away. They are the core of the Tea Party, and they are back with bells on ... (via Capital Gains and Games)

The Rise of the Budget Fundamentalists -- Daily Intel

... There’s a growing consensus that the government could be forced to shut down next month as emboldened Republicans demand spending cuts that Democrats can’t stomach, and that even some conservative experts say aren’t feasible...

... “What you’ve got to understand is this is an emotional issue, not a rational issue," says budget guru Stan Collender, a veteran of both House and Senate budget committees who puts the likelihood of a shutdown at 90 percent. “As far I can tell it has no theoretical economic underpinnings, which is why it’s so difficult for the budget these days to be discussed, because statistics don’t mean anything, equations don’t convince anybody. It is almost a religious belief.”

Perhaps more than “almost.” The tea party has a reputation for secularism, but in fact it’s deeply rooted in the religious right. The GOP’s tea party freshmen made their leanings clear by going after insurance coverage for abortion and funding for Planned Parenthood, but their faith informs their economic stance as well. “It's no coincidence that socialist Europe is post-Christian because the bigger the government gets the smaller God gets and vice versa,” Senator Jim DeMint, one of the Tea Party’s major Senate supporters, told the Christian Broadcasting Network last year ...

From Climate Science to economics, the GOP has been the party of UnReason since the age of Reagan.

So will the GOP indeed destroy the US economy in the next few months? My prediction is that they won't, because while individuals can be both powerful and irrational, Corporate entities are more predictable. I think the Tea Party House will heed their true master's voices.

See also

Wednesday, February 23, 2011

Health insurance - Americans are sheep

Health reform discussions are boring. I wish could resist health care reform posts. It's a compulsion, but at least I only do them every few months.

We've known for decades where will end up. We will guarantee every American good enough health care. Good enough care means 21st century American versions of "barefoot doctors" using relatively cheap technologies that have been fully depreciated. People with money will still buy more luxurious care; sometimes it will be genuinely better care.

Good enough care will use more physician assistants, not because they're wonderful people [2], but because they're paid like teachers instead of like radiologists [1]. It will outsource pathology and imaging to New Zealand and Israel. It will negotiate cut-throat prices with manufacturers of off-patent drugs, and it will fight patent law dodges. Good enough care will have simple contracts and pricing, reducing the overhead of care provision.

ObamaCare is a significant first step to good enough care [4], and, unlike ClintonCare, it leaves lots of room for the concierge-care end of the luxury health market.

Darn, this isn't quantum mechanics. It's not even relativity. It's arithmetic. So it's agonizing that we Americans are such sheep. We elected a House of loonies dedicated to preserving this status quo (emphases mine) ...

Money Won’t Buy You Health Insurance - Donna Dubinksy [3] -

... Unlike many others, my family can afford medical care, with or without insurance.

Instead, this is a story about how broken the market for health insurance is, even for those who are healthy and who are willing and able to pay for it.

Most employees assume that if they lose their job and the health coverage that comes along with it, they’ll be able to purchase insurance somewhere. The members of Congress who want to repeal the provision of last year’s health insurance law that makes it easier for individuals to buy coverage must assume that uninsured people do not want to buy it, or are just too cheap or too poor to do so.

The truth is that individual health insurance is not easy to get...

... An insurance broker helped me sort through the options. I settled on a high-deductible plan, and filled out the long application. I diligently listed the various minor complaints for which we had been seen over the years, knowing that these might turn up later and be a basis for revoking coverage if they were not disclosed.

Then the first letter arrived — denied. It never occurred to me that we would be denied! Yes, we had listed a bunch of minor ailments, but nothing serious. No cancer, no chronic diseases like asthma or diabetes, no hospital stays.

Why were we denied? What were these pre-existing conditions that put us into high-risk categories? For me, it was a corn on my toe for which my podiatrist had recommended an in-office procedure. My daughter was denied because she takes regular medication for a common teenage issue. My husband was denied because his ophthalmologist had identified a slow-growing cataract. Basically, if there is any possible procedure in your future, insurers will deny you.

... As I filled out more applications, I discovered a critical error in my strategy. The first question was “Have you ever been denied health insurance”? Now my answer was yes, giving the new companies reason to be wary of my application. I learned too late that the best tactic is to apply simultaneously to as many companies as possible, so that you don’t have to admit to a denial.

I completed four applications for each of the three of us, using reams of paper. ... I was accepted by exactly one insurance company. So was my daughter, although at a 50 percent premium over the standard charge for a girl her age. My husband was also accepted by one insurer but was denied by the company that approved me.

Our premiums, which were reasonable at first, have increased substantially over the last six years; the average annual increase has been 20 percent. I now am paying premiums that are more than double what they were initially. And because these are high-deductible policies, we still are paying most of the medical bills ourselves...

... If members of Congress feel so strongly about undoing this important legislation, perhaps we should stop providing them with health insurance. Let’s credit their pay for the amount that has been paid by the taxpayers, and let them try to buy health insurance in the individual market. My bet is that they all would be denied. Health insurance reform might suddenly not seem to them like such a bad idea.

Americans tolerate this. We have tolerated a broken system for a decade.

It's worse than mere tolerance though. Against enormous resistance, with zero help from the Opposition, the Obama administration manages to get some form of health insurance reform done. So what do Americans do? We elect bozos who can do nothing but strive to preserve the status quo that feeds them.

We are such sheep. We deserve the GOP.

[1] Many family physicians are closer to teachers than to radiologists than teachers, however. Also there should be a way for PAs to train up to a medical degree, but that's a different story.
[2] The ones I've personally known were pretty fine people. 
[3] This Donna Dubinsky. A legend in the Palm days.  She is wealthy and can self-insure if she prefers.
[4] It only lays the groundwork. Politics and economics will do the rest.

Monday, February 21, 2011

A taxonomy of American politics

The weak are inescapable. Live long enough? Probably weak. Child? Weak. Wrong genes? Not so strong. Blacksmith post-horses? Tribe out of power? Parents not wealthy? Don't own a Senator? Organic in the machine age? Ok, so you get it.

In America weakness and poverty trend together. and, to a first approximation, American political tribes can be classified by their attitudes to the weak...

Branch I The strong should help the weak because ...

  • I need help -> Weak person, not in denial
  • My religious tradition tells me I will be rewarded for compassion -> Theist
  • Seeing suffering makes me feel bad -> Normal human
  • I choose to assume this obligation because ...
    • I am perverse [3] ->  liberal secular humanist
    • Some of those I love are weak -> Social interest
    • I may be weak some day -> Rational self-interest
    • I favor civilization and prosperity -> Rational social interest
    • My tribe is defined by its service -> Noblesse obliges

Branch II The strong should not help the the weak because ...

  • I am strong because I am of the strong tribe, non-tribe is non-person -> Weak person, in denial
  • Misfortune is the will of God/The Market which I must support -> neo-Calvinist [1], Marketarian
  • I am strong, and the weak serve me -> Authoritarian
  • I don't care about the suffering of others -> Sociopath
  • I like seeing others suffer -> Psychopath
  • Obligation is an infringement on my liberty ->  Libertarian
  • The health of the tribe requires the sacrifice of the weak -> Social Darwinist [2]
  • Charity makes people weak, for weak must win or fall on their own -> Tough Lover

I guesstimate that about 70% of Americans belong in Branch I and 70%of them vote Democrat. Of the 30% of Americans in Branch II about 95% of them vote GOP. Branch II defines the heart of the GOP, though Branch II alone can't win elections.

Of all the twigs of this tree there are three that are in play during elections.

  • non-Calvinist theists can vote Democrat or Republican. They are why we can have a Black President, but never an atheist President.
  • GOP voters who are weak,  but yearn to be of the strong tribe. They may realize they are dupes, that they are sheep funding wolves. They can then change sides. (Today many of these are Beckians.)
  • The Tough Lovers

The last are the most interesting. From my secular humanist perspective, they have a point.

Sure, some TLs are just sociopaths in denial, but most of us are capable of more than we, or others, imagine. Sometimes hunger or homelessness helps someone overcome a social phobia and accept an unpleasant public facing job. Sometimes loss of child care benefits leads to rational choices about contraception. Parents in particular know that children love to win by their own ends against the odds (although we rig the game in the child's favor).

Tough love has its limits though. Sometimes people break. They become homeless. Their dependents suffer. This is why Food Stamps are usually a very good thing. Even the core GOP voters of Branch II often support some sort of publicly funded education, thought they want it to be locally funded and thus favor the strong [5].

The trick for those of us who want to help the weak be stronger, but also recognize that humans are not not rational actors, is to fake "Tough Love". We need systems and solutions that allow the weak to seem "win on their own" , perhaps by rigging the game in a way that seems 'fair'. So instead of doing affirmative action on the basis of ethnicity, we achieve similar ends to by providing affirmative action on the basis of poverty. Instead of directly subsidizing employment, we make it easier to create a viable startup company.

Political systems are good at finding solutions like these, which is why politics is the worse form of governance save for all the alternatives. We'll need to get very good at this form of kindness, because the 21st century will soon be seen as the age of mass disability, when fewer skills are needed, and more skills are as redundant as blacksmithing in the age of the automobile ...

[1] Calvinism is the best "Christian" example I know of, but this is common to many traditions. It is perhaps the only rational answer to the "problem of evil" in a religious tradition.
[2] Apologies to Darwin, who was a remarkably compassionate human being.
[3] It's a "worker Bee thing". Some are programmed this way. It isn't perverse if you think as humans as bipedal naked mole rats.
[4] It's been a long time since I'd given this much thought. I'm indebted to a substantially younger person for refreshing topics I'd internally settled long ago. 
[5] Note to foreigners. Americans typically fund education through local property taxes. Shocking, isn't it? The most shocking thing is that Americans think of this as a good idea.

Thursday, February 17, 2011

Where now for the iOS Borders eBook reader?

Borders is in bankruptcy. Its future is quite uncertain.

Of course the books we bought there are still good. The paper ones that is ...

Borders launches eBook reader for iPhone

... Borders has entered the battle for dominance of the iPhone eBook market. Well sort of. Today Borders launched an official eBook app for the iPhone, iPod touch, and iPad. But it’s basically just a rebranded version of the Kobo app which has been available since last week.

Kobo and Borders are partners in the eBook space, with Kobo powering the Borders eBook store. Kobo also sells a physical eBook reader with an E Ink display that competes with the Amazon Kindle, and which has access to the Borders eBook store...

I've read elsewhere that Kobo is still in business, though I suspect Borders was their primary partner. This is probably not a good time to buy a Kobo reader.

The average lifespan of a Fortune 500 company is 40-50 years. I think we can assume that the lifespan of file formats in general, and Digital Rights Management standards is significantly less than that. Make your purchases accordingly.

Sunday, February 13, 2011

How a small company acquisition works

I've been around enough acquisition pieces to recognize that this is an excellent summary of a business acquisition.  M&A Case Studies: WhatCounts Sale Process. Keep a copy handy just in case you need it some day.

8 banks with low fees - per CNN

CNN Money's list of the 8 least evil banks. They seem largely next-generation banks; they're least good at what we use a bank for - managing and depositing checks.

The problem with "Everyday Mathematics"

We've lived with Everyday Mathematics through the last six years of my son's primary school education.

It's a lousy way to teach arithmetic and basic symbol manipulation to the non-mathematically gifted. This means it's a lousy way to teach, since the mathematically gifted would be better off playing with Mathematica.

The interesting question is what makes it lousy. I've wondered about that intermittently, and I think I've got the answer.

The problem with Everyday Math is that it asks too much of the math teacher. Most math teachers are just a bit about average (yes, I'm mathematically gifted); Everyday Math requires a 75th percentile teacher to really work. So it fails.

Saturday, February 12, 2011


I haven't had anything novel to say about the Egyptian Revolution of 2011...

The 2011 Egyptian revolution was a series of street demonstrations, marches, rallies, acts of civil disobedience, riots, labour strikes, and violent clashes that began in Egypt on 25 January 2011, a day selected to coincide with the National Police Day. The protests were largest in Cairo and Alexandria, with significant activities in other cities of Egypt ... On 11 February, Mubarak resigned from office as a result of determined popular protest...

My one connection to this revolution is I've been reading the Facebook posts of a high school friend. She's been visiting Tahrir square. I hope she stays safe. Egypt has surprised the world, but of course their journey is far from over. They need many more miracles to follow Turkey's path. It is possible; the Berlin Wall proved that humans can exceed expectations.

Surprisingly, I have a remote connection to another Egyptian Revolution -- one from 1919 and the Russian-Ottoman war [1] ...

The Egyptian Revolution of 1919 was a countrywide revolution against the British occupation of Egypt and Sudan. It was carried out by Egyptians and Sudanese from different walks of life in the wake of the British-ordered exile of revolutionary leader Saad Zaghlul and other members of the Wafd Party in 1919. The event led to Britain's unilateral grant of independence to Egypt in 1922, and the implementation of a new constitution in 1923...

... Although the Ottoman Empire retained nominal sovereignty over Egypt, the political connection between the two countries was severed by the British occupation of Egypt in 1882. From 1883 to 1914, actual power in Egypt was exercised by the British Consul-General through the Khedive and his council of ministers. When war broke out between the Russian and Ottoman Empires, Britain declared martial law in Egypt and announced that it would shoulder the entire burden of the war. On December 14, 1914, Egypt became a separate sultanate and was declared a British protectorate, thus completely detaching the country from the Ottoman Empire ..

... Over the course of the war ... dissatisfaction with British rule spread amongst all classes of the population. This was the result of Egypt’s increasing involvement in the war, despite Britain's promise to shoulder the entire burden of the war. During the war, the British poured masses of foreign troops into Egypt, conscripted over one and a half million Egyptians into the Labour Corps, and requisitioned buildings, crops, and animals for the use of the army...

I learned of my connection when discussing Mubarak's fall with my 80 yo mother. She referred to my "Egyptian relatives". Her maternal grandmother's sister, Catherine (Kitty) Maxfield of Manchester England, married an Egyptian around 1909 and moved first to Cairo and then to Alexandria.

I thought I'd never learn more, but when I shared this story on Facebook Emily's sister, Martha, provided some context ...

In those days it was not uncommon yet still very controversial, for Egyptian men to take English brides. It led to a trumped-up "marriage crisis" because the state was worried about how to take care of unmarried Egyptian women ... [and] ....  worried about men not setting up "proper" Egyptian families ...

Basically it was a Nationalism problem.

This is detailed in a journal article "Stolen Husbands, Foreign Wives: Mixed Marriage, Identity Formation, and Gender in Colonial Egypt, 1909-1923" by Hanan Kholoussy. There is also a book by the same author, "For Better, For Worse: The Marriage Crisis that Made Modern Egypt" (Stanford U Press, 2010). [Google Preview]

Kitty may have lived through the Egyptian Revolution of 1919. She had two children, so it's possible that their grandchildren were in Tahrir square.

It's a complicated world.

[1] No, I'd never heard of this either. I added a link from the 1919 article to the Caucasus Campaign article.

North Korea

Netflix streaming to the Wii attached to our ancient CRT used to require a physical disk. It has recently switched to using Wii internal storage [1]. I did the update today and looked for a documentary to test with [3]. I hoped for the BBC, but had to settle for National Geographic [2]. Since I have some Korea connections, I chose Inside North Korea (2007, 52 min).

It's a remarkable video. There was nothing there I haven't read, but video communicates a rich awfulness even photographs can't manage. In a history full of astounding cruelty and evil, Kim Jong Il's North Korea stands tall with Stalin's Russia, Pol Pot's Cambodia, Mao's China, Hitler's Germany and the Congo's Congo.

On the other hand, Nat Geog is no BBC. There's room for a more complex documentary about what they omitted. The family members of the team's minders, in particular, have probably spent the last four years dying in an NK concentration camp for their failure to stop covert filming. It's never explained why the remarkable team of Nepalese surgeons agreed to the undercover journalism. They may exaggerate the isolation and control of NK.

I was reminded of the Maoist era documentaries of China I saw as a child. The control of the party seemed complete, the population genuinely brainwashed. This was a time when millions were dying of Mao's famine, but that was not well known at the time. The brainwashing turned out to be mostly illusions born of fear and terror, and, for most, readily reversible.

There's a good chance that NK's government will collapse sometime in the next ten years. I hope then that someone will then be able to safely interview some of the people from this documentary, and ask them what they were really thinking when they wept tears in praise of one of humanity's great bastards.

[1] The install required a firmware update and is mildly geeky, but the streaming works remarkably well. Even with our feeble DSL service, and an AirPort router 2 floors above the Wii, the video quality was excellent. Of course our low res TV isn't very demanding ...
[2] BBC licensing discussions must be hellish.
[3] The Netflix-Wii UI is atrocious. I recommend locating streamable movies on computer, then searching them on the Wii.

Friday, February 11, 2011

A guide to better websites in two comics

Most organizational and commercial websites truly suck.

It's Bizarre. It's really not that hard.

Between XKCD and The Oatmeal, here's how do it well in two comics.

Adjust these examples to your site, and the world will reward you.

PS. Nobody does $&!# parking info.

Tuesday, February 08, 2011

Dementia prevention: reason enough for road tolls and public transit

I was a persistent skeptic. I didn't believe that exercise slowed the inevitable [1] onset of age related cognitive decline.

The animal models broke my resistance. Now we're exploring mechanisms (emphases mine) ...

Observations: Aerobic exercise bulks up hippocampus, improving memory in older adults
... adults aged 55 to 80 years who walked around a track for 40 minutes on three days a week for a year increased the volume of their hippocampus, the brain region that is implicated in memory and spatial reasoning. Older adults assigned to a stretching routine showed no hippocampal growth. The 120 previously sedentary older adults recruited for the study did not yet have diagnosable dementia but were experiencing typical age-related reduction of the hippocampus, according to pre-study MRIs. "We think of the atrophy of the hippocampus in later life as almost inevitable," ...
The growth of the hippocampus was modest, increasing 2.12 percent in the left hippocampus and 1.97 percent in the right hippocampus, which effectively turns back the clock one to two years in terms of volume. The stretching group, on the other hand, experienced continued reduction in pace with expected age-related losses, losing on average 1.40 percent and 1.43 percent in the volume of their left and right hippocampus, respectively...
In addition to the increased size of the hippocampus, the aerobic exercise group also tended to have a higher level of brain-derived neurotrophic factor (BDNF), a compound that is associated with having a larger hippocampus and better memory. The researchers did not see any changes in the thalamus or caudate nucleus, two other parts of the brain that are involved with spatial sense and memory, respectively. Because only the hippocampus seemed to be affected by the aerobic exercise regime, the researchers reasoned that the activity might be acting specifically on certain molecular pathways to prompt "cell proliferation or dendritic branching," they noted...

This was a randomized (non-blinded of course) therapeutic trial and it's backed up by persuasive animal model studies. I think this is real.

I would not call the effects "modest". Over one year there was a 3.4% difference in hippocampal volume between the control and experimental groups. This corresponds to a 2-4 year age gap. There is no reason to assume the groups would not continue to diverge for additional time.

This is a big enough difference that ethics panels may not approve further experimental studies of this sort. Future control groups will have to include significant exercise (I would not call 40 minutes 3 times a week modest.)

So now we have a few known ways for individuals to reduce their personal risk of cognitive disability:

  1. Don't hit your head. That means no football for your kids (and, worse, maybe no hockey).
  2. Exercise (without hurting your head) a lot.
  3. Don't smoke, drink to excess, eat too much, etc.

We know things that don't work at all ...

  1. Playing bridge, cognitive work, crosswords, etc.
  2. Nutritional supplements

And we're waiting to find out if sleeping 7-8 hours a night will matter. I have a hunch sleep duration will be found to be a key to amyloid turnover ...

Insights Give Hope for New Attack on Alzheimer’s - Gina Kolata -

...  Dr. Bateman was his own first subject. He then did the test on people in their 30s and 40s, as well as healthy older people and people with Alzheimer’s...

The problem in Alzheimer’s, he found, is disposal. Beta amyloid, he found, normally is disposed of extremely quickly — within eight hours, half the beta amyloid in the brain has been washed away, replaced by new beta amyloid.

With Alzheimer’s disease, Dr. Bateman discovered, beta amyloid is made at a normal rate, but it hangs around, draining at a rate that is 30 percent slower than in healthy people the same age. And healthy older people, in turn, clear the substance from their brains more slowly than healthy younger people.

... “What we think may be happening is that a clearance mechanism is broken first,” Dr. Bateman says. Slowly, as years go by, beta amyloid starts to accumulate in the brain. If that clearance can be fixed, or enhanced, the buildup might never occur...

Of course exercise helps regulate sleep as well ...

We know enough to make some policy decisions. The economic payoff to delaying cognitive disability across the US population is enormous. It's enough of a savings, for example, to justify a shift to public transit, which leads to higher levels of ambulation. A carbon tax, which makes sense in many other ways, can pay for public transit, reduce automobile use, and reduce dementia rates.

Friday, February 04, 2011

Science is stuck in a rut. What now?

I was surprised when I did my 2008 family medicine board exams...

Gordon's Notes 2008: Challenges to medicine and science – medication invention hits a brick wall

... To put it delicately, progress has sucked. If you put a good physician to sleep 7 years ago, and woke her up today, she’d be reasonable competent on day one. A week later she’d be fully up to speed ...

Sure, there were lots of new drugs, but they were mostly incremental improvements. Medicine got stuck around 1984. Smolin claims physics is just as bad. Now people are writing books about the "Great Stagnation".

This is good. The first step to getting out a rut is to stop spinning wheels. Even better, scientists are doing meta-science on this problem ...

Biologists Ignoring Low-Hanging Fruit, Says Drug Discovery Study  - Technology Review

The entire set of kinases in a given organism is called its kinome. The human kinome consists of 518 kinases. Unsurprisingly, biologists and pharmaceutical companies are intensely interested in understanding how these enzymes work and developing drugs that control their behaviour.

So it may come as a surprise to find that three quarters of the research in this area focuses on just 10 per cent of these enzymes, as measured by the number of times the kinases are cited in research papers. By contrast, 60 per cent of the kinome, some 300 kinases, is virtually ignored by the community and mentioned in only 5 per cent of the work.

This is known as the Harlow-Knapp effect after the researchers that discovered it a couple of years ago. The question it raises is why biologists ignore most of the kinome when there is good reason to think that careful study should pay off in silver dollars

Today, Ruth Isserlin at the University of Toronto in Canada and a few buddies take a more detailed look at the effect. They say it is more widespread than previously thought and also affects the study of other biological molecules too....

... One common idea is the Matthew effect--from the biblical reference that the rich get richer and poor get poorer. For example, it is common for well-known scientists to be awarded prizes, making them more famous, even if all the work was done by a graduate student who is ignored.

At first glance, it's easy to imagine that the Harlow Knapp effect is good example of this. Isserlin and co point out that current molecular biology is so rich that it is possible to ask important questions even of the most well-studied systems. And since its easier to get grants, to do good science and to get published in higher impact journals by sticking to well known systems, that's exactly what scientists do. So the best known systems become better studied.

That alone might explain this distribution. But there is something else going on too, say Isserlin and co. Biologists commonly screen the entire genome of an organism looking for interesting proteins. But when they find one, the amount of work they can do with it depends on the chemical tools available to interact with it.

In many cases, these tools are not available. And when that happens, the proteins are ignored. This, say Isserlin and co, is one of the important underlying reasons why so many kinases and other interesting biomolecules are so poorly studied...

Some good clues there, but we should look also into other domains of historic stasis. Music and art have gone through periods of stagnation and renaissance. So has religion ...

... Around the Godde there forms a Shelle of prayers and Ceremonies and Buildings and Priestes and Authority, until at Last the Godde Dies. Ande this maye notte be noticed... [1]

"Priestes and Authority"? Sounds like the NIH.

So we've recognized the problem. How do we get out? It might be we'll get unstuck any minute now, but this is a good time to rethink how we fund and reward scientific endeavor. Should we be doing more prizes for discoveries instead of grants for research? Should we declare certain domains "boring" and off limits for NIH funding? Should we accelerate the demise of tenure?

I expect we're going to hear some interesting ideas over the next couple of years.

[1] Terry Pratchett, Small Gods.  Famous scholarly work. In some circles anyway. Ok, so I just like the book.

Bayes and the infinite universe

I used to teach Bayesian reasoning to informatics students. I couldn't justify to them why such simple math felt both spooky and profound. I still can't, but this story fits.

Cosmologists tell us that, comparing a subset of models to available data using Bayesian methods, the 14 billion year old universe is somewhere between 3,500,000,000,000 and an infinite number of light years across (emphases mine) ....
Cosmos At Least 250x Bigger Than Visible Universe - Technology Review

... the photons in the cosmic microwave background have travelled ... 45 billion light years to get here. That makes the visible universe some 90 billion light years across.

... one line of thinking is that if the universe expanded at the speed of light during inflation, then it ought to be 10^23 times bigger than the visible universe... .... Other estimates depend on a number factors and in particular on the curvature of the Universe: whether it is closed, like a sphere, flat or open. In the latter two cases, the Universe must be infinite.

... in recent years, astronomers have various ingenious ways of measuring the curvature of the Universe. One is to search for a distant object of known size and measure how big it looks. If it's bigger than it ought to be, the Universe is closed; if it's the right size, the universe is flat and if it's smaller, the Universe is open.

Astronomers know of one type of object that fits the bill: waves in the early universe that became frozen in the cosmic microwave background. They can measure the size of these waves, called baryonic acoustic oscillations, using space observatories such as WMAP.

There are also other indicators, such as the luminosity of type 1A supernovas in distant galaxies.

But when cosmologists examine all this data, different models of the Universe give different answers to the question of its curvature and size. Which to choose?

The breakthrough that Vardanyan and pals have made is to find a way to average the results of all the data in the simplest possible way. The technique they use is called Bayesian model averaging ...

... Instead of asking how well the model fits the data, its asks a different question: given the data, how likely is the model to be correct. This approach is automatically biased against complex models--it's a kind of statistical Occam's razor.

In applying it to various cosmological models of the universe, Vardanyan and co are able to place important constraints on the curvature and size of the Universe. In fact, it turns out that their constraints are much stricter than is possible with other approaches.

They say that the curvature of the Universe is tightly constrained around 0. In other words, the most likely model is that the Universe is flat. A flat Universe would also be infinite and their calculations are consistent with this too. These show that the Universe is at least 250 times bigger than the Hubble volume. (The Hubble volume is similar to the size of the observable universe.) ...
This is Occam's razor statistics - "... we should tend towards simpler theories .... until we can trade some simplicity for increased explanatory power".

Given the available information, the universe is most likely infinite, but it could be as "small" as 3,500,000,000,000 light years across. Big enough for one human like civilization for every human that has ever lived.

Probably though, much bigger than that.

It is a bit much. Surely, there is a simpler, less extravagant explanation. I'd like to see the authors rerun their analysis with a broader range of explanatory models. I think I know what the answer would be [1] ...

See also (Gordon's Notes unless otherwise noted)
- fn --
[1] An omniscient universe-creating deity is equivalent to the "Boltzmann's Brain" explanation, so creationists are in good company. Alas, this "deity" is not the one they're looking for.

Thursday, February 03, 2011

Economics of POW Camp - whatever happened to R. A. Radford?

The conclusion of an essay beloved to Krugman and many other economists ...
Economics of POW Camp, R.A. Radford 1945
.... In January, 1945, supplies of Red Cross cigarettes ran out: and prices slumped still further: in February the supplies of food parcels were exhausted and the depression became a blizzard. Food, itself scarce, was almost given away in order to meet the non-monetary demand for cigarettes. Laundries ceased to operate, or worked for £s or RMk.s: food and cigarettes sold for fancy prices in £s, hitherto unheard of. The Restaurant was a memory and the BMk. a joke. The Shop was empty and the Exchange and Mart notices were full of unaccepted offers for cigarettes. Barter increased in volume, becoming a larger proportion of a smaller volume of trade. Thus, the first serious and prolonged food shortage in the writer's experience, caused the price structure to change again, partly because German rations were not easily divisible. A margarine ration gradually sank in value until it exchanged directly for a treacle ration. Sugar slumped sadly. Only bread retained its value. Several thousand cigarettes, the capital of the Shop, were distributed without any noticeable effect. A few fractional parcel and cigarette issues, such as one-sixth of a parcel and twelve cigarettes each, led to monetary price recoveries and feverish trade, especially when they coincided with good news from the Western Front, but the general position remained unaltered.

By April, 1945, chaos had replaced order in the economic sphere: sales were difficult, prices lacked stability. Economics has been defined as the science of distributing limited means among unlimited and competing ends. On 12th April, with the arrival of elements of the 30th U.S. Infantry Division, the ushering in of an age of plenty demonstrated the hypothesis that with infinite means economic organization and activity would be redundant, as every want could be satisfied without effort.
The essay has a very English style. Radford's upper lip was rock solid.
A Caracas Chronicles 2002 post has a bit of background and some analysis of the article ...
In 1941, a British officer by the name of R.A. Radford was captured by the Nazis and confined to a POW camp. At the camp, Radford and 2400 other inmates were forced to live on meager rations delivered by the Red Cross. The rations issued to each prisoner contained a bit of bread, some sugar, biscuits, jam, margarine, tea and chocolate bars, with small rations of canned meat sporadically made available. They also included 25 cigarettes per prisoner per week. Radford, who had been trained in economics before the war, noticed how even in the extreme conditions of a Nazi prison camp, a rudimentary market system developed as prisoners traded with one another to maximize their satisfaction. The British army's Gurkahs, for instance were eager to trade their meat for other foods, since as Hindus they were strict vegetarians. Prisoners who didn’t smoke were eager to trade their cigarettes for food. At first, each of these trades was a simple barter. But soon enough, the inmates realized the need for a more sophisticated system of exchange. Lacking money, they started using cigarrettes as prison currency. A ration of margarine might be bought for seven cigarrettes, which could then be used to buy one and a half chocolate bars, and so on.
Soon after his release, Radford described the system that developed in a classic paper entitled “The Economic Organization of a POW Camp,” a write-up that's much appreciated by undergraduates everywhere for its skill at explaining the mysteries of monetary systems. What interested Radford the most was the way that cigarrettes, as a means of exchange, were subject to all of the fluctuations of normal currency. So long as there was a roughly steady relationship between the number of cigarettes in circulation and the goods those cigarettes could be traded for, “prices” in terms of cigarettes remained more or less stable. But when a shipment of cigarrettes unexpectedly arrived, an inflationary spiral was set in motion. With the camp suddenly awash in “unbacked cigarettes” (additional cigarettes that circulated without a corresponding increase in the amount of other goods they could buy) prisoners would demand more and more of them in exchange for other goods. Alternatively, when cigarettes failed to arrive for one reason or another (an allied bombing raid, for instance,) a liquidity crunch took hold of the camp. These currency shortfalls would actually lead to recessions at the camp: with inmates eager to hang on to their scarce cigarettes, it became more and more difficult to find people to trade with.
So what happened to Radford after the war? There's no Wikipedia entry for him, and I couldn't find a biography or a reference to anything but his 1945 publication. I couldn't even find out what the initials "R.A." stood for.

It is a mystery.

Update 10/21/2011: Mystery solved in a comment on this post. R stood for Richard, he moved to the US to work for the IMF. See:

Tuesday, February 01, 2011

Google Art Project

Google Art Project hosts seventeen museums worth of paintings with gigapixel imaging - including Rembrandt's Night Watch...

Screen shot 2011-02-01 at 10.10.40 PM.png

Yes, it's Flash based. More's the pity. Churlish to complain though.

This is a glorious marvel. Most of these paintings can be seen only at a distance. Now you can put your eye next to them.

Google moves into positive Kharma territory with this one.

From the FAQ ...

Why is there a difference between the museums in terms of the number of galleries, artworks and related information?

Google approached the museum partners without any curatorial direction, and each museum was able to chose the number of galleries, artwork and information they wanted to include, based on reasons specific to them. All content in the information panel pertaining to individual artworks was also provided by the museums.

Why are some areas or specific paintings in the museum Street View imagery blurred?

Some of the paintings and features captured with Street View were required to be blurred by the museums for reasons pertaining to copyrights.

Are the images on the Art Project site copyright protected?

Yes. The high resolution imagery of artworks featured on the art project site are owned by the museums, and these images are protected by copyright laws around the world. The Street View imagery is owned by Google. All of the imagery on this site is provided for the sole purpose of enabling you to use and enjoy the benefit of the art project site, in the manner permitted by Google’s Terms of Service.

Update: Unsurprisingly, given the use of Flash, it's buggy on a Mac. I had more luck using Chrome for OS X than using Safari. I created a shareable collection but it took a few tries to get it saved. Doubtless a part of Google Social to be. Did I mention Flash sucks?