A brief education in modern genetics

If your last genetics class involved wrinkled peas, you need to read Pharyngula's (a distant colleague actually, he's a tenured U of MN prof and I'm a very part-time adjuct faculty person there) modern genetics 101: evolution of a polyphenism.

Clinical practice hasn't changed much in the past 20 years, but genetics has seen a few updates ...

Power corrupts: the tyranny of the lowly immigration officer

Lowly bureaucrats in the immigration services, emboldened by increased powers and stressed by the threat of harsh punishments, are abusing "foreigners" (emphases mine):

Seized With Heavy Hand at Border, for Paperwork Errors - New York Times

...Though there are no statistics on such cases, the lawyers say they are seeing harsher treatment in situations involving paperwork errors or minor infractions. A political climate more hostile to foreigners, fears of being faulted for leniency and a lack of coordination among immigration agencies, they say, are leading officers to go overboard in cases that fit the government guidelines for prosecutorial discretion.

"I'm desperate," Emily Arroyo, the mother of the second grader, said last week, after prosecutors refused an immigration judge's suggestion that they drop the two-year-old deportation case against her son, José Arroyo Rodas. Instead, they demanded that she buy him a one-way ticket to Canada by next week.

"I'm American — they're making me leave my country, too, because of course I'm not going to let him go alone," said Ms. Arroyo, a hairstylist raised in Guatemala, who calculates that she has spent $10,000 in legal fees trying in vain to fix José's paperwork problem. But on Wednesday, hours after this reporter asked United States Immigration and Customs Enforcement officials in Washington for comment about the case, an agency spokesman, Marc Raimondi, said that prosecutors reviewing the matter had found that it met the guidelines for prosecutorial discretion. "A dismissal recommendation to the immigration judge is planned," he said.

... case like José's only confirms that without exceptional outside attention or high-level intervention, rigidity prevails, said Diane M. Butler, a Seattle lawyer who heads the American Immigration Lawyers Association committee that works with Customs and Border Protection.

Most officers, she said, "are trying to do the right thing" but lack training in how to apply discretion. But, in some instances, she added, officers seem newly emboldened by campaigns against illegal immigration to express their resentment of foreigners by denying or delaying entry whenever possible. She said her business clients reported remarks like, " 'You're just trying to take jobs away from Americans.' "

Other immigrant advocates say that low-level employees often act out of fear. "The people on the front line are told that if they make a mistake, their jobs are gone," said Amy L. Peck, an immigration lawyer in Omaha who heads the association committee that works with Immigration and Customs Enforcement. "So that translates into this rigid — what one could also describe as extreme — policy of turning away and not using discretion in cases that scream for it."

Immigration officials combine the power of police, judge and jury. Such power is an intoxicating drug, especially for those with little experience in its use. Low level immigration staff suffer from both the intoxication of power and the fear of punishment for errors -- and errors are impossible to avoid in their job. Being human they have to make mistakes, and naturally they now err towards punishing the innocent.

The story caught my attention, however, because of some personal experiences. Even as a melanin-deficient euro immigrant from Canada I was told by an immigration security official that I was marrying my Yankee girl simply to enter the US (I managed to avoid laughing -- I'm not that dumb). I learned when overseas that there was a sharp rise in quality towards the top of the consular hierarchy, with very smart and capable people at more senior levels and remarkably ineffectual sorts lower down. My family has also run into minor but scary issues when traveling due to our motley family mix (the trick there is to avoid the immigration worker who's ethnicity matches the non-euro children -- and to carry documentation beyond a full set of passports).

The solution is to put more high level, higher paid staff in place to provide backup and make judgment calls. The folks at the bottom will need to err on the side of rigidity and suspicion, but they need to have experienced senior staff on call at all times to help make corrections. In the meantime, never ever look cross-eyed at any immigration or transportation official.

Countries can't downsize

The Big Picture: BusinessWeek Cover Story: Disingenuous or Denial had this rather interesting comment:

... In a nutshell, countries can't downsize. Bizweek (and others) are trying to suggest that America as a whole is benefiting from this enlightened leverage of IP and low cost manufacturing availability. Not true, not by a longshot.

The reality is that there is a small contingent of folks in the US reaping the benefits of the iPod economy, and a much larger group of folks feeling the brunt of wage stagnation even as downward pressure on manufactured goods gets offset by upward pressure elsewhere (the natural result of a static inflation policy). America is not like a jack-be-nimble startup, or even like a General Electric where Neutron Jack can lay off 100,000 workers.

As borders dissolve, opportunity spreads more evenly. This is very good for rich world players with leverage (knowledge, know-how etc) and developing world players looking for a leg up (88 cents an hour better than 0 cents an hour). It is very bad for rich world wage workers who were previously insulated from developing world competition.

A great short essay. The pithy phrase is worth bearing in mind.

Google vs. PayPal: world's shortest fight

Based on my personal PayPal experience, I think of them as a great solution for shady operators. It turns out I'm not alone in my feelings about PayPal (and eBay). A rumor that Google might enter the transactional marketplace has generated a remarkable Slashdot consensus; PayPal's natural customer base want PayPal to be crushed like a bug.

Companies can last quite a while when their customers hate them -- if switching costs are high.

In this case, the switching costs are not high. If Google makes this move PayPal is toast.

Of course I've overestimated the significance of Google's moves before. Google Base has not set the world aflame, in part due to a lack of a security model. I did say, however, that the next step was the payments system. (Yeah, I wasn't the only one to draw that obvious conclusion.)

NSA traffic analysis: the seduction of data and the creation of conspiracy

I heard a part of the senate hearings on the NSA intercepts today. The GOP Senator was lobbing softball questions at the Bush attorney, who answered them well and carefully. Of course none of the questions were about the more interesting issue -- how the intercepts are selected and whether that process is legal. Cringely, who's done some good summaries to date, adds a bit more to the picture:

PBS | I, Cringely . February 2, 2006

... last thought comes from an old friend of mine who is conservative in the very best sense and knows what he is writing about:

"Traffic analysis, at the NSA? I'm tempted to be sarcastic, but I won't be. As you might know, I started a company a few years ago with a former NSA guy -- somebody who was a cryptographer and Russian linguist on those submarines that snuck into Soviet harbors to tap their phone lines -- and we applied traffic analysis to Internet discussion groups to identify opinion leaders, conversation trends and so forth. We used a lot of techniques that were developed or applied to law enforcement. And we didn't use anything that violated anybody's security clearances... really!

"(My company) was acquired by a business intelligence company funded by the CIA venture capital outfit. Apparently the stuff I invented is now in the hands of a couple of intelligence agencies, including Homeland Security.

"I'll tell you what I think the most troubling thing about all this is. It's easy to see whatever pattern you're looking for. It's like curve fitting in the stock market -- looks beautiful historically and maybe even in the short run, but it's a disaster in the making. So we have these guys running the country who saw a non-existent pattern in Iraq that justified a war ... and now we're going to give them software that will make it easy to create the illusion of patterns of conspiracy.

"Your friend from the NSA was right, but it's worse than he suggests. It's not just that social network analysis casts a wide net. It's that without oversight by people who really grasp the mathematics and have some distance from the whole thing, they're going to see patterns where there aren't any.

"They have a history of that."

The history of lie detector testing is informative. Current lie detector technology is very unreliable. It falsely implicates and falsely absolves. It's only somewhat better than a random guess, and some observers do better without the technology. Nonetheless, it is immensely abused by law enforcement. We can expect the NSA, FBI, and CIA to make the same mistakes with traffic monitoring technologies. Geeks don't get promoted in these agencies, and only geeks understand the limitations of this technology.

Bush's apparatchik in NASA: obnoxious youth

A few weeks ago we read that some NASA 'public affairs' officer had been attempting to silence of NASA's senior climate researches. Apparently Dr. Hansen wasn't following the part line; he needed a handler present lest he talk too honestly to the press.

What we didn't hear, and what's buried at the back of recent NYT article, is a feature of that apparatchik that made him particularly annoying -- he's a kid, a presidential appointee with zero credentials. A classic Soviet era apparatchik...

NASA Chief Backs Agency Openness - New York Times

The Big Bang memo came from Mr. Deutsch, a 24-year-old presidential appointee in the press office at NASA headquarters whose résumé says he was an intern in the "war room" of the 2004 Bush-Cheney re-election campaign. A 2003 journalism graduate of Texas A&M, he was also the public-affairs officer who sought more control over Dr. Hansen's public statements.

In October 2005, Mr. Deutsch sent an e-mail message to Flint Wild, a NASA contractor working on a set of Web presentations about Einstein for middle-school students. The message said the word "theory" needed to be added after every mention of the Big Bang.

The Big Bang is "not proven fact; it is opinion," Mr. Deutsch wrote, adding, "It is not NASA's place, nor should it be to make a declaration such as this about the existence of the universe that discounts intelligent design by a creator."

It continued: "This is more than a science issue, it is a religious issue. And I would hate to think that young people would only be getting one-half of this debate from NASA. That would mean we had failed to properly educate the very people who rely on us for factual information the most.

... Mr. Deutsch did not respond to e-mail or phone messages. On Friday evening, repeated queries were made to the White House about how a young presidential appointee with no science background came to be supervising Web presentations on cosmology and interview requests to senior NASA scientists.

Bush's team appoints a flunkee to be their apparatchik for NASA. Said flunky starts drafting very annoying memos, implying dire consequences to those who disobeys. He's particularly concerned about affirming intelligent design and blocking talk of global climate change. An interesting story. So why did it get buried at the little read end of a NYT article?

The more I see Bush in action, the more convinced I am that he's a KGB implementation of 'The Manchurian Candidate'. It was a rogue mission by a Putin clique in the KGB, and it was thought to have failed. Their vehicle was far gone in alcohol and drug abuse. Miraculously he turns his life around and becomes president. Putin is astounded but he activates the original programming. Bush begins to transform the US into a satellite of the Soviet Union ...

How amantadine became useless

Symmetrel (amantadine) and Flumadine (rimantadine), have lost their value against this year's strain and should be shelved. Ok, but why?

That's the interesting question, and most of the media reports I've seen don't address it. NPR did, however. It turns out that over the counter cold remedies in China and Russia often contain amantadine. Sigh. That's so sad, and so stupid. Very human.

Of course the same thing is true of antimicrobials, they are widely available over the counter in many nations. The difference is that pathogenic bacteria don't travel nearly as quickly as flu viruses. The CDC expected we'd get a few more years of life out of amantadine/rimantadine, but resistance spread more quickly than expected.

The ACLU's estimate of NSA activity

So what's the NSA up to that Bush couldn't use the FISA courts? The current consensus is that the most controversial things they're doing are:

1. Using messaging metadata and algorithmic analysis to target individuals for wiretaps that would otherwise not be identified.
2. Applying wiretaps to the individuals identified via #1 based on evidence (algorithmic ratings) that, by itself, would be very insufficient to justify a wiretap.

If you listen to what Bush says, he focuses on the intercepts, not on the legality of how the intercepts were selected.

The upshot of this is they're probably monitoring a lot of journalists, and a lot of family members of the true targets. They may learn interesting things in the monitoring of journalists, such as the identity of anyone in the government, NSA, or CIA who's blabbing about the NSA's programs.

The ACLU fills in the details:

American Civil Liberties Union : Eavesdropping 101: What Can The NSA Do?

Data mining is a broad dragnet. Instead of targeting you because you once received a telephone call from a person who received a telephone call from a person who is a suspected terrorist, you might be targeted because the NSA's computers have analyzed your communications and have determined that they contain certain words or word combinations, addressing information, or other factors with a frequency that deviates from the average, and which they have decided might be an indication of suspiciousness. The NSA has no prior reason to suspect you, and you are in no way tied to any other suspicious individuals %u2013 you have just been plucked out of the crowd by a computer algorithm's analysis of your behavior.

If we don't put a stop to this, we will pay a very high price. I really do believe that, at the moment, the Bush administration is a greater threat to our future than al Qaeda (in large part, of course, because the non-Iraq part of the 'War on Terror' did make sense and al Qaeda appears to be both weak and to have a very thin bench team).

Bush on cutting imports: really, it was a joke

Rarely does the leed of an newspaper article cut so deeply (via Shrillblog):

KR Washington Bureau | 02/01/2006 | Administration backs off Bush's vow to reduce Mideast oil imports

WASHINGTON - One day after President Bush vowed to reduce America's dependence on Middle East oil by cutting imports from there 75 percent by 2025, his energy secretary and national economic adviser said Wednesday that the president didn't mean it literally...

Bush's people feel they've proved beyond a reasonable doubt that 20% [1] of the voting American public are blithering idiots. Maybe they give him lines like these to test the resilience of this hard-core non-sentience. Perhaps they're trying to tell us "stop me before I kill again".

[1] Bush's approval rating is usually about 42%. About half of his hard core base feel he is serving messianic duties. I don't agree with that, but if that's one's belief then it's not idiotic to support him. That leaves my 20% estimate.

How often will sentience evolve on earth? From anthropology to the Fermi Pardox - via the Drake Equation

Hawks reviews research that suggests that "modern" evolutionary innovations are more likely to be repeatable (non-singular) than "ancient" innovations. He connects this to the Drake equation, the companion to the Fermi Paradox that attempts to estimate the prevalence of technological civilizations in our galaxy. He points out that since the only instance of sentience we know of is quite recent, it is likely that sentience is not a particularly singular innovation.

Personally, I'd bet we're not the first. Stephen Baxter wrote an immensely underappreciated science fiction novel (Evolution) that painted a rather persuasive picture of how sentience might come and go across the history of life on earth -- only once and briefly producing interplanetary technology (after this transiently spacefaring species passes, there's not much left for others to work from).

Hawks is inclined to think we're the first, but most likely not the last. Indeed, if we live out this century, I think it's likely we'll create other sentiences, both biological and otherwise. If we don't make it, the biological ones will still emerge some day, some place. Maybe they'll do a better job that us.

Back to the Drake Equation. The more we start to shift our estimates for the terms of the Drake Equation, the more the Omega term, L, looms larger (sorry). This term is often estimated based on the Fermi Paradox. Wikipedia (currently) has an excellent discussion of this relationship:

The remarkable thing about the Drake equation is that by plugging in apparently fairly plausible values for each of the parameters above, the resultant expectant value of N is generally often >> 1. This has provided considerable motivation for the SETI movement. However, this conflicts with the currently observed value of N = 1 — one observed civilization in the entire universe. Other assumptions give values of N that are <<>

This conflict is often called the Fermi paradox, after Enrico Fermi who first publicised the subject, and suggests that our understanding of what is a "conservative" value for some of the parameters may be overly optimistic or that some other factor is involved to suppress the development of intelligent space-faring life...

... L = the expected lifetime of such a civilization

Estimated by Drake as 10 years.

The value of L can be estimated from the lifetime of our current civilization from the advent of radio astronomy in 1938 (dated from Grote Reber's parabolic dish radio telescope) to the current date. In 2005, this gives an L of 67 years.

In an article in Scientific American, Michael Shermer estimated L as 420 years, based on compiling the durations of sixty historical civilizations. Using twenty-eight civilizations more recent than the Roman Empire he calculates a figure of 304 years for "modern" civilizations. Note, however, that the fall of most of these civilizations did not destroy their technology, and they were succeeded by later civilizations which carried on those technologies, so Shermer's estimates should be regarded as pessimistic.

The Wikipedia article estimates a low value for "safe" earth like planets, I read the most recent findings as much more encouraging but I'm far out of my expertise range.

If "safe" planets turn out not to be rare, then we're back to Drake's solution to the Fermi Paradox -- a 10 year lifespan for a technological civilization. My bet is that the small number is not so much L, as it is fc*L, so even if L is not short something happens to technological civilizations that causes them to lose interest in both physical exploration and communication with the likes of us. Something that produces a communicative sentience for no more than 10-40 years.

The passing of the Telegram

Western Union no longer sends telegrams. If I'd known they still sent them, I'd have tried to send one just for history's sake. Typewriters, telegrams, carbon paper ... these are some of the things I used to know.

The secret to better crime results: don't record the data

The St. Paul Police department is practising the time-honored method of improving one's results -- don't record troublesome data points. It works as well for crime measurement as it does for Texas schools.

In this case some low life smashed our rear van window -- in bright daylight outside our local library. When they were called, the police said they don't do police reports on this kind of crime.

What is not measured -- did not happen. It works for Bush, and it works for the local police.

Ampulex and the cockroach slave: another Zimmer zinger

Karl Zimmer is a great help to those on diets. Read his articles just prior to lunch.

The Wisdom of Parasites. The Loom: A blog about life, past and future

... As an adult, Ampulex compressa seems like your normal wasp, buzzing about and mating. But things get weird when it's time for a female to lay an egg. She finds a cockroach to make her egg's host, and proceeds to deliver two precise stings. The first she delivers to the roach's mid-section, causing its front legs [to] buckle. The brief paralysis caused by the first sting gives the wasp the luxury of time to deliver a more precise sting to the head.

The wasp slips her stinger through the roach's exoskeleton and directly into the cockroach's brain. She apparently using sensors along the sides of the stinger to guide it through the brain, a bit like a surgeon snaking his way to an appendix with a laparoscope. She continues to probe the roach's brain until she reaches one particular spot that appears to control the escape reflex. She injects a second venom that influences these neurons in such a way that the escape reflex disappears.

From the outside, the effect is surreal. The wasp does not paralyze the cockroach. In fact, the roach is able to lift up its front legs again and walk. But now it cannot move of its own accord. The wasp takes hold of one of the roach's antennae and leads it--in the words of Israeli scientists who study Ampulex--like a dog on a leash...

We have insufficient respect for the Emergent Designer (ED) -- the pseudo-deity of evolution. The ED is not a cuddly sort. Its humor is bleak indeed.

How many human psychiatric disorders (think OCD) are the result of adaptive mutations that compensate for a parasitic influence, but subsequently become disorders when the parasite is absent?

Google's feet of clay: Gmail and spam

Google's share price had a minor hit the other day when they "disappointed" on earnings. I can't make sense of their valuation, even though I do think they're a great company.

I can, however, point out that one of their flagship products, Gmail, has serious issues. For historical reasons I get to see how five different spam filtering systems work: Yahoo, Earthlink, Spamcop, the open source systems used by many smaller ISPs, and Gmail's system.

Gmail is not just slightly inferior. It is qualitatively inferior. It is so bad it's mindboggling. The other four all work quite well, making relatively few false positive or false negative errors. Gmail errs in both directions, misclassifying spam as mail and mail as spam.

This isn't new. They've had the same problem for over a year. The only reason I stick with them is their fantastic UI and amazing search capabilities, but if Yahoo ever updates me to their new UI I may switch (I can redirect my mail flows fairly easily since I control the routing domains).

Why doesn't Google invest in the open source systems that work for everyone else? The scale they work on is rather different from that of a small ISP, so they may face impossible scalability challenges. I wonder though, if arrogance plays a role -- the belief that their algorithms will devise a better solution. If it's really arrogance, then their share price may fall more than 10% over the next year.

The best commentary on the state of the union address

Fafblog is marvelous ...

Fafblog! The State of the Universe Address

...Would you take all that away by letting isolationist courts tax the Jesus fetus? Never! Because history is written in courage, and courage will remember us in the future how we were today: pandering, desperate and barely coherent!

My prediction on the Bush health care plan ...

The smart Republican (they're all dead now, but they once existed) thing to do would be to eliminate the corporate tax break for health insurance and apply the funds to a mixture of subsidies and individual tax breaks. That would be a Reagan type of move -- the guy who brought us the Earned Income Tax Credit. (I used to think Reagan was an idiot. True, he was demented during his second term, but compared to Bush II he was a brilliant pillar of light.)

Instead, Bush the Incoherent will introduce a meaningless tax credit that will complicate the tax code, transfer wealth from the Weak to the Strong, worsen the deficit, and have no material impact on healthcare.