Tuesday, July 03, 2007

Ensembl Genome Browser: Take a walk on the wild side

Feeling adventurous? Visit the ensemble genome browser. Really, it's safe for work. All you have to do is click the link.

If you dare.

Come on, you know you want to. Browse a bit ...

There. That wasn't so bad, was it?

One link away.

Now, if you're old enough, remember the world of 10 years ago. I know it's hard, but try.

Things have changed more than we know.

Smarter terrorists: this seems ominous

Anyone who thinks physicians are particularly immune to evil needs a quick history lesson. Or maybe they just need to be reminded that Al Qaeda's true leader, Zawahiri, is a surgeon. Or that Serbia's genocidal murderer, still at large, was a psychiatrist. And, of course, there's dear old Mengele.

So it would not be surprising if the principals in a recent set of terrorist attacks were physicians. Not surprising, but ominous.

The last few years the terrorist attacks and plots in the UK and US have, as nearly as I can tell (I try to track this) involved pretty incompetent people. No geeks. Nobody clever. Many persons with obvious psychiatric ailments or cognitive disorders.

This group is not like this. Maybe they were incompetent, or maybe we were just very lucky, but they're not naive or disabled. They more resemble the terrorists of Hamas than of the past few years of al Qaeda.

I'd very much like to know why they're getting smarter.

Future expected, future forgotten: ubiquitous robotics

I was chatting with a colleague recently about the impact of robotics on infrastructure repair costs. Many older cities, most catastrophically New Orleans, have deferred infrastructure maintenance. In most cases this doesn't result in the annihilation of the city, but it does produce collapsing roadways in Montreal.

There's an upside to deferring infrastructure maintenance, assuming one is willing to risk a few motorists or, in the case of New Orleans, much of the city. The cost may shrink. Modern robotics is making a lot of everyday tasks, such as replacing gas mains, far cheaper. Roads are no longer torn up, instead robotic tunnelers wend their way beneath the asphalt.

Which makes me think about how the future arrives. Sometimes it arrives with great fanfare and long anticipation. Other times, though, it builds off to the side, sleepily and beneath our attention, and merges to take us unawares. I think robotics may be like that. They've been getting smarter and better in the deep ocean, on the battlefield, flying simulators with organic components, vacuuming, mowing ... Incrementally improving.

Japan is highly incented to lead in robotics. Korea is likely to take the same track. It seems inevitable that within 10-20 years most of us will own, and become dependent upon, many increasingly sophisticated robots. A future so long predicted that we've almost forgotten about it, will abruptly be upon us.

The implications for immigration, and for much of the work done by non-knowledge workers, will be substantial. (American knowledge workers, of course, are already doomed by globalization.)

Monday, July 02, 2007

Silencing Libby - Bush acts

Bush has acted as expected. It would be interesting to know what deals were made, what role Cheney played, and what Libby threatened to reveal.

Gordon's Tech is not gone -- but feeds may require a manual update

The short version: I moved Gordon's Tech to a new address: tech.kateva.org. Subscriptions (like bloglines, google reader) were supposed to auto-update, but it's not working. If you read that blog, you'll need to update your feed. Sorry!

The longer version: Gordon's Tech is one of my 3 public blogs (Gordon's Notes is this one, Be the Best You Can Be focuses on cognitive disorders). GT consists almost entirely of technical notes and discoveries I'm interested in; instead of storing them in a desktop file I put 'em into a blog. Works for me, and the results are available for search. Most readers find those posts when solving a tech problem with Google. A small number of readers subscribe to the feed, though the blog doesn't make many concessions to a subscriber audience.

Yesterday I moved Gordon's Tech from a blogspot domain to a Google custom domain. In theory Google's Blogger uses a "301 redirect" to tell feed readers to update their feeds. In practice, that's not working. So subscribers need to update manually. The new URL is tech.kateva.org.

We now return you to your regular programming ...

The joy of parasitism and the strategic wisdom of the cat

I'm a dog person, but I'm kindly inclined to the Dog's historic rival in exploiting the human host. Not that Dogs and Cats are pure parasites, though the cat's role as a toxoplamsa vector arguably moves them closer to the dark side. Dogs do eat garbage and thus reduce disease (like toxoplasma, which can't live in dogs), cat's do kill pests, which reduces disease (do cats get plague?) and food loss.

Quibbles aside, as a happy host to my current canine parasite, I'll raise a toast to the strategic brilliance of the cat, an animal that went from chewing on primates to switching sides when the time was right ... (emphases mine)

The Near Eastern Origin of Cat Domestication (Science)

... Some 10,000 years ago, somewhere in the Near East, an audacious wildcat crept into one of the crude villages of early human settlers, the first to domesticate wheat and barley. There she felt safe from her many predators in the region, such as hyenas and larger cats.

The rodents that infested the settlers’ homes and granaries were sufficient prey. Seeing that she was earning her keep, the settlers tolerated her, and their children greeted her kittens with delight.

At least five females of the wildcat subspecies known as Felis silvestris lybica accomplished this delicate transition from forest to village. And from these five matriarchs all the world’s 600 million house cats are descended....

a subsequent NYT editorial comments:

Cats Among Us - New York Times

... This new genetic evidence resolves the puzzle of cat remains turning up in Cyprus before the rise of the Egyptian civilizations that were supposed to have domesticated the cat.

The wild subspecies that gave up their DNA for these tests still exist, though barely. That is one of the painful ironies of domestication. Creatures who come in from the wild eventually prosper — domestic cats number, after all, in the hundreds of millions — while those who don’t almost inevitably fall upon hard times...

Humans are the ultimate predator, compared to which the old saber tooths were ... pussy cats. We may not last long, but in the meantime we are pretty sure to wipe out every large animal that doesn't find a way to serve us. The cat made a good strategic move. With luck they might outlast us, and return to having primates for lunch long after we're gone ...

Sunday, July 01, 2007

Flash and Silverlight in the iPhone's crosshairs

There are two complementary articles out discussing the big time battle for control of the web's presentation layer. I wrote about this in my tech blog a week or two ago, but it's really more a technological and marketing battle than a "how to" issue -- hence the crossover to this one.

The first article is by Cringely. An AIR of Invisbility is about Abobe's flash descendant, once Apollo and now AIR. It's compact, responsive, and Cringely thinks it will beat Microsoft's Silverfish ... err ... Silverlight on the web and as the presentation layer for the post-PC era.

The second is by a Mac geek site, Roughly Drafted. RD thinks the iPhone's exclusion of Flash is the declaration of a war that Apple will win. It's a nice bit of work, I learned a few things about Flash and the Flash video codec.

My experiences with Adobe's products doesn't make me happy about them winning this battle. I might even prefer Silverlight, except that would be the death of the non-Microsoft web. Since Apple is pushing a suite of non-Apple standards that Google and Mozilla also favor, I hope they win, but I don't expect a knockout victory.

I don't think Silverlight will win -- with enemies like Google, Adobe, Apple and everyone else that's too much even for Microsoft. I hope.

I don't think Flash will die, I think Google will want to keep it around to fight Silverlight, but I could see it's advance slowing.

So I'm cautiously optimistic.

Justice takes a surprise turn - the man that got away goes to prison

What?! This inverts my entire sense of how the world works. Can I rely on nothing?!

Two years ago Richard Scrushy escaped what seemed to be a slam dunk conviction. The outsider consensus at the time was that the charismatic Mr. Scrush used his nefarious talents, and the language of the southern baptist, to persuade a religiously inclined jury to disregard the evidence. Certainly the people I personally know who knew him well felt that way.

Today, accidentally, I read that he's gone to jail. Here's what happened, emphases mine:

TheStar.com - Business - Richard Scrushy's road to prison

Richard Scrushy, the rehabilitation king turned TV preacher, is trading his 92-foot yacht for a jailhouse bunk.

The former HealthSouth Corp. chief executive – cleared in a landmark corporate fraud trial in Birmingham but convicted on unrelated bribery charges in Montgomery – was sentenced late Thursday to nearly seven years in prison.

Scrushy's third wife, Leslie, a former HealthSouth secretary, cried as marshals took the millionaire with nine children into custody.

The term was imposed two years after Scrushy beat charges in Birmingham that he presided over a $2.6 billion (U.S.) accounting fraud at HealthSouth, a sweeping acquittal in sharp contrast to high-profile corporate convictions won against Enron Corp., WorldCom Inc. and Tyco International Ltd. executives.

After losing the case involving false earnings reports at the rehabilitation company Scrushy founded, federal prosecutors targeted his dealings in 1999 with then-Gov. Don Siegelman, who was also convicted and sentenced to seven years and four months in prison.

So Scrushy – the brash guy from small-town Alabama who mostly recently cast himself as a minister trying to save lost souls – is being sent far from his big boat, the Chez Soiree, and his estate in Birmingham, where HealthSouth is based.

A judge ordered him to serve six years and 10 months in federal prison, where there's no chance of parole. He must pay $417,000 in fines and restitution, serve three years on probation, and perform 500 hours of service work once freed.

It's a long fall for a man who once hobnobbed with celebrities and politicians. Asking the judge to spare him from prison, Scrushy, 54, portrayed himself as a humble man of God who did nothing wrong. "I'm just a pastor," he said.

Scrushy studied respiratory therapy before coming up with the idea in the early 1980s for a company focused on rehabilitation in outpatient clinics rather than hospitals.

Pooling money from investors, Scrushy launched what became HealthSouth, which billed itself as the nation's largest rehabilitation company with some 2,000 locations worldwide. Reported revenues exceeded $3.5 billion.

But something sinister was going on. Evidence at Scrushy's first trial showed a group of executives who called themselves "the family" began fudging earnings in a bid to bolster sagging stock prices. The company overstated earnings by $2.6 billion from 1996 through 2002.

Fifteen former executives pleaded guilty, and some said Scrushy directed the scam. But in a stunning defeat for the government, Scrushy was acquitted on 36 counts of fraud, false corporate reporting and making false statements to regulators.

Then came the bribery charges. Scrushy was accused of arranging $500,000 in payments for a seat on a board that regulates Alabama hospitals. He was convicted.
I'm sure there will be an appeal, but even so! The south is not what it was. An ex-governor and a wealthy evangelical con man both sent to prison for 7 years - without parole? What planet am I living on again?

The only thing that seems believable about this is how quietly the media has treated the story.

Did leaking gas intoxicate the london bombers?

The bright side, so far, of several failed attacks in London, is that the attackers seem incompetent and undersupplied. I wonder, reading this description, if the primary bomber failed because s/he was intoxicated by leaking petroleum fumes:
Scotsman.com News - UK - Second car bomb 'aimed at rescuers':

THE terrorists who attempted to bomb central London last week deliberately placed the second vehicle to catch rescuers attending the injured from the first explosion, Scotland on Sunday can reveal.

The senior security source also said the primitive gas and petrol devices were most likely the work of determined terrorists struggling - because of the security crackdown - to get their hands on the ingredients needed to create high explosives.

Yesterday, a huge police manhunt was under way for the terrorists responsible as forensic experts continued to examine the vehicles involved for clues.

The attack was thwarted after fumes were spotted leaking from the first vehicle, parked outside the packed Tiger Tiger nightclub in London's West End in the early hours of Friday morning...

Saturday, June 30, 2007

The good news on global warming: not enough fuel

Dyer recently wrote of the CO2 "game of chicken" -- China and India vs. the post-industrial world in a race to see who can fry the world first.

FuturePundit (warning, he is irrational about global warming) posts a more optimistic view -- we can't fry the world because we don't have enough coal. His writing is referring to this blog post. If you buy this argument we can only roast the world a bit.

That's the most optimistic thing I've read all week. Of course I suspect it's not true, but one can dream ...

Why the Iraq war is a great thing for America

No, really. It's great. George Bush is a strategic genius, a farsighted visionary far beyond anything the world has seen before.

Yes, hundreds of thousands of Iraqis have died. Millions have suffered terribly. Over 30,000 allied solders will have significant lifelong disability. Thousands are dead. A trillion dollars has been vaporized. America's shame will live a hundred years. The middle east's problems are even less tractable than they were 10 years ago. Pakistan may yet collapse, becoming an arms dealer for nuclear terrorists (ok, so that would be particularly bad).

All this, thanks to George Bush.

And, yet, this would be much worse. If the fiasco, the horror, of the Iraq war makes America more cautious, less strident, wiser ... then we may avoid war with China. If we avoid war with China, future historians may decide that Bush's fiasco was a good thing for America and for most of the world, excepting, perhaps, Iraq.

Update 7/4/07: James Fallows makes a similar point from a different angle. Brrrr. There are worse fates.

Apple victorious

I've been reading the iPhone reviews. Grumpy geek iPhone fans like Coding Horror say to wait for 3G support and a few more physical buttons next year. More desperate sorts, less enamored of Microsoft's solutions, say to wait at least until this fall. Maybe then we'll have search, cut and paste, tasks, better synchronization, an external keyboard, disk mode, fewer crashes, etc.

No matter. This review, late to the game, sums it up best. It's quite possible, if AT&T can hold itself together, and if the phone crashes no more than once every few days (with no data loss), that Apple has won. They've put a serious OS, with serious multimedia and network capabilities, on a phone with serious graphics capabilities. They've established a cross-platform distribution mechanism (iTunes) for updates, software, backups, media retail, etc. They're allied with Google (for now).

Does Apple want to raise a few millions? Sell a "task" add-on for $20 a pop. Does Apple want to raise a few hundred million? Sell games.

You did notice that Apple now has a handheld gaming platform, didn't you? (With an accelerometer too.)

It's great news for Apple stakeholders and, in the near term, it's good news for AT&T. More importantly, it's fantastic news for the decaying American mobile phone industry. There will be a desperate scramble by AT&T's competitors to deliver better products faster, and the handset manufacturer will get whatever they want. And once the 3G iPhones start appearing overseas ...

Did I mention that Minneapolis is putting in metro-wide 802.11? The iPhone will work quite nicely there, including the VOIP services Jobs is promising.

Anyone who has a mobile phone number should be very grateful that Apple, it seems, has delivered.

7/2/07: Yes, victory indeed. When a US mobile phone stokes anxiety in Korean manufacturers, something radical has happened. It's bit like Brazil suddenly launching a star ship.

7/2/07: More proof. I really didn't think Apple could do it out of the gate.

Race returns as ancestry, this time with better brains from China

A few years ago race was on the ropes, but it's back and looking as though it will persist, though possibly with a new name. The base "genetic clusters" (races) are:
  • Africans
  • Australian aborigines
  • East Asians
  • American Indians
  • Caucasians (Europeans, Middle Easterners and people of the Indian subcontinent)
(The "genetic cluster" breakdown in the graphic that accompanies the article is incomplete, the above list was taken from the article)

Not only is race back, but so are race-specific mutations affecting brain development. DAB1 is said to be "Chinese only", but I suspect the researchers are using "Chinese" as a proxy for "east asian". Anyway, the mutation sounds suspiciously like an upgrade:
Humans Have Spread Globally, and Evolved Locally - New York Times

Another puzzle is presented by selected genes involved in brain function, which occur in different populations and could presumably be responses to behavioral challenges encountered since people left the ancestral homeland in Africa.

But some genes have more than one role, and some of these brain-related genes could have been selected for other properties.

Two years ago, Bruce Lahn, a geneticist at the University of Chicago, reported finding signatures of selection in two brain-related genes of a type known as microcephalins, because when mutated, people are born with very small brains. Two of the microcephalins had come under selection in Europeans and one in Chinese, Dr. Lahn reported.

He suggested that the selected forms of the gene had helped improved cognitive capacity and that many other genes, yet to be identified, would turn out to have done the same in these and other populations.

Neither microcephalin gene turned up in Dr. Pritchard’s or Dr. Williamson’s list of selected genes, and other researchers have disputed Dr. Lahn’s claims. Dr. Pritchard found that two other microcephalin genes were under selection, one in Africans and the other in Europeans and East Asians.

Even more strikingly, Dr. Williamson’s group reported that a version of a gene called DAB1 had become universal in Chinese but not in other populations. DAB1 is involved in organizing the layers of cells in the cerebral cortex, the site of higher cognitive functions.

Variants of two genes involved in hearing have become universal, one in Chinese, the other in Europeans...

... A genomic survey of world populations by Dr. Feldman, Noah Rosenberg and colleagues in 2002 showed that people clustered genetically on the basis of small differences in DNA into five groups that correspond to the five continent-based populations: Africans, Australian aborigines, East Asians, American Indians and Caucasians, a group that includes Europeans, Middle Easterners and people of the Indian subcontinent. The clusterings reflect “serial founder effects,” Dr. Feldman said, meaning that as people migrated around the world, each new population carried away just part of the genetic variation in the one it was derived from...

... The concept of race as having a biological basis is controversial, and most geneticists are reluctant to describe it that way. But some say the genetic clustering into continent-based groups does correspond roughly to the popular conception of racial groups....

... David Reich, a population geneticist at the Harvard Medical School, said that the term “race” was scientifically inexact and that he preferred “ancestry"...
Ethnicity reflects your cultural identity, so that word is clear enough. I think "ancestry" is too vague -- Japanese and Koreans may feel they have very different "ancestry" (and in a sense they do), but they're not two "races". I think we're stuck with race for now.

So what year will we start tweaking human brains with the "best" (heh, heh) upgrades? I'm guessing 2040, because it will probably be pretty hard to get right.

Friedman on the "transparent society" (without mention of Brin)

Friedman, a celebrity whose reputation has cruelly fallen, writes about the implications of global reputations ... 

The Whole World Is Watching - Friedman -New York Times

... When everyone has a blog, a MySpace page or Facebook entry, everyone is a publisher. When everyone has a cellphone with a camera in it, everyone is a paparazzo. When everyone can upload video on YouTube, everyone is filmmaker. When everyone is a publisher, paparazzo or filmmaker, everyone else is a public figure. We’re all public figures now. The blogosphere has made the global discussion so much richer — and each of us so much more transparent.

The implications of all this are the subject of a new book by Dov Seidman, founder and C.E.O. of LRN, a business ethics company. His book is simply called “How.”..

Alas, Friedman is not much of a reader or a researcher, otherwise he'd know of David Brin's 1999 book, The Transparent Society. Friedman, presumably recycling Seidman, predicts youngsters of today will have to carefully manage their public actions from now through adulthood, avoiding any smirch on their record that would impair their future promotion path. So predictable. He doesn't even manage to mention that the vast majority of human history has been lived in small communities where reputations were as robust as memory.

If Friedman were to open his mind a wee bit, he'd take in a bit of science fiction. Reputation management has been a recurring theme of the genre for at least 20 years. There are many alternate paths, including identity obscuration (create false paths to confuse the story, an application of fraud techniques to blur recollection), identity fraud, and tools and methodologies to support the creation of multiple transient identities. In some paths one's "True Name" is guarded as closely as in LeGuin's fantasy novels, while alternate identities are juggled throughout life. Or, most likely of all, we'll only have to worry about any of this stuff for the short period of time in which our everyday environment is even marginally comprehensible to our feeble primate brains.

Incidentally, the relationship between John Gordon and me will become one degree more obscure sometime in the next few weeks....

Friday, June 29, 2007

Four new Dyer essays

Dyer 2007

June 14 The Islamic Republic of Gaza
June 18 Kosovo and the Law
June 21 China's Shoes
June 23 The Middle East After Iraq
Some points of interest from this series:
  • In 2006 China emitted 8% more CO2 than the US
  • Cement and coal are the two reasons China puts out far more CO2 per capita than it should
  • China, India and the US are playing a monstrous game of "chicken" on CO2 emissions
  • Dyer on Israel's future: "Israel faces another generation of confrontation and quite possibly of war, and the Palestinians face another generation of military occupation. Significant chunks of the Arab world face Islamist revolutions that would bring more poverty and a new kind of oppression. It is a mess, and it's too late to fix it.
  • Dyer is as pessimistic about Kosovo as he is about Israel, and he regrets ever supporting the US attack on Serbia. He sees it as a "precedent" for the invasion of Iraq. I think he's overestimating how much "precedent" Cheney/Bush needed.
Of the four essays the China one is by far the best and the Kosovo essay the weakest.