Caffeine and apoptosis

This is not necessarily good ...

Coffee and plenty of exercise could cut risk of skin cancer | Science | The Guardian

...A combination of coffee drinking and regular exercise may help to lower the risk of developing skin cancer, according to scientists in the US.

The two are thought to work together to kill off precancerous cells whose DNA has been damaged by ultraviolet-B radiation from the sun....

... Previous studies have suggested that exercise and coffee may each play a small role in protecting against skin cancer, but the latest research shows for the first time that when combined, the two may offer far more protection.

Scientists led by Allan Conney at Rutgers University, New Jersey, examined the effect of ultraviolet light on mice bred to be hairless, and so particularly vulnerable to the effects of sunlight.

Four groups of mice were exposed to UV-B radiation, but were given different diets and exercise regimes. One group drank caffeinated water, giving them a caffeine intake equivalent to one to two cups of coffee a day. A second group was fed pure water but allowed to exercise on a running wheel. The third group was given caffeine and access to a running wheel, while the fourth did no exercise and had no caffeine.

The scientists later took samples and checked for signs of UV-induced genetic damage. They also looked for evidence of a natural survival mechanism called apoptosis, in which damaged and potentially cancerous cells are forced to commit suicide before they can form tumours.

The tests showed that caffeine alone led to a 95% increase in programmed cell death and there was a 120% increase from exercise alone. But when combined, exercise and caffeine led to a four-fold increase in cell death, suggesting the body was able to rid itself of pre-cancerous cells much more effectively....

A 400% increase in programmed cell death?! Omigod, that's a lot. It turns out there's a burgeoning literature on caffeine and apoptosis.

Yech. I have both an affection (heck, addiction) to caffeine and a family history of skin cancer, so one might think I'd find this lighthearted good news. Alas, biology doesn't work that way. If this effect occurs in humans we're looking at a significant impact of caffeine on the fundamental behavior of cells. It would be surprising if that effect were always benign. Apoptosis of pre-melanoma is fine, but apoptosis of dopaminergic neurons ... maybe not so fine.

Fallows on the media: a 1996 article is even better today

Fallows, writing in his personal blog, called attention to an article he wrote in 1996 - before Bush, before 9/11, before the crash -- at the very height of our Glory Days: Why Americans Hate the Media. In brief, Fallows was merciless. Americans dislike the media, he concluded in 1996 because ... they had performed miserably. Everything he wrote then is true today. There are some great exceptions (some print journalists turned bloggers, Fallows himself, some astounding science writers) but there are lots of disasters. The punditry is an almost complete mess, and the beltway media is as bad today as it was 11 years ago.

Today Fallows writes "several times I have considered revisiting the whole what's-wrong-with-the-press question and have instead plugged on with other topics -- Iraq policy, China -- for reasons that boil down to: what's the point? The problems with the media are the same as I tried to describe 11 years ago -- just worse, and with new technology. But there's always tomorrow..."

The media didn't reach the basement by itself of course. Advertisers and bottom-line editors and owners drove many there, though some made it through egomania alone. Americans, above all, spent the money that justified those decisions. In consumer action as in American politics, the blame ultimately falls on the American citizen. Of course since newspapers are hemorrhaging money, maybe Americans have reformed a bit ...

NSA 2004: the loons were right, of course

In 2004 cynical geeks were convinced that Total Information Awareness, Poindexter's program of data mining, was continuing under an assumed name. Mainstream journalists classified this as "lunatic fringe". Now, of course, the "loons" have gone mainstream.

Which brings us to Gonzales. Why hasn't he gone? Why the intense focus on GOP election rigging strategies and telecom monitoring when there are so many other GOP/Cheney/Bush crimes to investigate? It's not unreasonable to assume that there's more going on that meets the eye. Something Gonzales has to cover up, something that will come to light too soon if he's gone ...

Data Mining Figured In Dispute Over NSA
By Dan Eggen and Joby Warrick
Washington Post Staff Writers
Sunday, July 29, 2007; A04

A fierce dispute within the Bush administration in early 2004 over a National Security Agency warrantless surveillance program was related to concerns about the NSA's searches of huge computer databases, the New York Times reported today.

The agency's data mining was also linked to a dramatic chain of events in March 2004, including threats of resignation from senior Justice Department officials and an unusual nighttime visit by White House aides to the hospital bedside of then-Attorney General John D. Ashcroft, the Times reported, citing current and former officials briefed on the program.

Attorney General Alberto R. Gonzales, one of the aides who went to the hospital, was questioned closely about that episode during a contentious Senate hearing on Tuesday. Gonzales characterized the internal debate as centering on "other intelligence activities" than the NSA's warrantless surveillance program, whose existence President Bush confirmed in December 2005.

FBI Director Robert S. Mueller III contradicted Gonzales, his boss, two days later, testifying before the House Judiciary Committee that the disagreement involved "an NSA program that has been much discussed."

Although the NSA's data mining efforts have been reported previously, neither Bush nor his aides have publicly confirmed that, in connection with the surveillance program, the agency had combed through phone and e-mail records in search of suspicious activity.

Nor have officials publicly discussed what prompted the legal dispute between the White House and the Justice Department.

The report of a data mining component to the dispute suggests that Gonzales's testimony could be correct. A group of Senate Democrats, including two who have been privy to classified briefings about the NSA program, called last week for a special prosecutor to consider perjury charges against Gonzales.

The report also provides further evidence that the NSA surveillance operation was far more extensive than has been acknowledged by the Bush administration, which has consistently sought to describe the program in narrow terms and to emphasize that the effort was legal.

The White House, the Justice Department and the Office of the Director of National Intelligence declined to comment last night. Calls placed to the NSA, which collected and analyzed the data, were not returned.

The warrantless surveillance program, which was authorized by presidential order after the Sept. 11, 2001, attacks, was first revealed publicly by the Times in December 2005. Bush confirmed aspects of the program at that time, defining it as monitoring communications between the United States and overseas in which one party was suspected of ties to al-Qaeda.

The Washington Post reported in February 2006 that the NSA targets were identified through data mining efforts and that thousands of Americans had been monitored. USA Today later reported that the government had the help of telecommunications companies in collecting millions of phone records.

The practice of sifting through mountains of privately collected data on phone calls and Internet communications raises legal issues. Although the contents of calls and e-mails are protected, courts have ruled that "metadata" -- basic records of calls and e-mails kept by phone companies -- are not...

I'll bet it wasn't merely international phone data. I suspect if they got a "hit" they ran through every database they could get their hands on -- and that they're false positive rates were significant. The media needs to read up on the original TIA plans, and assume that they were all implemented under different names.

Stories sunk without a trace: Feb 2004 bioweapon scare

I was searching my blog for a post and came across this old story ...

Gordon's Notes: WaPo: Chemical and bioweapon attacks on planes (2/1/2004)

... Intelligence indicating that al Qaeda terrorists are seeking to release a chemical or biological agent aboard an airliner, or transport a radiological device in cargo, was one of the factors that prompted the cancellation of six international flights scheduled for today and tomorrow...

I've long wished newspapers would routinely review stories written 2-5 years ago and tell us how it turned out...

Paying doctors: Room for huge cuts

The New York Times points out that physician reimbursement is one of the reasons that Amerian healthcare is more costly than european (or Canadian, Israeli, etc) health care.

I think they're mostly correct, though the discussion is necessarily simplified. They so point out that the discrepancy is far larger for specialists than primary care, but I think that when one adjusts for differing social costs and workload that primary care physicians in Europe and the US are similarly compensated. The gulf is entirely in the specialties, and particularly the procedural subspecialties (gastroenterology, radiology, etc.). The vastly greater compensation for specialty care in the US has shifted the physician workforce to being largely specialty based, amplifying the total cost to American healthcare. Of course lawyers in the US are probably paid several times as much as European lawyers, but that doesn't change the conclusion.

There's no way to figure out what one should pay physicians because there's no true market in healthcare; the best guide we have is people who pay cash and they tend to be atypically impoverished. It's likely, however, that one could slash US orthopedic reimbursement by 30-40% [1] and still get excellent orthopedic care once the dust settled (though the dust would take years to settle).

There's one point in the article where things went quite wrong however (emphases mine)...

...Dr. Goldman of RAND said that doctors are misleading themselves if they think the current system serves patients’ needs.

For example, if a diabetic patient visits a doctor, he said, “the doctor is paid to check his feet, they’re paid to check his eyes; they’re not paid to make sure he goes out and exercises and really, that may be the most important thing.”

“The whole health-care system is set up to pay for services that are rendered,” he said, “when the patient, and society, is interested in health.”...

I assume Dr. Goldman is not terminally naive, so he must be dissembling. I'm sure his job requires some creative dishonesty, but I wish he wouldn't. There's no real evidence that Americans, or anyone really, is happy shifting healthcare resources from treatment to prevention. Humans simply are not that rational. It's not even close. If Americans were spending their own dime, meaning we had a true healthcare market, I bet we'd spend even less on preventive care than we spend now.

Other than Dr. Goldman's misdirection I agree with the thrust of the article. We could slash healthcare administrative overhead by 70% chop 30% or more off drug costs, and cut procedural/subspecialty reimbursement by 30-40% [1] and still end up with better quality healthcare, by any measure, than we have now. We'd also, with no increase in primary care compensation, end up with a better supply of primary care physicians. The subspecialty offices, however, would have thinner carpets and rattier furniture.

[1] I originally wrote 70%, but that was the result of too quick math. The contrary argument is that, barring continued importation of non-citizen physicians, the US healthcare system is competing for talent with the corporate sector. If US corporate compensation is much higher than European compensation, then that might necessitate higher proceduralist compensation. I don't think that's true however.

The erratic non-progress of the personal information manager

The Personal Information Manager (PIM) has had a difficult 24 years, since Borland's "Sidekick" more or less launched the genre. We're coming up on the 25th anniversary of Sidekick, and I think it's fair to say a geek of 1983 would be shocked by how little progress we've made. The iPhone has no tasks. What more can I say?

The PIM has been a longstanding interest of mine. At various times in my life I've had a pre-web listserv dedicated to the personal information manager, a now-defunct blog dedicated to the Palm and its alternatives and an abandoned web page or two on related topics. I thought of the PIM as I cleaned out some old files, with clippings about (some of these were groupware too) the golden years from 1983-1994. It was in 1994 that the reign of Sauron began.

• Arabesque's Ecco (much mourned)
• Lotus Organizer (ok, so it wasn't too fancy)
• Act for Windows (still around I think)
• CrossTies (object oriented model)
  
• MeetingMaker (cross-platform)
  
• Lotus Agenda (a classic)
• Attain Corp's "In Control": outliner/calendar combination
• GrandView: calendar/task/outliner/spreadsheet
• Ascend
• Commence
• Arrange 2.0 (Mac - bit of an object oriented database I think)
• InfoDepot
• FullContact
• First Things First (outliner, calendar)
• NewtonOS: a PIM that was an Operating System

Outlook came later, and the combination of Outlook/Exchange crushed the genre on the PC -- and finished off Palm as well (though by then Palm's owners had shot both feet off). Reinvention continues on the Mac, with a vast array of small vendor products that have various combinations of features of all of the 1983-1994 PIMs. On the web we have Backpack and a range of Web 2.0 apps, most of which will vanish in the next few years. Along with all your data.

Fifteen years ago I thought the salvation of the PIM would be application embedding, what we then thought of as OpenDoc. We'd have applications for projects, tasks, calendars and the like, and they'd all seamlessly interoperate with one another. That was a bit before I got into the interoperability business myself, building applications that tried to talk to one another about lab studies, diseases, genetic history, procedure history, consultations, etc. In that world software is relatively easy, the hard part is "meaning" -- having a common, or at least reasonably interoperable way to represent knowledge about things between systems. It starts with being able to generate a common data model (even if it's only used for communication), but it gets much harder than that when you need to store and create bits of data. That's when you get into really painful things, like formally maintained ontologies. (Engineers love emergent ontologies, which is more like the way our minds work, but interoperability between minds requires more CPU power than we have on the desktop.)

I think the 25 years of non-progress in PIMs springs from the same roots as 25 years of very slow progress in interoperable clinical systems (whether you want them to actually be able to share data is another matter - one of which I've blogged before). The domain of the PIM is far simpler semantically than that of the clinical record, but there's far less pressure for the grindingly hard work of common semantics and mutually agreed upon data models. I think we'll be at roughly the same point in 2033 that were were in 1983 ...

How worthless is the no fly list: 20,000:0 false to true positive

We have long history in medicine of worse-than-useless tests. Tests that produced ten false alarms for every genuine alarm, causing more harm from misguided retesting and treatment than the disease being tested for. The PSA test in men may turn out to be one of those misguided tests; at best it's a borderline test.

I can't recall any diagnostic test in modern medical history, however, that produced 20,000 false positive results and no true positives. I think for a test like that you have to go back to the pre-rational era.

The pre-rational era in which Homeland Security lives today:

Schneier on Security: Terrorist Watch List: 20,000 False Alarms

The Justice Department's proposed budget for 2008 reveals for the first time how often names match against the database, reporting that there were 19,967 "positive matches" in 2006. The TSC had expected to match a far fewer number 14,780. The watch list matched people 5,396 and 15,730 times in 2004 and 2005 respectively.

The report defines a positive match as "one in which an encountered individual is positively matched with an identity in the Terrorist Screening Data Base, or TSDB."..

How do I know they're all false alarms? Because this administration makes a press splash with every arrest, no matter how scant the evidence is. Do you really think they would pass up a chance to tout how good the watch list is?

I've written about this before, often reacting to Schneier's prior posts:

• June 2007
• October 2006
• March 2006
• Dec 2005
• Oct 2005
• Aug 2004

There are two classes of problems with stupidity like this. One is that it causes potential harm to all the false positives, from travel delays to targeted data mining to harassment and false arrest. The other class of problem is that it harms our security. We have only limited resources to use against our enemies, spending them on chasing false leads leaves less for the real work.

Why you may want your child on the third place team ...

If your child is keen and a strong ball player, you probably want her to join the team that will contend for the championship. On the other hand, if your child is a marginal sportsmen, you may want him on the team that will contend for third place.

At least that's the conclusion I came to from my first season coaching (assistant/manager) a 10-12 yo ball team. In our league the teams start out reasonably equal (there are some inequalities with pitching that can't quite be eliminated), but at the end of the season there's a wide range of abilities. There are really three major determinants of success -- coaching input, chance (injuries), and natural selection.

The natural selection bit isn't hard to game. If you drive hard, push a bit, yell a bit, tone down the encouragement, it's not hard to eliminate two or three of the weaker players. If your numbers get too low you get to bring up the very best players from the lower league -- who will play well above the weakest players you gave up. I really doubt this is done consciously; I think these coaches would be profoundly offended if the topic were broached. It's just the way the world works.

The winning team this year had a superb coach (I've been learning from him) and, as near as I can tell, just this kind of natural selection. I suspect it's a universal rule in all team sports, no matter how egalitarian the league. On the other hand, I think in a league of nine teams a very good coach (better than I am now) can probably contend for third or fourth place with their original squad.

BTW, the optimization problems of a full-rotation 14 player ball team roster are pretty darned impressive ...

Hinduism, Mormonism and more - Fundamentalist America in disarray

How the mighty have fallen.

Only seven years after inflicting Cheney/Bush upon the world the American Fundamentalist faces ruin on every front. Gay relationships barely draw notice (do they draw any notice?) in the Twin Cities -- at the very heart of fly-over land. The creationist movement, though far from spent, is in disarray. Polls suggest a dramatic increase in the number of Americans without religious affiliation (though still a smallish minority). Wiccans have their symbols in military cemeteries, and are an identified religious group in the military. Islam has come to Congress. So many evangelical figures have gone down to flames that scandals barely draw notice any more. Perhaps worst of all, current GOP presidential candidates range from incredibly lapsed Catholic (3 marriages?) to a flip-flopping non-Christian.

Into the ruins comes .... Hinduism [1]. Along with Jains, Hindus challenged the display of the ten commandments in the court (though they lost that fight). Now there've been Hindu prayers in the Senate, six years after Bush's post-9/11 invocations pointedly ignored "non-biblical faiths" and non-faiths:

Hindu Groups Ask '08 Hopefuls to Criticize Protest - washingtonpost.com

... Ante Nedlko Pavkovic, Katherine Lynn Pavkovic and Christan Renee Sugar -- identified in the Christian media as a couple and their daughter -- were removed from the Senate floor and arrested by Capitol Police on July 12 after they began shouting, "This is an abomination," and asking for forgiveness from God...

... A brief prayer was then delivered by Rajan Zed, a chaplain from Reno who was invited by Senate Majority Leader Harry M. Reid (D-Nev.).

Several Christian organizations spoke out against the prayer, before and after it was delivered. The American Family Association circulated a petition, urging its members to contact their senator to protest the prayer. "This is not a religion that has produced great things in the world," it read. The Rev. Flip Benham of Operation Rescue/Operation Save America issued a statement saying the prayer placed "the false god of Hinduism on a level playing field with the One True God, Jesus Christ."...

... A focus of the Christian organizations was the perception that Hindus are polytheistic. "Our national motto isn't 'In gods we trust,' " Janet L. Folger, president of Faith2Action, said the day before the Senate prayer.

However, the U.S. Hindu groups say this criticism reflects ignorance of the monotheistic underpinnings of their faith. Hinduism has many deities, all manifestations of one god.

According to the foundation, there are 2 million Hindus in the United States.

Hindusim is monotheistic? Umm, I don't think it's that simple (read the eb article by the way, it's fascinating). Mormonism, Islam (excl Sufism), Judaism, and Christianity are all pretty different theologies -- roughly equidistant from one another in some multi-dimensional doctrinal space. Hinduism is an order of magnitude away from the those four, as are Bahai, Unitarianism, Shinto, etc.

There's no way to paper over those differences, and they are disastrous for American fundamentalists. The world is moving on, and American politicians want those Hindu, Jain, Bahai, Buddhist, Shinto votes ...

[1] After reading the EB article it's not clear that "Hindu" is a theologically meaningful label, but I'll stick with it for this post.

Obesity: correlation, not causation

Wailing. Gnashing of teeth. Rending of garments.

That's my reaction to the continuing inability of even semi-informed humans to remember the distinction between correlation and causation, of fully informed specialists to "forget" the distinction ...

Find Yourself Packing It On? Blame Friends - New York Times:

.... The answer, the researchers report, was that people were most likely to become obese when a friend became obese. That increased a person’s chances of becoming obese by 57 percent. There was no effect when a neighbor gained or lost weight, however, and family members had less influence than friends.

It did not even matter if the friend was hundreds of miles away, the influence remained. And the greatest influence of all was between close mutual friends. There, if one became obese, the other had a 171 percent increased chance of becoming obese, too...

...Dr. Nicholas A. Christakis, a physician and professor of medical sociology at Harvard Medical School and a principal investigator in the new study, said one explanation was that friends affected each others’ perception of fatness. When a close friend becomes obese, obesity may not look so bad.

“You change your idea of what is an acceptable body type by looking at the people around you,” Dr. Christakis said....

Christakis knows better of course, but he also knows how to play the game. He's discovered an interesting correlation in the Framingham data set, and no doubt he thinks he's "controlled" for confounders like education, smoking, socio-economic status, exercise, hobbies, and attitudes towards food. All factors that may play a role in both friendship and obesity (and all of which are affected by genes, which is another topic).

Grr. If the NEJM had better editors they'd publicly slap the hand of researchers who pretend to be unable to tell the difference between causation and correlation. No wonder the media gets confused.

We have a long history of studies like this that demonstrate our ability to control for confounders is weak -- no matter what statisticians say. (Why it's weak is an interesting question.) I am very much doubt that a true study (impossible to do), one that randomized people to be "friends" would find any correlation.

Update 7/27/07: Other variables plausibly correlated with both obesity and friendship include term pregnancy, child rearing, and marital-equivalents. There are likely several others ...

Addiction and disease: My comments on the TIME Science blog

Here's a fragment from Lemonick's blog post:

Addiction is NOT a Disease??? - Eye on Science - Science Blog - Michael D. Lemonick - TIME

A couple of weeks ago, Alice Park and I wrote a cover story about addiction. In it, we kept talking about the fact that addiction is a disease of the brain.

Silly us. While that's admittedly the view of the National Institute on Drug Abuse and the vast majority of addiction specialists, we forgot to talk to Sally Satel and Scott Lilienfeld. If we had, we would just have said "never mind." Yesterday, this dynamic duo published this essay at Slate.com, in which they set the record straight.

Satel and Lilienfeld, a psychiatrist and a psychologist, respectively, explain that addiction is no disease. It's a habit. "But like other bad habits," they write, "it can be broken." Which is to say, it's kind of like picking your nose in public, evidently, except that it's more expensive...

And here's my comment:

This is a deeper topic than you're suggesting. The past twenty years of neuroscience have been putting a tighter and tighter box around what "free will" can be. Much of what we are and do is determined by our genes, and the rest is pretty much set in-utero (the primary environmental component). The next 5-10 years may add another 10-15% of variation, and we don't have much control over that, do we?

After age 10 we're pretty much on cruise control -- or so it seems.

So the contrarians aren't really arguing about addiction, they're arguing about the fundamental basis of responsibility. If all we are and do is determined by our genes and uterine residence, then what does punishment mean?

So their arguments are nonsensical, but their anxiety is completely understandable. If our civilization survives I am reasonably certain that within 40 years our concepts of punishment and responsibility will be dramatically different.

Torturers may not sleep well ...

Libya imprisoned and tortured innocent people because they were convenient scapegoats for a disastrous HIV outbreak. Libya received a $400 million ransom to free them.

The torturers, however, may not always sleep so well ...

Freed medics describe Libyan captivity - International Herald Tribune

...Asked if they were ready to testify in a Bulgarian court in a future case against her torturers, Valcheva said calmly, 'Yes, we are ready.'

The courts will grind on. One day, a small semblance of justice will be done.

I wonder if Cheney ever thinks about the day he gets off a plane in Germany and finds handcuffs waiting for him ...

Please don't buy an iPhone. Yet.

Apple's iPhone may not have launched quite as well as Apple might have hoped. I like that. Apple is more likely now to second guess some of their mistakes, like a headphone jack that, for no sensible reason, doesn't fit most headphones. Maybe they'll even create a task list, enable notes synchronization, open the phone to signed Cocoa apps, put FileMaker Mobile on the phone, provide synchronization to Google Calendar, fix the broken Outlook synchronization (255 character contact notes?!?!) etc, etc.

On other side of the iPhone equation, AT&T may rethink pricing, and in particular rethink how much an iPhone is worth given their weak coverage and demonstrably slow and unreliable data support.

So if you've been thinking of buying an iPhone, please hold off a bit. I very much want to buy an iPhone, but I want Apple and AT&T to suffer enough to bring it a bit closer to what I need. (Voice dialing and GPS wouldn't hurt either, but I can live without them.) If you're still feeling tempted, contemplate this list of iPhone v1.0 Bugs (AppleHound). There, don't you think you can wait another three to five months?

You can wait a bit longer ... really. Apple's got tons of cash -- they're not going away. We just want them to suffer a bit. Heck, if the share price drops 20% you can make a good investment too ...

Iraqi feelings theoretically meaningful?

The very latest research suggests to some that Iraqi feelings should be treated as meaningful, even human ...

Study: Iraqis May Experience Sadness When Friends, Relatives Die

CHAPEL HILL, NC— A field study released Monday by the University of North Carolina School of Public Health suggests that Iraqi citizens experience sadness and a sense of loss when relatives, spouses, and even friends perish, emotions that have until recently been identified almost exclusively with Westerners.

"We were struck by how an Iraqi reacts to the sight of the bloody or decapitated corpse of a family member in a not unlike an American, or at the very least a Canadian, would," said Dr. Jonathan Pryztal, chief author of the study...

... "We are, in truth, still a long way from determining if Iraqis are exhibiting actual, U.S.-grade sadness," Mayo Clinic neuropsychologist Norman Blum said. "At present, we see no reason for the popular press to report on Iraqi emotions as if they are real."

The Onion has produced another bitter classic. I would applaud any newspaper that routinely followed "3,500 US dead" with "and over 300,000 Iraqi dead" .... (Thanks FMH)

Let us not mention this to our space alien visitors ...

There's really no need to bring up this sort of thing ...

Damn Interesting: The Thugs of India

...Their extreme secrecy combined with their mastery of murder made the Thugs the deadliest secret society in all of history. In the early 19th century they were credited with 40,000 deaths annually, stretching back as far as anyone cared to count. Some estimates put the overall death toll as high as 2,000,000, but with the cult potentially operating for more than 500 years before formal records were kept, the true number is impossible to determine.