About JPL

JPL lives the humid southeastern climes of North America. He enjoys the languid, directionless existence of the graduate student, but laments its low pay. Occasionally his volcanic temper overflows with rage. He inflicts this rage on others through blog posts.

Natty

So, one of the joys of Ubuntu is upgrading your OS every 6 months or so, getting kicked in the teeth, and spending the next week figuring out how to get back the functionality you used to have.

For me (this time) this meant figuring out why third-button emulation didn’t work on my two button mouse anymore (ancient, I know, but it ain’t broke).  This turns out to be X.org’s fault, and to fix it I have to do the same thing I had to do to enable it 15 years ago when I was running FreeBSD — edit the X config file in vi.  It’s all covered here.  At least xorg.conf is not the godawful mess that XFree’s config file was.  Still, one of Ubuntu’s most consistent failings is the way graphical configuration utilities consistently lag the functionality they support.  Ubuntu switched to pulseaudio as the default sound system two full releases before a pulseaudio configurator was available.  This was a real problem since pulse frequently chose the wrong output device as the default, leaving users with no sound and no way to fix the problem except hand-hacking the pulse config file.

What really reminds me of pulseaudio, though, is Unity, Canonical’s new graphical shell.  I don’t want to be a “the new interface sucks because it’s not the old interface” guy, but Unity is not fully thought out and not ready to be the default desktop.  This guy has it pretty much right (although I don’t hate the new scrollbar).  I wanted to like it, but the mechanism for running applications is fundamentally broken, and that happens to be the main function of an OS.  I could go on for a while about how stupid I think it is for an OS to depend on 3D acceleration, but that just makes me sound like a curmudgeon. As the link points out, though, it’s self-evidently stupid to ship a 3D-only desktop if your OS doesn’t install 3D drivers by default because of its philosophy on proprietary software.

Readers (if there were any) might rightly point out that these things are my fault for upgrading a perfectly working system.  It turns out six months is just about long enough to decide that the things you had to go through last time weren’t so bad, and to convince yourself that the shiny new features you’ll get from updating will be totally worth it.

Now I’m off to figure out why xsane doesn’t work anymore.

On WikiLeaks

I’ve been reading as much about WikiLeaks’ release of the State Department cables as I can find, and trying to get a handle on what I and others think about it.  The reaction to these leaks by the media, politicians, and various public figures has been far more hostile than to WL’s previous releases.  The key question seems to be whether the release of the cables is a responsible action, in the manner of the classic whistle-blower, or whether it is egregious and unwarranted.

I think the hostility stems primarily from two causes, a misunderstanding of exactly what has taken place, and a bit of good old-fashioned American navel-gazing.

On the first point, I think most people are under the impression (as I was, based on the initial coverage), that WikiLeaks has dumped it’s entire cache of documents on the Internet for everyone to peruse.  In fact the documents are being released in redacted form by WikiLeaks’ media partners at a rate of about 100 per day.  As far as I can tell, the balance of the documents are not available anywhere on line, nor were they available on the old wikileaks.org site.

My main point though, is aimed at the people who don’t think these documents are significant enough to warrant a deliberate breach of American security.  It’s only natural that these documents (being records of US diplomacy) are primarily of interest to people in other countries.  For instance, I think people in the UK are pretty interested to find out that their government lied to them about the cluster bomb treaty and the fate of Diego Garcia natives, and residents of the Middle East might want to know how the Qatari government manipulates al-Jazeera.  If someone sends you that kind of information, it seems to me that you’re morally obligated to disseminate it as widely as you can.

Perhaps the saddest part of this chapter is the vehemence with which the American media have attacked Assange and WikiLeaks, and the ambivalence they’ve shown in reporting the stories.  Glenn Greenwald has really been on top of this, check out the way the MSNBC host talks about Assange in the clip linked here.  Liberal media indeed.  Coverage in the New York Times, which has all the cables, has been, to me, significantly poorer than that of the Guardian, and even the English-language coverage by Der Spiegel.  Check out this list of stories broken by all of the outlets for a comparison (admittedly biased towards the Guardian).

I think the media has particularly dropped the ball on reporting the ideology behind WikiLeaks.  They have spelled out quite clearly the reasons behind what they’re doing, but I had to read about it on the blog of a grad student in California, because I haven’t heard it mentioned (much less engaged) by the mainstream press.  I suppose this is a little unfair, because the mainstream press does a bad job of reporting ideas and ideology at the best of times.

Why has the US media not embraced this treasure trove of information?  Maybe this is too simplistic, but I blame jealousy.  Once upon a time Daniel Ellsberg took the Pentagon Papers to the NYT, but the cables leaker(s) went to WikiLeaks instead.  Some potentially good reasons are spelled out in these videos.  This is yet another way in which new media is eating old media’s lunch, and a certain amount of hostility is only natural (if deeply unprofessional).

I’d like to close by saying that I don’t see a millimeter of moral difference between the releases by WikiLeaks and those of any other major media organization.  The reason they have been targeted is that they enjoy less status than more established organizations, and because they are a choke point in the information flow.  Next time you hear Eric Holder or some other Obama apparatchik call Julian Assange a criminal, just imagine they are talking about Marcus Brauchli or Bill Keller instead.  Better yet, ask yourself why those guys haven’t done anything to get themselves talked about that way.

Scientific Meta-Journalism

This post is almost two months old at this point, but I’ve just seen it. It’s a meta-article from the Guardian about science journalism, and it’s quite good. The biggest thing he misses is that the actual results of the study, which are probably quite technical and several steps removed from any general conclusion, will be fundamentally distorted to make them seem to have a massive impact on daily life.  This, however, might be done by the Journal’s PR people and not necessarily by the reporter.

The Global Game

A friend wondered, while watching Ghana v. Serbia on Saturday, how many countries in the 2010 World Cup have been bombed by the USA.  The ensuing discussion became led inevitably to this:

Countries bombed, shelled, invaded, occupied or attacked by the US:

  • Serbia (Kosovo War, 1999)
  • North Korea (Korean War)
  • South Korea (Korean War)
  • Japan (WW2)
  • Italy (WW2)
  • France (WW1/WW2)
  • Germany (WW1/WW2)
  • Mexico (Wilson administration and Mexican war)
  • Spain (Spanish-American war)
  • Algeria (Tripolitan war)

Countries where the US has organized, sponsored, or supported coups d’etat (not including the above):

  • Chile (Allende)
  • Ghana (Nkruma)

Countries where the US has supported brutal totalitarian regimes (not including the above):

  • South Africa (National party)
  • Argentina (Jorge Rafael Videla)
  • Greece (Colonels regime)
  • Paraguay (Stroessner)

That’s 16, or half of the teams in the Mondial.  I’ve probably also forgotten something obvious and embarrassing.

Honorable Mention goes to Honduras, whose banana republican governments were backed by the United States and the United Fruit for much of the 20th century, and to Portugal under the Estadio Novo, with which the US was allied through NATO.

It should be emphasized that if the US had not supported these regimes and organized these coups, the communists would have won, and we’d all be speaking Russian today.

A bit on Cell Phones and Cancer

I finally made time to read the results of the Interphone retrospective study on cell phones and brain cancer that were released last week.  What persuaded me to do it were the radically conflicting media interpretations of the announcement.  Here’s what seems to be the consensus view, as reported on the Washington Post’s “Post Tech” blog:

A large international study into the link between cellphone use and two kinds of brain cancer produced inconclusive results, according to a report to be released Tuesday in Geneva.

But researchers of the report noted flaws in the methodology of the long-awaited study. … The study’s results echo past research that the cellphone industry has cited for nearly two decades — a murky picture that there is not a conclusive link between cellphone use and cancer nor conclusive results that such a connection isn’t possible.

That’s the kind of summary I wish were written more often.  Ambiguity is probably the most common scientific result, although the press seems determined not to admit it in science reporting or elsewhere.  Contrast that with this take from, of all places, the BBC:

Analysis of more than 10,000 people by the International Agency for Research on Cancer (IARC) found no relationship between years of use and risk.  There is no known biological mechanism by which mobiles could cause cancer, but there has been public concern.  It is hoped this study will allay some anxieties, as research continues.

In other words: “You superstitious idiots only think phones cause cancer because you don’t know anything about Science.”  It’s one thing to say that no link was found, but to basically insult people who believe it could exist is pretty rich.  That first sentence is also carefully worded to focus on the one thing the study did rule out, instead of the many things it didn’t.  Logically one would expect the amount of use to be a driver of risk rather than length of use.  Why didn’t they lead with that?  Because the findings about the amount of use are inconsistent, and the way the two articles deal with them is telling.  One problem is that for most people there appears to be a risk-reduction associated with moderate, regular cell-phone use. Here’s the BBC’s take:

In fact, most regular users – defined as people who made use of their phone at least once a week – appeared to have a lower risk of brain cancer than those who rarely used a phone. The report authors stressed however this was unlikely to be down to any protective effect of phone use, and more a quirk of the study.

In the WaPo article this is seen as more than a mere quirk, indicative of a “flaw” and a “source of possible inaccuracies”.  The other key point is that people in the highest usage category (more than 30 minutes per day) did appear to show an increased risk.  Here’s how the WaPo handles that point:

The 10-year study, which was conducted by the World Health Organization’s International Agency for Research on Cancer, concluded there were “suggestions” that heavy use could increase the risk of glioma but “biases and error prevent a causal interpretation” that would directly blame cellphone radiation for the tumor.

According to the BBC story, these results were “dismissed as problematic.”  The Beeb story tries pretty hard to blame this on errors in reporting, citing the fact that ten people (out of over 5000 with tumours) claimed to have spent 12 hours per day on the phone.  They punch this further with a quotation from the report that the cancer “interferes with memory and cognition, undermining the accuracy of the recollections of such extreme use.”  That may be true, but what it adds up to is that you don’t know if that risk is there or not.  It doesn’t mean the risk should be discounted.

On the issue of funding for the study (about $24 million total), the BBC says that it “received some funding from the mobile industry”, while the Post tells us that it was “almost a quarter”.  Weirdest of all is the difference on further reports.  The BBC story seems to be pushing the idea that it’s a waste of taxpayer money, with this quote from the leader of the UK arm of the study:

“Whether it is worth doing more research, that is a question for society. These are expensive studies, and there are many other things in the world that should be investigated.  It is society which has to answer the question of how long you continue to investigate something that does not have a biological basis.”

He has clearly made up his mind.  According to the Post however, the lead researchers “urge more investigation into the topic to account for how cellphone use is affecting the health of youths” and because “the behavior of cellphone users has changed since the study was launched in 2000″.  That’s a bit different.  Either way, both articles report that a 30-year prospective study started last month.  So 30 years from now we ought to know, although that study too is funded in part by the cell phone industry.  If it gets canceled early, I might throw my phone away.

Do Fruits and Vegetables Prevent Cancer or Not?

A friend linked this Times blog post today, and it made me seethe with rage.  The headline is “Eating Vegetables Doesn’t Stop Cancer,” which seems reasonable enough.  It’s based on a recent study in the Journal of the National Cancer Institute which, unfortunately, reaches the opposite conclusion.  The journalist is forced to admit, in the sixth paragraph, that there was a statistically significant reduction in risk – 1-4% for eating 200 grams/day above the average.  Ok that’s small, but it’s still the exact opposite of what was in the headline and the first five paragraphs.  How does she reconcile this?  Unconvincingly:

While the findings suggest at least a small lower risk of cancer among those who eat lots of vegetables, the slight difference could be explained by a number of variables, like reporting errors among the study subjects or the fact that vegetable eaters also are less likely to smoke or drink to excess. In addition, a 4 percent reduction in relative risk offers very little practical benefit to an individual.

Of course, reporting errors could also cut the other way.  I suspect people are much more likely to exaggerate the amount of fruit and vegetables that they eat, particularly those who eat relatively little.

There is news here, which is that the reduction is much lower than was previously hoped, as this editorial in the same journal makes clear.  This point is totally absent from the Times post.  My biggest problem would be that the overly reductive title implies that no fruit or vegetable confers any benefit against any cancer.  There is a lot of evidence that some do, which they mention briefly at the end.

Will calorie restricted diets help us live forever?

As a nerd, I like the idea of reading science news.  Unfortunately, science coverage in the general interest press is almost uniformly awful.  There are a lot of reasons for this: reporters can’t possibly be current in every area of science (and in fact are probably not current in any of them), editors don’t seem to think the general public is interested in science except as it immediately applies to their lives (and they’re probably right), and the process of writing a science news article is like a giant game of password.  When you read a story in a newspaper, what you’re reading is an article summarizing a press release summarizing a journal article summarizing a study.  Clearly, information is lost, distorted, and spontaneously generated at every step of that process, so what you see in the newspaper often bears little resemblance to what was actually done.  Some amount of that distortion is deliberate:  Scientists try to make the data tell a story, the journal’s marketers try to write a press release that will get the journal’s name in papers around the country, the journalist tries to write a story that will get printed, and the editor tries to shape it into something he thinks will sell papers (or magazines, or page views, or whatever).

This rant was brought on by a story in today’s L.A. Times called “Permanent diet may equal longer life“.  It’s about a 20-year longtudinal study of reduced calorie (RC) diets in Rhesus macaques (n=76).  As you can guess from the title, the angle is that reduced calorie diets can help humans live longer.  They don’t take any time getting there, here’s the first graph (thanks to The Wire, I can throw newsroom slang around like a seasoned pro):

For a country in which roughly 200 million people are overweight or obese, scientists today have discouraging news: Even those who maintain a healthy weight probably should be eating less.

In the second we get “It has been shown to significantly extend the lives of yeast, worms, flies, spiders, fish, mice and rats” followed by

“It adds to the evidence piling up that caloric restriction, independent of thinness, is a healthy way to stay alive and healthy longer,” said Susan Roberts of the Human Nutrition Research Center on Aging at Tufts University, who wasn’t involved in the study. “Less diseases in old age has to be something most everyone wants.”

and then “Mild caloric restriction is beneficial to everybody,” said Dr. Luigi Fontana, a medical professor at Washington University in St. Louis.” Oh man, I want to live longer, how do I cut my own calories!?!  That question is answered, and the answer is followed by a competent summary of the study’s methodology.  But wait a minute… for those who are still reading, the fifth graph from the end, after the jump, finally comes clean with

It also isn’t clear whether caloric restriction would extend human lives by very much, Phelan said. … He calculated that reducing intake by 35% would extend the human life span by just two years.

Huh, but I don’t understand, calorie restriction is going to make me live longer, and prevent heart disease, cancer, and diabetes!  It’s going to improve my brain health!  Except it’s not.  The study doesn’t support any such conclusions about human health.  I became convinced of that when I checked out the lovely inset graphic.  If I count those dots correctly, 16 of the control group monkeys got diabetes during the study period.  That’s almost half of the group (the text of the journal article reveals that most of those actually have pre-diabetes, for which they received medical treatment).  Maybe what’s actually happening here is that the diet they feed the monkeys, referred to in the story as “lab chow”, is actually really bad for them.  The comparison to human nutrition that the Times story wants to imply rests on the assumption that the control regime is somehow equivalent to a typical human diet.  Instead monkey chow*, like most pet food, is a cereal made from the castoffs of human food processing, designed to have low cost and a long shelf life.  All the stuff you can read about it being “scientifically formulated” and “nutritionally balanced” really just means that it has enough micronutrients (vitamins, minerals, etc.) so that the monkeys won’t get any of the deficiency diseases (that we know about), and that it’s balance of macronutrients (fat, protein, carbohydrates) falls within the nutritional consensus.  Of course, we’ve known for a long time that nutrition is much more complicated that keeping fat low and getting enough B12.

I should note here that this story is also a summing-up of a lot of prior research on reduced calorie diets, which has been an ongoing area of research since about 1935.  This study is far from the only one on which to base claims that such a diet would benefit from humans, but it doesn’t seem to make nearly as strong a contribution to that argument as the story wants to claim.

*The study does not indicate what food was fed to the monkeys, presumably they made at least the reduced calorie formulation themselves.  All they say is “Animals in this study are fed a semipurified, nutritionally fortified, low fat diet containing 15% protein and 10% fat.”