2007/05/02

Hacking Your Body's Bacteria for Better Health -

Wired recently ran an article on probiotics. It had so many interesting observations that I've had a hard time summarizing it.

Okay, the summary is that we need bacteria in order to stay healthy.

Hacking Your Body's Bacteria for Better Health:

We assassinate microbes with hand soap, mouthwash and bathroom cleaners. But some scientists say ... all this killing may actually cause diseases like eczema, irritable bowel syndrome and even diabetes.

"Probiotics have resulted in complete elimination of eczema in 80 percent of the people we've treated," says Dr. Joseph E. Pizzorno Jr., a practicing physician and former member of the White House Commission on Complementary and Alternative Medicine Policy. Pizzorno says he's used probiotics to treat irritable bowel disease, acne and even premenstrual syndrome.

"After the Second World War, when our lifestyles changed dramatically, allergies increased. Autoimmune diseases like diabetes and inflammatory bowel disease are increasing," says Kaarina Kukkonen, a University of Helsinki allergy expert.

Microbial exposures early in life, scientists believe, cause mild inflammation that calibrates the body's responses to other pathogens and contaminants later in life. Without exposure as infants, researchers say, people can end up with unbalanced immune systems.

"Many of the most difficult problems in medicine today are chronic inflammatory diseases," says Blaser. "These include rheumatoid arthritis, lupus, atherosclerosis, eczema and multiple sclerosis. One possibility is that they're autoimmune or genetic diseases. The other possibility is that they are physiological responses to changes in microbiota."

2007/05/01

Microsoft's Silverlight

Microsoft has announced details of their competitor to Flash -- and to JavaScript, and to ... It's called Silverlight.

To me the most interesting thing about it is that it allows developers to build browser-side web apps using Python and Ruby instead of JavaScript.

Silverlight apps can use a subset of the .NET framework. Embedded video can run at HD revolutions up to 1280x720.

It all looks pretty interesting. It'd be more interesting if it provided a 3D API; but so far I see no evidence of that.

2007/04/27

Sun eyes a JavaScript alternative to AJAX

Sun eyes a JavaScript alternative to AJAX:

"

(InfoWorld) - Sun Microsystems is working on Web application development technology that presents an alternative to AJAX (Asynchronous JavaScript and XML), a Sun official said on Thursday.



The company's Project Flair is an open-source project now in development... A version of Flair for developers to experiment with is eyed for release later this year.


Small and simple, Flair presents a 'great vehicle for experimenting with [what] I guess what you would call, sort of, collaborative object development, that kind of thing,' said Ingalls.


'AJAX sort of deals with all of the old way of doing things. It makes it simpler ... but underneath it’s still all this junky HTML, Document Object Model, CSS, all that stuff, where 30 years ago, we knew how to do that stuff cleanly with a dynamic programming language and a simple graphics model,' Ingalls said.


'Flair takes us back to that simple model and adds the collaboration [and] Web access to it,' he said.




Anybody have links to more details on Project Flair?

2007/04/23

American's imprisonment in Kazakhstan sends chilling message - International Herald Tribune

American's imprisonment in Kazakhstan sends chilling message - International Herald Tribune:

"Despite all the Western donor money and American-financed projects aimed at reforming the judiciaries here," said Michael Hall, an analyst in Bishkek, Kyrgyzstan, with the International Crisis Group ... "this is all part of a bigger Central Asian trend to make their judicial systems subordinate to their presidents."

"The result is a significant retreat in America's ability to project its public and business interests in the region," he said.

"Plus, the U.S. has suffered a massive loss of credibility when it comes to talking about the rule of law and independent judiciaries in the wake of the abuses we've been hearing about in places like Guantánamo." (emphasis added)


The last paragraph is a sideline to the main story. But it shows again that it's in the best interests of the United States to treat its prisoners humanely. Any abuse we lay on our prisoners (call them what you will) can be used as a justification for the mistreatment of U.S. citizens.

Duck and Cover: Ancient Mass Extinctions Caused by Cosmic Radiation

Ancient Mass Extinctions Caused by Cosmic Radiation, Scientists Say:

"Cosmic rays produced at the edge of our galaxy have devastated life on Earth every 62 million years, researchers say."


Not all mass extinctions are explained by this theory. For example, the KT boundary event probably has another cause.

But what an interesting idea: our galaxy is moving "flat-faced", like a pie in a pie fight, relative to surrounding material. A shock wave is generated where galactic matter comes into contact with the surrounding hot gases, and cosmic radiation is generated at that same point.

Periodically on its 225-million-year galactic orbit, our solar system rises up out of the galactic plane, closer to the shock wave, where it is exposed to more of the incoming cosmic radiation than normal.

Researchers aren't sure about the consequences of the increased radiation. Greater ozone depletion may allow more of the radiation to reach the earth's surface and into its oceans. Other effects may include changes in cloud cover, etc.

One possibility is that organisms receive harmful doses of radiation from high-energy particles known as muons, which are produced by cosmic rays colliding with Earth's atmosphere.

"Cosmic rays themselves are not really that dangerous," said Medvedev. "They create [charged particles] that propagate down through the atmosphere—especially muons that can go below the sea level."

Russia's former president Yeltsin dies: Kremlin | Reuters

Russia's former president Yeltsin dies: Kremlin | Reuters:

Many Russians initially viewed Yeltsin as a hero for dismantling Communist rule. His finest hour came when, in 1991, he clambered onto a tank and raised his fist in defiance of hardline coup plotters who wanted to turn back the clock.

...in 1989 he was elected to the new Soviet Congress of People's Deputies and in June 1991 he was elected president of Russia -- still within the Soviet Union -- in a landslide.

Two months later, he faced down tanks in the Moscow streets...


2007/04/18

Make your own Ghost Map

From Paul Kedrosky: Twitter for Hypochondriacs:

Who is sick? is a clever idea, and similar in many ways to my 'what's going around?' idea. It allows people with symptoms of something or another -- bloody stool! sniffles! cough! muscle ache! -- to add their location and symptoms to a map.

Why clever? Because it is the data-rich beginnings of grassroots epidemiology via capturing the kinds of conversations that usually only happen in doctors' offices. You, know, 'You have a cold. That's going around'.


Gee, it's like a modern, collaborative version of The Ghost Map.

2007/04/04

Why it's called "good" cholesterol

Technology Review: Imaging Cholesterol Buildup in the Heart: " Normally, HDL passes through arteries and attaches to low-density lipoprotein (LDL), or 'bad' cholesterol, carrying it out of arteries to the liver."

'Course that's not what the article is about. Researchers have found a way to attach markers to segments of unstable arterial plaque, using altered HDL. As a result, they can better see where unstable plaque has built up in a patient and can better identify problems which increase the risk of heart attack.

2007/04/02

Light Therapy Spares the Scalpel and the Chemo -

Light Therapy Spares the Scalpel and the Chemo -


Imagine you could treat cancer by taking a pill, then directing a laser light toward the location of the tumor. The growth would dissolve with no chemotherapy, and no harm to healthy tissue.

It might sound futuristic, but a select number of cancer patients already benefit from the method, called photodynamic therapy. An upgrade for the procedure could save thousands more cancer patients from the horrors of chemotherapy.

Although chemotherapy has improved over the past decade, the treatment still damages healthy tissue and causes other unpleasant side effects like nausea and a weakened immune system. The researchers hope their work will spare patients from chemo's ravages and even the surgery usually necessary to remove a tumor.

2007/03/27

TI demos its movie projector in a phone | CNET News.com

TI demos its movie projector in a phone | CNET News.com


At the CTIA Wireless 2007 show, TI is providing public demonstrations of its digital light processing (DLP) 'pico' projector, a tiny movie projector that can fit inside a cell phone.

TI showed off the components and a prototype at the Consumer Electronics Show earlier this year to a few reporters. Now the company is touting a working prototype in a phone. The phone is fake, but the projector works.


I expect someday this is what laptop displays will look like. Why waste physical space and weight, provided you can find or create a flat viewing surface?

2007/03/05

TextMate, Parallels, and Visual Web Developer 2005 Express Edition

I've been using TextMate for the past two years, and like it so well that I have a hard time adjusting to most other text editors. Even my old favorite, XEmacs, is now painful to use.

I recently started work on my first ASP.NET project. The customer wants the whole thing to be done with VB.NET -- another first for me.

Lots of bundles are available for TextMate, and among them is an "ASP vb.NET" bundle. Yippee! Since my Windows XP "machine" is a VM hosted under Parallels, I can develop my project in a shared folder. [Edit 2007/03/06] On the Mac side I can use the Finder's "Network" sidebar entry to connect to my VM and mount the shared folder. TextMate sees it just fine. I get to use all of the toys at once.

Almost... I think it's because of filename limitations in NTFS, but I can't check out a working copy of my subversion repository into such a shared folder -- not from the Mac side. Trying to do so fails when subversion tries to check out a file whose name contains more than one period (".").

The simplest solution seems to be to to install the excellent TortoiseSVN under XP, and to check out the working copy from Windows. In order to avoid entering my ssh password 400 times, I've also installed PuTTY and used it to generate a private/public key pair for use with the subversion server.

Parallels really makes for some head-twisting fun. Recently I attended a web meeting using GoToMeeting, running in a Parallels VM. Instead of scrambling madly to keep notes on paper, I recorded the whole thing as a QuickTime movie using iShowU, running natively on Mac OS X. Let's see, that's a screencast recorded on a Mac, of a web conference running in a Win XP virtual machine hosted on the Mac.

2007/03/01

Mars Melt Hints at Solar, Not Human, Cause for Warming, Scientist Says

Mars Melt Hints at Solar, Not Human, Cause for Warming, Scientist Says: "Simultaneous warming on Earth and Mars suggests that our planet's recent climate changes have a natural—and not a human-induced—cause, according to one scientist's controversial theory."

"Man-made greenhouse warming has made a small contribution to the warming seen on Earth in recent years, but it cannot compete with the increase in solar irradiance," Abdussamatov said.


Abdussamatov is not alone in his beliefs. Last fall a group of German researchers also concluded that the sun was the primary cause of the historically recent increases in global mean temperature. [insert URL here]

Humans have a significant effect on this planet. Pick a satellite image, any image, and it's obvious that we've been here :) And of course we could soil our environment so badly that we die out.

Still, the hand-wringing over climate change often sounds like an oblique claim to importance. Dominion over the animals, created in God's image, etc. It's an anthropocentric world-view that even atheists can embrace. So reminders of the relative importance of the sun are good for our humility.

Unfortunately, the article notes several reasons why Abdussamatov's claims are met with skepticism. Mars has much bigger orbital wobbles than Earth, so it endures bigger climate swings. Greenhouse gases are important to our climate; without them life probably wouldn't have flourished here. Etc.

Abdussamatov does offer a way to test his claims, but it will take some time:
"The solar irradiance began to drop in the 1990s, and a minimum will be reached by approximately 2040," Abdussamatov said. "It will cause a steep cooling of the climate on Earth in 15 to 20 years."

N. Korea vows to denuclearize in talks - Yahoo! News

N. Korea vows to denuclearize in talks - Yahoo! News: "SEOUL, South Korea - North Korea's No. 2 leader pledged his country's commitment Thursday to giving up its nuclear program amid intensifying diplomacy aimed at implementing Pyongyang's pledge to disarm."

Based on seismic readings, North Korea's nuclear test last fall might have been a dud. Could this be one reason (coming as a distant second to the prospect of mass starvation) for the North's commitment to disarmament?

2007/02/28

Spotlight, LaunchServices and backup volumes

When I select a file in the Finder and right click to "Open With ->", the system pauses, my backup hard drive spins up, and I get a menu showing 5 or 6 duplicate entries for, say, VLC.app.

My backup volume is often online, so it's visible to LaunchServices and Spotlight, et al. Maybe this is the root cause of my problem. But I need to leave the backup volume online because it shares a hard drive with other volumes that I need.

What to do? Is this a problem with Spotlight? With LaunchServices? Regardless of Finder misbehavior, I don't want Spotlight indexing my backup drive; it's just a mirror of my boot volume. Time for some googling.

Spotlight Indexing



From ~stevenf: Disabling Spotlight for a Volume: To see if indexing is on for a volume:
$ sudo mdutil -s /Volumes/Backup


To get rid of the index for a volume and ensure that it is not re-indexed in future:
$ sudo mdutil -i off -E /Volumes/Backup


I've just performed these steps and will see if it works following my next backup.

I'm using SuperDuper to do periodic, full backups. Their forum says that SD will honor Spotlight indexing preferences for a target volume:
As of v2.0, when used with Tiger 10.4.3 or later... just add the volume to the Privacy tab of the Spotlight preference pane. We'll automatically ensure that that state is maintained, and all should work fine.


Of course I can't figure out how to add the volume to the Spotlight preference pane. I've tried dragging it in, but it doesn't show up in the list. Hence the above shell commands.

LaunchServices Caching



Since LaunchServices is already caching redundant references to my backed-up apps, with apparent disregard for duplicate (Unix) pathnames. So I also need to clear its cache. I've used these steps:

$ cd /Library/Caches
$ sudo rm com.apple.LaunchServices-*.plist


I've also restarted my system, since I didn't know whether it would suffice to log out and back in, or to simply kill launchd from within Activity Monitor.

Just now everything is looking good.

2007/02/26

A Breath of Fresh Air: To Fight TB, Open a Window: Scientific American

A Breath of Fresh Air: To Fight TB, Open a Window: Scientific American: "Escombe says the riskiest areas of hospitals are waiting rooms and other places where people congregate before being diagnosed. In a prior study, he and co-workers found that 30 percent of emergency department staff in a Lima hospital became infected with TB during a year."

Installing mod_python for Python 2.5 on Mac OS X

Django wants to be served from behind Apache, using mod_python. I want to use Python 2.5, but the MacPorts/DarwinPorts mod_python port wants to use Python 2.4.

I downloaded mod_python 3.3.1 from the mod_python downloads page and was able to install in a few easy steps:

$ ./configure --with-apxs=/opt/local/apache2/bin/apxs
$ make
$ sudo make install
$ sudo vi /opt/local/apache2/conf/httpd.conf
# Add this line
LoadModule python_module /opt/local/apache2/modules/mod_python.so


Then restart the web server.

All of the warnings in the mod_python README about Mac OS X 10.2.x and Python and libtool and static libraries appear not to matter for OS X 10.4.

Testing w. Django



To test the installation I set up a virtual host pointing to my Django app, following the instructions in the Django docs.

The hardest part was realizing I needed a virtual host (the IP address for which I hardwired into my /etc/hosts file). That was the easiest way to let my app continue to use its absolute URL paths; learning how to adapt to different installation "mount points" looked a bit harder.

The next hardest part was putting the subversion workspace for my project where the web server user (www) had permission to traverse to it.

Integrating MacPorts Apache 2 with System Preferences

Just returned from PyCon 2007, and wanted to try out a few of the new web frameworks tools I'd seen. To get started I needed to be running my own installation of Apache, instead of the system default installation. The latter does not AFAIK include sources, and that makes it difficult to add things like mod_fastcgi.

Install Apache 2


I used the MacPorts/DarwinPorts version of Apache 2:
$ sudo port install mod_fastcgi


Configure /etc/hostconfig


Following hints from elsewhere on the web, I tried to ensure Apache 2 would start at system boot by adding this line to /etc/hostconfig. (Haven't tested this yet.)
WEBSERVER=-NO-

APACHE2=-YES-



Fake Out System Preferences


To tell System Preferences Sharing->Personal Web Sharing to start Apache 2 rather than the system default Apache 1.3:
$ cd /usr/sbin
$ sudo mv apachectl apachectl-1.3
$ sudo ln -s /opt/local/apache2/bin/apachectl apachectl
$ pushd /opt/local/apache2/conf
$ sudo cp httpd.conf.sample httpd.conf
$ sudo vi httpd.conf
# Add this line somewhere near the DocumentRoot directive
PidFile "/private/var/run/httpd.pid"


Move Static Content and CGIs


I made sure System Preferences was able to start the new web server, and then double-checked that I actually was getting content from my new document root :) Then it was time to move static content from /Library/WebServer/DocumentRoot to /opt/local/apache2/htdocs, and cgi-bin executables from /Library/WebServer/CGI-Executables to /opt/local/apache2/cgi-bin.

Copy CGI-Bin Configuration Directives


Finally I had to copy the configuration section for my Trac projects to /opt/local/apache2/conf/httpd.conf.

All done.

Update



Oops, not quite. I want the log files to be under /var/log/httpd, where Console.app expects to find them. So CustomLog and ErrorLog need to be fixed up in all of the *.config files under /opt/local/apache2/conf/.

2007/02/04

New Scientist: Vaccine zaps allergy in record time

Vaccine zaps allergy in record time - health - 04 February 2007 - New Scientist

I've often wondered why an effective treatment for an allergy is to expose the sufferer to more of the allergen. According to the article (emph. added):

Existing vaccines for allergies involve three to five years of regular injections with increasing amounts of allergen... All the while the immune response slowly changes from a predominance of T-helper 2 (TH2) cells, immune cells responsible for triggering allergic reactions, to T-helper 1 (TH1) cells, which stimulate the production of protective antibodies.


So the trick is to make sure the vaccine contains only a small dose of the allergen -- so as not to kill the subject? And yet, as the article says,
Because nothing is directing allergens to the right place in immune cells, it takes a lot of allergen to generate a response.


The new vaccine is structured to deliver the allergens/antigens to the right places.
"[Components in the new vaccine] lower the dose needed to induce a T-cell response by a factor of about 100," says Reto Crameri of SAIF, lead author of the study.

2007/02/02

What made the 1918 flu contagious?

Pandemic flu may be only two mutations away - health - 01 February 2007 - New Scientist Space

What a virus needs to spread, the CDC team concluded, is an ability to bind 2,6 sugars, whether or not it needs this to replicate... One clue, they speculate, is that ferrets with non-contagious viruses... do not sneeze. Contagious ferrets do.

“The cells with 2,3-sialic acid receptors have been associated with the bronchial mucins,” Tumpey told New Scientist. This viscous secretion might inhibit these viruses, and prevent the irritation that causes sneezing, which “may contribute to the spread of influenza, at least in ferrets”.

...the CDC results suggest finding out what mutations make H5N1 bind to 2,6-sialic, as those could make it contagious.