Getting Cable

July 27, 2010

There’s an article at the Wired site reminding us that it was on July 27, 1866 that the first successful undersea cable between Europe and North America was completed.  (This was a telegraph cable — sorry, no streaming video in this release.)  In some ways, it represented a very impressive rate of technological progress.  It had been just 22 years since Samuel Morse’s historic first telegraphic transmission between Baltimore and Washington DC.  Not only had the use of the telegraph spread, but the US found the time to have a Civil War.

From today’s perspective, it’s almost impossible to imagine living in that era.  The telegraph was the first widespread means by which information could be spread faster than a person could travel.  Before the completion of the trans-Atlantic cable, an event in London could not be known in New York until enough time had passed for a ship to cross the ocean.

Thinking about the change in communications possibilities implied by that cable may help us make some more sense of the changes we’re experiencing today.

Spontaneous Prion Generation

July 26, 2010

One of the scarier health threats that has been in the news in the last few years is the family of neurodegenerative diseases, including Bovine Spongiform Encephalopathy [BSE, often called “Mad Cow Disease”], and the similar diseases scrapie in sheep and goats, and variant Creutzfeldt-Jakob Disease [vCJD] in humans.  Besides their devastating effects, they are frightening because they typically have a long incubation period, measured in years, between the time of first exposure to the disease and the appearance of symptoms, and are essentially always fatal.  They are thought to be caused by prions, a pathological form of a normally occurring protein that differs by being “folded” differently in space.

(Many biological molecules depend for their effects not only on their chemical composition, but also on their physical shape.  It is quite common, for example, to have two forms of the same compound that are mirror images of one another [these are called stereoisomers], where one form is biologically active, and the other is not..   To take another example, the three simple sugars — glucose, fructose, and galactose — all have the same basic formula, C6H12O6, but differ in the arrangement of those atoms within the molecule.)

The prions themselves are not in any sense living organisms; they contain no DNA or RNA.  Nonetheless, introduction of a small quantity of prions into normal protein causes the normal molecules to “re-fold” themselves into the pathological shape.   The mechanism of transmission of these diseases has been thought to be eating infected animals.  For example, the original outbreak of BSE in the United Kingdom was attributed to cattle (which are naturally vegetarians) being fed protein supplements derived from the meat of diseased cattle or sheep.   This transmission mechanism is reasonably well accepted, but it of course begs the question of how the whole thing got started — although a random mutation is always a possibility.

In a new study reported at the site, researchers from the Scripps Research Institute in Florida and the Institute of Neurology at University College London have shown that infectious prions can be spontaneously developed in normal tissue.  The scientists placed normal tissue on very fine steel wires, and were able to observe the spontaneous formation of infectious prions.  It is possible that the metal somehow acts as a catalyst for the formation of these molecules.  Dr. Charles Weissman, of Scripps, one of the study leaders, is careful to say that there is another possible explanation of the results:

Weissmann noted that an alternative interpretation of the results is that infectious prions are naturally present in the brain at levels not detectable by conventional methods, and are normally destroyed at the same rate they are created. If that is the case, he noted, metal surfaces could be acting to concentrate the infectious prions to the extent that they became quantifiable by the team’s testing methods.

The paper reporting the results is to be published in the Proceedings of the National Academy of Sciences, and is available online as a pre-publication open access article [doi:10.1073/pnas.1004036107]; the lead author is Julie Edgeworth of UCL.

I doubt that many people will find these results particularly reassuring, but at least we are making progress in understanding the mechanism of these strange diseases.

New Firefox Versions

July 26, 2010

Mozilla last week released, not one, but two new versions of the Firefox browser.   Version 3.6.7 was released on July 20,  and was quickly followed by version 3.6.8 on July 23.   The first release, 3.6.7, fixed a number of stability bugs, and 14 security vulnerabilities; unfortunately, as sometimes happens, these fixes introduced another bug, which caused crashes on some pages using plug-ins.  This bug was fixed in the second release, 3.6.8, which is obviously the one you want, and the one you will get using the built-in update mechanism.

Release Notes, with more detailed information, are available for both versions, 3.6.7 and 3.6.8.   Installation binaries for all platforms (Mac OS X, Windows, and Linux), in your choice of more than 70 (human) languages,  can be downloaded here.

Windows .LNK Flaw Exploit

July 20, 2010

I posted a note last week about a new Windows security vulnerability, related to its processing of shortcut (.LNK) files.  The Internet Storm Center  [ISC]at SANS is now reporting that  code to implement an attack on this vulnerability has been published within the Metasploit  framework.

The ISC has raised its assessment of the overall Internet threat level from Green to Yellow.  (Who decides these colors, anyway?)   I think this is a potentially serious thret, because it requires so little in the way of user action to succeed.

Microsoft has not yet issued a patch for this, but there are some mitigation steps listed in its Security Advisory.

I’d expect Microsoft to issue a patch for this in its regular update in August.  If I discover anything further, I’ll post a follow-up note.

Top Secret America

July 19, 2010

Three can keep a secret, if two of them are dead.
— Benjamin Franklin

The Washington Post has a long history of investigative journalism.   I was a regular reader when I was in  college, when the Post reported on the Watergate break-in, and (along with the New York Times) on the Pentagon Papers.  So I was most interested  to see, in this morning’s Post, the first article in a new series, “Top Secret America”, which discusses the explosive growth in domestic intelligence and security services since September 11, 2001.  There is also an accompanying Web site that includes not only the articles, but also additional graphic and video content.  This is all as the result of a two-year investigation by the Post‘s staff.   Not surprisingly in an area that has “growed like Topsy”, the structure and organization of this effort seem to leave something to be desired.

These are some of the findings of a two-year investigation by The Washington Post that discovered what amounts to an alternative geography of the United States, a Top Secret America hidden from public view and lacking in thorough oversight. After nine years of unprecedented spending and growth, the result is that the system put in place to keep the United States safe is so massive that its effectiveness is impossible to determine.

According  to the Post, there are 1,271 governmental and 1.931 private organizations involved in this effort, scattered across ~10,000 locations in the US.  There are something like 854,000 people who now have Top Secret security clearances.  One wonders how secret anything can be that is (potentially) known to so many people.

I have not, obviously, had time to read and digest all this material yet.  But, assuming the facts are rougly correct, it is hard to imagine that anyone really has an overall grasp of what is going on.

More Bugs Inside

July 18, 2010

I’ve written here before about the hygiene hypothesis, the idea that our focus, at least in the developed world, on maintaining an environment that is extraordinarily clean by historical standards, coupled with excessive use of antibiotics, may be contributing to a rise in conditions like asthma and auto-immune disorders.  The hypothesis is that the developing human immune system needs to be exposed to a diversity of different microbes in order to calibrate itself.  There is also the possibility that all of this emphasis on hygiene is getting rid of beneficial micro-organisms that are part of our internal bio-system.  Although we know that there are many different species of bacteria that call us home, we’re still at a very early stage in cataloging all the pieces of the puzzle, never mind how they go together.   The Human Microbiome Project, at the National Institutes of Health, is one effort to build our understanding of how our own personal ecosystems work.

The New York Times has an interesting article reporting on some of the recent developments in this field.  One of the obstacles to cataloging all the microbes that call us home has been that many of them cannot be grown in culture outside the human body.   This is a problem, especially since one might reasonably assume that the organisms that can’t survive in culture are those most specifically adapted to their host(s), and therefore of especial interest.  Researchers have now taken the approach of trying to collect and sequence bacterial DNA from the body.   The process is laborious, because the underlying microbiome is extremely complex.

To make sense of the genes that they’re gathering, they are sequencing the entire genomes of some 900 species that have been cultivated in the lab. Before the project, scientists had only sequenced about 20 species in the microbiome. In May, the scientists published details on the first 178 genomes. They discovered 29,693 genes that are unlike any known genes.

Scientists estimate that there are between 500 and 1,000 different species that colonize just the mouth, although any given person has only a subset of these.   They are even finding that internal organs, such as the lungs, which were previously thought to be sterile, because no one had ever been able to culture bacteria from healthy lungs, have their own set of microbial “colonists”.

A team of scientists at Imperial College London recently went hunting for DNA instead. Analyzing lung samples from healthy volunteers, they discovered 128 species of bacteria. Every square centimeter of our lungs is home to 2,000 microbes.

The Times story starts with a dramatic example of what can happen when this ecosystem is severely disrupted.

In 2008, Dr. Khoruts, a gastroenterologist at the University of Minnesota, took on a patient suffering from a vicious gut infection of Clostridium difficile. She was crippled by constant diarrhea, which had left her in a wheelchair wearing diapers. Dr. Khoruts treated her with an assortment of antibiotics, but nothing could stop the bacteria. His patient was wasting away, losing 60 pounds over the course of eight months.

(Clostridium is a genus of bacteria that includes the species responsible for tetanus, C. tetani, and for botulism, C botulinum.)

Dr. Khoruts finally tries treating his patient by introducing a sample of bacteria, collected from her husband’s feces, into her gut.  The results were fairly dramatic.  Both the diarrhea and other indications of infection disappeared within a couple of days.   The doctors compared specimens of bacteria from the patient’s gut before and after the treatment.

Before the transplant, they found, her gut flora was in a desperate state. “The normal bacteria just didn’t exist in her,” said Dr. Khoruts. “She was colonized by all sorts of misfits.”

Two weeks after the treatment, the patient’s internal microbial census had returned to normal.

This is a fascinating (if sometimes slightly gross) area of research. It is clear that there is a lot happening right in front of our eyes, as well as inside them, that we are just beginning to understand.

WD-40: Canny Marketing

July 17, 2010

Today’s Washington Post has an article about a new social marketing campaign being launched by the WD-40 Company, for its eponymous product.  The product, WD-40, is a familiar sight in many workshops.  It was originally developed as part of “a line of rust-prevention solvents and degreasers for use in the aerospace industry”; according to the product lore, the “WD” stood for Water Displacement, and the formula was supposedly the 40th one tested.  The company has introduced a commemorative “Twin Pack”, with one modern can of WD-40, and one can with a “retro” design from the 1950s, complete with the company’s original name, Rocket Chemical Co. (the product was apparently originally developed for the Atlas Missile program)

WD-40 Twin Pack, courtesy WD-40 Co.

There is even a WD-40 Fan Club at the company’s site, where users are invited to contribute their favorite applications of the product.

Although you will find a can of WD-40 in many serious mechanics’ shops, the product has also acquired the reputation of being, like duct tape and baling wire, a favorite tool of the un-handy handyman.

If you didn’t own or couldn’t identify the right tool for the job, there was always WD-40 and a hammer.

If lawnmowers wore cologne, it would smell like WD-40, the Old Spice of the two-stroke engine.

WD-40 is to bad handymen what cream of mushroom soup is to bad cooks.

It is handy, and often seems a good short-term fix for things like squeaky hinges and stubborn locks.  But the temptation is to overuse it, and in places where it is not the right tool for the job.

Back in the 1990s, when USENET discussion groups were still active, and had not yet been rendered almost entirely useless by spam, I was a frequent participant in the group.  A question that came up regularly there was whether WD-40 was a good lubricant for bicycle chains.  The consensus answer is no, although it can be useful for cleaning really crappy chains.  In these discussions, it was almost inevitable that various more or less fanciful ideas would be advanced about what was actually in WD-40.  One of these discussions led to my own small contribution to the group’s FAQ:

Subject: 8a.8 WD-40
From: (Rich Gibbs)
Date: Wed, 09 Sep 1998 04:03:00 GMT

There have been many opinions posted here on WD-40's composition, but here is what the Material Safety Data Sheet [MSDS] says (it's from Oct 93, the latest I could find):

50% Stoddard solvent (mineral spirits) [8052-41-3]
25% Liquified petroleum gas (presumably as a propellant) [68476-85-7]
15+% Mineral Oil (light lubricating oil) [64742-65-0]
10-% Inert ingredients

(The numbers in square brackets '[]' are the CAS numbers for the ingredients, as listed in the MSDS.)

Mostly, WD-40 is a solvent, with a bit of light oil mixed in. It doesn't contain wax (except incidentally, since it's not exactly a reagent-grade product).

Personally, I use it sometimes for small cleaning jobs, but it's not a particularly good lubricant for anything that I can think of, offhand.

The composition of the product is still proprietary, although it does seem that it might have changed slightly, looking at the current MSDS [PDF].

Still, there is always a can of WD-40 in my toolbox, because sometimes anything that works is better than unobtainable perfection.

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