Bugs Inside

December 26, 2009

I’ve talked here before about the hygiene hypothesis: the idea that our environments, which are extraordinarily clean by evolutionary standards, are keeping some children’s immune systems from developing normally, because they are not exposed to the range of microorganisms that the immune system needs to “see” in order to calibrate itself.

There is a recent article at Scientific American that raises another unsettling possibility: that a combination of excessive hygiene and other anti-microbial measures, such as antibiotics, may be decimating the population of helpful organisms that live on, and in, us.  The human body contains ~10 trillion cells; however, there are about ten times as many bacteria, fungi, and other microbes that live on the skin, in the gut, or elsewhere in the body, most of which are benign or actually beneficial. (This does not count the mitochondria that are present in most cells, which probably evolved from bacteria.)  We have evolved along with these organisms, and the concern is that we may be engaged in a giant uncontrolled experiment to see what happens if some of them are removed from the scene.

With rapid changes in sanitation, medicine and lifestyle in the past century, some of these indigenous species are facing decline, displacement and possibly even extinction. In many of the world’s larger ecosystems, scientists can predict what might happen when one of the central species is lost, but in the human microbial environment—which is still largely uncharacterized—most of these rapid changes are not yet understood.

As with hygiene in general, most of these changes have occurred as a result of medical interventions that were well-intentioned and in fact have had an overall positive effect on human health.  Antibiotics are a case in point.  It is certainly a good thing that we are able to prevent many people from dying as a result of bacterial infections every year.  But the perspective of evolutionary biology that took a while for us to grasp is that antibiotics  create selection pressure for antibiotic resistance, and that has led to the development of new nasties like MRSA (methicillin-resistant Staphylococcus aureus).  There are subtler effects, too.  Yeast infections can be a side effect of antibiotic treatment, because the antibiotic, as it attacks the primary infection, can also wipe out large numbers of the beneficial bacteria that normally keep the yeast organisms in check.

Another potential example is the vaccine for pneumonia.  It has been a success in reducing the number of cases of pneumonia, which can be life-threatening in susceptible individuals.  But the organism against which it builds immunity, Streptococcus pneumoniae, is frequently present in healthy individuals.  Moreover, it is a natural competitor to S. aureus; the concern is that getting rid of one bacterium may make the environment more congenial for another that is at least as nasty.

We’ve begun to see some reflection of this in popular culture, with the introduction of so-called “probiotic” products, like yogurt, that are claimed to replenish the helpful microorganisms in the body.  At present, though, this is something of a “Ready, Fire, Aim” approach, since it is hard to adjust things to a normal state when we don’t know what a normal state looks like.

The first step in understanding these systems is simply taking stock of what archaea, bacteria, fungi, protozoa and viruses are present in healthy individuals. This massive micro undertaking has been ongoing since 2007 through the National Institutes of Health’s (NIH) Human Microbiome Project.

This project is an enormous undertaking, and is unlikely to produce any definitive results quickly.  Yet it is fascinating to realize how much of what happens not only under our noses but inside them (not to mention other places) we don’t understand.

Molecular Transistors

December 24, 2009

We are all familiar with the amazing progress in electronic technology — Moore’s Law, and all that — that has gotten us ever smaller, cheaper, and more powerful devices.  It is almost boring to say that the laptop on which I’m writing this is much more powerful, by virtually any measure, than the first mainframe computer I used back in 1970, which filled a good-sized room and costs several million dollars.  But how small can these things be made?

Ars Technica has a report on some new research being done by an international team that has led to the successful creation of a voltage-gated transistor using a single molecule.   (The paper has been published in the journal Nature; the abstract is here.)  A transistor is conceptually a simple device.  It consists of two electrodes, separated by a gate that controls the flow of current between them.  In a conventional transistor, the gate is a semiconductor attached to a third electrode; varying the voltage applied to this third electrode controls the flow of current through the device.

It is relatively easy to find chemical compounds whose molecules can conduct electricity.  The trick is figuring out how to implement the gate.  A few previous experiments have managed to produce something like a transistor, but only by fairly complex “trickery”, such as manipulating the spin of the electrons passing through the molecule.  Although this is a very nifty trick, it is not really practical, since doing the trickery is far too complicated.

In the new experiment, a very fine gold wire is coated with an organic compound.  The wire is placed above an aluminum oxide electrode, and then a nano-scale gap is introduced into the wire.  If the construction is successful, a molecule of the organic substance will remain in the gap to become the gate, controlled by the aluminum oxide electrode.

The team used tried two organic compounds containing sulfur, and had the best results with 1,4-benzenedithiol.  The benzene ring is hexagonal, and this compound has the sulfur atoms at opposite vertices of the hexagon.  If you took an introductory course in organic chemistry, you may remember that the geometry of the benzene ring, with its alternating double and single C-C bonds, means that the electron orbitals form a “cloud” around the ring.  This makes it much easier to affect the electron energy by applying an external voltage via the gate electrode.

What is particularly interesting about this work is that the experimenters were actually able to get a “picture”, of sorts, of the function of the molecular transistor:

A technique called inelastic electron tunneling can detect the vibrational modes available to the atoms in the molecule; the researchers used it to demonstrate that applying a voltage to the gate changes the energy of the orbitals, with a corresponding impact on the vibrational energy.

This is a much clearer result than any previously obtained, since it avoids potential red herrings due to contaminants or fabrication problems.

This is still, of course, just a research result; you should not expect to see it in your iPhone anytime soon (the Steve Jobs Reality Distortion Field notwithstanding).  But it is a demonstration of how much scope there is for further amazing technology.

The iWorm

December 23, 2009

Apple’s iPhone is sold as a closed device: it can only be used on the AT&T network, and only applications that are approved by Apple can be used on it.  It is, of course, basically a small general-purpose computer at heart, and some people have succeeded in an iPhone “Jailbreak” — they have managed to work around the iPhone’s security restrictions to gain access to the underlying operating system (which is basically a variant of Mac OS X, which is at heart a variant of BSD Unix).

There has been speculation for some time about the likelihood of malware attacks on smart phones, like the iPhone.  Ars Technica has an article about a worm that attacks “jailbroken” iPhones that are vulnerable in a particular way.  Although the specific worm in question is not, as a practical matter, a particularly important threat, it does serve as a “proof of concept” for constructing something considerably nastier.

Here is how this worm works.  Apparently, some users that jailbreak their phones like to leave an ssh daemon running on the phone (ssh is the secure shell remote login, which uses an encrypted connection).  The iPhone’s OS has a default password set for the root account (the super-user).  The worm uses standard port-scanning techniques to look for iPhones running ‘ssh’ with a default password. The initial version of the worm just displayed a warning message about unchanged default passwords.  However, more malicious variants have been spotted.

One of these, ‘iKee.B’, was studied by researchers at SRI International.  Despite being a fairly small piece of software, it incorporates the three key functions of a botnet worm:

  • It can self-propagate
  • It has a malicious payload (which steals personal data)
  • It periodically contacts a “command & control” server for new instructions

The real worry here is not this particular worm, which can only infect a small subset of iPhones (those that have been “jailbroken” and that still have the default root password).  It is that there is an attack platform already in existence that could be easily adapted to work via an OS exploit, or on other smart phones:

Though this example can only infect a small subset of iPhone users, extending the software to rely on a future iPhone OS exploit, or to merely infect other smartphone platforms that don’t have the same security measures as the iPhone, is relatively trivial. This has the researchers worried that smartphones could quickly become an important target for malware writers, since we continue to entrust so much personal data to the devices.

Smart phones could prove an extremely attractive target for Bad Guys who want to steal personal information, since they are frequently used to store that information, and because the limited selection of applications makes it quite easy to scan for potentially valuable data.

Big Time Cyber-Crime

December 22, 2009

I’ve written here a couple of times before about a trend that has become apparent in worm, virus, and other malware attacks: whereas they were once most like vandalism, they are now serious (criminal) business.  The attacks are often targeted at specific organizations or individuals, with the aim of stealing credentials that can be used for further mischief.

A new article on the “Threat Level” blog at Wired is another example of this development.  It describes how an international group of crooks, apparently assembled ad hoc via the Internet, carried out a chain of operations to net more than $2 million stolen from Citibank ATMs.  The article is full of interesting details, but the key sequence of events went something like this:

  • Two Russian hackers attacked the public Web site of Seven-Eleven (the convenience store chain), apparently with an SQL injection attack, and managed to gain access to the company’s servers.
  • The hackers used this access to collect ATM card numbers and PINs from machines located in 7-11 stores. (These machines were provided by Citibank, and apparently at least some of them were especially vulnerable, because the offered “advanced” functions, such as selling money orders, that had to be supported by a server at 7-11.)
  • Using local workers recruited via the Internet, the gang then manufactured phony ATM cards, and used the captured PINs to withdraw money from ATMs in and around New York City.

The deal was organized so that the Russians provided the card numbers and PINs, the local workers got the money, and the take was split:

The deal was straightforward: They’d use the information to encode fraudulent ATM cards and withdraw cash, sending 70 percent of the take to the Russian and keeping 25 percent for themselves. Another 5 percent went for expenses.

One of the local participants also was allegedly involved in another scam to loot iWire pre-paid MasterCard accounts, which resulted in 9000 attempted withdrawals from cash machines around the world in just two days, and caused losses of approximately $5 million.

It should be apparent that this kind of organized crime operation is not the work of bored teenagers.  If you run a business, or are responsible for systems security at one, this is another wake-up call.  Just making sure that you put anti-virus on all the PCs doesn’t cut it anymore (if it ever did).  Any machine that is connected to the outside world (meaning the Internet, in particular) is a potential attack point.

New Cyber-Security Czar

December 22, 2009

The White House announced this morning that President Obama has appointed Howard Schmidt as Cyber-Security Coordinator (or “Czar”, as he will undoubtedly be called).   Mr. Schmidt has considerable experience in the area, having served as a security advisor in the Bush administration, and also as security chief at E-Bay and Microsoft.  He has worked for the FBI in computer forensics.  People in the security field generally regard him as competent and well-qualified; the major reservation about his appointment, shared by many, is that his position has a broad scope of responsibility, but very limited real authority (for example, he has no budgetary authority). Whether the position may evolve into one of greater influence remains to be seen.

The New York Times also has an article on Mr. Schmidt’s appointment.

Quantum Batteries

December 21, 2009

I’ve written here several times about potential advances in battery technology (including sodium ion batteries, rechargeable zinc-air batteries, and nuclear batteries).   Now Technology Review has an article describing another new battery technology: digital quantum batteries,  a concept proposed by a physicist at the University of Illinois at Urbana-Champaign, Alfred Hübler.  The proposed device is actually a sort of hybrid battery/capacitor:

The concept calls for billions of nanoscale capacitors and would rely on quantum effects–the weird phenomena that occur at atomic size scales–to boost energy storage

A conventional capacitor stores energy in an electric field that is created when electric charge is applied to two parallel plates. (A conventional battery, by contrast, stores chemical energy which it converts to electricity.)  Capacitors can be charged and discharged much faster than batteries, but their storage capacity is limited; apply too much charge, and electrical arcing between the plates will occur.

In Hübler’s design, the “battery” is actually an array of a large number of nanoscale capacitors.  In theory, quantum effects that manifest themselves only at such small scales would act to reduce arcing:

If capacitors were instead built as nanoscale arrays–crucially, with electrodes spaced at about 10 nanometers (or 100 atoms) apart–quantum effects ought to suppress such arcing.

If the device can be fabricated successfully, and if the theoretical calculations of its properties prove accurate, the improvement in energy storage could be substantial:

Hübler claims the resulting power density (the speed at which energy can be stored or released) could be orders of magnitude greater, and the energy density (the amount of energy that can be stored) two to 10 times greater than possible with today’s best lithium-ion and other battery technologies.

Today, the quantum battery is only a research concept, but Hübler believes that the devices could be fabricated by existing lithographic technologies used to manufacture semiconductor chips, using metals such as iron or tungsten on a silicon substrate.  He thinks that a lab prototype might be developed in about a year.  Nanoscale capacitors have been fabricated, by researchers in Korea, but the quantum battery would require millions of them to be practical.  (The concept is discussed in more detail in a paper [PDF], of which Hübler is the lead author, to be published in the journal Complexity.)

As I’ve noted before, developing new batteries and other types of energy storage technologies are critical in allowing us to shift to greater reliance on renewable energy sources like solar or wind power.  The quantum battery is one of the moe exotic concepts that has been proposed, and it’s not clear that it will become a viable product; but this kind of research is of tremendous importance to developing a sensible energy strategy for the future.


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