nov 2009 / greg goebel
* This weblog provides an "online diary" to provide notes on current events, interesting items I run across, and the occasional musing. It promotes no particular ideology. For update notifications, follow "gvgoebel" on Twitter.
* THE IMMUNE SYSTEM (1): Having become curious about the human immune system, investigation showed that it was a bewilderingly complicated subject. I was able to track down a relatively short introduction to the immune system from the US National Cancer Institute. That proving interesting but inadequate, I obtained Lauren Sompayrac's book HOW THE IMMUNE SYSTEM WORKS to find more details and flesh out these notes for the blog.
* We live in an environment loaded with a wide range of microorganisms, many of which are malign, or are "pathogens". Pathogens include viruses; bacteria; and a remaining grab-bag of unpleasant organisms such as infectious worms technically referred to as "parasites", though in the broad nontechnical sense viruses and bacteria are parasites as well.
If such pathogens were able to casually invade our bodies and replicate at will, we would have been exterminated a long time ago. The first line of our body's defenses consists of external barriers that can block entry of intruders:
However, pathogens can get through those barriers, for example through a wound. Once they do, they are dealt with by our "immune system" -- an extremely elaborate complex of organs, cells, and molecules that protects us from invaders, blocking their entry and targeting them for destruction after the invasion. Humans have an "innate" immune system that can recognize broad classes of pathogens from birth, backed up by a subordinate "adaptive" immune system that can "learn" to target unfamiliar pathogens in detail.
* The immune system is fundamentally based on an ability to distinguish "self", -- the body's own cells -- from "nonself" -- intruders from the outside world. The body's cells identify themselves as "self" through protein structures on their surface known as "major histocompatibility complexes (MHC)" or "self-marker proteins". The MHC proteins are variable; they are effectively never the same for any two people aside from identical twins. Occasionally the immune system will "go off the rails" and attack the body's own cells, resulting in "autoimmune disorders" such as multiple sclerosis, where the body attacks nerve cells; or lupus erythymatosis, where the body performs a broad-spectrum attack on itself. The immune system also very often identifies transplanted organ as nonself -- their MHC proteins don't "look right" -- and attacks or "rejects" them.
Any foreign material that the immune system targets as "nonself" is referred to as an "antigen". An antigen can be a whole nonself cell, a bacterium, a virus, or a protein from a foreign organism. The distinctive markers on antigens that trigger an immune response are called "epitopes". There are actually two types of MHC: all our cells have "Type I MHC" or "MHC I" molecules, while certain specific cells also have "MHC II" proteins.
* The immune system is arranged around a set of specialized organs, cells, and biochemicals. It is useful to outline this elaborate "cast of characters" before trying to describe how they operate to deal with invaders.
The immune system is supported by a set of high-level organs and body structures distributed through the body, known as the "lymphoid organs". The root of the lymphoid system is the "bone marrow" the spongy tissue in the core of our bones, which produces:
Among the other lymphoid organs, the "thymus" is a gland under the breastbone; it is where stem cells mature into the class of lymphocyte known as "T lymphocytes" or "T cells", the "T" of course standing for "thymus". The "spleen" is an organ in the abdominal cavity near the left kidney; it filters out old red blood cells and pathogens, and provides compartments where immune system cells can confront antigens.
In addition to these organs, clumps of lymphoid tissue are found in several parts of the body, especially in the linings of the digestive tract and the airways and lungs, these organs being gateways to the body for pathogens. These tissues include the "tonsils", ringing the throat; the "adenoids", at the back of the throat and usually lost by adulthood; and the "appendix", which is a minor extension of the small intestine. It is actually uncertain that the appendix really serves much purpose, possibly being a vestigial feature from our distant ancestry, but lymphocytes congregate there, suggesting it may have an immune system function.
Lymphocytes can travel throughout the body to and from the lymph organs through the bloodstream; the cells also travel through a system of "lymphatic vessels" that link the lymph organs and closely parallel the blood system. Cells and fluids are exchanged between blood and lymphatic vessels, allowing the lymphatic system to monitor the body for invading pathogens. The lymphatic vessels carry "lymph", a clear fluid that essentially amounts to blood with very few red blood cells and very many white blood cells. Incidentally, unlike the blood circulation system, the lymphatic system is not pumped; lymphatic fluid travels through it in response to body motions.
Small, bean-shaped "lymph nodes" sit along the lymphatic vessels, with clusters in the neck, armpits, abdomen, and groin. Each lymph node contains specialized compartments where immune cells congregate and encounter antigens, with the immune cells then being sent out to patrol the body for intruders. [TO BE CONTINUED]
* GIMMICKS & GADGETS: The idea of using camera phones to scan barcodes is not completely new -- an article here from some years back discussed its use in Japan -- but it is now starting to become popular elsewhere. Camera phones can be used to scan barcodes on products and automatically look up information, such as comparisons between prices at different retailers. Two-dimensional barcodes, designed with camera phones in mind and carrying more data, are also becoming common -- one simple example of usage being a 2D barcode printed on a poster for a movie or event, with the barcode scanned to obtain more relevant data or tickets online. In Japan, 2D barcodes are found in train stations, to key camera phones to convenient listings of train schedules; in magazines; on coupons; and even on tee shirts.
There are three 2D barcode specs in use in the USA and Europe, including "QR Code", "Data Matrix", and "Ezcode". QR Code and Data Matrix are open standards, available to all; Ezcode is proprietary, owned by a New York firm named ScanBuy, but gives it away free to users, with the company making money from advertisers and publishers who are linked by the Ezcodes. ScanBuy has closed or is working on deals with cellphone operators in the USA, Europe, and Latin America to provide cellphone-based Ezcode reading software. Other vendors are working to leverage the technology as well.
Microsoft got into the 2D barcode game early in 2009, releasing the "Tag" scheme, which uses color to increase the information density of a barcode. Tag has about eight times the density of other 2D barcode schemes, and can be applied to irregular objects, with Microsoft even showing pictures of barcoded jellybeans. JAGTAG of Princeton, New Jersey, has gone in the other direction, creating 2D barcodes that are low density -- but which can be read by cheap camera phones that can't run barcode reader software. The trick is that the phone sends an image of the JAGTAG barcode to a server, which reads the barcode and sends back the appropriate data. Exactly which of these schemes will end up being a standard is anyone's guess, but it seems very likely that within a few years, the technology will be so commonplace that people will take it for granted.
* THE ECONOMIST reports that Pirelli Tires of Italy is now working on a "smart tire", containing an internal sensor unit the size of a large coin. The unit carries micromechanical accelerometers to monitor the motion of the tire, plus a wireless interface to allow it to communicate with the car. The sensor generates its own power from the vibrations of the tire.
Pirelli engineers believe the smart tire could optimize braking and suspension action to improve mileage. It could also increase the use of low-friction tires, which improve mileage at the expense of poorer grip; the smart tire would be more easily controlled in wet road conditions. The company believes that cars with the wireless reader and control system should be on the market no earlier than 2012.
* THE ECONOMIST also reported on work by a researcher named Mehdi Saiidi at the University of Nevada in Reno on building bridges that can ride out earthquakes. Modern bridges are actually very good at standing up to quakes, but they're not safe to use afterwards, which can hamper the work of emergency services and evacuations. Saiidi performed tests of model bridges on "shake tables" that simulated earthquakes, and found that bridge structures do not simply fall apart all at once; instead, some critical components fail first, leading to failures of other components, and so on in a cascade until the bridge goes down. Saiidi's big idea is to make the critical elements out of "shape memory alloy", which is metal that returns to its original configuration after being deformed.
There is nothing particularly unusual about that property in itself. Most solid materials will return to their original configuration, at least until the deformation reaches the "elastic limit" -- and then the deformation becomes permanent. However, shape memory alloys have a very high elastic limit; Saiidi's nickel-titanium shape memory alloy has an elastic limit twenty times greater than that of the steel bridge components that would be replaced. The alloy is expensive, but it would be only used in the most critical components. Saiidi believes that the concrete around these components could be poured mixed with short polymer fibers, permitting it to flex. The bridge may still need to be replaced over the long run, but it should be serviceable enough for emergency use.
* SEABASES: As reported in an article from THE ECONOMIST ("All At Sea", 30 April 2009), the USA is currently in the somewhat uncomfortable role of playing the world's policeman, fighting "dirty little wars" in remote corners of the globe. It gets more uncomfortable when supposedly friendly nations near those hot spots refuse to allow US forces to operate from their soil.
However, nobody owns the high seas, and while insurgents are clever about planting roadside bombs, they have little capability to attack defended targets offshore. As a result, the Pentagon is considering the construction of military bases on the oceans, made up of modules that could be plugged together like Lego blocks. They could be moved to the seas near an operational theatre, assembled and modified as desired, and then sent home when the war is over. Such "seabases" are of course a technological challenge, demanding living quarters and support systems for soldiers; facilities for handling stores and munitions; and platforms for the operation of cargolift aircraft, helicopters, small vessels, unmanned aerial vehicles, and other "tools of the trade".
An experiment in seabasing was conducted in the spring of 2008, with a set of rafts built on pontoons linked by hinges set up off the coast of Liberia in West Africa to support a reconstruction project. Supply vessels offloaded materials for building a school and hospital supplies, with the cargoes then delivered by landing craft onto a beach. The experiment was judged a success, but there was skepticism about going any further: the platform was obviously vulnerable to high weather, and building a platform that could provide a stable airstrip for transport aircraft was seen as a challenge for a modular system.
New thinking envisions the construction of ships designed to act as seabases, with the US Navy considering acquisition of 35 such vessels. The core of the seabase is currently referred to as the "Maritime Pre-Positioning Force (Future)". The US Marines already use pre-positioned supply ships as floating warehouses, and the 14 future vessels in the class will perform the same function -- but they will also have accommodations for 2,000 troops, or from 20 to 30 vertical take-off aircraft (including helicopters), or hundreds of ground vehicles. Each will also have a folding bridge, about 30 meters (100 feet) long, to link to a sister ship. The bridges will be stable in swells of up to 2 meters (6.5 feet) and will allow vehicles the size of trucks to drive from one vessel to the other.
A second element in the seabase concept is the "mobile landing platform (MLP)", a ship longer than two athletic fields, featuring a large, flat platform. The platform will make the MLP easier for other vessels to load using the platform's cranes and bridges. It will have facilities for almost 1,500 troops, who will be transferred to shore operations with a half dozen landing craft or hovercraft, amphibious tanks and trucks, and a handful of vertical take-off aircraft. The MLP will have ballast tanks, allowing it to sink low in the water to make access by hovercraft easier. A modern hovercraft can carry a main battle tank at a speed of 74 KPH (40 knots).
The vessels are the most visible elements of the seabase scheme, but they are dependent on being supplied with the proper materiel to conduct operations. This has always been an issue with overseas force projection and it is very easy to make a mess of it. These days, the materiel can be conveniently stored and handled in standard shipping containers, but making sure that the right materiel is provided in the right sequence is a tricky task.
The US military awarded a contract to BEC Industries, a Florida-based engineering firm, to design a container-management system. The result of the effort, named GRID, was introduced early in 2009. GRID consists of a shipboard hold full of containers with a grid of raids laid over the top. An automated winch moves over the rail grid, shuttling containers around as necessary -- it can relocated six containers in ten minutes. A software system decides how to access and shuffle the containers to get the job done; the scheduling software was actually the hardest part of the work, since it needed to optimize what amounted to a complex puzzle with large numbers of parts. GRID is now being installed on some US Navy vessels.
Once a container has been selected, however, it has to be transferred ship to ship, usually by crane. That is a difficult, even dangerous task, except in extremely calm seas. The US Office of Naval Research (ONR), in collaboration with Oceaneering and German industrial giant Siemens, has developed a "smart crane" that uses laser and other sensors coupled to processing power to compensate for the movement of the vessels involved in the transfer. The ONR plans to test the crane in the fall of 2009. The seabase may seem like a wild idea, but the pieces are now falling into place.
* In related news, the WIRED Danger Room defense blog tipped me off to an interesting paper by Commander Henry Hendrix in the US Naval Institute PROCEEDINGS for April 2009. Much of the paper required a fair context in naval technology and nomenclature that I don't really have, but the general vision was clear.
Right now the US Navy has 11 fleet carrier groups; Hendrix suggested that while they provided heavy force projection when and where it was needed, they weren't the best tool for the kinds of jobs associated with the era of "dirty little wars" and that the number of groups could be cut to 9 or 10 to allow funding of less expensive naval groups, which Hendrix cast into two groups.
One group, the "Expeditionary Strike Force (ESG)", would be centered on an LHA -- a helicopter assault ship, essentially a relatively small aircraft carrier intended primarily as a helicopter-based landing ship. With vertical take-off & landing (VTOL) fighters like the Harrier or the new VTOL F-35, the LHA can also operate as an air power asset, with future developments in small robot unmanned air vehicles (UAVs) only enhancing its effectiveness in that role. The ESG would of course include escorts with their complement of missiles and UAVs. With its missiles and other air assets, the ESG would be able to conduct strikes deep inland, while it would still be able to send in the Marines for military operations, as well as for humanitarian missions. Hendrix envisions 10 ESGs.
The second type of group is the "Influence Squadron (IS)". The ESG is interesting from a "war geek" point of view, but the IS is definitely a Zen approach to warfare, not being specifically intended for combat operations at all. The least expensive way, in Hendrix's view, to deal with hot spots in poor lands is to help the locals lead stable and prosperous lives. The core of the IS would be a large amphibious operations ship, capable of delivering humanitarian supplies and providing medical care, but also capable of sending in small anti-terrorist or policing teams. It would be backed up by a destroyer to provide defense or offense against air, surface, or underwater threats, as well as a "Littoral Combat Ship" for clearing mines or performing other shallow-water operations, along with other small support vessels.
Hendrix envisions 16 Influence Squadrons. They can be seen as a complement to the ESGs: an ESG would be a combat asset that can perform humanitarian missions, while an IS would be a humanitarian asset that can perform combat missions. One might suspect that Barack Obama finds this a very interesting idea: the president has clearly embraced the necessity and utility of American military power, but he also has a bent towards the use of "soft power".
* Incidentally, the article identified the likely core vessel for an Influence Squadron as new SAN ANTONIO class "Landing Platform Dock Type 17 (LPD-17)", and I got curious enough to check up on it. The LPD-17 is a modern replacement for traditional landing ships in the range of the big "Landing Ship Dock" down to the mid-size "Landing Ship Tank (LST)". The first LPD-17, of course the SAN ANTONIO, was commissioned in 2006, with three more commissioned to date. The fourth, the NEW YORK, was built partly of steel salvaged from the World Trade Center towers as something of a tribute to his namesake city and the 911 attacks.
The LPD-17 doesn't look all that warlike, having obviously been designed for support operations instead of shooting it out directly with the Black Hats. It does look clearly military, with a helicopter deck in the rear plus the sloped sides and pyramid "masts" associated with "stealthy" vessels. There are barely noticeable cluster launchers fore and aft for "rolling airframe missiles (RAMs)", the RAM being a heavily-modified derivative of the well-known Sidewinder air-to-air missile for ship air defense -- one important feature added to the missile being a secondary seeker to home in on the radar emissions of antiship missiles homing in for the kill. The LPD-17 also has defensive countermeasures systems, plus two 30 millimeter automatic cannon and four 12.7 millimeter (0.50 caliber) machine guns -- adequate firepower for protection against attack and suicide boats.
The LPD-17 has a length of 200 meters (660 feet), a crew of almost 400, and can typically carry 700 Marines. It can perform landings from over the horizon with helicopters or Osprey tilt-rotors, as well as the two hovercraft landing craft it carries and discharges from a bay in the rear. The LPD-17 has two surgeries, two dental clinics, and a hospital ward with beds for 24. Ship systems are linked by a fiber-optic network. Crew facilities were not ignored in the design of the ship: the bunks have enough headspace to sit up, while the vessel also offers a ship services mall, a gym, and an education center.
* BIOHACKING: As reported by an article in THE ECONOMIST ("Hacking Goes Squishy", 5 September 2009), the cost of biotech instrumentation has been dropping rapidly. The price of sequencing a human genome is gradually falling to a thousand dollars, while other biotech gear is going through a similar cost reduction curve. As the price falls, more and more amateurs are getting involved in what is being called "biohacking".
One symptom of this trend is a group named "Do-It-Yourself bio (DIYbio)", which holds meetings in the US and the UK, with about 800 members on its newsletter mailing list. DIYbio's efforts are starting out modest, with a plan emerging for members to swab public objects in different cities to determine their microecology of microorganisms. Other biohackers are working on more ambitious projects, for example modified microorganisms that can make biofuels cheaply or measure the alcohol content of a person's breath.
The prototype for the future of biohacking may be the "International Genetically Engineered Machine (iGem)" competition held annually by the Massachusetts Institute of Technology (MIT). The contest challenges undergraduates to hack an organism using a "kit" provided by a gene bank named the "Registry of Standard Biological Parts". The kit is made up of standardized chunks of DNA known as "Biobricks", a scheme that was discussed here a few years ago.
The BioBricks are open-source, with data available online; they help provide some structure to a field that even the professionals admit is still well more art than science. Using the BioBricks, students have come up with some remarkable schemes: a Taiwanese team conceived a bacterium that could do the work of a failed kidney, while another team from Britain worked on a "biofabricator" that could build desired biological materials. The iGem competition began quietly in 2003, and has now grown to include 84 teams and 1,200 participants, who generally leave the effort with considerable expertise under their belts.
Using such expertise at home has been troublesome, not because of any legal restrictions on the use of biotech tools -- for all practical purposes, there aren't any -- but because the tools have traditionally been expensive. That has led to a trend among biohackers to focus on the development of ever cheaper tools. Tito Jankowski, who participated in iGem and is now a member of DIYbio, was exasperated with the high price of gel electrophoresis systems, commonly used in analyzing protein composition. Despite the fact that a gel electrophoresis system can be very simple, consisting of a few panes of colored plastic over a heating element, such gear can easily cost more than $1,000 USD. Jankowski has been working towards building his own version with a far lower pricetag, explaining: "This equipment is only expensive because it has never been used for personal stuff before." The cost of DNA synthesis is falling so quickly that automatic DNA synthesis "printers" are expected to be available for home use before long.
* Biohackers believe that they are entering an age resembling that of the early days of the personal computer revolution, when an Apple or a Google might be dreamed up in a garage or university dormitory. There is another angle to that metaphor that comes to mind: makers of computer malware. Building malicious computer viruses is troublesome enough, synthesizing malevolent viral pathogens is a potential nightmare that everyone immediately recognizes as a threat.
The authorities are certainly aware of this potential, to the point of extreme paranoia. The most high-profile example so far is Steve Kurtz, a professor of art at the State University of New York in Buffalo. Kurtz is an anti-establishment type whose presentations have addressed issues in biotechnology; he occasionally obtained harmless bacteria for his presentations. When his wife Hope stopped breathing one day in May 2004, he called the paramedics, who were not able to revive her.
Police came along with the paramedics, noticed petri dishes in the Kurtz home, and called the Federal Bureau of Investigation (FBI). Kurtz was detained for a day and not allowed to return to his home while Federal agents went over the residence with a fine-toothed comb. He went back home a week later after it was confirmed that Hope Kurtz had died of a congenital heart defect, and the New York State Commissioner of Public Health reported that no threat to public safety had been discovered there.
That might have been dismissed as an unfortunate but understandable mixup; however, the FBI wouldn't relent, managing to get Kurtz indicted on mail and wire fraud charges in July 2004, claiming he had obtained (harmless) bacteria through the mail on false pretenses. After an extended legal nightmare, in 2008 a Federal judge simply threw out the charges, saying the indictment was "insufficient on its face" -- essentially discarding it as trash, that even if all the accusations were true, no crimes had been committed. There was no appeal against this judgement. The FBI clearly overreacted in the Kurtz case, but the bureau does have reason for concern. Rumors are now circulating among the biohacker community that the Feds are discreetly discouraging suppliers of reagents from selling to private individuals, though no law is in place to stop them from doing so.
* Legislators have not demonstrated any urge to pass any such laws, either. If they try to do so, it may prove difficult to keep the genie in the bottle. The biohackers at DIYbio are making progress in the development of tools that would not only be cheap to buy but easy to build at home. Many DNA sequences, including those of dangerous pathogens, are easily to find on the internet, and a clampdown would hardly take them out of circulation. Some substances may be controlled, like the reagents used in dealing with DNA, but that could end up like gun control laws: clamping down on ordinary citizens, while the black hats get what they need on the black market anyway.
Biohacking enthusiasts can admit there is a threat, but also point out there is a potential. We are still vulnerable to a wide range of dangerous natural pathogens; the garage-shop biohackers represent an immense potential resource for coming up with new ideas for dealing with such threats. Physicist Freeman Dyson, noted for his sparking blue-sky speculations in a wide range of fields, is a biohacking enthusiast, writing of options such as trees that sponge up greenhouse gases and termites that can digest old cars. Regulation is inevitable, but it will have to walk the line between ensuring public safety and stifling valuable innovation.
* ANOTHER MONTH: Having become increasingly aware of YouTube, I started checking it out on a daily basis in hopes of finding some gems there. Alas, although there are indeed some very fine gems there, they are embedded in a video trashdump. Of course, any mass agglomeration of user-contributed videos is likely to be varied lot, but it's not just that YouTube tends toward the trivial ("here's a jerky video of my cat"), it can also go below that, into exhibitions by folks trying to be clever -- while lacking the gear to realize that they aren't, much less realize that everybody else knows it.
I also ended up getting sidetracked by "911 Truther" videos for a short time. I have a fascination with the lunatic fringe, and the Truthers come across as an extreme case. I once remarked to a friend with regards to the Kennedy assassination that "there's just enough there to make you a little bit suspicious." In contrast, as far as 911 goes, it would never occur to me on my own that there was anything suspicious there. The overheated claims of the Truthers don't convince me of anything different, either, since they make a message from a Nigerian email scammer -- claiming to be the son of a deceased African dictator with $20 million USD to put in my bank account -- sound relatively credible in comparison.
However, the lack of credibility is not the issue. The real problem is that I am tempted to be drawn into the dispute. Alas, sad experience has taught me that arguing with the lunatic fringe ends up being a mean-spirited lunatic activity in itself. I recall somebody who described arguing with cranks as a hobby, "sort of like trainspotting, but more like spotting train wrecks."
I have a slush fund with a few thousand bucks in it for trips and the like. I finally made a decision that every time I got into any such argument, I'd take $100 USD from it and donate it to charity. So now if I'm tempted, I ask myself: Is this worth a hundred bucks to me? OK, that's a no-brainer. So far my slush fund is safe.
As far as YouTube goes, now I only give YouTube a quick scan once in the mornings, or check it for specific videos that I'm after. I still do get sidetracked on it a bit, and not always for entirely sensible reasons. Videos of girls giving instructions on makeup and beauty hints are fairly common fare on YouTube; for some reason I'll occasionally watch through them. Exactly WHY I find watching pretty girls fussing with their makeup and hair so fascinating is of course a COMPLETE mystery to me. But it certainly beats listening to Truthers.
* As far as comments about Twitter in earlier installments, I'm starting to feel a bit more confident with it now. For the time being, weeding out the spammers isn't too difficult, and Twitter now has a "Report As Spam" link. It might have been there all along, but since it's something I was looking from the start, I would have been unobservant to miss it. Given the seemingly marginal nature of Twitterspam, it may well help push the spammers down into the noise level. It's certainly fun to use in any case.
More significantly, I've got ten followers now. The pattern is interesting: there's only two Yanks on the list, one a GI stationed in Iraq; two Britons; a Dutchman; a Frenchman; a New Zealander; a Hungarian; a Spaniard; and somebody who lives in Australia but, backtracking from his Flickr account, seems to be from Malaysia or maybe Indonesia -- someplace in Southeast Asia where the femmes wear headscarves. He had some spectacular wedding pictures, bride and groom in glittering golden clothes that almost hurt the eyes.
Some of the followers have locked accounts and I'm not sure they're on the level. There were some folks who signed up who turned out to be following hundreds or thousands of people, but didn't seem to be spamming anything; I finally figured out that some people just set up automated signups and let them free-run, with the signups to my account triggered by some tweet I sent out. I shrugged and blocked them. What sense it makes to rack up hundreds of followers until the tweets are lost in the noise is hard to understand -- but it's not like it concerns me much, either.
