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DayVectors

nov 2009 / last mod nov 2015 / greg goebel

* 21 entries including: immune system, Southwest road trip, Second Life disappointment, falling global population growth, farming mushrooms, toxic risk assessment reconsidered, Demand Media churns out cheap data, biochar against global warming, seabases, and biohacking.

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[MON 30 NOV 09] NEWS COMMENTARY FOR NOVEMBER 2009
[FRI 27 NOV 09] THE IMMUNE SYSTEM (4)
[THU 26 NOV 09] GIMMICKS & GADGETS
[WED 25 NOV 09] WHO NEEDS A SECOND LIFE?
[TUE 24 NOV 09] BABY BUST
[MON 23 NOV 09] SOUTHWEST ROAD TRIP (4)
[FRI 20 NOV 09] THE IMMUNE SYSTEM (3)
[THU 19 NOV 09] SCIENCE NOTES
[WED 18 NOV 09] MUSHROOM FARMING
[TUE 17 NOV 09] RECONSIDERING TOXIC RISK ASSESSMENT
[MON 16 NOV 09] SOUTHWEST ROAD TRIP (3)
[FRI 13 NOV 09] THE IMMUNE SYSTEM (2)
[THU 12 NOV 09] SPACE NEWS
[WED 11 NOV 09] INFORMATION ON DEMAND
[TUE 10 NOV 09] CHARCOAL VERSUS GLOBAL WARMING
[MON 09 NOV 09] SOUTHWEST ROAD TRIP (2)
[FRI 06 NOV 09] THE IMMUNE SYSTEM (1)
[THU 05 NOV 09] GIMMICKS & GADGETS
[WED 04 NOV 09] SEABASES
[TUE 03 NOV 09] BIOHACKING
[MON 02 NOV 09] ANOTHER MONTH

[MON 30 NOV 09] NEWS COMMENTARY FOR NOVEMBER 2009

* NEWS COMMENTARY FOR NOVEMBER 2009: US President Barack Obama went on Asian tour this last month, making a particular splash on the Chinese public, where his trademark crew cut became something of a fad. Chinese state media gave the visitor entirely positive coverage -- with "entirely positive" meaning "criticisms of Chinese human rights issues trimmed out". That wasn't too difficult, since Obama's critical comments were muted and few in number. No sense in offending his hosts, after all.

Hu Jintao & Barack Obama

Back home, Obama is nearing the first anniversary of his inauguration, and as reported by THE ECONOMIST'S rotating American columnist, some disillusionment has set in. As the cover of NEWSWEEK magazine put it: "Yes He Can (But He Hasn't Yet)". During the campaign last year, Obama promised to fix health care, tackle global warming, and sort out America's wars -- but none of those things have been accomplished. One young woman in the audience for a recent presidential event said she was no longer buying "all the hype of hope and change."

Nobody doubts that Obama is a first-class orator, which was one of his most powerful tools to win him the Oval Office. Unfortunately, his silver tongue helped to raise great expectations, convincing many of his supporters that he would perform wonders on health care and global warming without raising taxes -- except of course on the "fat cats". He promised a new era of bipartisanship, and an end to dirty tricks in the name of the "war on terror": in his inauguration speech, the president proclaimed: "We reject as false the choice between our safety and our ideals."

However, what we've ended up with is a political war of attrition on health care, while global warming remains stuck in the wings. As far as the "fat cats" went, they have been the beneficiaries of an expensive bailout that has helped drive up the deficit. Obama doesn't hesitate to snipe at the Right, or even take an occasional kick at the dead horse of the Bush II Administration -- an action all the more gratuitous because George W. Bush has been careful not to take potshots at Obama from the gallery. Predator drones continue to make strikes at terrorist targets in Pakistan, each strike requiring direct authorization from the White House. Throw firepower around when innocent civilians are in the area and they can get caught in the crossfire; kids get killed along with terrorists.

Obama has clearly failed to live up to his campaign promises. However, nobody sensibly takes campaign promises at anything more than the best face of hopes and aspirations, presented with as little emphasis on specifics as possible. On the basis of what might more reasonably be expected of him, matters seem to be moving along, if not energetically.

Health reform means tinkering with a sixth of the US economy, and the president has to have a strong consensus with a divided Congress to get it done. Global warming legislation could have an even greater effect, and so it will be even harder to push through. The financial system has stabilized; although propping up ailing banks and insurers with taxpayer dollars wasn't popular, the collapse of these businesses would have been a disaster, dragging the rest of the country down with them.

Despite the president's high-flown rhetoric, there was no way to evade some sort of "choice between our safety and ideals" -- and though Obama wants to shut down the detention center at Guantanamo, he knows he can't do it without making sure dangerous individuals aren't set free. American forces are being withdrawn from Iraq in a gradual and cautious way. Hawks are not happy about the president's equivocation on Afghanistan, but others point out that Obama's careful deliberation on the matter contrasts well with the "ready-fire-aim" approach that discredited the previous administration. Obama's election did greatly improve the US brand name elsewhere, though so far it hasn't yielded much in the way of tangible benefits. His willingness to talk with Iran and North Korea haven't proven very useful so far either, but nobody thinks diplomacy is easy, particularly with cantankerous states.

Obama also ends up having a peculiar advantage in that the dominant expressions of discontent for his administration on the blogosphere and elsewhere are skewed towards the hysterical. If Obama's performance so far hasn't been much to write home about, his limitations end up being masked by the over-the-top rants of his ill-wishers. Compared to the tinfoil-hat fantasy Obama conjured by those who hate him, the real Obama ends up looking not so bad.

One might still be unhappy at the continued inclination of Obama to oversell himself, at his disappointing partisanship. However, the president has at least three more years to deliver. There was talk in August that the Obama Administration was reaching a "crunch point" that would "make or break" his presidency. Rubbish. As the saying goes, it's not over until its over, and a lot more can and will happen. The Obama presidency may well prove a bust, but it's still too early in the game to call.

* On 9 November, South Korean and North Korean patrol boats had a brief shootout, with South Korean officials saying they had sent a North Korean vessel off in flames with no harm to the South Korean vessels. North Korean sources insisted that they had sent the South Koreans packing and that South Korea needed to apologize. There is nothing much new in such clashes, occasional shootouts being a hazard when living alongside a dysfunctional neighbor. The last naval dust-up was in 2002, with six sailors killed. It is likely the incident was just jumpiness with guns and not planned, but the North Koreans are at least a little bit crazy, and it's hard to tell what they might be up to.

An article discussed that the North Korean Army, while rich in warm bodies, has little heavy gear or fuel. Pyongyang knows perfectly well that if it came to a serious shooting match, the troops wouldn't provide much more than a "target rich environment" for South Korean and US firepower, all the more so because to get south North Korea forces would be channeled through mountain passes that would make good "killboxes". Fortunately for all concerned, the North Koreans seem to realize that provoking such a head-on confrontation would be madness. As a result, they have been focusing on special operations units that would infiltrate south and simply raise hell, using tactics such as assassinations and improvised explosive devices (IEDs). The idea is not to win a war, they can't -- just to make sure they can inflict pain if it comes to that.

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[FRI 27 NOV 09] THE IMMUNE SYSTEM (4)

* THE IMMUNE SYSTEM (4): Having outlined the players in the immune system -- its organs, cells, and molecules -- it is now possible to describe how the immune system operates. As mentioned, the skin and various secretions are the first line of defense against intruders. It should be obvious now that they are not simply passive barriers, instead being integrated into the immune defense with players such as IgA in the tears and saliva.

If an intruder gets through the barriers, it encounters the innate response. The body does have certain coarse innate defenses, such as sneezing to get rid of intruders in the nose, plus vomiting and diarrhea to get rid of toxins and the like. If pathogens arrive through a wound, an inflammation response occurs, with histamines released by immune cells causing blood vessels to become dilated and leaky, resulting in swelling. The aggravated blood flow and leaky blood vessels help wash out the wound, and also allow more oxygen, nutrients, immune system components, and blood clotting system components to reach the wound in quantity.

During the inflammation reaction, cytokines are released to call macrophages and other immune system components to the wound. The enhanced metabolic activity in the wound results in heat, which has the useful side effect of limiting pathogen activity. Incidentally, in more general infections the added metabolic load of the body due to the immune system can result in a fever, which at least in moderation can be helpful by suppressing pathogens.

In any case, the nonspecific immune cells and chemicals back up the innate response. Macrophages perform the initial counterattack, eating up intruders. Neutrophils then arrive from the bloodstream, moving into the region of infection in large numbers. Complement molecules link up onto pathogens, attacking them directly and opsonizing them for attack by other immune system components.

The innate response is fairly "dumb"; macrophages, for example, have receptors, known as "Toll-like receptors (TLRs)", that can identify certain components common to a number of particular types of pathogens, but they have no ability to target anything else. If the invasion persists, the action of the innate immune system calls in the "smarter" adaptive immune system to take more precisely targeted action against the threat. [TO BE CONTINUED]

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[THU 26 NOV 09] GIMMICKS & GADGETS

* GIMMICKS & GADGETS: WIRED Online had a little article on a robot designed by Nissan Motors of Japan. The EPORO, as it's named, is pure cutesy Japanese in appearance, being barrel-shaped with a vaguely fishlike appearance. The fishlike appearance is a hint at the point of the exercise: the EPORO emulates the behavior of fish in schools to allow a set of the robots move effectively at high traffic density down test roadways.

EPORO robots

Each robot has a laser rangefinder, plus a wireless spread-spectrum link with its "schoolmates". The schooling algorithms mimic how fish avoid collisions, fall in neatly with each other, and remain closed up fin-to-fin. Diagrams showed how the robot school would converge into a single file to handle a constricted roadway or flow around an obstacle. Nissan is tinkering with such concepts with an eye towards future "smart" traffic flow control schemes.

* WIRED Online also discussed how the military is making use of a software product named "MultiPlayer" from company named EchoStorm that works on video and data management systems. The military makes considerable use of surveillance systems that produce vast floods of still imagery and video; MultiPlayer allows a user to access such data, both from archives and in real time.

MultiPlayer allows searches on various criteria, with the data pinned to map locations. It's sort of like YouTube for warriors with laptops; not only can locations be monitored for activity via an array of sensors -- with new sensors, such as cameras on ground vehicles or even on an infantryman's helmet, added at will -- but archival footage can be inspected, for example to see if insurgents have planted a roadside bomb along a route that a truck convoy. If adversaries are spotted by a real-time sensor, MultiPlayer can be used to call in artillery or strikes by other "shooters". No doubt the system either includes or could be extended to include video analysis to alert users to events of interest, and validation schemes to help prevent "friendly fire" incidents.

* BBC WORLD Online had an interesting article on a transportable waste-to-energy plant obtained by the US Army from the UK defense research firm QinetiQ (pronounced "kinetic"). The "PyTec" system accepts waste and heats it in an oxygen-deprived chamber to produce "synthesis gas" or "syngas", consisting mostly of hydrogen and carbon monoxide. The syngas can then be burned to drive a power turbine.

PyTec can be hauled in two trailers and can handle up to 100 kilograms (220 pounds) of waste an hour, reducing it to 5% of its volume while generating up to 400 kilowatts of power. That reduces the amount of waste to be disposed of while providing electricity. The Royal Navy installed a similar system on the ship HMS OCEAN last year.

* As discussed by a note from the SCIENTIFIC AMERICAN website, researchers at the Missouri University of Science & Technology have come up with a scheme for growing algae for biofuels -- in abandoned mines. Since algae need light to grow, that might seem obtuse, but it turns out that algae only need the red and blue parts of the spectrum, and they can get by very efficiently on pulsed light -- since they require a bit of time to actually process the light energy. The researchers are considering the use of arrays of LEDs to provide the light.

The mines have an existing infrastructure that would make it relatively easy to place the bioreactors for the algae and their associated arrays. The mines can provide an environment where temperatures are relatively easy to control and contamination -- from or to the outside world -- is minimized. The algae could also provide bioremediation in contaminated mines, since the algae is good at sequestering heavy metals. Of course LED arrays are more expensive than sunlight, but the mines would be able to work in any weather, 24 hours a day. It's an interesting idea, but not one I'd put a lot of money on myself.

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[WED 25 NOV 09] WHO NEEDS A SECOND LIFE?

* WHO NEEDS A SECOND LIFE? The Second Life online virtual environment was a hot topic not so long ago, being reported here in 2007 as the Big New Thing. As reported by an article from BBC WORLD Online ("What Happened To Second Life?" by Lauren Hansen), as it turns out -- it wasn't.

Second Life was established by Linden Labs in 2003. The environment allowed users to move around in virtual cities that they could design themselves, interact with other virtual users in the form of cyber avatars, and conduct transactions using a virtual currency. In 2006, Second Life started to get media attention that ramped up rapidly. Corporations like IBM bought virtual properties to promote their products; Reuters set up a news service to report on activities in the environment. In 2007, the number of users jumped from 450,000 to 7 million.

Then came the crash. By 2008, the media had lost interest, as had many of the corporations. Some businesses had spent a fair amount of money designing and implementing their virtual storefronts in Second Life, only to have nothing to show for it. One observer described the experience of opening a store in underwhelming terms: "They would have 20 or 30 people there when it opened, and after that no one would bother going in there again. It just wasn't worth the spend." The Reuters correspondent who was assigned to the Second Life "beat" was less forthcoming: "It isn't a subject we like to revisit."

Where is everybody?

To be sure, Linden Labs claims Second Life is still a going proposition, saying that a million people log in each month, that usage is growing at present, and pointing out that some companies, most prominently IBM, are holding on. However, even taking the login stats at face value, that's a big comedown from the high expectations of 2007. What happened?

Partly the difficulty was that Second Life lacked a clear identity. Second Life seemed to many like combining a social networking site with all the overhead of a massively multiplayer online role playing game (MMO-RPG), and one that tended towards the slow and klunky at that. For social networking, the virtual environment was just so much excess baggage, and far too much excess baggage for the emerging smartphone environment. Second Life was also a "real-time" system, and the "live chat" model isn't necessarily the best for social networking. There's intense competition among social networking sites, and Second Life could not keep up.

Similarly, as far as online shopping environment went, it was just more clunky overhead than Amazon.com to do the same sorts of things. The competition from MMO-RPGs hit Second Life from the other side: gamers are willing to learn complicated rule systems, but where was the game in Second Life? Sure, users could devise their own games, but that was too much like work, particularly given the anarchy and confrontational tone of online interactions.

Those who have stayed in Second Life shrug at the end of the hype, believing it still has its attractions -- for example providing a fairly rich environment for setting up simulations, such as the "virtual hospital" discussed here this last summer, or for "storyboarding" theatrical productions. Certainly the concept seems to have potential, though it may take improved technology and new ideas to achieve it. If "the future is NOW!" turned out to be exaggeration -- there may still indeed be a future.

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[TUE 24 NOV 09] BABY BUST

* BABY BUST: The notion of the "population doomsday" was popular in the 1960s and 1970s, envisioning an exponential increase in the human population of the Earth in the 21st century that would certainly lead to a disastrous crash. However, as reported by an article from THE ECONOMIST ("Go Forth & Multiply A Lot Less", 31 October 2009), that isn't exactly how things are working out: the global human fertility rate is falling and should go under the "replacement rate" by 2020.

The replacement rate is the average number of children born by each female in a population during her childbearing years, generally regarded as from age 15 to 49. In principle the replacement rate should be a simple value of 2, but not all females either have children or live long enough to have children. Childhood mortality has the strongest influence on the increment of births required to exceed break-even: in prosperous countries, where childhood mortality is low, the replacement rate is about 2.1, while in the most wretched countries, it can run at an appalling 3. The global average is about 2.33.

It has long been realized that prosperous countries have low fertility rates; the worry has traditionally been over the explosion of population in poorer countries. In the 1970s, only 24 countries had fertility rates of 2.1 or less. However, instead of remaining the exception, they have increasingly become the rule: now 70 countries have fertility rates of 2.1 or less. Between 1950 and 2000 the average fertility rate in developing countries fell from about 6 to 3. It took over a century for Britain's population to fall to the replacement rate; it only took 20 years in South Korea. In Mauritius, the fertility rate fell in half in only ten years.

The most spectacular example is Iran. When the Islamic Revolution took power, the mullahs dismantled family planning and encouraged more babies. The result was a fertility rate of about 7 in 1984. Obviously, that rate was unsustainable, but the rate of fall was breathtaking -- to a national average of 1.9 over the entire country, and only 1.5 in Tehran.

* The notion that organisms will continue to reproduce until they outstrip their food supply is an old one, established two centuries ago by the 19th-century English scholar Thomas Malthus, and not only did it seem to be borne out by the observation of animal populations, but of human populations as well. Traditionally, in agrarian societies, children were an economic benefit: they provided labor to support a family, with overhead of more children more than offset by the increase in resources. However, once societies reach a middle-class level of prosperity, the economic incentives for having more kids tend to reverse. Kids don't contribute much to family prosperity, while requiring that resources be invested in them to educate them for their future life as citizens. Wives may find steady jobs, providing income that goes away when they bear and raise kids. Women may also acquire positions of influence and authority that work against child-rearing.

Of course, couples still generally want to have children, but while the economics of poverty tend to mean "the more the better", the economics of prosperity ironically make large families more difficult to afford. The statistical inverse correlation between average income of a population and its fertility rate is a very strong one.

It is not, however, a perfect one, since in some countries rich families have as many kids as poor families. One issue is access to contraceptives. Comprehensive survey data suggests that in poor countries, women generally have about one more child than they actually want. In Africa, more women say they want access to contraceptives than actually have access to them. In other words, if contraceptives were universally available, regions with high birth rates would see a significant fall.

Another issue is simple literacy. Women who can read learn about contraceptives and planning a family; women who have full educations can obtain steady jobs and responsibilities, making them less likely to want big families. One of most significant positive achievements of Iran's Islamic Revolution was widespread education of women, with the level of female education well above those of its neighbors. The spread of female education in Iran is clearly correlated to the fall in birthrate.

* The question follows: Is the decline in population growth good or bad? An environmentalist would wonder how anyone would think it could possibly be a bad thing: it's unassailable logic that the planet cannot support an indefinite growth in the human population. Most greens don't think it can sustainably support the population it has now, and are quick to point out that even once population growth falls to the global replacement rate, the population is going to continue to grow for decades, until deaths start catching up with earlier births. Given current demographics, the world population stands to increase from over 6 billion now to a peak of over 9 billion in 2050.

However, the push towards lower birth rates has not always been benign. To be sure, few have objections to providing women with access to contraceptives and matching educational services: the right to reproduce implies the right not to. The problem is that in some ugly cases, women have been denied the right to reproduce -- the worst case being China, which has achieved a substantial reduction in population growth through a "one child" policy whose heavy-handed implementation would be flatly unacceptable on the basis of human rights in most other countries. In Russia, population has been on a clear decrease, not because of family planning gone out of control, but because of appallingly poor public-health standards and resulting short life expectancies.

There is also in principle an economic case for population growth: aren't humans a valuable resource in themselves? The more hands there are, the more work that can be done; of course, militaristic states also like to see boys born who can later fill out the ranks of armies. However, churning out more kids in an agrarian society where the per-capita productivity is low is a poorer path to national wealth than industrial development and automation. Even militaristic societies have also understood that automation has extended to warfare, and legions of "cannon fodder" that are of little value unless they're properly trained and equipped are less important than access to modern weaponry. In addition, a smaller population is less of a burden on resources, while parents with smaller families are more economically productive and can invest their savings in economic growth.

There is still a subtle economic problem with declining population growth: once the brakes go on, the relative number of nonproductive elderly who require care in the population starts to grow, placing an increasing economic burden on those who are still working. This is clearly a challenge for graying societies like Japan, and it may require changes in mindset, for example encouraging immigration from regions where population growth hasn't slowed off so much yet. The culturally homogeneous Japanese are not keen on this idea. If there are some who celebrate the idea of a declining global population, it will not be without its troublesome drawbacks.

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[MON 23 NOV 09] SOUTHWEST ROAD TRIP (4)

* SOUTHWEST ROAD TRIP (4): I spent Thursday night in Socorro. I had been thinking of spending it in Roswell to the west, but it wasn't that long a drive to Midland, Texas, from Socorro, and I didn't like the idea of going across the desert in the dark. I had a vague idea that I might get abducted by a UFO.

I left Socorro for Midland the next morning, Friday, 9 October. I wasn't in any particular hurry. The drive was about 640 kilometers (400 miles) and I could make it easily by the afternoon, but I doubted there was much entertaining to do in Midland for the rest of the day -- TripAdvisor's list of "Things To Do" in Midland was very short and unspectacular.

I had been thinking of going out of my way to visit the missile museum at White Sands, but on investigation I found it was inside the military post fence and I would have to put up with a security check before they let me in. NO WAY. I understood the need for security, but I figured that it they didn't really want me there, I wasn't going to beg to be let in. Somehow the scenario brought up half-amusing, half-irritating recollections from decades ago of how the military does things -- putting out the WELCOME mat and then handing the incautious a raft of service-issue hassle.

On some nosing around I found the "Bosque de Apache National Wildlife Refuge", not far from Socorro and effectively right on the road to Roswell and Midland. It was described as being a major watering hole on the flightways of seasonal bird migrations. However, on a brief checkout I found no unusual bird activity in progress, and had to satisfy myself with a shot of sunrise against the barren but scenic New Mexico mountains.

New Mexico sunrise

The land from Socorro to the Texas border tends towards the desolate, with juniper forests giving way to prairie marked by cactus. The only town of any size on the route is Roswell; out of curiosity I took a quick drive up Main Street. I had discovered before I left home that there was a military museum in town, and I figured it might have a tank or something out front I could shoot. I didn't find the museum, but the city hall had an old 90 millimeter anti-aircraft gun out front. I did a walkaround of the gun, taking about a dozen pictures to see what the best camera angle was -- annoying background clutter not always being obvious until the image is viewed later. That's one of the great things about a digital camera: images are effectively free, I can take as many as I like in hopes that one will work.

Anyway, Roswell turned out to be a fairly thriving and prosperous town. I wasn't sure what industries held it up, it appears to be mostly agritech; Wikipedia reports there's a big producer of mozzarella cheese there -- hey, it's got to be made somewhere, right? As far as the "aliens" angle, aside from a few gift shops in the old downtown area, it was hardly in evidence. Then again, maybe the 90 millimeter gun was for air defense against UFOs.

90 millimeter AA gun, Roswell NM

Once I got to West Texas, the prairie gave way to irrigated farmland -- cotton, sorghum, some other crops like sunflowers. I had heard the land there was flat, yep it's flat, only a dry lake bed might be flatter. There were signs that read WATCH FOR WATER ON ROADS; uh-huh, drainage might be a real problem, the water having absolutely no place to go.

On the leg south to Midland, the croplands gave way to brush again, with oil exploitation much in evidence. When I got down to Midland I was definitely surprised, having believed it was another small town like Socorro. Nope, as I got from Wikipedia the population of the Midland-Odessa twin cities area -- "Midessa" -- is over a quarter of a million people, downtown Midland has a cluster of significant high-rise buildings, and there were modern malls and industrial campuses. It appears oil money keeps it mostly afloat. Drainage did appear to be a problem there as well: hollows in the streets were fitted with vertical "yardsticks" to the side to tell a driver how deep the water in a puddle really was. [TO BE CONTINUED]

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[FRI 20 NOV 09] THE IMMUNE SYSTEM (3)

* THE IMMUNE SYSTEM (3): The cells of the immune system make use of a variety of molecules to get the job done. One of the most important are the "antibodies" or "immunoglobulins (Ig)", which are produced by B cells in response to an infection. Antibodies are closely tailored by the immune system to lock onto specific antigens. The core element of an antibody -- consists of two identical heavy protein chains and two identical light protein chains, shaped to form a Y-shaped structure. The tips of the arms of the Y are highly variable, generated to match any one of a wide range of antigens, much as a key fits into a lock.

There are different classes of antibodies. Some are "singlets", consisting only of one Y; while others are "multiplets", with multiple Ys joined together at the bases. The base or stem of the Y is constant for each class, though not between classes, and so is known as the "constant region". There is a total of nine classes:

In any case, when an antibody links up with an antigen, it creates an "antigen-antibody complex" that provides a lever for an attack on the intruder. This targeting process is known as "opsonization".

* The antibody system is backed up by another molecular defense known as "complement", because it complements the antibodies. Complement consists of about 25 proteins, produced by the liver, that circulate in the blood in an inactive form. When one of the complement molecules, known as "C1", encounters an antigen-antibody complex, it sets off a "complement cascade", with other members of the complement assembling to punch a hole in the cell membrane of the intruder, killing it. Complement also performs an opsonization function.

* As mentioned, immune cells communicate with chemicals known generally as "cytokines", with the cytokines used by macrophages known as "monokines". T cells and B cells secrete cytokines unsurprisingly known as "lymphokines" or "interleukins". Other cytokines included "growth factors" and "interferons".

After being produced and released, cytokines recruit other cells and substances to a "war zone". They encourage cell growth, promote cell activation, direct cell traffic, and command the destruction of target cells. When cytokines attract specific cell types to an area, they are called "chemokines". Chemokines are released at the site of injury or infection and call other immune cells to the region to help repair damage and defend against infection. [TO BE CONTINUED]

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[THU 19 NOV 09] SCIENCE NOTES

* SCIENCE NOTES: As reported by AAAS SCIENCE, careful measurements of global temperature have demonstrated that over the past decade, the Earth's average temperature has not risen at all. Global warming deniers have pointed to this as obvious evidence that global warming is not really happening and that the fuss over it is unnecessary.

Climate modelers do not dispute the fact that temperatures have remained level, but they claim it is not surprising. Climate models that show a future trend towards a hotter Earth do not show the temperature climbing steadily, year by year; in fact, it is nothing unusual for the models to repeatedly "flatline" for a decade or so before the temperature starts rising again. Pauses for longer than 15 years are rare, and the general belief is that the Earth will start getting hotter again in no more than five years. Says one climate researcher: "In the end, global warming will prevail."

* While the notion that increasing loads of atmospheric carbon dioxide will contribute to global warming has been generally (if not universally) accepted, the extent of the warning is still argued. Atmospheric CO2 concentrations are on track to doubling the 280 parts per million (PPM) found in the Earth's atmosphere before the Industrial Revolution; climate modeling being a tricky issue, it's not too surprising that the estimates of the impact of this change range from an average global temperature increase of 2 degrees Celsius to a much less tolerable increase of 6 degrees Celsius. It would be nice to get some real-world data to determine just how sensitive climate is to CO2.

A paper recently published by Aradhna Tripati of the University of California at Los Angeles (UCLA) and colleagues described a record of atmospheric CO2 concentrations going back 20 million years, using deposits of the shells of "foraminifera". "Forams", as they are known, are single-celled aquatic organisms that grow shells of calcium carbonate; they are very well known, the shells tending to be distinctive for different species, and are have long been used as "markers" of oil deposits by geologists.

The UCLA researchers knew that the way forams build their shells out of the minerals in sea water is dependent on ocean acidity -- which in turn is dependent on atmospheric CO2 concentrations, with more CO2 meaning higher acidity. Some boron is incorporated into the shells; as acidity rises, the ratio of boron to calcium falls, and the isotopic distribution of the boron changes as well. The researchers chose two species of forams that are known to be symbiotic with photosynthetic algae, meaning they lived in surface waters, where the ocean interfaced with the atmosphere.

Initially, the UCLA team analyzed Pacific Ocean drill cores going back 800,000 years that could be calibrated against Antarctic ice cores going back the same length of time. Having obtained the calibration, they then proceeded back in time. As it turns out, about 15 million years ago atmospheric CO2 levels were about the same as they are now; the average global temperature was about 3 degrees Celsius greater, while sea levels were tens of meters higher; there was also less ice at the poles, and the patterns of rainfall were much different. Overall, the pattern revealed by the forams showed that atmospheric CO2 levels had never risen as rapidly in the timeframe examined as they are rising now; and that relatively moderate changes in CO2 concentrations -- from 100 to 200 PPM -- could cause substantial temperature swings, strongly suggesting a sensitive climate system.

* THE ECONOMIST reported on interesting research being performed by Harvard University scientists to evaluate new antibiotic medicine candidates. Such evaluations are time-consuming and laborious, and the Harvard researchers have been working on ways to automate them.

The guinea pig being used in the effort is the C. elegans nematode worm. It is very well understood, being the first organism to have its genome completely decoded. It is small, only about a millimeter long, and easy to breed, making it an excellent test subject. The worms are spread on a culture bed of bacteria for a bit over half a day, then mixed in water to form a "solution" of worms. The solution is dispensed by a precision instrument called a "particle sorter" into an array of 384 tiny wells, with 15 worms per well. Each well contains an antibiotic candidate.

After five days, the wells are examined to see if the worms have survived or not. In the past, the only way to check to see if the worms were alive was to observe them through a microscope and see if they were still squirming, but that was laborious. The Harvard researchers instead use an orange stain that enters dead worms but not live ones; the wells are stained and then the array is read by a digital camera, with image analysis software able to use the imagery to determine if the worms in each well are alive or dead. The software analysis is just as reliable as visual analysis and much less time-consuming.

To date, the researchers have examined 37,000 antibiotic candidates and screened them down to 28 that seem promising for further investigation. Some of these candidates appear to work in entirely different ways from traditional antibiotics, meaning that they may be particularly effective against bacteria that resist existing antibiotics.

* The European Space Agency's Rosetta probe, on its way to rendezvous with and go into an orbit around a comet in 2014, performed its last Earth flyby this November, taking a spectacular picture of the Earth as it flew past.

Earth from Rosetta probe

* The WIRED Online science blog had a short report on yet another interesting new fossil discovery, this one from southwest China. It is known from fossil records that life has been around for about 3.5 billion years, but for almost 3 billion of those years it was just single-celled organisms. Multicellular organisms didn't make an appearance until about 600 million years ago, in the "Precambrian" period.

Early multicellular organisms had flat bodies with simple symmetry, these creatures being described as "living quilts" or "mattresses". The branch of animals to which we belong of course have "bilateral" symmetry, with two sides that mirror each other, along with a distinct front and back. The new fossils, from China's Doushantuo formation, which was laid down about 590 million years ago, and represent the earliest known examples of biological organization.

They are merely microscopic lumps of cells. Their external appearance is unremarkable, suggesting on a superficial inspection that they are just some sort of geological artifacts that just happen to resemble the remains of living creatures. However, their internal structure was examined using "synchrotron radiation microtomography" -- in which the fossils were X-rayed from thousands of angles, with the results digitally interpreted into a three-dimensional image -- shows them to be embryos of bilaterally symmetrical animals. Even more interestingly, there were two distinct sets of embryos with clearly different organizations, suggesting that they were derivatives of a common bilaterian ancestor that was even more ancient.

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[WED 18 NOV 09] MUSHROOM FARMING

* MUSHROOM FARMING: There's a certain fascination in learning how things we take for granted actually work. An article from SCIENTIFIC AMERICAN Online ("Making Mushrooms Environmentally Friendly" by Brendan Borrell, 3 April 2009) took a spyglass to the mushroom business and its problems with neighbors.

Welcome to West Grove, Pennsylvania, near Philadelphia. The Needham family raised mushrooms here for generations, but urban sprawl finally caught up with the operation. In 2004 the family announced plans to expand their mushroom farming operation, but the neighbors were unhappy enough with the status quo, which involved the Needhams hauling in dumptruck loads of horse and chicken manure every week to fuel their mushrooms. The neighbors had no tolerance for the idea of more of the same, and the authorities refused to provide permits.

The Needhams are far from alone. Pennsylvania is the biggest producer of button mushrooms, producing 225,000 tonnes (250,000 tons) a year, with the crop worth almost half a billion dollars. Despite the economic importance of mushroom farming there, resistance to the smelly business of raising mushrooms has been on the increase as city folk move to the country, to find out that, as anyone who lived there could have told them, that the air isn't always as fresh as TV commercials make it out to be. The "not in my back yard" mentality holds, even when somebody moves their back yard into a neighborhood where mushroom farming has been going on for decades. Pennsylvania State University researchers are now trying to see what they can do to make both sides happy.

There's a general perception that fungi are a kind of plant, but they are no more plants than we are. They do not photosynthesize, instead sending a network of rootlike tendrils known as "hyphae" to digest their surroundings -- manure, an old log, bread, or (in the case of athlete's foot) skin. Mushrooms are farmed in sheds containing troughs of manure, with the environment kept cool and humid. The mushrooms grow quickly under such circumstances, yielding about 24 kilograms per square meter (5 pounds per square foot), reducing the mass of their compost bed by about a fifth in the process.

Mushroom farmers get their manure from owners of stables and farms who are happy to see it carted off. It has to be "pasteurized" before use, being mixed with straw and fresh hay and then spread out for one or two weeks. Bacteria grow in the compost, raising its temperature to 50 degrees Celsius (120 degrees Fahrenheit), killing off unwanted organisms, including other fungi that could compete with the mushrooms. The compost doesn't smell so bad in itself, but as the temperature rises the oxygen levels in it fall, and anaerobic bacteria thrive. The bacteria produce hydrogen sulfide gas, famed for it's rotten-egg smell, which can make its presence known at low concentrations. Water runoff from the compost piles also pollutes streams and groundwater.

Penn State researchers have found that installing air jets in composting bunkers tends to keep down the anaerobic bacteria and their smell, but they decided that it would be even better if they could reduce the amount of compost -- since that would not just mean less smell for neighbors but also less material for farmers to handle. The issue is that, traditionally, one batch of compost can only support two crops or "flushes" before the yield becomes unacceptable, even though there's only been about a 20% decline in the mass of the compost. The scientists are now trying to determine what additives might permit a third flush.

Finally, there's the problem of what to do with the spent compost, which is a nuisance to dispose of. However, there are opportunities to put it to good use. Bark mulch in the area has a tendency to become infected with "artillery fungus", which has the interesting habit of blasting its spores at bright surfaces, like a house or car, and the spores are almost impossible to clean off. The Penn State researchers have found that adding spent compost to bark mulch kills off the artillery fungus neatly. Disposing of spent compost then became much easier, and in fact there's a possibility that it might even be salable. As the old saying goes, pollution can sometimes just be a misplaced resource. All the efforts of the Penn State researchers did not save the Needham's operation. After fighting through the courts for several years, a developer made them an offer they couldn't refuse -- and the family pulled up stakes in search of new pastures.

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[TUE 17 NOV 09] RECONSIDERING TOXIC RISK ASSESSMENT

* RECONSIDERING TOXIC RISK ASSESSMENT: In the USA and many other countries, the introduction of new drugs and other chemicals is subject to regulation by the government to ensure that the new products are safe. This is necessarily a troublesome process, prone to controversy and requiring laborious, expensive tests. As reported by an article in AAAS SCIENCE ("Putting Chemicals On A Path To Better Risk Assessment" by Erik Stokstad, 7 August 2009), it's also not all that effective.

To be sure, any chemical that is blatantly dangerous is going to be spotted, but sorting between chemicals that may have subtle hazards and chemicals that are actually harmless is tricky. Consider ethylhexyl methoxycyanate, a compound that blocks ultraviolet rays and is often used in sunscreens. Given hints that it might have toxic effects, the US National Toxicology Program (NTP) of the National Institute of Environmental Health Sciences decided to investigate, feeding large doses of the compound to lab rats and mice. The problem is that humans don't make a habit of eating sunscreen, and though such a procedure might demonstrate harm to lab rodents, that wouldn't prove the compound actually constitutes a real threat.

Both researchers and policy makers are starting to believe that toxicity testing needs to be rethought. The current approach, which involves giving animals large doses of chemicals, is slow and expensive, while its relevance to humans is often unclear. The US Congress is considering tighter regulations on chemicals, and in response companies and government agencies are working on new approaches to testing them to ensure that tougher laws don't end up being burdensome and ineffective.

In March 2009, the US Environmental Protection Agency (EPA) released a 20-year strategic plan, which leveraged heavily off a 2007 report from the National Research Council (NRC) of the US National Academies. The EPA report concluded that animal testing should give way to the use of computer modeling to predict toxicity, with practical data obtained from rapid assays of human cells. As an industry observer put it, the report has "created incredible momentum" for change in the way toxicology testing is performed. Setting up a new system for testing presents a formidable challenge, with costs estimated at one or two billion USD over one or two decades, but the EPA believes it can and should be done. Since industry has to meet EPA requirements, the affected companies are in complete agreement.

* The current approach to toxicology testing goes back to 1937, when a company released an antimicrobial drug named "Elixir of Sulfanilamide". It was a disaster, killing over 70 people from toxic side effects, and led to the passing of the "Food, Drug, & Cosmetic Act", which dictated toxicity tests using animals. A decade later, a second law was passed to require similar tests for pesticides.

Since its formation in 1970, the EPA has been one of the primary Federal organizations involved in regulation of chemicals. Not surprisingly, the agency has been the target of criticisms that the procedures it demands for toxicology tests are ineffective. In 2005, the EPA asked the NRC to suggest ways of doing a better job. The NRC report suggested that data could be obtained by quick tests of chemicals on human cells, with warnings obtained by disturbances in cellular signaling pathways. That was all very neat, except for the fact that it required a detailed knowledge of hundreds of possible pathways, which dictated a major long-term research effort.

In response, later in 2005 the EPA established the "National Center For Computational Toxicology (NCCT)", which has been working with the NTP and other government organizations to evaluate hundreds of rapid tests against hundreds of chemicals. Companies from the pharmaceutical and agrochemical industries have been highly cooperative, freely providing data that they would have traditionally kept secret. The companies themselves are doing plenty of research on new approaches to toxicology testing, performing rapid human cell assays -- as well as computer-based "quantitative structure-activity relationship models" to identify new compounds that seem likely to be toxic.

However, nobody is expecting quick results, since there are a lot of tricky factors to consider. For example, a chemical may break down in the human body, and even though the chemical itself may be harmless, such "metabolites" may not be. There is also the big question of assessing the validity of the new tests; some researchers suggest that animal testing might be used as a check, while others reply that animal testing is too crude and computer modeling will do a better job over the long run. Finally, there is ugly fact that the science and technology are only two parts of the equation of toxicology testing: the third is politics -- and that may well be the biggest challenge of all.

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[MON 16 NOV 09] SOUTHWEST ROAD TRIP (3)

* SOUTHWEST ROAD TRIP (3): After canvassing the Albuquerque zoo I hit the rest of the biopark -- I'd bought a "combo ticket" at the zoo so I could see it all. The western part of the biopark included an aquarium and botanical garden. I was looking forward to the aquarium, but though it was nice and clean and modern, it was also unexciting, with no particularly unusual exhibits to attract anyone who frequents aquariums fairly often. I wasn't thinking the botanical gardens would be that interesting, but I much preferred them, particularly the Japanese section, with its little shrine and Zen / sand garden. It looked like the garden would be fun at night, since it was littered with displays -- animal cutouts patterned with Christmas-tree lights.

Zen garden, Albuquerque

That finished up Albuquerque; next stop was Socorro to the south. I hit the Albuquerque airport for some planespotting on the way down, got a few helicopters but that was about it. I was intrigued to see signs marking an area for "aircraft viewing" -- I didn't find the area but it made sense, for good reasons airport security is suspicious of planespotters. I usually try to avoid doing anything to provoke security, and it was nice to see the administration taking measures to keep the planespotters happy, keeping them and airport security out of each others' hair.

I stopped to get a burger for lunch. New Mexico acquaintances told me that Latinos were the biggest ethnic group in the population, and this was getting hammered in everywhere I went. If I lived in New Mexico I'd definitely put a priority on learning Spanish. It's nothing unusual to hear Spanish spoken in northern Colorado, but in New Mexico is it at least as commonly spoken as English. I'm sure it would be easy to learn -- Mexicans tend toward the genial and I'd get a lot of informal tutoring, along with a certain amount of linguistic pranksterism.

My main objective in Socorro was the Very Large Array of radio telescopes in the desert to the west. I equivocated about taking that dogleg during trip planning, partly because I worried I'd end up driving all over the back of beyond in the desert to find it. On closer inspection that turned out to be no worry, it was just a straight shot about 80 kilometers (50 miles) west from Socorro on Highway 60. It wasn't like I would miss it -- as the satellite imagery showed, the rails on which the antenna moved actually crossed the highway.

I had worried I would get there too late to get shots, but I had plenty of light. There was a viewing turnoff along the highway and I stood there for about 15 minutes, getting various shots. What was intriguing was that the controllers were refocusing the array while I was shooting. I couldn't see the antennas move from where I was at, but I noticed between shots they had changed orientation; they started out pointing in various directions and finally all ended up pointing near straight up.

Very Large Array in Socorro NM

On the way back, I noticed a sign for the visitor's center and decided to check it out -- I wasn't in a hurry, and I wasn't likely to come back again, after all. I didn't regret it. Much to my surprise, the core of the telescope complex is open to the public, and I could take really spectacular shots from right up near the antennas. Oddly the place was quiet; I didn't see a soul, except for some other tourists.

The VLA was worth seeing, though it wouldn't have been worth a trip in itself -- as long as I was in the region, going a bit out of my way to see it wasn't a waste of time. When I got back to Socorro I prowled around a bit. I was thinking it might be one of these dusty decrepit small towns, but though the population was less than 10,000 it was a modern shiny little town, with all the basic amenities like a Walmart and a row of popular chain restaurants. The centerpiece of the town appears to be the New Mexico Institute of Mining & Technology, or just "New Mexico Tech" for short. The campus is extensive, clean, and modern as well, and I understand it has a good academic reputation. However, given the mining and industrial orientation it has a certain "dirty fingernails" mindset that doesn't fit well with the usual ivory tower academia stereotype. I hear it has a lab that performs research on commercial explosive technology that is regarded as one of the best in the world.

Incidentally, the National Radio Astronomy Observatories (NRAO) organization that runs the VLA has its headquarters on campus. Also incidentally, the "adobe motif" that characterized Santa Fe is not so predominant elsewhere, though buildings do often have a Latin flavor in their design. [TO BE CONTINUED]

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[FRI 13 NOV 09] THE IMMUNE SYSTEM (2)

* THE IMMUNE SYSTEM (2): As mentioned in the last installment, the bone marrow produces stem cells that eventually grow into different types of immune cells. The stem cells actually do so in two stages, initially growing into one of two second-level precursor cells -- either a "myeloid progenitor cell" or a "lymphoid progenitor cell", both of which then grow into specific types of immune system cells.

The immune cells produced by the myeloid progenitor cell are "early responders", supporting the nonspecific innate immune response. The early responders include:

The immune cells produced by the lymphoid precursor cell include:

Each of these different immune system cells provides specific capabilities in dealing with infections; they have an elaborate set of interactions to help coordinate their actions. [TO BE CONTINUED]

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[THU 12 NOV 09] SPACE NEWS

* SPACE NEWS: Space launches for October included:

-- 01 OCT 09 / AMAZONAS 2, GMS -- An Ariane 5 ECA booster was launched from Kourou in French Guiana to put the "Amazonas 2" and "GMS" geostationary comsats into orbit. Amazonas 2 was operated by Hispasat of Spain to provide communications services for Latin America. Amazonas 2 was built by EADS Astrium and was based on the Eurostar E3000 satellite platform. It had a launch mass of 5,440 kilograms (12,000 pounds), with the payload consisting of 54 Ku-band and 10 C-band transponders. Amazonas 2 was placed in the geostationary slot at 61 degrees West longitude to provide communications services to the Americas.

GMS was a German military comsat, also known as "COMSATBW 1". It was built by Thales Alenia Space and was based on the Spacebus 3000B comsat platform. It had a launch mass of 2,450 kilograms (5,400 pounds) and carried a payload of four SHF and five UHF transponders. It was placed in the geostationary slot at 63 degrees East longitude to provide secure and reliable military communications. It was to be joined by a sister craft to provide a communications network spanning from the Americas to East Asia.

-- 08 OCT 09 / WORLDVIEW 2 -- A Delta 2 7920 booster was launched from Vandenberg Air Force Base in California to put the "Worldview 2" commercial Earth observation satellite into orbit for DigitalGlobe of Longmont, Colorado. Worldview 2 joined the DigitalGlobe "Quickbird" satellite, launched in 2001, and "Worldview 1", launched in 2007. Worldview 2 improved on its predecessors by doubling the number of imaging bands to eight. Worldview 2's imaging system provided 46 centimeter (18 inch) resolution in grayscale and 1.8 meter (72 inch) resolution in color.

Worldview 2

-- 14 OCT 09 / PROGRESS 35P (ISS) -- A Soyuz booster was launched from Baikonur in Kazakhstan to put a Progress tanker-freighter spacecraft into orbit on an International Space Station (ISS) supply mission. It docked with the ISS Pirs module on 17 October.

-- 18 OCT 09 / DMSP F18 -- An Atlas 5 booster was launched from Vandenberg AFB to put the Air Force "Defense Meteorological Satellite Program 18 (DMSP 18)" low-orbit weather satellite into space. The Atlas 5 flew in the "401" configuration, with a 4 meter (157 inch) fairing, no solid rocket boosters, and an upper stage with a single Centaur engine.

-- 18 OCT 09 / ARES 1-X SUBORBITAL TEST FLIGHT -- The new US Ares 1 booster, derived from the shuttle solid rocket boosters, was launched on a suborbital test flight.

Ares 1-X

-- 29 OCT 09 / NSS 12, THOR 6 -- An Ariane 5 ECA booster was launched from Kourou to put the "NSS 12" and "Thor 6" geostationary comsats in orbit for SES World Skies of the Netherlands and Telenor Satellite Broadcasting of Norway respectively.

NSS 12 was built by Space Systems / Loral and was based on the LS-1300 comsat platform. It had a launch mass of 5,625 kilograms (12,400 pounds) and carried a payload 48 Ku-band and 40 C-band transponders. It replaced the NSS 8 satellite, lost on launch in early 2007. NSS 12 was placed in the geostationary slot at 57 degrees East longitude to provide communications services to Europe, Africa, India, and other parts of Asia.

Thor 6 was built by Thales Alenia Space and was based on the SpaceBus 4000B2 platform. It had a launch mass of 3,050 kilograms (6,725 pounds) and carried a payload of 36 Ku-band transponders. It was placed in the geostationary slot at 1 degree West longitude to provide direct-to-home TV services to the Nordic countries.

* OTHER SPACE NEWS: The US Lunar Reconnaissance Orbiter (LRO) launched in June -- discussed here a few months back -- included a secondary "crash lander" probe named the "Lunar Crater Observation & Sensing Satellite (LCROSS)". The Centaur upper stage of the launch vehicle was directed to impact on the Moon's south pole on 9 October, with LCROSS trailing behind. The impact of the Centaur upper stage, at a velocity of about 9,000 KPH (5,600 MPH). The 900 kilogram (1,984 pound) LCROSS performed observations with a camera and spectrometers, relaying data through the LRO, before crashing itself, fifteen minutes after the first impact. There was some disappointment that the impact of the upper stage was not visible from Earth, even through the largest telescopes, but mission officials were not disappointed with the "take" from the experiment.

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[WED 11 NOV 09] INFORMATION ON DEMAND

* INFORMATION ON DEMAND: The rise of the internet has led to an explosion in the demand for information, with vast numbers of users googling at every instant to find the answers to any conceivable question. As discussed by an article in WIRED magazine ("The Answer Factory" by Daniel Roth, November 2009), an online operation named Demand Media is trying to exploit this thirst for answers.

Every day, DM produces about 4,000 videos and articles, the objective being to get to the top of Google's hit charts on as many different queries as possible. Quantity is the goal; quality is a secondary objective, with DM churning out cheap & dirty instruction videos like "Dog Whistle Training Techniques", or guides to lunch meat and nonprofit administration. DM pumps out vast numbers of bulleted lists and tutorials on the most obscure subjects.

How does DM figure out what answers people are after? By automated data mining. DM's scheme crunches through search terms, the ad market, and competing available resources to figure out what answers to produce next that will bring in the most money. The algorithm answers the question: "What answers are people most after that will bring in the most ad money, and aren't being answered by existing internet resources?"

DM is becoming a feature of the internet, with founder and CEO Richard Rosenblatt grandly projecting that the company will be publishing a million items a month, four times the current content of the English-language Wikipedia. Want to know where the cheesy tutorial videos on YouTube come from? It's a good bet it's DM, with over 170,000 videos now on the service. DM also provides materials to 45 of the company's own slick-looking websites, with names like "eHow.com" ("How To Do Just About Anything"), health site "Livestrong.com", and even the "TheDailyPuppy.com" ("Your Daily Fix For Puppy Pictures.")

Of course, DM's business model looks somewhat like spamming, but the company's name says it all: the demand for answers is there, they're plugging it. In effect, the company's vision is make a reality of the old dream of being able to ask a computer a question, ANY question, and get an answer. They may not be the best answers, but DM is careful to avoid competing with questions that will be hit first by Wikipedia or hardcore enthusiast websites. DM wouldn't try to provide a history of the Chevy Corvette sportscar, but the company might explain where to buy one and how much it would cost. Answers to mundane "how to" questions end up bringing in a lot of money, like an estimated $200 million USD in 2009.

DM's algorithm requires live bodies to translate the suggestions for answers it obtains into actual answers. DM sits on top of a pyramid of grunt workers, paying about $15 USD for short articles and $20 USD for short video clips. Farther down the pyramid are workers who copyedit, fact-check, and proof titles -- the last of which pays eight cents a title. Payouts are disbursed through PayPal. So far, DM has paid out $17 million USD; if the company actually ends up producing a million items a month, it could be paying out tens of millions a month.

Rosenblatt, who has a long history of making big money in internet startups since he got out of college in 1994, began DM with human editors to determine what answers to produce. It worked -- but once the process was automated, the revenue per item jumped by a factor of five. Experience and judgement, it turned out, couldn't compete with a conceptually simple brute-force algorithm. Of course the algorithm churned out suggestions for answers at a vastly greater rate than the editors, who found themselves out of that line of work.

DM then formed what would become an ever-stronger alliance with YouTube. Google, which owns YouTube, has had problems making money from the video service, mostly because advertisers don't want to be matched up with videos that rip off copyrights or contain abusive material. YouTube didn't have the resources to screen all the videos -- but then YouTube executives noticed the hundreds of pre-screened, ad-friendly, cheap videos Demand Media was uploading every day, and called up DM to propose cooperation. The cooperation keeps getting tighter: YouTube people noticed there was a shortage of Spanish-language videos that could support ads, rang up DM to suggest Spanish-language videos, and so DM started churning out Spanish-language materials.

Demand Media is a fascinating idea, though the company's general indifference to quality is a little off-putting. However, does the quality really matter? The internet is a big place, with people providing more materials at all levels of quality on a continuous basis. DM is working at the bottom of the food chain, providing materials that just plain wouldn't be there otherwise. Rosenblatt himself believes that better quality is the way of the future, though he's not considering any fundamental change in his business model -- just coming up with ways to do better for the same cost, with more automation and better production tools; or maybe pay out a little bit more for a little bit better: "For instance, pay an extra dollar for fact-checking."

DM has only been around for a few years, so it is at an early stage in its evolution. Whether it ultimately proves a benefit to the internet, or ends up being just another variation on spam, remains to be seen.

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[TUE 10 NOV 09] CHARCOAL VERSUS GLOBAL WARMING

* CHARCOAL VERSUS GLOBAL WARMING: The idea of developing "scrubbing" systems to remove carbon dioxide from the atmosphere in hopes of heading off global warming was discussed here a few months back. Now, according to an article in THE ECONOMIST ("A New Growth Industry", 27 August 2009), a faction is advocating a remarkably low-tech way of sequestering atmospheric carbon dioxide: grow biomass, convert it into charcoal or "biochar", and then bury it.

The roots of the idea go back about a century, when an explorer named Herbert Smith noticed some unusually fertile patches of ground in the Amazon rainforest. Most of the forest's soil isn't very good, but the "terra preta (black earth)" was of high quality. The soil was found at the sites of ancient settlements, where the locals seemed to have acquired the habit of mixing the remains of burned plants into the ground. Some modern farmers -- most significantly a Dutch soil researcher named Wim Sombroek, who died in 2003 -- have tried the same trick, with impressive results. Savannah in Colombia carpeted with biochar made from corn stover (plant waste) will grow bumper crops, and researchers from the University of Georgia in the USA have found that burned chicken droppings provide similar benefits. Researchers from the US Department of Agriculture (USDA) have demonstrated that biochar helps soils retain vital nutrients, such as nitrate, phosphate, and potassium.

That's all very interesting to agriculturalists, but it's the prospect of using biochar to sequester carbon dioxide that has attracted wider notice. Sombroek suggested the idea in 1992, but it wasn't taken very seriously until recently. Plants of course soak up carbon dioxide as they grow, to release it again when they rot or are consumed. Charred plant matter, however, doesn't rot quickly or at all, because organisms have problems trying to metabolize pure carbon. Some of the deposits of terra preta are thousands of years old. The charcoal also seems to soak up methane and nitrous oxides, potent greenhouse gases naturally released by soils. Another benefit is that making the charcoal can provide heat as well as "synthesis gas", laden with carbon monoxide, that can be chemically transformed into synthetic fuels.

A recent study performed in the USA used a computer model to show that biochar might be able to sequester ten to twenty percent of carbon emissions per year. However, the researchers involved admitted the model was based on a large number of unproven assumptions. Critics of the biochar idea also suggest that it might not make sense to deliberately grow plants like switchgrass just to convert into biochar, since the tillage would release greenhouse gases, and the exercise would also encourage more conversion of land to grow crops displaced by switchgrass. The critics do concede that turning normal plant wastes like corn stover or lawn clippings into biochar seems to make good sense.

Producing the charcoal in quantity doesn't look like it will be a problem, the pyrolyzing stoves being easy to make, and available in sizes ranging from portable units to industrial systems; continuous-process stoves appear to be perfectly practical. The agricultural benefits of burying biochar should be attractive to farmers. If not, carbon offsets may help sell the concept, though that would demand some regulation and oversight.

Farmers in poor countries could obtain the same benefits, and would get a bonus because the pyrolyzing stoves burn much more cleanly and safely than primitive stoves and hearths now in widespread use. Current burning of wood, waste, and dung in villages generates soot, which is unhealthy to breathe, and which also enhances global warming since it soaks up solar heat; pyrolyzing stoves, in contrast, generate almost no soot, since the carbon remains locked up in the charcoal. Work is underway to developing simple, cheap pyrolyzing stoves for poor countries. Nobody thinks that biochar by itself can solve the global warming problem, but it could do its part, and on paper the range of potential benefits makes it an option definitely worth taking seriously.

ED: The WIRED Magazine Online blogs add that the Indian Ocean island nation of the Maldives is planning to use coconut biochar as part of a scheme to achieve carbon neutrality by 2020. The biochar project was put together with the help of a UK-based firm named Carbon Gold. Kilns will be distributed to villages in the islands, with the villagers using the kilns to dispose of waste and obtain fertilizer for their fields -- the soil is so poor that manure has to be imported from India at considerable expense, so the effort may be a paying proposition on the face of it.

Along roughly similar lines, the DISCOVER Magazine Online blogs discussed a scheme being floated by the UK Institute of Mechanical Engineers (IME) in which tubes filled with algae would be attached to high-rise buildings, with the algae used as biochar. It's an interesting idea but it's strictly a concept for the moment, with the IME admitting that such "bioreactors" are expensive. I'd have to add that growing algae sounds like a process highly prone to fouling.

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[MON 09 NOV 09] SOUTHWEST ROAD TRIP (2)

* SOUTHWEST ROAD TRIP (2): On the morning of Thursday, 8 October, I left the motel in Santa Fe to head down to Albuquerque. I dropped by the local municipal airport first in hopes of finding some interesting aircraft to shoot. That's always a hit or miss proposition, but this time it was a hit -- the Santa Fe municipal airport was small, but a number of "warbird" owners kept their aircraft there, the most significant being a red-painted Hawker Hunter jet trainer. I managed to get some adequate if not particularly special shots of it, holding up my camera over my head with the viewfinder tilted down to shoot over the wire fence while balancing uncertainly on a pile of stones. I also got shots of a Eurocopter Ecureuil helicopter in medical service colors.

Albuquerque is only about a hour down the road and I was a bit apprehensive about getting stuck in gridlock -- it's a fairly large city, well big enough for traffic jams. However, when I was approaching the north of the city I noticed a dot in the sky ... then two (helicopters in formation?) ... then three, four, five, six -- I stopped counting. Balloons. I knew Albuquerque had a "balloon fiesta" but I wasn't expected to be around when the balloons were flying. It was pure luck that I was there at the right time.

There were about fifty of them in the sky. I saw a portable sign lit up with BALLOON FIESTA NEXT EXIT and took it, quickly finding a gas station where I could park and get some shots. I ended up chatting with another shutterbug, from New Jersey, who had been there for the previous days of the balloon fiesta. He said the initial launch was of 500 balloons -- the fifty or so I saw in the sky were spectacular enough, 500 would be unbelievable.

balloons over Albuquerque

That worked out well since I got good shots and also avoided the crush of rush-hour traffic -- it was still a bit congested going downtown but the traffic never came to a halt. My objective was the zoo / biopark and my navigation was okay; I don't expect to get from place to place in a strange city by an efficient route, as long as I get there I'm happy, and my zigzag navigation in the proper general direction did get me there -- if in the back of the zoo grounds. No problem, it was just a turn around the corner to the parking lot.

* The Albuquerque zoo is a nice, extensive modern zoo with natural enclosures for the animals. I didn't really see much that was unfamiliar, however, the most interesting exhibit being African hunting dogs, playing among each other as dogs like to do. I also finally got a workable if not great shot of a koala, something I'd been after for a while.

Another interesting item was a zoo worker with an African porcupine on a leash. It was obviously a smell-oriented creature, sniffing at everything; I held out my fist like I would to a dog, it sniffed at it, sniffed at my clothes, moved on. I got to thinking how inconceivable it would be to put an American porcupine on a similar display. African and American porcupines are not closely related except for being rodents, and the African porcupine is not as nasty a customer, since its quills don't come out easily. I have heard of people keeping American porcupines around more or less as pets, but they require careful handling -- since if they get annoyed, they're liable to use their tail to slap a handful of quills into the annoyance that require pliers to get out. The quills have a "grain" and they demand muscle to remove.

Still another interesting item was the vulture enclosure, which had a tunnel covered with cyclone fencing. I looked up while I was walking through it to see them lying on top, looking back down at me. I got a wild idea, stood up on the pedestal of a support post, and shoved my pocket camera objective through the wire to get a point-blank shot of one of the vultures. It took me a while and the vulture kept trying to bite me, but much to my surprise I got a shot that worked.

gray vulture

The rest was generally nothing new. I tried to use my little old Coolpix camera to shoot a baby howler monkey through wiring of its enclosure, but it didn't work -- the Coolpix's lens is so small that it will rarely take clear shots without direct sunlight. I was impressed with the zoo's playground for kids, however, the play complex being very elaborate and obviously a lot of fun for the kids. [TO BE CONTINUED]

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[FRI 06 NOV 09] THE IMMUNE SYSTEM (1)

* THE IMMUNE SYSTEM (1): Having become curious about the human immune system, I started hunting around for materials on the subject. Immunology is bewilderingly complicated and it's hard to find writeups that make sense, but Lauren Sompayrac's book HOW THE IMMUNE SYSTEM WORKS provided a reasonable explanation. This series outlines the book.

* We live in an environment loaded with a wide range of microorganisms, many of which are malign pathogens -- including viruses; bacteria; and a remaining grab-bag of unpleasant organisms such as protozoans and 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. We have acquired defenses to protect ourselves. The first line of our body's defenses consists of external barriers that can block entry of intruders:

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 defensive complex of organs, cells, and molecules that protects us from invaders, blocking their entry and targeting them for destruction if they do get in. Humans have an "innate" immune system that is "hardwired" to recognize broad classes of pathogens, backed up by a subordinate "adaptive" immune system that can "learn" to target unfamiliar pathogens.

* 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. 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 also very often identifies transplanted organ as nonself -- their MHC proteins don't "look right" -- and attacks or "rejects" them. Occasionally the immune system will "go off the rails" and attack "self", resulting in "autoimmune disorders" such as multiple sclerosis, where the body attacks nerve cells; or lupus erythymatosis, where the body performs a broad attack on connective tissues.

Any foreign material that the immune system targets as "nonself" is referred to as an "antigen". The distinctive markers on antigens that trigger an immune response are called "epitopes".

* The immune system organs, cells, and molecules form an elaborate interacting hierarchy. The organs of the immune system are 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:

Other lymphoid organs include the "thymus" and the "spleen". The thymus a gland under the breastbone; it is where stem cells mature into the class of lymphocytes 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, which are 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; lymphocytes 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]

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[THU 05 NOV 09] GIMMICKS & GADGETS

* GIMMICKS & GADGETS: The idea of using camera phones to scan barcodes is not completely new -- an article here in 2005 discussed such usage 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 Scanbuy 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.

QR code writ large

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 barcode readout. Exactly which of these schemes will end up being a standard is anyone's guess.

* 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 after being deformed -- at least until the deformation reaches the "elastic limit" and 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.

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[WED 04 NOV 09] SEABASES

* 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 use of oceanic military bases, made up of modules that could be plugged together like Lego blocks. Such "seabases" could be moved to the waters near an operational theatre, assembled and modified as desired, and then sent home when the war is over. Seabases are of course a technological challenge, requiring:

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 along with 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 severe 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 self-deploying 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; the 14 future vessels in that 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 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.

seabase elements

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, thanks to the platform's cranes and bridges. The MLP 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 (35 MPH / 40 KT).

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. That has always been an issue with overseas force projection, and it's 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 needed 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 relocate 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's 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 base, with future developments in small drones only enhancing its effectiveness in that role. The ESG would of course include escorts with their complement of missiles and drones. 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 was 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 (LSD)" 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.

LPD-17 San Antonio

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 heat-seeking air-to-air missile for ship air defense -- one important feature added to the missile being a secondary seeker to target 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.

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[TUE 03 NOV 09] BIOHACKING

* 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 in 2006.

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; it has now grown to include 84 teams and 1,200 participants, who generally come out of 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 laws over the matter -- 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 unable 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, pointing out that even if all the accusations were true, no crimes had been committed. No appeal was made against the 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.

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[MON 02 NOV 09] ANOTHER MONTH

* 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 perverse 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 can be strongly 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 that can burn up time and energy while driving frustration through the roof. I recall running into somebody online who described arguing with cranks as a hobby, "sort of like trainspotting, but more like spotting train wrecks."

Now I only give YouTube a quick scan every now and then, 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.

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