Wednesday, June 30, 2010

They point every which way

kw: musings, physics, electrons

This is my 1,000th post! Recent reading about the behavior of electrons in atoms reminded me of work I did many years ago (as well as triggering my prior post). My first paying job (besides newspaperboy) was in spectroscopy. Though I worked primarily in infrared spectroscopy of molecular species, I did some visible and UV work, and got to know that field a little. Years before I took the relevant physics courses, I became familiar with the S P D F designations for the various series of atomic spectral lines.

It is amazing what early spectroscopy workers were able to discern about electron orbitals from the lines they examined on photographic film. SPDF is the earliest indication of substructure in the electron "orbits". These four letters refer to the terms "sharp", "principle", "diffuse", and "fundamental", as explained by Grant R. Fowles in Introduction to Modern Optics (1989):
The sharp and diffuse series are so named because of the appearance of the spectral lines.

The principal series is the most intense in emission...

...the frequecies [ratios] of the lines of this [fundamental] series are very nearly the same as those of the corresponding series in hydrogen. This is the reason for the name "fundamental."
[The bracketed words are mine.]

This image, from the article "Light and the Modern Atom" at Chemistry Land, shows the original designations of four series of spectral lines as seen in the absorption spectrum of sodium at high resolution. The two dark bands in the warmish yellow portion of the spectrum, one of which is designated as an example of a Diffuse line, are the diagnostic sodium D lines near 589 nm wavelength.

What is really happening here? The four spectroscopic series have a relationship to the quantized energy levels surrounding the nucleus, which allow electrons to have certain electrical and angular energies, but not others. There are shells and subshells in which electrons can reside, both in spectroscopic terms and as more and more electrons are gathered by heavier and heavier nuclei. However, the spectroscopic energy levels do not correspond exactly to electron subshell orbitals, so more modern nomenclature relies on quantum numbers. Shells are numbered n=1,2,3… and subshells as l=0,1,2… and there are other quantum numbers. Detailed quantum designations are a side issue to the point of this post, so please refer to the Wikipedia article Electron Configuration for a thorough discussion.

Now that we can use computers to calculate the probabilities of electron locations quickly, and to visualize them, I find the images we can create show most compellingly what the spectra are telling us. For example, the S series is sharp because the subshell that generates it is the simplest. It has spherical symmetry in all cases, and can be occupied by either one or two electrons, no more. The D series is more diffuse (and indeed, P and F lines are also broader than S lines) because the shell has a substructure, in which pairs of electrons occupy a shape that is distinguished not only by distance from the nucleus, but angle also. A few images will illustrate.

These images of S orbitals (quantum number l=0; that is an "ell") for the L, M, and N shells (n=2,3,4) show the spheres cut in half so you can see the inner shells of alternating phase that nestle inside. The boundary of the colored area is not a hard edge. It represents the 3-D contour of 90% probability that the electron is "located" within it. For any S subshell, there is both an inner sphere and an outer sphere that together define the 90% probability region. However, any electron can actually be anywhere in space with some probability, but that statistic is very close to zero for much larger distances or for locations much closer to the nucleus.

A characteristic of the other subshells that allures me is that a filled subshell has spherical symmetry. A particular orbital within such a subshell is, however, very far from spherically symmetric.

This illustration of the orbital shapes for the P subshell (l=1) shows the shapes of the 90% probability regions of these orbitals for L, M, and N shells. There are no P orbitals for the K shell (n=1). If we call this set of three orbitals a, b and c, then when we work through the periodic table and the P subshell is being filled, one electron goes into each of a, b and c, before a second electron is added to any of the three.

I recall my awe when a physics instructor went through the math to demonstrate that the actual probabilities for the filled P shell of neon actually added up to a purely spherically symmetric entity, with none of the bumps we might expect from seeing the component orbitals. He wryly pointed out that while "it may be shown" that any filled subshell is the same, he personally didn't know anybody who could actually work the math to perform the demonstration.

The orbitals of a D subshell, for M, N and O shells (n = 3,4,5) are more complex, with more lobes. The plethora of ways a D subshell could relate to the ground state of an atom explains the diffuse nature of the spectral lines. The broad D lines of sodium, under very high resolution study, are seen to consist of a veritable forest of lines. The energy splitting that underlies this line broadening is due to quantum effects caused by the other electrons in an atom with D subshells.

Finally, the F orbitals, here just shown for an N shell (n = 4), are dauntingly complex. So, why are the F lines in the spectrum above not even more diffuse than the D lines? It is mainly because the physical size of the F orbital greatly reduces the quantum effects of the other electrons, so that though the F lines have very complex structure, it all fits into a narrower spectral band. This also leads to a simple relationship between the wavelengths (or energies) of a series of F lines, that led to their being called "fundamental", as mentioned in the quote above. By the way, after F, the rather faint spectroscopic series just continue through the alphabet (G, H, etc.) but I've never seen any attempt to illustrate orbital shapes.

I wonder if anyone living can really add up the seven sets of probabilities analytically, to demonstrate that a filled F subshell has spherical symmetry, without any lumps? I know that computer solutions of the appropriate Schrödinger wave equation can be performed numerically, but that is almost cheating.

An atom of platinum (Z=78), with four completely filled shells and the first three subshells of shell 5 filled, is like a Matrushka doll: thirteen concentric spherical regions of high probability for locating any of the 78 electrons. This very high symmetry results in platinum having a less complex spectrum than elements 77 (iridium) or 79 (gold), though all of them have more complex spectra than much less massive elements such as iron.

Superconductors everywhere

kw: observations, physics

I read in an article an analogy to explain the orbital restrictions of electrons in atoms. The electron's "orbit" was compared to an organ pipe, which makes a particular tone because of a standing wave within it. Just as a standing wave doesn't "go anywhere", the electron forms a standing wave and doesn't go anywhere. Thus, it does not experience acceleration. This is important because a charged particle that experiences acceleration must emit radiation. Our entire electrical economy is built on this principle!

The electron, then, does not orbit the nucleus, strictly speaking, but forms a standing wave and remains stable. However, the source of the analogy, the organ pipe, is not stable. One must supply energy because the tone it emits removes energy from the system. There is, however, a standing wave system, which can be the size of an organ pipe, that does not emit any energy and is stable. That is a superconducting magnet. One uses conventional leads to feed current into a superconducting magnet to build up its magnetic field, then adds a superconducting link to short across the leads' terminals and switches out the leads. This system is stable, emits no radiation, and maintains the magnetic field until a resisting link is introduced to absorb the energy. Both charging and discharging a superconducting magnet must be done carefully, because some of them store the energy of a few sticks of dynamite.

Compare with a hydrogen atom. Its single electron is a stable standing wave that emits no radiation and maintains a magnetic field. A lone atom of hydrogen is a tiny magnet (but hydrogen normally exists in H2 molecules that pair up like two magnets stuck together, leaving no residual field). In this atomic magnet, the electron is effectively a superconductor! Superconductivity is a quantum property of electrons in their stable orbitals. It is fundamentally different from Cooper pair-induced superconductivity.

If this kind of quantum superconductivity could be expanded to large scales, room-temperature (and above) superconducting devices could become a reality. Ferromagnetism is one expression of intrinsic electron magnetic orientation, but is inefficient, because the electron that produces the magnetic field needs at least 25 "friends" to support the magnetic asymmetry required.

Monday, June 28, 2010

Good enough for me

kw: opinion, technology

Just about a year ago, in an article for Wired, Robert Capps discussed "the good enuf rvlutn", and why cheap was beating out superior on many fronts. This is nothing new; it has always been the case. Not only does the Flip outsell Sony camcorders that will record movies in HD, and the Kindle outsell some E-book readers with glitzier features:
  • Chevy outsells Cadillac, Ford outsells Mercury and Lincoln, and Camry outsells Lexus, in spite of the fact that each pair is produced by the same manufacturer.
  • Lower- and mid-level point-and-shoot digital cameras will always outsell more advanced models, and in fact many people with 5+Mpx cameras in their cell phones have "better" cameras sitting at home collecting dust.
  • Beer outsells wine.
In each case, the product that provides something a customer wants, and which passes a foggily defined "good as it needs to be" threshold, will succeed wildly, compared to "the best there is." It explains why the VW Bug (the old one) was the best-selling car to young Baby Boomers in the 1960s and early '70s: it got you from point A to point B and left you money in your wallet for something besides transportation.

It is said that MP3 files sound terrible compared to a CD. I guess I don't have a very good ear (in spite of the fact that I have been a professional musician): I can't tell the difference once the quality level reaches 128 whatever-it-is (Kbps?). So I have a ton of old (1930s and earlier) songs on MP3 to satisfy my Western Swing appetite, and a smaller amount of newer stuff in the Country/Family genre.

All this does not totally take account of the appeal of mid-level stuff, however. A significant factor is focus. I once belonged to a very active lapidary club. Most of the members were retirees, and their passion was spending frequent weekends in the Mojave Desert, collecting large amounts of "agates" (lotsa rocks get called that which are only agates in the loosest sense), and cutting-n-grinding cabochons or faceted stones to show off to each other, or at regional shows. Many of these folks had two expensive things: A motor home or camper truck, and a gem cutting workstation. At a time when I could barely afford a $2 lunch more than every other week, I spent $100 on a Diamond Demon (this is forty years ago). Many of them had spent $500 and more. But none of us had a really good camera, coffee maker, or pair of hiking boots. Oh, yeah; we did all have quite good rock hammers and chisels!

Most people don't really care to have the best possible example of everything. They want things that meet their needs and desires, affordably, and only splurge on a very few things. There will always be a market for products that support the focus of people with a dedicated passion, but the market for everyone else, for "good enough" products, will always be larger by far.

Sunday, June 27, 2010

Go jump off a building for fun and profit

kw: opinion, entertainment

There are very few TV shows that I watch with any regularity. One I took a liking for in its first season was Wipeout on ABC. Its new season has just begun, and it is being followed by another "win a million" sort of show, titled Downfall.

I've only seen the trailers, which indicate that you start with a lot of cool stuff on a conveyor belt at the edge of a skyscraper, and you have to answer trivia questions. Wrong answer? Something is shot off the roof to crash below. Too many wrong answers? You are also shot off (wearing a harness so you can scream all you want, but don't hit bottom).

I decline to watch Downfall. The premise is terminally silly. Now, Wipeout I like!

Half a review for half a book

kw: book reviews, fantasy, thrillers, religion

A family friend who knows I've read The Da Vinci Code said I should read Map of Bones by James Rollins. Well, I tried, I really did, but about halfway through I jumped to the last twenty or so pages to read the denouement, and to be done with it. Too much bloodshed, much too improbable in its hairbreadth escapes, and too sadistic.

It is in the genre made popular by The Da Vinci Code: an ancient conspiracy with roots buried deep in the Vatican, makes a discovery that threatens the world order, and tries to consolidate their power using it; an elite force of spies and "special operatives" defeats them in a thrilling climax.

In this case, the action centers on bones purported to belong to the Magi, the visitors "from the East" who brought gifts to the baby Jesus, and on themes in Christian and pseudo-Christian pagan art (such as labyrinths) which provide clues to an ageless crypt that magically protects its secrets. Nowhere is it explained how the ancients (including Moses) converted gold into an inert white powder (an "m-state metal"; a hoax so far as I can determine) or how they produced the lasers and room-temperature superconducting materials that protect their secrets. By the way, large amounts of m-state metals such as iridium are stated to reside in our brains. Not so.

Along the way, a harmless club of aging aristocrats gets slandered as the origin of some really gruesome monsters (human variety, such as Vlad Tepes, the original Dracula). Surprisingly, this novel has a more sympathetic view of Roman Catholicism than is common among the Da Vinci spinoffs. And, in a common sort of ploy, a few random Bible references are used to blow out of all proportion the historical excesses of some who followed the apostle Thomas and mixed his teachings with gnosticism. Much mischief has been done through the ages by taking verses that seem hard to reconcile and supposing a duality, where God's intention has always been inclusiveness.

Our friend certainly dotes on thrillers. Me? Not so much.

Friday, June 25, 2010

To know the unknowable

kw: book reviews, nonfiction, science, cosmology, philosophy

When I was a geology student in the late 1960s, the environmental movement was gaining traction, and the word "biodegradable" became fashionable. My classmates and I had just learned of the tectonic cycle, the understanding that on a scale of between 50 million and 200 million years, mountains rise, they are eroded to near sea level, all the sediments eventually wind up being subducted by trenches into the upper mantle, and new mountains arise. Somebody said, in a bull session, that there is a lot of waste "out there" that is not biodegradable. Someone else said, "Well, it is mostly geodegradable," to which I added, "and everything else is theodegradable."

Endings get better press than beginnings. A very popular country song of a few years ago crooned, "Let's go out in a blaze of glory," and quoted the proverb, "All good things must end." Just ask Chris Impey. In his book how it ends: from you to the universe (capitalization of the book's cover) he tells us not just that everything ends, but how it does so. Yet in the best tradition of the philosophy of science, you have to know what you have before you can predict where it is going, so much of the book is devoted to exploring what exists. It is a very good survey of the breadth of science as it relates to existence of people, species, planets, stars, galaxies, and universes. The doleful matter of how each might come to an end is nearly swallowed up in the discussions of how they are.

Let's begin with the biggest ending of all: the Universe. Can it end? Not too surprisingly, the jury is still out on that one. Hubble's discovery 80+ years ago that the universe is expanding led to much work (and speculation) about whether the expansion was being brought to a halt by gravity. Visible matter (stars and gas clouds) constitutes only a few percent of the mass needed to halt the expansion at any time. But star movements in galaxies and other lines of evidence indicate that a kind of matter we cannot detect except by its gravity, usually called dark matter, outweighs visible matter by a factor of six or seven. But that still falls short of the mass needed to "close" the universe. That would seem to answer the question negatively: the Universe cannot end; it will expand forever.

But wait, there's more. Just under twenty years ago, accelerated expansion was proffered to explain the unexpected dimness of distant supernovae. This would seem to emphasize the point, but some versions of "cosmic acceleration" postulate a singularity, perhaps one or two billion years from now, when the acceleration rate will rise infinitely (better stated as "without limit"), leading to a "Big Rip", after which spacetime cannot exist, at least not in any form that we can calculate (after all, the theory itself is simply a calculation). Dr. Impey follows his discussion of the big rip with a reference to data that it probably can't be so. Whew! So maybe something can be genuinely eternal after all.

Not so fast. Let us suppose that there is no cosmic acceleration, or that it stays within bounds, so that spacetime expands at some calculable rate, and just keeps doing so. In a few billion years, not much happens, but in a trillion years or so the galaxies have run out of non-star matter (gas and dust) to make new stars, and the oldest stars existing are running out of their own fuel. The lights go out and the universe cools, forever, toward absolute zero. Yet matter itself may also evaporate. In a trillion trillion trillion years (36 zeroes), half of existing matter will have turned into neutrinos and photons; add a few more zeroes and it is effectively all gone. Double the number of zeroes and most black holes will have evaporated via Hawking radiation. Do you dare to double the number of zeroes again? Spacetime may still be expanding, but there is no matter around to impede the passage of photons, most of which have wavelengths measured in billions or trillions of light years. Not too exciting. So photons are apparently eternal. Big whoop!

Well, with that for a backdrop, we can consider items with briefer existences, and more interesting ones. Stars, for example. The biggest stars that can exist burn off their nuclear fuel in a million years or less, briefly forge elements ranging to iron, then blow everything into space as a supernova. That allows planets to form that are made of something other than H+He. The smallest stars that can burn nuclear fuel might last a trillion years, but eventually just fade away as dimming cinders. In between, the Sun and similar stars can cook along for a number of billions of years, then they puff up into red giants and puff away a third of their mass into a planetary nebula before subsiding into white dwarfs, which slowly fade to black (in a few dozen billion years). But in midlife they provide a haven for planets that might harbor life for a while, say one to ten billion years.

But what of life? Earth has been a living planet for about four billion years. The Sun will probably cook all life off the Earth long before becoming a red giant. Theories differ: it may take as little as another half a billion years, or as many as 2-3 billion. Will humanity survive to that point? Here things get interesting. Will our technology allow us to overcome evolution, which so far seems to produce mammal species that last no longer than ten or twenty million years, and tend to average about two million years before going extinct or mutating beyond recognition, becoming a different species? Is there a "technological singularity," as Ray Kurzweil projects, that will make humanity into something different (and possibly part or all machine) within the lifetime of people a little younger than I am? Will these post-human creatures be longer-lived than we?

How long can a human live? Shigechiyo Izumi and Jeanne Calment are the only humans in the modern era who are thought to have lived more than 120 years. Darn few of us live more than 90 years. A few species of bird, turtle, and whale seem to have produced individuals that have lived 150 years or more, but the complex organ systems needed to keep a metazoan animal living are apparently not able to fend off irreparable damage more than 100-200 years.

There are two indicators of general senescence that, if you want to pay for a test or two, will probably simply cause depression. One is the Hayflick limit. Fetal cells in culture divide 40-60 times, then stop, enter senescence, and eventually all die. That 40-60 range is not quite absolute, but covers nearly all of us. Statistical analyses indicate that if nothing else gets you, you'll just wear out at some age between 60 and 120 years. The other test is to get an electron microscopic look at your mitochondria. Mitochondria look like crisp little sausages about two microns long, with baffles inside. They start looking rather ragged in your forties, and get positively snaggly with the passing decades. They are your energy system, and when they fall apart, so does everything else.

The amazing thing is, that we are continually driven to learn such things: the inner workings of mitochondria, the survival of species, the evolution of stellar interiors, and the structures of galaxies and universes. Even the least technical among us are interested in how things work, and indeed, many members of the local Astronomy club are not science majors. Same with the local Lapidary society. Humans are curious, and the best stimulation is to learn things. I read that Robert Feynman said on his deathbed, "I'd hate to die again. It is so boring." We are driven, and that makes us what we are.

Thursday, June 24, 2010

Coal burning cars

kw: opinion, technology, environmentalism

In the July 2010 issue of Scientific American, Michael Moyer has written an article that speaks directly to a concern I have long had about electric cars: Where does the electricity come from? The article, on pages 55-56, is titled "The Dirty Truth about Plug-in Hybrids".

To cut to the chase, the amount of benefit, or lack thereof, simply depends on where you live. A plug-in hybrid vehicle is expected to use about half the gasoline used by a first-generation hybrid such as the Toyota Prius or a Honda Civic Hybrid. An all-electric car, of course, burns no gasoline at all. Thus, in most parts of the U.S., an all-electric uses no gasoline, but not all. In New York state, in particular, where 2/3 of the electricity is generated by burning petroleum products similar to gasoline, you may as well be driving a gasoline-burning car.

In most of the rest of the highly-populated, industrial Northeast and in the deep South and upper Midwest, while little or no electricity is generated using petroleum, from half to 75% is generated using coal, making an electric vehicle that plugs in a worse producer of carbon dioxide than a pure hybrid vehicle.

The areas where an electric, whether all-electric or plug-in hybrid, will have a benefit in both reducing carbon dioxide and greatly reducing petroleum consumption are those areas that use no petroleum or coal to generate electricity: the Pacific Northwest, California, Texas, and Florida. In the lower Midwest and desert Southwest and New England, though a little coal is used, little enough is burned that an electric car is also a benefit there.

Now consider population. The coal-burning areas are mostly high-population areas, and the natural gas-burning (and nuclear-powered) areas are mostly areas of lower population density. The only highly-populated area in which an electric car is a distinct benefit is California.

If you are considering getting a greener car, find out where your electricity comes from. If you are in a coal-burning area, a pure hybrid is probably the best. Otherwise, a "more electric" vehicle just may be the right thing to get.

Wednesday, June 23, 2010

Planets, planets everywhere

kw: speculation, planets

I read an article in which the author used a chart like this one to argue that many small extrasolar planets are yet to be found. While the conclusion is right, some of the reasoning is flawed.
This chart shows a frequency diagram of the 432 exoplanets so far catalogued, plotted by their line-of-sight masses (mass times the sine of inclination). The "1" bin includes all those with a mass of one Jupiter or less. The strong inflection in the shape of the distribution is said to indicate that the smaller masses are underrepresented. And they are, as we will see.

The appropriate analysis of wide-ranging data is not linear but either logarithmic (power law) or lognormal. The same data, collected into bins with a range of 2:1 in mass, show a more useful picture:
Here, "1" is again "one Jupiter", but the mass range is 0.71-1.41 rather than 0-1. The parenthesis points out that one Earth mass is 0.0031 Jupiter mass; one Mj is 318 Me. Here the sharp inflection to the left of 0.5 Mj also indicates that the mass distribution is artificially cut off at low masses. But now we have the ammunition needed to estimate just how much.

The only stellar system for which we have a reasonably complete catalog of planetary masses is our own. This chart of the distribution of planetary masses is based, not on Mj but on Me, the mass of Earth. Looking closely, we see four pairs:
  • Mercury and Mars have very small masses, 0.055 and 0.11 Me.
  • Venus and Earth are the second pair: 0.815 and 1 (of course).
  • Uranus and Neptune are next, at 14.5 and 17.1 Me, respectively.
  • Saturn and Jupiter are the heaviest: 95 and 318 Me.
These fit a lognormal distribution with a logmean (base 10) of 0.57 and a logSD of 1.36. The confidence interval about both these parameters is rather large, but I'll use them to produce a fit from which we might learn something useful.

Here a Lognormal distribution with our system's parameters and the exoplanet data are cast in the same coordinates, re-figured so that unit mass is one Earth. The lightest exoplanet on this list (which includes only those found by astrometric means, rather than eclipses) is just under 2 Me. Making the quite unfounded assumption that the larger exoplanets are fairly sampled, I fitted a distribution with the logmean and logSD of the Solar System. This chart tells us that if our own Solar System is at all representative, a complete census of the stars already searched would yield about 4,000 planets, with a statistical peak near 4 Me (3.7).

Is this reasonable? For it to be anywhere close to true, we must also assume that the preponderance of "hot Jupiters" so far found is also due to selection bias, because they are so much easier to find than any other kind. I sure look forward to the first data from the Terrestrial Planet Finder mission (canceled last week by the President, but sure to be reinstated by a future administration).

Tuesday, June 22, 2010

Old but not obsolete

kw: history, education

Several news items recently discussed the case of thirteen Marines in leadership training who were caught cheating and discharged from the Marines. They had used the prior year's answers to the rally point identifiers in a navigation exercise. While their poor ethics are sufficient to make them unsuitable military leaders, they were also stupid. Any wise instructor will change the test answers from year to year or session to session.

I was intrigued by a point someone made, that they thought the exercise was futile because of modern navigation aids such as GPS. They considered the compass-and-pace methods they were learning were obsolete. Let me simply ask: suppose a low-yield nuclear device is detonated anywhere within a few hundred miles of your position? Do you know the result? Your GPS device will burn out; it is, after all, a very sensitive radio receiver, and the giant electromagnetic pulse from the blast will run right down the antenna and fry the innards. A side note to civilians: three properly placed one-megaton blasts, set off at an altitude of 80+ km, will destroy nearly all the electronics of any kind in the entire United States (lower 48).

So what technological device will still work after a nuclear battlefield attack? A compass (but give it an hour or so for the electromagnetic disturbances to die away). Then those "obsolete" skills learned in leadership training will be your lifeline. And by the way, don't talk to me about "militarily hardened" GPS units. There ain't enough hardening available in a 100-gram package to protect the transistors connected to the antenna. Besides, the attack itself just might blow out some of the satellites that GPS depends on; how hardened are they? Hmmm?

A couple dozen years ago as I was finishing graduate school, my major professor learned that I am an amateur radio operator, and he told this story: He had, two years earlier, been on the Glomar Challenger, the deep-sea drilling ship used for geophysical research. One day, when their "shopping list" was due to be sent to the next port, there was a solar flare. Radio communications on most bands were wiped out, and it was expected that radio disturbances would last a few days.

It so happens that Morse Code communications are about 100 times as "penetrating" as voice communications, and perhaps ten times as penetrating as radioteletype (RTTY), the usual backup. The ship's radio operator could not get through either with voice or RTTY, so he transmitted the information using Morse Code with a hand key, at 20 words per minute or so.

There is nothing like having an "obsolete" skill at your fingertips when the "modern" ones cannot be used.

Monday, June 21, 2010

Physicians, heal thyselves

kw: book reviews, nonfiction, medicine, polemics

The first general rule for finding a doctor or lawyer is to pick one who is between 35 and 60 years old. Professionals who are 35 or older have probably already made their worst mistakes, but by the age of 60, many have lost their "fire" and are more likely to be marking time until they can afford to retire (by their own lights).

The second rule is to find a doctor in a social situation and ask, "If you had [whatever], which doctor would you want to treat you?" or "If your child had [whatever], which pediatrician would you choose?" About ten years ago, with very fortuitous timing, a local group published a guide to physicians, which included, for a number of specialties, "Which doctor I would go to". The oncologist suggested by my surgeon is locally considered the best, so this helped me make the decision to have him treat me, rather than going to Fox Chase, a greater distance away. No complaints; I like him a lot, as a physician, not just as a friend.

But getting to the point where he could treat me was another matter. As I have mentioned in the past, I had to be my own doctor to get the cancer treatment I needed. My family physician at the time was not very proactive, and was taking a very slow, measured approach to finding out why I had abdominal pain. One day, after an inconclusive consultation, I asked his office scheduling clerk, "If the Doctor were to send me to a gastroenterologist, whom would he choose?" She told me, and I made my own appointment, then called that clerk to process a referral to him. It saved my life. The GE said I was days from death when he diagnosed my cancer, so I told (not asked) my doctor to get me a surgeon pronto, and went to the emergency room. They put me in the hospice! But they also gave me six days of IV feeding in two days to strengthen me for surgery. On a ward in which every program board had the notice "Comfort", mine read, "Comfort and Feed 3x". Now my GE, whom I still see for periodic colonoscopies, calls me a Trophy.

So my current doctor just turned 60. He is much more proactive, and wants me to get blood pressure medication. I'm amenable, but I decided to try a folk remedy first, and allowed our son to bring home a kitten. Three days after the kitten arrived, I checked my blood pressure. The long-term average for the past few months had been 148/90. The average of the past three measurements (post-kitten) is 132/80. While it doesn't bring me into the 120/75 range my doctor would prefer, it may mean I can use one of the less aggressive medications, with, of course, fewer side effects.

The cancer tale is one of four in which my wife and I have had to intervene in the medical process to get appropriate care. That makes Dr. Richard S. Klein a man after my own heart. It is just the kind of advice he offers in Surviving Your Doctors: Why the Medical System is Dangerous to Your Health and How to Get Through it Alive. The root of his concern is this: At least 100,000 people die every year in the U.S. from medical mistakes. Dr. Klein says this rampant malpractice constitutes a pandemic that is, numerically, equivalent to a jumbo jet crashing nearly every day. A web-based service called HealthGrades contains the claim that the number is actually closer to 200,000 yearly deaths by malpractice. Contrast either figure with 40,000 yearly deaths in auto accidents. Malpractice is the third or fourth leading cause of death.

How are we to avoid becoming a statistic in this race with untimely death? For starters, read this book. It has joined my reference library. Every chapter has, in addition to narrative and stories, particular advice in a certain area. A few themes show up repeatedly:
  • Prepare for any doctor visit by writing down everything you are taking, including vitamin supplements and over-the-counter pills; and write all your questions about what's currently bothering you (medically).
  • Get very, very good at finding medical information using the Internet, using sources such as MedlinePlus and the NIH and NIMH web sites, plus, which has a great drug interactions checker.
  • Whenever a nurse shows up with a pill or hypodermic, first ask, "Who is this for?" In a hospital setting, it is surprising how many times Mr. Jones gets an injection or pill intended for Mr. Johnson, or even Mr. Smith. Secondly ask to see the doctor's order, and thirdly ask what this medication is intended to accomplish.
  • Always ask what to expect after a medication or procedure, including side effects and expected course of recovery. Very few doctors will bring this up on their own.
  • If your doctor won't communicate with you, get another doctor. Any doctor who feels threatened by a patient's knowledge or questions should get out of medicine.
Dr. Klein is an internist, so while he has made his book as comprehensive as possible, he admits he can't cover everything. He recommends, as mentioned, researching anything new by yourself, using both internet resources and asking your doctor more questions, and then even more questions. Your doctor went to school and residency for ten years after finishing high school; drag some of that knowledge out of him or her.

He refers to HealthGrades frequently, so I spent some time at their web site (see link above). Some results are free, such as reports on nursing homes, but in general it costs $13 to get a full report on your doctor, and $18 to get a report on a hospital, for which you first have to pick up to 20 conditions out of a menu of 57, so if you wanted every condition covered, it would cost you $54. However, if I were again faced with choosing a hospital in which to spend a week after having my insides re-plumbed, I'd definitely spend the $36 to get reports on the two in my area that are available to me, and maybe another $18 to get a report on Thos. Jefferson Hospital in Philly for comparison.

Along with the theme of that daily jumbo jet crash (and statements such as "While you read this chapter, five people will die of malpractice"), Dr. Klein has a full chapter on reforming the medical system, in addition to recommendations that appear throughout the book. For example, there is a very strong inclination for doctors to deny ever having made a mistake, probably because their malpractice lawyer has advised them to minimize liability by never admitting wrong. They need to be convinced that correcting a mistake quickly is less costly than going through a malpractice trial (even if they win, as they do 70% of the time). But first a doctor has to admit that a mistake has occurred. A national medical climate that encourages the acknowledgment of mistakes and encourages learning from them is needed. But so is a climate that stops the rampant covering-up for those few physicians who are responsible for the great majority of actual malpractice that occurs. It is a kind of 80-20 rule, or more likely, 90-10: 90% of the malpractice is committed by 10% of the physicians, who need to be "encouraged" to find another line of work.

Since that is very unlikely, taking the proactive steps Dr. Klein recommends will make it more likely that you, the educated client (not patient) of your doctor, a collaborator with your doctor rather than a passive receiver of medical "services", will not just survive, but thrive.

Saturday, June 19, 2010

Squirrelly harbinger?

kw: musings, animals

When West Nile virus came to the Northeast, it was first seen in lots of dead crows and similar birds. I wonder if a sudden dearth of squirrels has any sort of meaning.

Last year (and for many years) we had lots of squirrels, which were very busy all Fall burying acorns from our oak trees. Since winter ended, I haven't seen any squirrels, and I've been pulling up lots of little oak trees that are coming up all over my yard. Just today, while cutting the lawn, I pulled out or mowed over more than 100 tiny oaks from all over the yard, even 200 feet from the nearest oak tree.

Considering that most human diseases began or begin as zoonoses (animal diseases), this could be an omen. It isn't likely, I know, but it is strange. No squirrels for the first time since we moved here in 1995.

Thursday, June 17, 2010

Summer photo workshop 1

kw: photographs, classes

For the second summer, I taught a 2-hour workshop in digital photography basics. This time we had more time outside taking example photos. One of the students wanted a wider wide angle lens, but balked at the price. I showed them all how to do simple panoramas (and gave them an ad for my Panorama/HDR workshop in July).

This photo is a composite of four. I stitched it with the Windows Live Albums "Make" tool. I plan to redo it with the Canon Stitcher tool, which will let me get rid of the glitch near the chimney.

As we were leaving, we noticed a pair of barn swallows had their nest on one of the posts near the front door of the studio. Here is the male bird feeding the young. One of the students is very interested in nature photography, and was quite gratified to get closeups just as good as this one (maybe better).

Wednesday, June 16, 2010

The bugs are winning

kw: book reviews, nonfiction, medicine, pandemics

This is one face of a pandemic (Image from this Wikipedia article). The colors indicate accredited cases of H1N1 influenza in 2009 by country, from 50,000 or more (black) through brick red and red to pink, in steps from 5,000, 500, 50 to 5, to the palest pink of between 1 and 4 cases.

The color pattern shows, for one, that H1N1 was spread by tourists, so those areas too poor to attract many tourists were actually largely spared. As influenza outbreaks go, this was a mediocre one, having led to "only" 12,000 excess deaths in the U.S. Compare this with more ordinary flu seasons, in which excess mortality ranges from 5,000 to nearly 70,000, averaging 36,000. On average, in the U.S. at least, influenza is on a par with auto accidents as a cause of death.

Let's put this against the backdrop of a real epidemic, one that goes on and on: Malaria, which infects about half a billion people and kills between one and three million yearly (a more accurate figure is not known). That makes the malaria parasite the most dangerous pathogen, and the mosquito the most dangerous vector, on Earth.

In 2002 Madeline Drexler published Secret Agents: The Menace of Emerging Infections. The 2003 paperback has recently been reissued with a new chapter and a new title, Emerging Epidemics: The Menace of New Infections. A blurb on the cover scratches the surface of the content, mentioning H1N1 flu, SARS, anthrax, and E. coli.

An opening chapter presents some recent history and enough bacteriology to help us understand the phrase, "A millennium in a fortnight", meaning that microbes evolve about 25,000 times as rapidly as humans. It is actually worse than that. A human generation is 20-30 years; a bacterium's generation is 20-30 minutes. There are half a million minutes in a year… This ushers in a major theme of the book, that viruses, bacteria and protozoans can quickly evolve ways to tolerate or defeat the medicines we use in our attempts to eradicate the diseases they cause. (A case in point is Penicillin, which went into widespread use in the early 1940s during World War II, and was losing effectiveness by the time I was born in 1947. By the time I was ten, I'd had my last Penicillin shot.)

The mosquito-borne disease theme is used in Chapter 2, focusing on the West Nile irruption a few years ago, to illustrate just how chancy is our public health system. It took the incredible persistence of a zoo veterinarian, who happened to be a middle-aged woman whose questions and date were ignored for months, for the CDC and other "official" medical organizations to recognize the connection between a rash of dead birds and a syndrome they at first attributed to St. Louis encephalitis. The dots are still not connected. How West Nile virus traveled to New York is still unknown.

In areas of the world that are free of malaria, the most frequent disease outbreaks are foodborne, including E. coli O157:H7, Listeria, Salmonella, Chlamydia, Campylobacter and Cyclospora. The third chapter focuses on these and on the difficulty of discerning a genuine outbreak from sporadic clusters: separating the signal from the noise. In a 1998 case of widely-scattered clusters of Shigella toxin poisoning, the trouble was finally traced to a single parsley grower in Mexico, from where fresh parsley was distributed worldwide. It made me look askance at the next parsley-garnished bowl of soup I ate at a restaurant. Nobody really eats the stuff; why use it?

The scariest chapter is the fourth, on superbugs, including MRSA and VRE (multiply resistant Staphylococcus aureus and Vancomycin resistant enterococci), plus the aforementioned E. coli strain and multiply resistant TB. The author points out that all antibiotics so far developed are members of just 16 molecular families, and every one of them is resisted by at least one organism. The thing about bacteria, they all seem to be a single, highly-variable species, because they all can have a kind of single-celled sex and exchange DNA. Certain viruses that prey on bacteria only make things worse, because they also inject DNA into the bacteria that may carry either resistance factors or "virulence factors" that make it easier for a pathogen to spread among us. I remember learning years ago that we all have plenty of Streptococcus living in and on us. It is only when the Strep is attacked by a certain virus that it makes a toxin, manufactured using the virus's DNA, and the toxin produces "strep throat". We get sick because one of our "passengers" is sick! The scary point: we are all out of weapons with which to fight certain battles.

Chapter 5 focuses not just on influenza, but on the 1918 pandemic that was so deadly, it killed more people than the bullets and bombs of World War I. It could return, or something like it. The 2009 pandemic was a weaker relative, which spread almost as fast, but wasn't nearly as deadly. By the way, H1 and N1 refer to protein factors that stud the surface of influenza virus particles. There are 15 H types and 9 N types, leading to 135 basic serotypes, each of which comes in other variations based on internal DNA variations. That is what makes it necessary to produce one or more new flu vaccines every year.

Chronic diseases were once considered to have other causes, such as "bad" cholesterol (heart and vascular disease), "autoimmune dysfunction" (arthritis and diabetes), excess stomach acid (ulcers), and random genetic damage (cancer). Evidence is accumulating that all of these, and others, are actually the result, or side effects, of infections. These days, your ulcer can be eradicated by a round of antibiotics. Maybe someday, an antimicrobial treatment will eradicate heart disease, cancer, and even juvenile diabetes. What'll kill old folks when there's no more chronic diseases? Maybe then we'll find out about "just dying from old age."

The seventh chapter treats of bioterror, going into quite a detailed history of germ warfare since the Medieval practice of throwing rotting bodies into besieged towns with catapults, and the use of "smallpox blankets" to decimate one Native American tribe 250 years ago; but focused much more on the U.S. and U.S.S.R. programs during the cold war. While "weaponized pathogen" stockpiles are reduced at present, there is still an uncomfortable tonnage of bio-weapons in existence, and it is evident that there are numbers of disaffected terrorists crazy enough to use them if they can steal some.

The last chapter tackles the information question. The public health apparatus has performed poorly in the past, and is still unready in the face of discerning a bioterror case from a restauranteur's error. There is hope that an internet tool such as ProMED will enable the right people to connect the dots sooner. It worked "sort of well" for SARS a few years ago. Newer web sites like GVFI (Global Viral Forecasting Initiative) are a big step in the right direction. I see a problem, though, that too many such initiatives will cause even more noise in the system, until they settle out to two or three really good ones.

What are the chances that a really nasty bug will come along and kill 10%, or even 50%, of the human population? Asteroid fans, take note: The chances are much, much greater than the chance of a 10-km asteroid such as the one that wiped out the dinosaurs. Our own lack of readiness is our greatest risk.

Tuesday, June 15, 2010

There's mud and then there's mud

kw: observations, efficiency

There was a news article today about drilling practices. Though it was focused on drilling for natural gas, it applies equally well to all petroleum drilling. A bit of debate was presented about the health risks of living near an active drill rig, and not just because of the hydrocarbons that are the target of the drilling. No, this was about drilling mud. Drilling companies have declined to tell what components and additives are used in their drilling mud, and people with health problems are frustrated because they can't find out what they are being exposed to.

What is drilling mud? It is primarily the lubricant for a drill bit. It is pumped down the drill string (the pipe that supports and drives the drill bit) to the drill bit, which has holes, where it is forced out and returns up the drilled shaft outside the drill string. At the top, it is recycled: rock chips are filtered out, possibly additives are put in, and down it goes again. It consists mostly of water and a clay such as Bentonite.

There are two kinds of additives. One kind is various petroleum products that increase its lubricating qualities. These are the target of all the secrecy. Each drilling company uses proprietary formulas that they hope give them a competitive advantage so they can drill the most feet for the dollars spent. The other main additive is a density additive, the most common being Barite, because it is best to keep pressure in the hole to avoid blowouts. If the target is known to be under great pressure, a lot of Barite is used. Without any Barite, the drilling mud is only about 70-80% as dense as the rock it is drilling through. All that rock pressure may be focused in the gas or oil reservoir, so it is necessary to hold it back and control its rise once the drill bit breaks through into the producing layer.

This latter point produces little controversy. The secrecy surrounding the first issue, the lubricant additives, is the point of contention. In my opinion this secrecy must be breached. This is not just a matter of keeping trade secrets. Obviously, there are differences in optimum formulas for best drilling efficiency, which differ from rock type to rock type. Each drilling company thinks it has the best formulas. Even more obviously, only one of them is right in any particular instance! ALL the others are less efficient.

It would make better sense to get those formulas out in the open, and compare them in real-life situations. Let a set of best practices for each rock type be codified, and all the drilling companies will benefit. So will the people who could then find out just what it is that they are breathing or otherwise being exposed to as drilling proceeds, perhaps right in their neighborhood.

To those who would protest that a lot of drilling research has been published, the key formulas have been published only in quite general form, and all the article of which I am aware are rather old. This needs to be brought up to date and made completely explicit. This is an area for which trade secrets cause more harm than good.

Monday, June 14, 2010

Eyes now a window to dementia?

kw: observations, science, medicine, dementia

This article in The New Scientist describes a new test that allows an ophthalmologist to see cells dying in the retina of the eye. An abnormally high rate of apoptosis is an early warning of probable Alzheimer's dementia.

At present, the test has been developed in mice, comparing cell death in the retina between mice that are prone to Alzheimer's and mice that are not. The test involves injecting a fluorescent dye into the back of the eye, so I don't expect it to become popular!

Saturday, June 12, 2010

Don't touch that dial

kw: observations, history, cliches

BMUS-THILH. It used to be fun to say, "Beam me up, Scotty; there's no intelligent life here," or just the first four words; the rest were understood. I haven't heard it in years, though the more sardonic BMUS-FTP lasted a while longer, mainly as a T-shirt slogan.

Come to think of it, T-shirt slogans aren't that pithy any more. A great many are almost short stories printed on cloth, and if the wearer is a bit too curvaceous, you'll never get to read all of it anyway. One of the shorter ones is at least witty:
I want to be like Gandhi and Martin Luther King and John Lennon, but I want to stay alive.
But back to sayings…

The inexorable progress of technology has made a bunch of things we used to say totally incomprehensible to today's youngsters. If you're under 40, you have no memory of any moon landing, nor of our pullout from Vietnam, nor of the resignation of a President.

How much longer will the icon of an idea be a light bulb? And how about this post's title: How long has it been since the last TV was made with a channel-changing dial, or two dials even, one for channels 2-13, and one for 14-69? Now we just push the up and down buttons, or poke the keypad on the remote, except when its batteries die just before the Super Bowl. Oh, yeah; a bit over forty years ago there was no Super Bowl. It started in 1967.

More than half the people alive would never say, "You sound like a broken record." Vinyl phonograph records would skip when scratched, or repeat, repeat, repeat… But a scratched CD probably works just fine, or at worst it makes a loud POP and keeps going. And you can often polish the CD and make it work better. There was no rescuing a scratched Vinyl record! Vagrant thought: CD sales are reducing as more and more people just suck albums off the Web into their IPods.

"Give me a ring" has given way to "Give me a jingle" and now to "Text me." Funny thing, though, Soap Operas are still called Soap Operas (except the ones called Telenovelas), even though their advertisers are no longer selling laundry soap. They're selling knee replacement surgery, asthma medicines, and Viagra.

The phrase "Let's get cranking" almost predates me. It refers to autos that had no starter motor. I have an ancestor (actually a great-uncle) who forgot to put the car out of gear to start it with the crank, and was run over. Luckily, a Model A didn't weigh much; he just broke a leg. Not that many years later, my father's first auto was a Model A, but the brand was getting old already by then. It was kind of like having a VW "old bug" today. You don't see many.

You also don't see many of the old E tickets, outside a museum. I went with my family to Disneyland the year it opened, and for its first several years, you bought packets of tickets of different values. There were plenty of A, B, and C tickets for the less thrilling rides, like the Submarine or Teacups. There were usually only two D and two E tickets in the packets we could afford. We could take half an hour deciding which two E rides to go on. Today an E-ticket gets you a boarding pass at the airport. Now, that's a lot more expensive ride than anything Disney had to offer, and a lot less thrilling (I love a nice, boring airplane ride!). Until Scotty arrives with his Transporter, airplanes are still the fastest way to get away.

Thursday, June 10, 2010

Care or cure?

kw: musings, aging, dementia

Yesterday's post about Making the Rounds With Oscar renewed my consideration of aging and dementia. I found a document online that gave me some numbers ("Prevalence of Dementia in the United States: The Aging, Demographics, and Memory Study" by B. L. Plassman et al, found here).

Of course, the most important variable is age. In the sample, made in 2002, the breakdown of people 71 and older is thus, by decade:
  • 71-79 5.0%
  • 80-89 24.2%
  • 90+ 37.4%
Considering that those over 85 are the fastest-growing segment of the population, those are grim numbers. Absent effective treatments for, primarily, Alzheimer's Syndrome, end-of-life care for demented elderly will take up great amounts of caregivers' time, and prove very costly.

As an example, my Father found the most economical option he could for caring for my Mother, supplementary care in addition to his own efforts. This was enough for a time, and the cost was a few thousand dollars monthly. But once her care required round-the-clock attention by professionals, the cost rose to $9,000 monthly, and he was still wearing himself out doing just a portion of the care, and with some help from one of my brothers who lived two hours away.

In a few years, the numbers of Americans requiring such care will be about ten million. $90 billion per month comes to $1 trillion per year. Public spending for dementia care in 2009 was about $170 billion. Contrast either figure with the national budget for dementia research, just over a billion dollars (I found it hard to determine any figures at all, let alone accurate ones).

We need to do better than that. An effective preventive or treatment will always be less costly than meliorative care. It will be even more economical of the time and emotional well-being of family members.

Wednesday, June 09, 2010

How does the cat know?

kw: book reviews, nonfiction, animals, dementia

A couple of years ago Dr. David Dosa was told about Oscar, a somewhat standoffish cat who always seemed to know when someone was about to die, and would snuggle up to them during their last hours. One of six cats resident in the nursing home where Dr. Dosa works, Oscar seems to take seriously his role as an end-of-life comforter to both the dying ones and their families. The doctor, initially skeptical, finally decided to investigate, and interviewed the families of all the former residents who had most recently passed away. They all had stories about Oscar, and how they had appreciated his attention and presence at the end of their loved ones' lives.

Their stories make up a large part of Making Rounds With Oscar: The Extraordinary Gift of an Ordinary Cat. Dr. Dosa's own story makes up the rest. He had more than stories to go on. He had his own experiences. He observed Oscar's "vigil" with more than one patient. He noted how Oscar, usually so quick to bat away a hand that tried to pet him, willingly received caresses from the dying person's family members. He even observed how Oscar stayed in the room of one patient who was sent to the next-door hospital (a place the cat could not go), until that patient died over there.

Doctor Dosa's main charges are 41 dementia-afflicted patients, who die with great regularity. Steere House is apparently one of the better places to die with dementia. However, it was only after he began his interviews that the doctor learned the most important lessons about dementia and the people who care for a loved one who has it. Two major points stuck with me: Learn to love who he or she is now, for whoever the person was before is gone; and Live in their world, because they can't return to ours.

The first point really means saying goodbye to someone whose body is still present, then learning to care for them as they have become, perhaps becoming a friendly stranger because they don't know you any more. I only knew my grandfather as a silent, friendly man who enjoyed being led around the block by one of his grandchildren. We were born too late to know him "before". This made it easier to recognize what we had to do with our mother when she slipped away, mentally.

I had heard the second point before, from my brother. He told of going to visit our mother right after a cancer operation. She wasn't in her room, but was found in the hallway, having unplugged all her tubes and needles. She was trying to escape. In the midst of a dementia-induced episode of paranoia, she was convinced she was a prisoner being held captive by phony doctors. My brother went along with this, and explained to her that he needed her to stay put and gather information about what the doctors and nurses were doing; that he was able to get in to see her "without getting caught"; and that in a few days he would "spring her". She happily settled into a day or two of spying on everyone until she gradually forgot her fears. And my brother and father did indeed "spring her" a few days later.

I also remember how flat exhausted our father got, caring for her as she deteriorated over a ten-year span. Eventually, he had to have round-the-clock help to take care of her. In my opinion, he waited longer than he should have to "rent" some help. Since none of us live close, though, that is what he had to do. My parents eventually both moved into a "retirement hotel" where help was easier to get, and less costly, and my parents were both much happier during my mother's last year. Having cats around would have made it even better, even if none were as prescient as Oscar.

Dr. Dosa has medical troubles of his own (mainly arthritis), but he is rather young, with a young family. He learned from the families of former patients just how precious is his own family time, and he learned from Oscar just how "in the moment" a cat is, and how that is also possible for people. Whether this cat has senses we don't understand, or is simply able to empathize with grieving families, he is a working cat. He gets tired after a person he's been with dies, and takes time for himself. There is a lot to learn from a cat like Oscar.

I got a book about a cat; its real story is about coping with terminal dementia.

Tuesday, June 08, 2010

To think is to . . . what?

kw: book reviews, nonfiction, scientists, biographies, neuroscience

Let's see, the process goes something like this:
  • Neural theta bursts occur about five times per second (the rate of a small mammal's sniffing, which is significant).
  • Theta bursts open neural channels AMPA and NMPA, in sequence.
  • Ions enter, inducing disassembly of portions of the cytoskeleton.
  • The cytoskeleton reassembles via actin polymerization, making certain synapse bulbs larger (they are about a micron or two across, smaller than an E. coli cell).
  • Molecules called integrins lock in these shape changes, that make room for more channel receptors.
  • The greater numbers of receptors increases the likelihood this neural circuit will be retained.
And that is how a memory is made. The process is called LTP or Long Term Potentiation. The early steps take milliseconds, the ones in the middle take seconds to minutes, and the later steps take up to an hour and can persist for a lifetime.

Figuring it all out did take a lifetime, that of Gary Lynch, PhD, in his lab at 101 Theory Drive in Irvine, California. The lab's address provides the title for Terry McDermott's book 101 Theory Drive: A Neuroscientist's Quest for Memory. This is a biography not just of Dr. Lynch, but of the lab itself and the motley collection of graduate students, postdocs and others he assembled over the past thirty-plus years as he drove single-mindedly to determine the mechanism of memory.

By all accounts, Gary Lynch is a champion jerk. He is as famous for his feuds as for his science. Luckily for him, his science made him rich, in spite of a long list of offended collaborators and competitors. Nearly from the beginning, he has commercialized key discoveries, and it may be that the recent ones, including ampakines, may yield effective treatments for memory diseases such as Alzheimer's Syndrome and RETT.

As I read, I remember wondering, "What if Superman had a bad personality? Would he retain his popularity?" Lynch is like Superman with an attitude. He spent much of his life knowing he was right, frustrated by the lack of tools to prove his ideas (his lab partners had to invent most of those tools over the past thirty-plus years), and alternating between elation and despair. Even in his sixties, he wears his heart on his sleeve as clearly as any four-year-old (a man after my own heart!). Though a lot of people don't like him, very few try to deny he gets results, tons of results!

Early on, he realized that the key to the great memory abilities of the mammalian brain is the very randomness of the cortex. Instinct works like pre-stored programs, which never change. Learning changes all the time, as Lynch said, "…the thing's random. The key to understanding it is, ninety percent of the human brain uses the same basic circuitry." But this randomness has its drawbacks:
We've made a deal with the devil here. It isn't the secret of our existence that we have so much plasticity. It's that we have so much stability. These dendrites have to last a lifetime. Now, if anything happens to one of them…you can't get it back. (p 105)
Put another way, we know neuron death occurs at a steady rate. Those that encode a particular memory might last a century, but whenever they die, that memory is gone. Memories are made and committed at a low rate to begin with; we have no room to recall every little thing. What we do remember is remarkable, but it is less than a percent of what we could remember if we were like DVD recorders with an infinite number of disks to fill. So we keep only the "memorable" memories, plus an assortment of less critical ones that happened to, quite randomly, rise above the noise level long enough for LTP to fix them permanently.

It is all a testament to the contingent nature of evolution. However the first collection of randomly-assembled neurons arose, they were found useful for learning stuff, and the newly-"invented" cortex just grew and grew ever since. It must have started in the olfactory bulb (the "smell center"), where a small mammal's sniffing rate of five per second became fixed as the theta rhythm that triggers learning. Smell is the oldest of the senses that utilizes learning as a key element in its working. Other parts of the LTP mechanism were cobbled together from existing molecules, such as the ones that cause blood platelets to stick together during clotting.

One albatross around the neck of neuroscience has been the term Engram, popularized by Karl Lashley. While in neuroscience an engram refers to the physical "whatever" that make(s) up a memory, the term was co-opted by Scientology to refer to only painful memory traces that their "auditing" is supposed to erase. Actually, if you remove all your engrams you'll become a wholly blank slate, no memory, no language, no nothing. The science is thus still devoid of a good replacement term. LTP is a poor substitute because it refers to only part of the process, strictly speaking.

McDermott's book covers the whole of Dr. Lynch's career, but focuses on the past ten years, during which the most sensitive tools were developed that finally proved the LTP hypothesis. The cover of the book is dominated by an image from the microscopic evidence for synaptic rearrangement on the dendrites during learning. You'd think Lynch would be ready to rest on his laurels at that point (late 2008), but you can't get an old plow horse out of the traces quite that easily. Science never stops, and neither will he.

Monday, June 07, 2010

When keyboard was king

kw: computers, history

My first desktop computer at work (1982) and my first home desktop computer (1984), both by TI, did not have mouse or hard disk. Once the operating system (MS-DOS) was loaded from a 360 Kbyte floppy, I'd use a runtime disk for WordPerfect or Lotus 1-2-3 in drive A, and a data disk in drive B.

It wasn't until I got my second computer in 1987 that I got both mouse and HDD, and I could run MS Windows 3. However, the mouse was a "new thing", and the menu-oriented software it could take advantage of was still rare. I used keyboard-oriented WordPerfect 4 and switched to Quattro Pro in place of Lotus 1-2-3.

Yesterday, cleaning out old stuff, I came across the Function Key templates for these two programs (click on the image for a really close look). I was really good with function keys for both these programs. It stood me in good stead at work, where WordPerfect was guidelined until 1995, and QP was an acceptable substitute for 1-2-3. Only when I transferred to corporate research in 1995 did I get in an environment in which MS Office products were guidelined, and nobody wanted me to send them files in WP or QP (or even 123) formats. I switched.

I've been fully into using Word and Excel (and PowerPoint) ever since. I still use as many keyboard shortcuts as I can remember, learned mainly from the help screens. But I've become such a heavy mouse user that I had to have an operation for deQuervain's tendinitis a couple years ago. I also switched the mouse to the left hand. Considering that I use the 10-key pad for most numbers, this balances the work between my two hands.

Just as I have fond memories of the Elephants I couldn't see over, I fondly remember the floppy-and-keyboard days, which I'm careful not to equate with walking to school "uphill both ways".

Saturday, June 05, 2010

The fort at the end of the runway

kw: history, historic sites

Returning from our trip last week, we flew over New Jersey to approach the Philadelphia Airport from the east. As the plane made its last turn toward the runway, I saw this fort out the window. I had no idea there was an old fort so near the airport.

This is Fort Mifflin, built in 1771, the site of the greatest bombardment ever on the North American continent (more than 10,000 cannonballs over a 3-week period). It is called "The Fort That Saved America." By withstanding the British attack for those three weeks, its 400 defenders allowed General Washington to withdraw his troops to Valley Forge late in 1777, too late for their enemies to pursue them.

Had the British taken the fort quickly and re-established their supply lines, they could have cut off Washington's retreat and probably would have brought an early end to the Revolutionary War, one that retained the Colonies in their former status, as subject to British law.

This is the only Revolutionary-era fort that remains intact. Now that I know it is there, I'll have to pay it a visit.

Friday, June 04, 2010

Not a wannabe

kw: book reviews, nonfiction, autobiographies, education, culture

At my parents' 50th anniversary celebration, my youngest brother spoke of growing up with three older brothers, and mainly of his school years. One or another of us was always showing him something new, so that he had a head start in some parts of his schooling, but ran crosswise in others. He had other experiences also, ones he felt were the most relevant to living life. His closing remark really stuck with me: "Education is what happens when you aren't being schooled."

Kurt Caswell makes a related remark in his book In the Sun's House: My Year Teaching on the Navajo Reservation. On p121: "…life at home was an education too, a better education in how to be Navajo, perhaps, than any classroom could provide." Considering that Borrego Pass School has half the class day held in the Navajo language, this is telling. Just as my brothers and I learned to be who we are by growing up in a certain family, the Navajo kids learned who they are by growing up in their families, and the author became who he is by growing up in his Idaho/Oregon family.

By age 26, having traveled the world more than most of us, having lived and taught in Japan for a year, he would be, one might expect, more cosmopolitan, more resilient in the face of different cultures. Perhaps he is, but in Borrego Pass he was completely out of his element. He didn't help himself by getting into a staring contest with one of the first school children he met; that's a good way to make a lifelong enemy out of a Navajo (and the same holds true for Native American men in general).

I believe the cluster of buildings in the foreground of this Google Earth image is Borrego Pass School. It is less than a mile from that point on the map known as Borrego Pass, where the Continental Divide wriggles through northwestern New Mexico.

The school grounds and surrounding buildings are nestled up against a mesa on and around which the author took frequent walks. In the afterword to the book, Rex Lee Jim has a few complaints, that Caswell didn't experience certain things that might have affected his outlook. He writes of the Navajo tendency to celebrate things like a child's birth or first steps, of the rich family life Navajos lead, and states, "He never sees it."

Indeed, this is true, but what options were there for him? I've spent a total of a few months on various Indian Reservations, and with very few exceptions, they are Third World enclaves buried in the lost corners of the First World US. Borrego Pass (really a part of Crownpoint, NM), is such a case. Poor people everywhere celebrate what they can, for there is little else to take the grinding edge off a poor life. While Caswell has definite loner tendencies—he seems to prefer long walks with his dog to most everything else—he was up against cultural tendencies that excluded him.

Like idealistic young people everywhere, the author hoped he could "make a difference", though he muses more than once over just what such a vague term that is. What he experienced was that Borrego Pass began to make a difference to him. He didn't change anyone much, but he was himself changed. At some point, he began to find the desert beautiful. He almost admits to finding the people beautiful, but he never goes that far. This fits the loner profile, with which I much sympathize; we are more comfortable with landscapes and mechanisms than we are with people.

Every teacher lives for those moments when someone's face lights up, or to hear a quiet "OH!" from the back of the room. He had a few similar moments, and was in the end quite impressed with a student he calls Renee (all names are made up to protect the people he lived among). Of all the kids (he taught 6-8 grade children), she alone seemed to look beyond the New Mexico horizon, for opportunities to grow beyond "the rez" and be able to return to "help the Navajo." Perhaps she will, just as Rex Lee Jim did in his own generation.

Kurt Caswell moved on after that one school year. But Borrego Pass didn't leave him so easily. It took him a few years to settle it in his mind, then he wrote this book. It exposes and reveals him in a way he'd have found painful at the time, but he has matured. He may think he had little effect, but he is like the man on the seashore, throwing starfish and snails back into the ocean. If someone asks, "How can that make much difference? There are so many," he will reply, "It matters to this one" as he throws it back in. For the uninitiated: that ocean is within.

Wednesday, June 02, 2010

The end of Moore's Law?

kw: observations, computers, analysis

This chart (click to see detail), from the Wikipedia article Moore's Law, shows the total transister count for CPU chips for nearly forty years. As Gordon Moore originally stated it, the density of transisters per square inch was doubling each year. For at least the last thirty years, the doubling time has actually been closer to 18 months. The total transistor count is a bit different, because total chip sizes have increased also, but it is easier to determine (not all transistors are the same size due to power flow requirements).

The "feature size" of chips circa mid-2010 is 45nm, or about 200 silicon atoms across. Integrated circuit engineers keep finding ways to make transistors work as the feature size decreases. If we suppose that the minimum feature size is two atoms, there is a factor of 100 yet to go, or about seven doublings. That means that Moore's Law will reach a limit in ten years.

Smaller transistors switch faster, so chip speeds have increased also. The relentless push of technology has increased the speed and capacity of disks, motherboards, and all components. The "personal power law" I have experienced centers on two measures, CPU clock speed and hard disk capacity. I've had a variety of "boxes" since 1985 when I first got a TI Pro "PC compatible" with a 4Mhz processor and no hard disk (nor mouse; there was no MS Windows yet). Since then, the progression has been:
  • 1987 - PC/AT - 10 Mhz - 40 Mby HDD
  • 1991 - Pentium - 75 Mhz - 500 Mby HDD (2d disk 1995 - 2.5 Gby)
  • 1998 - Pent III - 800 Mhz - 30 Gby HDD
  • 2000 - Pent IV - 1.3 Ghz - 40 Gby HDD
  • 2008 - Core 2 - 2.7 Ghz - 160 Gby HDD
Note how CPU speed increases have become less aggressive. Now, even though 4-, 6- and 8-core processors are available, the top speed of a single core is 3.5 Ghz, and this hasn't changed for three or four years. However, hard disks are continuing to grow in capacity. Current "standard" is 1-2 Tby, which costs less than $100. There is more room for disk capacity to continue to grow than there is for CPU speeds to increase. Suppose 100 atoms will do, for a persistent "on" or "off" bit. A 15-cm disk could hold 200 Tby, and multi-platter stacks are common. The Pby (petabyte) personal disk drive is probably no more than twelve years away. At that point, the exponential law for disk capacity will also be about played out.

Personally, I once thought I'd never use a full Gby. Now I have 10 Gby of pictures! (and a similar size stash of music files) But what will we do about a decade from now when the limits I've noted are reached? I suspect technology has some surprises in store for us. The Moore's Law that I can see may be coming to an end, but I'm probably not much of a prophet.

Tuesday, June 01, 2010

More fish

kw: photographs, animals, fish

A few more pictures taken at the Georgia Aquarium May 27, 2010. We spent the whole day there.

Jellyfish. They are white; the color is from colored lights that change slowly. A kind of living light show.

A manta about to do a backflip in front of the big window.

Freshwater tropical fish, just a bit bigger than you can usually get at the pet store. There were also neon tetras in this tank, but these are the size of a hand and larger.

Some ghostly sea anemones. I had to take this at very high EV, so it looks grainy.

Across from the aquarium is Centennial Olympic Park, which is paved with engraved bricks. Take a second look at the one in the center (click on any of these for an image about twice the size).

Genius versus Brilliant

kw: book reviews, nonfiction, biographies, crime

In 1698, Isaac Newton, after two years as Warden of the Royal Mint, found his work called into question because of allegations made by…a counterfeiter. Though not quite called up before the dock, he had to defend himself because at least some in Parliament had been swayed by the claims of malfeasance in the Mint made by one William Chaloner. Chaloner had some fame as a betrayer of a Jacobite plot, which gave him a measure of unwarranted credit. It was unknown at the time that he had set up the plot with the intent to betray it and thus gain that very credit. His aim, however, was to obtain an official post in the Mint, the more easily to corrupt the currency. This, on the heels of an effort, led by Newton, that de-corrupted a famously vulnerable monetary system.

Fortunately, Newton was able to fend of this attack and brush off others. He finally had Chaloner brought to justice a year later. But how did Isaac Newton, mathematician extraordinaire, the most famous scientist in England, become first Warden then, after 1700, Master of the Mint? What turned this academic don into a hard-boiled detective, who hired little crooks to catch bigger ones, and did not hesitate to send "clippers and coyners" to their doom on the gallows? A large biography of Isaac Newton that I read years ago hardly provides five paragraphs on this portion of his life.

Thomas Levenson begins Newton and the Counterfeiter: The Unknown Detective Career of the World's Greatest Scientist with two mini-biographies, one of the young Newton, the other of the young Wm. Chaloner. Each rose to the pinnacle of his chosen profession, the one to riches and honor, the other to temporary riches and then the end of a short rope. We see how the laboratory habits of mind that served Newton so well were equally useful in criminal investigation. Indeed, he seems to have invented the kind of network of informants that is so routinely used by modern police detectives. And we see how another brilliant mind was always and ever turned to criminal pursuits, to playing a deep game that kept him far from the bleeding edge of blame, at the center of his own network of minions.

Criminal detection thrives on information. Even today, many investigations are hampered by the tendency of some enforcement agencies to keep their information close. Sharing is rare. Nobody can "connect the dots". The problem was much keener in the 1680s. Newton, who spent a year and more on the effort to reform British coinage and eliminate clippable coins, had no way at first to know his post was being stalked by a criminal bold enough to attempt to take over the Mint, a criminal who produced gilded pewter/lead slugs that looked better than the real thing. Newton knew none of this for many months. It was only once he had built up his own information network that he could learn who the players were in the great counterfeiting enterprises, and focus upon the most dangerous of them all, William Chaloner.

Chaloner epitomizes the theme of an old popular song: "I fought the law and the law won." By betraying the Jacobite plot he had set up, he won a monetary reward from Parliament. By dint of clever accusations, he persuaded that august body to reward him further for demonstrations of superior coining techniques (in spite of the fact that any Member with the brain of a turtle might have realized he was eminently skilled in counterfeiting). But his attempts to attain access to the Mint failed, because the Warden, Newton, would have none of it, and once he realized that his accuser was his prime target, he relentlessly pursued the evidence he would need to hang him.

It is likely that the criminal didn't realize, until perhaps a day or two before his demise, the quality of mind he'd set himself up against. The very lack of information flow that hampered Newton also hampered Chaloner, so that he thought slow action bespoke a slow mind. He learned instead, one must beware a patient man. Newton, patient? With his scientific peers he could be short, even abrupt, but he had the patience to spend decades upon the equations of gravity. He was equally patient and persistent, treating Chaloner's case as an equation to be solved, and solve it he did.

A fascinating account, which rounds out Newton's character compared to the more standard biographies I have read.