Thursday, July 31, 2008

Broken brain, maimed mind

kw: book reviews, nonfiction, psychology, psychopaths, social predators

The year before I married, I rented a bedroom from a family with two young boys. The parents were strict with them, but basically cheerful and, I think, pretty good parents. They did practice corporal punishment, based on the Biblical verse to "beat with a stick", on occasion. Both boys were mainly cheerful and sweet, but I soon learned that the younger one, age seven at the time, had a criminal disposition. I know he stole from me, for example. He also committed petty vandalism and had set a fire or two. When confronted with a crime, he usually openly defied anyone who didn't actually have a stick in hand with which to spank him...and sometimes even then. Decades later, his father informed me that he'd spent most of his adult life in prison. At the moment, that is where he is. The older boy has had no scrapes with the law. To my observation, the two were raised as much the same as possible, but they turned out very different.

Over time I have encountered people who simply cannot be wrong...that is, they never admit to being wrong. It is clear that they cannot imagine wrong in themselves, so they shift blame, they "gaslight" others, and commit emotional blackmail instead. I know a woman who threatened a lawsuit against her daughter and son-in-law to prevent their moving further from the "family base", which would reduce her "access" to the grandchildren she actually had nearly no time for.

Troublesome people range from simple jerks to totalitarian dictators. If we consider the human race an ecology of similar "species", they are the parasites and predators of the ecology. To me, they seem to share four characteristics:
  • They can be both charming and horrific, and their emotional expression can switch in an eye blink.
  • They thrive on attention, and will take steps to get as much adulation as possible.
  • They may seem to know right from wrong, though some seem to have no conscience at all. The key is, they don't care for the distinction and can severely abuse someone or even kill without compunction.
  • Their world really does revolve about them, and they eliminate any elements that don't or won't comply.

Adolph Hitler and Joseph Stalin are probably the third- and second-worst (in that order) leaders in all history. Hitler supervised the killing of twelve millions, or more, and Stalin at least twice that number.

This cartoon by David Low appeared in the September 1939 issue of Life. It was already clear to many people that these guys were monsters. Yet they were at the same time being praised by many. Here the cartoonist brings out a key characteristic: outwardly charming, they revile one another.

And who, by the way, is number-one most evil? My vote goes to Mao Tse-Tung, who is responsible for the deaths of at least fifty million Chinese, and perhaps twice that many. Historical monsters such as Nero or Caligula are far, far behind. As long as we're on dictators, "Who's the Worst Dictator?" by Nicholas D. Kristof lists, among the living, Kim Jong Il of Korea, Omar Al-Bashir of Sudan, and Than Shwe of Myanmar/Burma. These three also top this Top Ten Dictators list at Parade Magazine.

There may be reasons for all this, buried in our evolutionary history. In Evil Genes: Why Rome Fell, Hitler Rose, Enron Failed, and My Sister Stole My Mother's Boyfriend, researcher Barbara Oakley gathers the social, psychological, and biological evidence that underlies psychopathy and the clinical designation of borderline personality disorder.

I found it disturbing to read the book, both disturbing and fascinating, just like the people whom it examines. Evolutionarily, there is a clear reason for the persistence of genes that underlie predatory personalities: in most settings predators have reproductive success. To add another example, we have a good friend in Asia, whom we met when she was a student here, who is raising her beloved son, the offspring of a man who stayed married to her only long enough for a healthy son to be born. His serial polygamy has resulted in a dozen or more offspring, and an equal number of broken hearts.

The four characteristics I mentioned above can be abbreviated as Machiavellian manipulation, Narcissism, lack of Conscience, and utter Ruthlessness. All four of these are exaggerations of normal traits that convey fitness. For example, a good negotiator can use both charm and warnings to secure a favorable deal; some folks can twist your emotions until you let them steal you blind, and thank them for doing so. I learned long ago to beware of people who try to make others feel guilty for their virtues. By reading Oakley's book I was appalled to find how broad and deep the syndrome really is. No wonder Jesus said we must be "wise as serpents, but harmless as doves"! It seems to me it is necessary to forgo the harmless part sometimes, to escape the coils of the serpents!!

I know that I like to be liked. I've learned to be civil with those I can't like, or who can't like me. Some of the people I mentioned in the opening paragraphs, however, will cut a person off cold, or even kill them, to remove themselves from dislike or disdain.

Dr. Oakley has a personal reason to study Machiavellian personality: her sister Carolyn. The book is also a memoir of that disturbed life. The brain of such persons works differently than ordinary (I hesitate to use the word "normal"). Brain scans reveal that key brain areas are larger or smaller than is usual. Also, the polio that Carolyn had at age seven may have attacked key parts of her brain, for she seems to have had a change of personality (As a polio survivor, I feel lucky that I had it before I was one, as it doesn't attack the brain at that age). Carolyn had a sad life, and made those around her unhappy with her predatory ways. She really did steal her own mother's boyfriend, but it didn't do her much good.

Her studies reveal that the brains of such people really are different, and most people would call them "broken". Of course, they think they are the normal ones, and the rest of us are passive cattle to be harvested as required. The author speculates about gene treatment to "cure" young psychopaths and BPD subjects. I don't agree; it is more likely that the predators will suborn such technology to make the mass of humanity even "better" passive victims.

One great benefit of reading Evil Genes was being steered to the book Stop Walking on Eggshells by Mason and Kreger. It has practical advice for coping with a Borderline person that you can't escape (sibling, parent or child, spouse, boss...). As a church leader, I can't just throw people out of the church, so I have a pill or two that I cannot escape! I'll post a review once I've read the's three or four down in my stack. Meanwhile, do take a look at the authors' website BPDCentral.

Oakley's book is useful to begin to raise awareness, to arm us, the potential victims. The discussion of business and political cycles shows an ebb and flow of predatory persons in such organizations. New organizations may soon gain a manipulator or two in or near the top ranks, but are relatively "pure" to start. Systems can be gamed, however, and predators naturally flock to power. Over time, seemingly minor changes in policies and practices can throw a cloak of secrecy over the workings of the executives, and then it is free-for-all time. The predators produce an Enron-like setup in which massive fraud is the norm and non-predators need not apply for any position of power. Finally the whole structure collapses, often toppled from without by a newer, leaner competitor, or by a (perhaps slightly) more law-keeping power structure such as the Justice Department in the US.

I have another word for these predators: Vampires. They are probably more damaging than the mythical Dracula ever could be. Let us not be their willing victims.

Wednesday, July 30, 2008

His last, but not mine

kw: musings, poems, mortality

In the wake of Randy Pausch's passing last Friday, I watched "The Last Lecture". I didn't get the chance to see it all when it first came out a few months ago. There is no way to do justice to such a monumental, wise accomplishment. I've been a few of the internal places Randy has been, because of my own cancer and chemotherapy. He didn't beat the odds. I did.

While on chemotherapy, I had stamina enough to join a group on a short canoe ride. I wound up saving someone's life, someone who remains a good friend to this day. I've done a few other things I might not have done had I not been faced with my mortality: taken piano lessons, talked a music school director into hiring me to teach guitar, and making a few more mobiles. But in memory of Randy, all I can really accomplish is to offer this poem I wrote as I was completing my chemotherapy, knowing at the time that I had slightly better than 50:50 odds of one more year...but I expected to beat those odds. This poem is copyrighted in 2001, under my real name (Google knows who Polymath07 is):

©Polymath07, 2001

Let me tell you what it’s like
When the nurse has put a spike
   Into your arm, and poison drips into your vein.
You may contemplate your fate,
Though it’s getting rather late
   To be preparing for what cannot come again.

Oh, you never can prepare
For the sudden, chilling scare
   When the doctor sighs, with sorrow on his brow:
For you knew it all along,
But you hoped that you were wrong—
   For when he says the words, “It’s cancer,” you think, “How?”

In the middle of the night
I awakened in a fright,
   And then I realized, the surgeon’s done with me.
That mechanic spent his day
Digging deep, to take away
   What once was “me”, but now became my enemy.

I can scarce recall the days—
For I spent them in a haze—
   The fight to overcome the pain and lassitude.
And the nurses were so kind
That I really didn’t mind
   It when they made me stand and walk, and eat my food.

Now, this poison is my friend,
And this ordeal soon will end;
   Soon another stage of living can begin.
Having faced my own demise,
Fear is gone, and I arise
   To live this new life that’s returned to me again.

Saturday, July 26, 2008

The Fusion Solution - and Opus 500

kw: book reviews, nonfiction, polemics, opinion, education

All our oil imports come from hostile Islamic nations, right? I thought so until I looked it up. I got the motivation to look it up from Glenn Beck, upon reading his new book An Inconvenient Book: Real Solutions to the World's Biggest Problems. If you can't stand the suspense, look at the bottom of this post for an eye-opening table. The conclusion is that about half our total petroleum imports come from Canada plus Mexico plus Venezuela plus a few other South American nations. That is, from the Western Hemisphere. Saudi Arabia is the second-biggest supplier, after Canada. Surprised?

Inconvenient puts energy matters in the middle of a 22-chapter volume that offers information, commentary, and realistic solutions to everything from boosting our memory of names to political correctness, which underlies many of our most thorny issues.

Beck calls his radio and television programs "the fusion of entertainment with enlightenment", and that is certainly a fair description of this book. I must certainly agree with Beck when he advocates the elimination of tipping. In Japan, for instance, offering a tip is considered an insult. It is just a way to get overly hopeful wait staff to accept wages below the "minimum" (another item Beck prefers we abolish)...and has become some kind of institutionalized bribery scam. Now we get "tip advice" from the newspaper deliverer (not a paperboy any more)!

I also agree that professorial tenure ought to be abolished. It just perpetuates mediocre instructing. And I agree that the human component of global warming is likely to do more good than harm. In fact, I find it hard to disagree with Glenn Beck. He is fast with a quip on his live programs, but his basic facts are always well researched, including an analysis in chapter 22 of this question: Why has no administration done more than pay lip service to border security? His conclusions are scary.

Beck is fond of saying that some things "cause blood to shoot from my eyes." Whether you like and enjoy him, or shoot blood from your eyes, this book has plenty of food for thought.

Based on statements in Beck's seventh chapter, I copied the following tables from the U.S. Energy Information Administration:

Crude Oil Imports (Top 15 Countries)
(Thousand Barrels per Day)
Country May-08 Apr-08 YTD 2008 May-07 YTD 2007


Total Imports of Petroleum (Top 15 Countries)
(Thousand Barrels per Day)
Country May-08 Apr-08 YTD 2008 May-07 YTD 2007


Wednesday, July 23, 2008

The man who made science modern

kw: book reviews, nonfiction, science, physics, biographies

When someone asked Paul Langevin, whose room at Cavendish Laboratory was next to Rutherford's, if they were friends, he replied, "One can hardly speak of being friendly with a force of nature." The remark supplied the title for a new book by Richard Reeves: A Force of Nature: The Frontier Genius of Ernest Rutherford. The book is not simply a biography; Rutherford has many biographers, most notably David Wilson with Rutherford, Simple Genius. This volume focuses on Rutherford's 1909 discovery of the atomic nucleus and that of particle-induced fission in 1923.

Along the way, Rutherford's life is covered in a brief way, from his boyhood in New Zealand, winning a scholarship to Cambridge in 1895, to professorships in Montreal and Manchester. He was a rare scientist who was an able administrator and promoter of science. Indeed, many of his students became Nobelists, and he introduced, almost unwillingly, the era of large machinery such as particle accelerators. The largest machines of human invention today are particle accelerators that cover several square miles of territory.

It started with a few milligrams of radium, a wisp of gold foil, and a lead block with a slitted hole, all enclosed in a vacuum chamber the size of a hatbox, holding a detection screen and a viewing microscope. Rutherford or an assistant had to sit in the dark for a half hour or so before looking through the microscope to see tiny specks of light produced when an alpha particle, having passed through the foil, or scattered at some angle, struck the screen.

When the foil was a lighter metal, the scattering seemed to be confined to a very narrow band around the image of the slit one would see if the foil were not there. But heavier metals such as gold and platinum produced a wider band and occasional sparkles further away. At one point, realizing these off-center sparkles were telling him something, Rutherford asked for the apparatus to be modified so they could look for scattering at all angles. It was found that a few particles were scattered right back in the direction from which they had come.

Rutherford later remarked that it was "as if you fired a fifteen-inch shell at a piece of tissue paper and it came back and hit you." Alpha particles are heavy and fast. Atoms were then thought to consist of a rather smooth mix of positively- and negatively-charged "somethings" that somehow avoided destroying one another. This experiment indicated that there was something heavy at the center of each atom, containing most of its mass, and that this central mass had a diameter smaller than 10-11cm (now known to be of the order of 10-13cm). In the case of gold, this Nucleus with its 79 positive charges had a long reach and scattered the alpha particles away from quite a distance, in terms of its own size.

Rutherford was a great experimenter (something in which I stand in awe, as I am a rather poor one). He was nearly the last of the "sealing wax and string" workers. Some of the students he inspired became the first room-full-of-big-machines experimenters.

Two of them were John Cockcroft and Ernest Walton. I'd wondered about them since using a Cockcroft-Walton accelerator when I was a physics senior. This image of Walton in his protective cage almost inside the first such accelerator shows what one had to do to avoid being impaled on a bolt of artificial lightning! No matter how you produce it, a large static charge with a potential of half a million volts or so can jump a few feet and fry you just as quickly as your bug zapper destroys a mosquito. At such levels, you don't get electrocuted, you get annihilated! In spite of the risks, Rutherford's "boys" were the first to split a Lithium atom by whacking it with fast protons. Though circular machines soon took over the race to greater energies, a C-W accelerator is a powerful tool even today for certain experiments...and this one is the 1923 model.

Through and behind it all, it was Rutherford's drive and personality that inspired and drove student after student to invent whole new branches of science; he was not just a giant of science but a maker of giants. We need more like him.

Tuesday, July 22, 2008

Preview the sights

kw: observations, travel

I am a bigger and bigger fan of Google Earth! I am planning a trip to Oregon and Washington, and decided to drive through the Cascades from Portland to Tacoma. Recent versions of Google Earth can tilt the view to horizontal, so I decided to see how the mountains would look from different vantage points.

I quickly discovered that Highway 5 runs through a valley and the mountain views are blocked by foothills nearly all the way. I decided to take the slow way: WA-503 to NF-90 past Mt St Helens on the east, then US-12 to WA-123 and Stevens Cyn Rd past Paradise on the south side or Mt Rainier, before taking WA-161 north into Tacoma. Then I used Google Earth to scope out which sections of these roads provide good views of the two mountains. I clipped images from the screen and pasted them into PowerPoint to make two montages. Click on the images below to see 1200x900 versions (so you can see the roads better).

First, the southern target, Mt St Helens. The montage shows two views (one pretty poor) on the approach, and two as one leaves to the northeast. Together, they provide views covering about 120 degrees of the south and east sides of the mountain. I won't go to Spirit Lake, which is at the end of a very winding road.

This montage shows five views, though I don't plan to go up WA-123 far enough to see one of them...time will tell.

All together, the drive time on this route is more than six hours, compared to 2.5 hours via the highway. It is my hope that the previews will help me plan the trip efficiently. It sure helped me avoid a road or two that would have provided a view of little more than nearby ridges.

Quick trick with the newest version of Google Earth: to tilt the image toward a more horizontal view, hold Shift while scrolling the wheel on a wheel mouse. You can also use Shift plus the Down Arrow to tilt toward a horizontal view, and Shift plus the Up Arrow to tilt toward a more vertical (straight down) view.

Sunday, July 20, 2008

Life on the ragged edge of eccentricity

kw: book reviews, nonfiction, asperger's syndrome, memoirs

The DMS-IV calls it "Asperger's Disorder", and distinguishes it thus:
  1. Severe and sustained impairment in social interaction.
  2. The development of restricted, repetitive patterns of behavior, interests, and activities.
  3. The disturbance must cause clinically significant impairment in social, occupational, or other important areas of functioning.
  4. In contrast to Autistic Disorder, there are no clinically significant delays in language.
  5. There are no clinically significant delays in cognitive development or in the development of age-appropriate self-help skills, adaptive behavior (other than in social interaction), and curiosity about the environment in childhood.
  6. The diagnosis is not given if the criteria are met for any other specific Pervasive Developmental Disorder or for Schizophrenia.
Let's compare point A with these items:
  • Have very high standards for performance, which they apply to themselves.
  • Independent and original, possibly eccentric.
  • Work best alone, and value autonomy.
  • Have no desire to lead or follow.
  • Live primarily inside their own minds, and may appear to be detached and uninvolved with other people.
Looked at positively, these five items are characteristic of good workers in almost any creative field. However, taken a little too far, these characteristics can be very off-putting; Criterion A might be a natural result.

Item B above is written to sound weird. Think another way: "Has narrow interests, enjoys a few, focused activities, is very consistent and persistent." These could describe virtues. Think of a prototypical trial lawyer: consistent and persistent is what you want, in spades! But these characteristics are also seen in people described by the five bulleted points above: those who fit the Myers-Briggs Type Indicator INTP.

INTP abbreviates Introverted, iNtuitive, Thinker, Perceiver. This personality type tends to be creative, withdrawn, and inwardly-directed. Take the INTP personality to an extreme, and you pass first through Asperger territory, then into Autism. I am INTP, about which more later...

I know several people with varying degrees of Asperger's Syndrome, and I've known several people in the past that, in retrospect, also fit the pattern. On the "mildly impaired" end of things, I think of Robert Leighton, the Physics Department chair at Cal Tech, and my boss for a few years. Brilliant, eccentric, and much better as a scientist than as an administrator, though he managed to do a pretty good job running the Department. Having myself learned to "build a personality", having found my natural endowment somewhat lacking, I could recognize the same in him. We got along very well.

At the "more impaired" end, but still a far cry from being Autistic, I think of two Operating Systems Analysts I knew who worked for Control Data in the 1970s and '80s. There was a running joke about the company's top programmers, who were "kept in cabins in the Minnesota woods and fed infinite amounts of pizza and Pepsi." On an occasion when these gentlemen were permitted to attend a developers' conference, they were painfully asocial. Not that they didn't try...they just couldn't. But if you got either one going on his favorite corner of the "deep code", watch out! You'd get a force-fed education in just how that stuff worked. It was amazing to see these shy guys, who couldn't raise their eyes above the floor, become eloquent, passionate, and engaging. None of us then had ever heard of Hans Asperger or the condition named for him.

I count John Elder Robison as my newest Aspergian acquaintance, having read his memoir look me in the eye: my life with asperger's. As he describes himself in later life, I see someone a lot like Dr. Leighton. He learned, over a span of decades, how to be liked by others, something that comes almost without effort to personality types with an "E" (for Extrovert) at their beginning. E types outnumber I types about 8 to 1, and as author Robison discusses where he fits into the spectrum of human life (not just the Autistic spectrum), he explains that a touch of Aspergian traits seem to be part of the creative personality.

Aspergians have a rough time growing up. They experience more rejection than most kids. I was particularly taken with an item that Dr. Asperger noted, but that is not part of the modern diagnosis: clumsiness and athletic ineptitude. This part of Robison's experience really mirrors mine: the last chosen for a team, the first ejected. In my case, I have a secondary explanation. I had polio.

On a side note, I am not self-diagnosing myself as Aspergian. I recognize that I have a bit of the hypochondriacal tendency that makes one speculate, "Do I have that" about almost anything. While I did undergo some psychoanalysis as a pre-teen for being "withdrawn", my experiences are much milder than those described by John Robison. He seems to be one in a line of Aspergians, which he did not really scope out until he'd made peace with his father, shortly before his father died. And his son is somewhat Aspergian, to a milder degree.

In his 20s, Robison had become a sound and special-effects technician for KISS (smoking guitars, for example). He could have continued a career as an electronic savant. He thinks now that would have led him further toward full Autism. Somehow, he had it in him to make the choice for a more "ordinary" life. But he found that he didn't like being a corporate drone, even a high-paid one. For twenty years he has owned and run a very valued repair shop for high-end European autos. Being the owner is what it took for him to get the degree of autonomy he needed.

That is one strong characteristic of the Aspergians I know, a need for autonomy. It is a cruel reality that many of them are so bad at the social relations needed to actually live well as their own boss, or to carve out an autonomous niche in a corporation. It takes enormous energy.

I consider this book required reading for everyone. We all know some people who are a bit weird, and in many cases, Asperger's condition is why. Let's begin to think of it as Asperger's Condition, rather than "Disorder" or "Syndrome". That makes more sense, and is kinder.

Friday, July 18, 2008

The clocks in the rocks

kw: book reviews, nonfiction, geology, geological history, radioactive dating

In the early 19th century, once William Smith had discovered the correlation of strata by index fossil assemblages, and published Strata Identified by Organized Fossils, you could use illustrations such as these to identify the key fossils for rocks of a certain formation. "Formation", to a geologist, refers to a sequence of rock strata with a certain range of ages. In 1820 those ages were not known, but their relative order was known. Cambrian rocks were the oldest layers with fossils, Permian was in the middle, and the Tertiary and Quaternary formations were the youngest. Debates over just how old these were went on for generations, until the discovery of radioactivity. This image is from a lovely site that reproduces William Smith's book for us: William Smith on the Web.

By 1950 it was possible to measure the amount of trace elements in certain rocks to determine their ages. Some radioactive isotopes, primarily C14, have half-lives of a few thousand years, making them ideal for dating (determining the age) artifacts younger than forty or fifty thousand years. Others have much longer half-lives: U235, for example, has a half-life of 710 million years, making it one of several very long-lived isotopes that are ideal for measuring the ages of rocks as old as the formation of the Earth 4,540 million years ago.

The main Uranium isotope, U238, decays through a dozen steps to produce an isotope of Lead, Pb206, with a half-life of 4,470 million years. When only this was known, the first age date on a Uranium-bearing mineral was done by extracting the lead and weighing it. In the two or three generation since that was first done, our techniques have improved somewhat...

This image, scanned from a recent (2003) article, shows a magnified Zircon crystal and associated facts discovered from it. The crystal was mounted in plastic, sectioned and polished, then attacked with an ion microprobe that made the eight pits that are numbered in the illustration. The pits are small, just twenty microns in diameter, and perhaps equally deep, but Zircons typically contain as much as a percent of Uranium, or sometimes a few percent. That means, among the Zirconium and Oxygen vaporized to make each pit, there were a few billion atoms each of Uranium and Lead, and millions of atoms of the rarer isotopes.

Modern instruments count each atom of an isotope of interest. Poisson statistics indicate that the uncertainty in a counted measurement is roughly the square root of the number counted. If you count a million atoms of Pb207, the uncertainty (formally, the standard deviation) is about a thousand counts, or 0.1%. In pits this size you can zap several times each, getting several counts for each isotope, and get a very precise result. All that from a crystal nearly too small to see! No more dissolving a big lump of Uraninite to extract a few grams of lead!! The curved line on the chart is a Concordia Curve, and deviations from it indicate either contamination or reheating of a sample. One typically measures a number of samples because trends of the measurements can often help discern both the age of reheating and the age of original formation, and distinguish reheating from contamination.

The development of these and other methods of dating using radioactive isotopes is outlines beautifully by Doug MacDougall in Nature's Clocks: How Scientists Measure the Age of Almost Everything. Dr. MacDougall, a retired professor of Geology, takes a strictly geological and radiological approach, so this book actually doesn't cover all the kinds of "natural clocks" that exist (such as mitochondrial DNA mutation rates or circadian rhythms). The radioactive elements decay with mathematical precision; other processes are more variable.

Come to think of it, although C14 decays with a half-life of 5,730 years, it is not produced at a very steady rate. Let us first suppose that C14 were produced at exactly the same rate always. Then it would be incorporated into all plants in exactly the same proportion to C12, and spread throughout the herbivorous and carnivorous animals in short order, so that every creature when it died would contain exactly the same proportion. All one need do then is measure how much of it is left to calculate the time since the creature died. There is the tiny complication that some of the Carbon in your bones and teeth has been there for decades, but compared to the 5,730-year half life, it is insignificant.

As author MacDougall explains so well, however, C14 is produced at a slightly variable rate. It forms when cosmic rays hit Nitrogen atoms in the upper atmosphere. The rate that cosmic rays reach Earth varies with several things: variations in Earth's magnetic field, the 11-year solar-magnetic cycle, and longer cycles that probably have cosmic origins. So calibration is needed.

This image shows a small part of a calibration curve known as Intcal98. It is used thus: The remnant C14, say in a piece of old bone or charcoal, is measured and used to calculate a "C14 age". Such ages are always referenced to 1950 as the zero age, meaning you subtract out any years from 1950 to the current year. Then, roughly speaking, you draw a line across from that age on the Y axis to the calibration data shown, and read off the age range from the X axis. So from this graph, a C14 age of 11,000 years turns into a Calendar age of about 12,850 years. In actual practice, the 11,000-year age would have some uncertainty, and this would be combined with the calibration data using an operation called convolution.

What is that telling us? When the C14 age is smaller than Calendar age, it means that more C14 was found than the true age would indicate, because there was more C14 being produced some 13,000 years ago. The symbols on the graph show the calibration data, mostly from tree rings, which have ages that are known exactly. At the lower left you can see part of the Intcal98 consensus curve without its "data cloak".

This image is a small portion of a more recent revision called Intcal04. See this PDF for the whole thing. The different data sets used for calibration are distinguished, and they are explained at the PDF's web site.

For both of these calibration curves, the wiggly nature of the data mean that some eras can be dated more accurately than others. On this curve, you can see that if you were to measure a C14 date of 6,250 years, the Calendar age would be quite uncertain, ranging from 7,000 to 7,150 years before 1950 (or 5050BC to 5200BC). On the other hand, a C14 age near 6,500 years would be much more accurately converted to a date near 5450BC (7,400 years BP).

And let us not forget the people (a tendency of mine). The very human stories, the triumphs and troubles of the players who worked all this out over the past hundred years make for enjoyable reading. The earliest measurements of radioactive isotopes and their decay products required nearly superhuman laboratory skills and skull-cracking effort. With today's knowledge, building an instrument to measure Uranium and Lead isotopes is tedious and rather costly, but not particularly difficult. What is difficult is gathering "clean" specimens and maintaining their cleanliness. The processing isn't hard, otherwise. But what big shoulders we are standing on!

Thursday, July 17, 2008

Bushiness of our family tree

kw: musings, evolution, human origins

You'll need to click on this image to see a version you can read. The chart shows the known historical existence of humans and sixteen other hominids, plus a number of inferred relationships. I obtained this image from Ancestral Lines (

It is most likely that, if Homo antecessor is ancestral to H. sapiens, its ancestor species is either H. ergaster or an un-found species intermediate between the two. Alternatively, H. antecessor could have branched from H. erectus by population isolation. The smaller population would have diverged the most, while the large population remained comparatively stable. Indeed, H. erectus seems to have been stable for a longer period than any of the others that are shown. It is likely that there are dozens of hominid species yet to be discovered, though a good number of them might have left no fossil remains at all.

As I considered this chart, I realized that the genus Ardipithecus may be the direct descendant of the common ancestor species of humans and chimpanzees. It is at most one or two species removed. Then I realized that, if we could find the fossils, the evolutionary path leading to chimps is probably just as complex as the human one. Finding proto-chimp fossils is much less likely than proto-humans because chimps live in more humid environments.

A September 2005 article in the Washington Post (here) reports on the sequencing of the chimpanzee genome, all three billion base pairs. The number of differences between chimp and human comes to forty million, or 1.3 percent. While most of these are probably SNP's (single nucleotide polymorphisms), a number of larger changes and rearrangements also exist. For example, chimps have 48 chromosomes and humans have 46. Further, the scientists are reported to have a list of 250,000 DNA changes that define the differences between the two species. That is 0.6% of the changes, which seems a reasonable number; it is about one-third of the ratio of coding to non-coding DNA: coding DNA is about 2% of the total in both species (and a tiny fraction is regulatory DNA which doesn't code for proteins but controls DNA coding or produces RNA that does so).

I call that reasonable because changes happen more freely and usually without consequence in non-coding (and non-regulatory) DNA, while DNA that codes for proteins or regulatory sequences is resistant to change because so many of the changes are deleterious.

Within the human species, each of us carries a million or so molecular changes to our DNA, including the three or four thousand that affect "real stuff" and make us visibly and behaviorally unique. These account for human diversity (The amount of genetic diversity among chimpanzees is much greater, but I haven't seen a particular value).

Backing off a few more steps, it seems logical that every species living today has a similarly bushy "family tree" that lies behind its existence. This is why paleontologists say that only a tiny fraction of fossil species will ever be found. We're lucky to have the fossils we do have!

Tuesday, July 15, 2008

The bridges to everywhere

kw: book reviews, fantasy, alternate worlds

Will Rogers famously said, "Invest in land. Nobody is making any more of it." In Shadowbridge by Gregory Frost, somebody has been making, if not land, a good substitute: immense bridges that connect islands in a world of archipelagos. Whether newer bridges are still being built is left open.

The people's creation myths posit the sudden appearance of the bridges out of dreams, the infertile dreamer(s) then becoming fertile and peopling the planet.

I found myself puzzled as, having read 80% of the book, I considered the setting-up just about finished, until I re-checked the cover where it states there is a second book to come. Thus, this first novel, to be followed by Lord Tophet (probably next spring), primarily introduces the characters: Jax (stage name of Leodora), a gifted storyteller whose medium is shadow puppets; the magical musician Diverus; and Leodora's old mentor Soter. They share the setting with demons, elves, and stranger creatures.

For me, the attraction is the stories. Frost has evoked new ways to clothe old archetypes in the psyches of an imaginary world. It has been said that there are but four stories, and we re-tell them with new characters and new environments that suit our generations. Actually, whether there are four or four dozen, every story is re-told many times in every generation. Just think of Romeo & Juliet, Paramus & Thisbe, and every story of star-crossed lovers. Today's preferred stage is the tragic lives of "celebrities", re-telling their foibles upon the tapestry of our imagination, ennobling or debasing them as needed.

Though Jax is a puppeteer, only the merest sketch of puppet technique is mentioned. The power is in the storytelling, and at this, author Frost is a master. Jax/Leodora collects stories, and the scenes where new stories are told are easily the most powerful: Jax and Diverus in a haunted park, learning a new creation myth from a were-fox, or Leandra on shipboard, hearing a large water-snake tell how death came to the snakes.

This then is the lesson of the book. A story teller is a story maker. The stories we are told are like groceries that we re-combine and cook up into new stories, the stories of our own lives.

Friday, July 11, 2008

A Narrow, narrow miss

kw: book reviews, nonfiction, viruses, biology

The Colonels Jaax, Nancy and Jerry. In 1983, Nancy Jaax came within a few microns (the thickness of a surgical glove) of being infected with Ebola Zaire, the "hottest" strain of Ebola virus. It was her second time working in a BSL 4 containment, in a "blue suit", and her first experience doing any work there.

BSL 4, BioSafety Level 4, describes a total isolation (as near total as is technically possible) between specimens containing infectious viruses or bacteria, and those who work with them. This very costly sort of "clean room" (or very, very dirty room, if you think of it) containment for specimens, including living (temporarily) lab animals such as infected monkeys, is reserved for a handful of the most dangerous agents, including several strains of Ebola and the Marburg virus.

These two relates species make up the genus of the filoviruses, or thread viruses. They and other BSL 4-rated species kill 10% or more of their victims, typically within a week or two of exposure. By contrast, the much-feared AIDS virus, HIV, though it seems to kill at least half, takes one or two decades to do so.

Have you ever had surgery, with the antiseptic washes, the surgeons and nurses in scrubs, masked and gloved? If so, you were in a BSL 2 containment, and it was you who were being protected. It costs tens of thousands of dollars (or Euros) to set up BSL 2 facilities, and tens of millions for BSL 3 or 4.

This is the Marburg Virus. Ebola looks about the same. It takes an expert to distinguish the various thread viruses from photographs. Biochemical and DNA tests are needed to be sure which strain and which species is which.

In a way, these are very primitive viruses. The thread is a protein structure about 70nm in diameter, or about 1/20th the diameter of an E. coli bacterium. The structure is hollow, containing a simple coil of RNA and another protein or two that initiate RNA transcription and duplication once the virus is taken into a cell.

Cells can be remarkably stupid. They tend to take anything into themselves that is coated with protein. Many viruses take advantage of this.

Once a cell contains an active ("living" is not really the right word) virus particle, it changes completely. Enzymes in the cell help the virus remove its protein coat, and others get suborned by the RNA and replicase proteins. The cell begins to make copies of the virus's RNA. The raw RNA is a (-) strand. Copies from this strand are (+) strands. The (+) strands and the cell's ribosomes begin making virus proteins (there are fewer than ten for a filovirus).

Once some (+) strands have been made, the replicase proteins will, by chance, produce equal numbers of (+) and (-) strands of RNA. The (-) strands and the virus proteins self-assemble into new virus particles (the uncoating enzymes have been deactivated by this point). The (+) strands keep churning out new proteins. In the case of Ebola and Marburg, the cell gradually fills with one or more "bricks" of compacted virus particles. When a brick contacts the cell wall, the cell ruptures, spilling out a few million viruses that infect all the cells in the vicinity.

The above sequence takes no more than a few hours. Because filoviruses travel through the blood stream, they invade the whole body in short order. Cells of every kind, in every imaginable location throughout the body, become filled with virus bricks, then burst, and so on. Within a few days, to at most two weeks, symptoms such as headache begin. Depending on which specific strain one has, there is a chance between 24% and 90% that the whole body will melt down and turn to a mixture of destroyed cells and viruses. This kind of explosive amplification can result in an ounce or more of each pound of body weight becoming virus. That is whole continents, whole planets, whole galaxies full of viruses, billions of billions of billions, taking over a body in just those few days.

It is not known what species is the reservoir for any strain or species of filovirus. One of the very few things we think we know: All known filoviruses are very, very deadly to primates, including humans.

The above is good background to prepare your mind for reading The Hot Zone by Richard Preston. Just nineteen years ago, around Thanksgiving time in 1989, there was an outbreak of a new strain of Ebola in a "monkey house" in Reston, Virginia. Reston is a suburb right outside the Washington, D.C. beltway. The monkey house in question housed 500 monkeys from the Philippines, that were being prepared to be sent to laboratories around the country. These 500 never made it out of the building...

The Hot Zone chronicles the Reston outbreak, sandwiching it between a clear, chilling introduction to Marburg and the two main strains of Ebola, and an account of the author's pilgrimage in 1993 to Kitum Cave, in Kenya. The Marburg virus is thought to originate near there, perhaps in one of the species endemic to the cave...but we don't know for sure.

The book lacks an index. It lacks little else. It has been called a bio-thriller, but it is much more than that. The language is not hyped in the way you'd expect of a fictional thriller. It is as matter-of-fact as butter on bread, but as compelling as a ride on a roller coaster. Early on, I looked up some of the principal players, such as the Jaaxes shown above, especially because I couldn't bear the thought that she might have died.

She lived, and lives today. She and her husband were central to the military operation that (with the company's permission) cordoned off the monkey house, made the whole place into a BSL 4 containment, and destroyed all life within it, first the monkeys and the viruses they contained, then every insect, bacterium, and virus within its walls. That is, everything was killed that the team was able to detect and verify as dead. One can never know for sure.

Strangely, the Reston strain of Ebola is not known to have caused any human deaths...yet. We can't say if we dodged a bullet, or if the bullets simply were a strain that kills monkeys but doesn't affect humans. We simply don't know if there are lots of other filoviruses out there that can't infect people. We only know of the six or seven that can.

Author Preston makes it clear that there is no way to ensure that this won't happen again. The tropics are a day away by modern aircraft. A person infected with Ebola has three to ten days of no symptoms, in which to travel to London, New York, Paris, Tokyo, New Delhi or Beijing...and at least the Reston strain and one other can be transmitted in the air, by a cough or perhaps just by speaking. At any time we could be less than a month away from the near-depopulation of planet Earth.

Wednesday, July 09, 2008

Possibly the luckiest man still alive

kw: book reviews, nonfiction, war, journalism

It is amazing that I can read two books, very similar in size, but I finish one in two days and the other takes a week or more. I usually get through fiction faster than nonfiction, but not always. The current two-day marvel is In the Hot Zone: One Man, One Year, Twenty Wars by Kevin Sites. The book comes with a 90-minute DVD that covers about half the wars, and the videography and editing make it even more compelling. I managed to survive watching it while eating lunch; not a practice I recommend...

A summary of the wars, not in the order presented:
  • Hot shooting wars ongoing [9]: Afghanistan, Colombia (50+ years, continuing), Iraq (& West), Kashmir, Israel (& Palestinians + allies), Chechnya, Somalia, Sudan, Uganda
  • Unstable but not currently active [1]: Haiti
  • Cease-Fire or under negotiation [5]: Congo, Lebanon (Hezbollah & Israel), Myanmar, Nepal, Sri Lanka
  • Conflicts of the somewhat recent past [3]: Cambodia, Lebanon (& Syria), Vietnam (& West)
  • Potential [2]: Iran (& West), Syria (& West)
The author's relentless focus is not on the military operations themselves, but on their effects on the populations. I once invented an epigram for a college paper: "History is made by the rich, suffered by the poor, and forgotten by their grandchildren". As the four current African wars reported here make clear, I was wrong, or at least one-third wrong. Not all history is forgotten when it involves atrocities between ethnic groups. The northern Iraqis, the Kurds, do not forget.

With the exception of a very few of the very rich, war makes all into paupers. It may seem that the fighters, at least on the stronger side, are able to live relatively well, but they suffer a relentlessly growing poverty of spirit. Nobody really wins a war.

The book is full of personal stories. A dying old man in Iraq whom the author could have at least comforted a little, but did not. He accuses himself for that, and is much comforted when he is able to render help to another, though he must break the journalist's code of noninvolvement to do so. As the segment in the DVD makes clear, all the journalists got involved that time, carrying people out of the rubble on doors made into stretchers. A child bride in Afghanistan, who suffered more tortures in six years with her "future father-in-law" than nearly any abused prisoner of war. This woman or that one, a victim of "rape as a weapon of war". Terrorism isn't just bombings.

In fact, since the old rules of gentlemanly engagement (which were honored mostly in the breach anyway) were swept aside in favor of "total war" just over ninety years ago, every war has been carried out primarily by terrorist methods. The "shock and awe" campaign that began the most recent Iraq war was intended to terrorize. I have read that the 21st Century American "battlespace" is a defined zone in which no opposing force can survive more than a few minutes.

Yes, indeed, we're getting better at war. At least during the two Great Wars of the 20th Century, slightly more than half the total casualties were military forces, for most countries involved (no, I'm not forgetting the Holocaust, and there were actually three of those). These days, a civilian population needs to count itself lucky to "only" have ten to one hundred civilians killed per military casualty.

Kevin Sites must count himself very fortunate to be among the living. To spend ten to twenty days in each of the war zones mentioned above, and survive, is so stunningly against the odds, I'd have to say God had something to do with it. This book is full of stories that need to be told. I am thankful that the Kevin Sites blog and Hot Zone web site are presenting them to anyone with an internet connection.

Monday, July 07, 2008

Passing one by

kw: opinion, book note

As my most recent "wild card" choice, I picked Blood on the Table by Colin Evans. It is subtitled The Greatest Cases of New York City's Office of the Chief Medical Examiner. Having read the first chapter and half the second, I've decided not to continue.

The book is clearly superbly written and well done. However, as a person determinedly wrapped up in the dispensing of life, I found its emphasis on murder and suicide just too much. I should have guessed, considering that the title and introduction make clear it is about the "super coroner" position, pioneered by New York City just ninety years ago. Of course, coroners' "great cases" have to do with figuring out the How's and Why's of death.

So I'll pass it by, in favor of a book of war correspondence. The focus in this book, at least, is on the lives of people affected by war, more than upon the deaths of those the survivors are bereaved of. Stay tuned.

Sunday, July 06, 2008

Seeds of discord, winds of change

kw: book reviews, nonfiction, biology, genetic engineering

Contrasting statements:
  1. From the Statement of Policy of the FDA, "Ultimately, it is the food producer who is responsible for assuring safety."
  2. From Monsanto's director of corporate communications, "Monsanto should not have to vouchsafe the safety of biotech food. Our interest is in selling as much of it as possible. Assuring its safety is the FDA's job."

Dr. Richard Strohman of U. Berkeley has written, "DNA is most definitely not the secret of life...the idea that there is a direct relationship between a single gene and a single trait is completely erroneous...[this is] the myth of genetic determinism."

This myth underlies the entire biotechnology industry today. In Uncertain Peril: Genetic Engineering and the Future of Seeds, Claire Hope Cummings chronicles how the misapplication of genetic ideas is undermining the foundation of the world's farming enterprises. Her charges against the biotech industry are as numerous as they are large. In whatever measure they are correct, they foretell a greater threat to the sustenance of civilization than any other effect of human activities.

Did you know that tomatoes and potatoes, being related and being members of the Nightshade family, are potentially quite poisonous? A large salad of tomato greens can stop your heart. Yet the fruit is nutritious and quite safe to eat! How can this be? The fact is, many, many plants produce various pesticides as they struggle to grow to maturity without being eaten down to the roots, yet their food parts contain no trace of these pesticides. So why are such critters as the Tomato Hornworm able to eat the leaves without harm? In the perpetual arms race that is evolution, this worm is one critter that has evolved a way to inactivate the Nightshade toxin in its food.

In the perpetual struggle of science to imitate nature, and it is hoped, do her one better, biotechnologists have sought to take potent natural pesticides such as the toxic proteins of B. thuringiensis and cause their expression in food plants. These plants then grow with less need for the application of chemical pesticides. Getting them to produce their own "BT toxin" has been seen as a simple matter of getting the right gene from the BT bacterium into the genome of the plant you want to grow. But there is a catch, a big one.

The scatter-shot methods being used to get novel genes into the genomes of crop plants seldom work, but when they do, they work too well. "BT corn" (BT maize), for example, expresses the BT toxin proteins in equal amounts in all its cells, even though the pests that BT affects mainly attack the roots, and the leaves a bit less. They don't attack the kernels much at all, leaving that to a different array of pests that aren't bothered by BT! The problem comes when we find that many people are harmed by BT residues.

Many farmers rely on sprays of BT organisms, the natural bacteria. These effectively kill pests, and the toxins can be washed right off the kernels after harvest. People can't avoid ingesting BT toxin if it was produced right inside the cells of the kernels.

So why haven't folks done the extra work to get the BT genes into a section of the genome that is "turned off" in the kernels? There is a nice, convenient stretch of DNA that contains the plant's natural pesticide-making genes, which are switched off in the seed cells.

Such precision of placement is quite out of the question with "modern" technology. Simply developing the methods that would allow it is prohibitively costly. Oh, it will get done anyway, but slowly, almost as a side effect of other studies. But this is only one instance, and in this case, the relevant target is pretty well known. For most plants, they'll also have to do more science to figure out exactly where to put new genes, to take advantage of such natural switching mechanisms.

All this digression is my own, an introduction to the troubles we are getting ourselves into by creating GMO's, Genetically Modified Organisms. And this is just one of those troubles. Ms Cummings outlines several areas of peril, but the greatest is the loss of seed diversity.

Industrial processes rely on control, and control requires uniformity. Industrial agriculture, which is now almost universal in the West, controls its markets by controlling seed varieties. Each seed company boasts of its "broad line" of varieties, and such lines do seem broad: ten or twenty varieties of a particular species. But contrast that with the contents of seed banks, that have existed or do exist today, with their tens of thousands of natural varieties per species.

For example, around the world there are more than five thousand varieties of rice being grown, and most of this diversity is in the hands of small planters who share seed among themselves, continually seeking the best variety for their combination of soil type and climate. Because all the grains are wind-pollinated, rice growers know that their own fields will produce best if they and their neighbors all grow good, strong varieties. It is thus in their interest to give the seeds of better varieties to any of their fellows who are having trouble with their harvests, in hopes that the winds will carry a good mix of the strongest rice varieties, to the benefit of them all.

Contrast this with the grower who buys seeds of only one variety for a million-acre planting, a variety that is a sterile hybrid, so that he cannot even keep back a part of the harvest for planting the following year. Not only that, he must sign a contract not to try to do so, in order to get these special seeds at all!

The dirty secret behind the bumper crops that super-seeds produce is that their harvest will utterly fail without constant, costly application of fertilizers and "crop protection" chemicals. The upshot is this: the small farmer using traditional seeds may have a lower yield per acre, but the cost to produce it was much less.

The risk of large monocrops is not just that a new pest will arise to decimate the entire season's crop. It is that a huge number of non-patented varieties is ignored, many are no longer planted, and many go extinct.

This is a tiny tip of the iceberg. Author Cummings sees hope, in spite of the perils. Increasing numbers of farmers, seeing the hypocrisy in the two statements I began with above, are rejecting the industrial model of agriculture. One promising trend is illustrated by Wes Jackson of the Land Institute in Salina, KS. He has sought to produce a plot of ground that will "produce like a farm field but act like a prairie". A healthy bit of prairie, say a meter square, contains dozens or even hundreds of species. It has the wherewithal to respond effectively to the vagaries of almost any year's weather.

I remember reading, years ago, of the efforts at Malabar Farm in Ohio, Louis Bromfield's experimental farm at which he sought to rebuild the topsoil. He was a particular advocate of multi-cropping, though in his book Malabar Farm he primarily illustrated the idea with a duo-crop of alfalfa and corn. Organic farmers are busily working at ways to extend this idea, taking advantage of natural synergies that abound around us.

Here is a question for you: Why is the ground kept so clear in an orchard? I lived across the street from fruit orchards as a boy. I remember the farmer saying that the right kind of undergrowth made the trees healthier, rather than "robbing" them of water or nutrients. But the ground was kept clear for the convenience of farm workers and harvesters. A pity.

There are many good ideas in Uncertain Peril, and lots of hope. May the hopes outstrip the perils, for our future rests upon them.

Thursday, July 03, 2008

The Singularity approacheth

kw: musings, cultural evolution

I once read a SciFi (or SpecFi, perhaps) that chronicled, at breakneck speed, one night in a future society. In this one night, fortunes were made and lost, and made again, marriages were forged, consummated, and dissolved, and it seems the only thing you couldn't pass through in a single night was carrying a baby to term. The term wasn't mentioned in the story, but it was a day just before a "singularity", when the pace of cultural evolution becomes infinite...or it collapses.

As a member of the Sandwich Generation, I have been observing the cultural expectations of my son, my father, and myself. This is the more keen as I consider courtship, which seems to be approaching just such a singularity, in the light of the letters I am collating and curating. I found a touching photo in a letter sent late in February 1944.

One day my Dad-to-be and two friends borrowed a Brownie camera and took pictures of one another, then one of the friends developed and printed the film in the darkroom on the post (They were newbies in Officer Candidate School in Australia). The friend was at least as clumsy as I am, and this image shows the best print of my future father that he was able to produce!

He promptly sent it to his fiancée Ruth, who kept it with the letter, so I found it today. He sent on average 2-3 letters per week, and she sent probably more like 4-6 weekly, from late 1942 until the very end of 1945. If I had all of my Mom's letters, there'd be several hundred, but I have only the first hundred; I think I have nearly all of Dad's, some four hundred.

The letters chronicle a young couple falling more and more in love. No "Dear John" letter for them. They were married 58 years, until my mother's death a few years ago. In a generation that thought a two year engagement "just about right", theirs lasted four. So far as I've noted, they only saw one another once after Dad joined the Army. Telephone contact was incredibly expensive, when it could be made to work internationally at all.

One letter details Dad's attempts to get a plane ride from Virginia to California and back, because he had only a ten-day leave; not enough time to drive it, though he was game to try! The plane fare was $300, round trip. Not only was that more than today's fare on Southwest, it was something like $10,000 in today's terms!

It takes a lot of communication to make love properly (using the old sense of the term). A convenient wartime separation of three years was just about right for them.

My own experience in my current marriage (I had a brief, disastrous one at a too-young age) had a much shorter courtship. But we also took a long time to fall properly in love. My wife and I spent six months in 1975 "engaged". I realize now how lucky we were to stay together. It took us also about three years to become a loving couple who knew how to properly care for one another...and another twenty or so to get good at it. This August it will be 33 years. Amazing.

Now I have been observing my teenage son learn how to cope with young women. He's had a few girlfriends, and made his mistakes. He probably has plenty of mistakes yet to make. He's just nineteen, after all. But he's living in the X generation, culturally. X for eXtreme. With his crowd the X games are more popular than the Olympics. When my generation dies out, the Olympics will have either withered away or changed radically.

Anyway, it is a good thing he has free night and weekend minutes on his cell phone, and his girlfriend the same, because he manages to talk to her 1500+ minutes per month, without incurring extra charges on our 500-minute family plan. I guess if he can bear waiting to marry until he finishes college, they'll also have a huge dollop of conversation to base a solid relationship on. I sometimes wonder if they won't run out of things to talk about...but my wife and I have been talking for 33 years and haven't run out yet, so there's hope.

Everything else he and his generation do, they do at breakneck speed. The ones who never give themselves leisure to communicate, over months and years, are those who become the "50% divorce" statistics. I hope better things for my son.