Innovation can take its sweet time

 kw: book reviews, nonfiction, biology, culture, sociology, evolution, innovation

The cover of the book really catches the eye, being decorated with lovely shells of the Cuban land snail Polymita picta. Interestingly, these snails are never mentioned in the text. These golf-ball-sized snails are considered by many to be the most beautiful snails in the world.

For your delectation, here are some more, from one lot in Berlin's Museum für Naturkunde. 

I happen to consider a different species the "most beautiful", and I'll show some examples below.

The term Sleeping Beauties is used by practitioners of scientometrics (measuring the effectiveness of scientific ideas), to describe articles or monographs that receive few or no citations by other scientists, for years or decades, until they suddenly become "popular", possibly receiving hundreds or thousands of citations in literature. A real "blockbuster" idea might then be cited, and even enter the popular press, for many years. One learns this rather late in the book Sleeping Beauties: The Mystery of Dormant Innovations in Nature and Culture by Andreas Wagner.

The thesis of the book is that innovations crop up all the time but are seldom "on time". They may need to arise a few times before factors in the environment permit them to spread. The first example in the book is grass. Grass evolved about 70 million years ago, but widespread grasslands did not appear until about 25 million years ago in South America and Asia, and 10-15 million years ago in North America. From that time, grasses radiated into thousands of species, from cm-high Alpine grasses to 20-meter-high timber bamboo. Although grasses had several innovations that made them more efficient—growth from the base rather than the tip; drought and heat resistance; SiO2 granules in the tissues—these did not favor them when Earth was mostly moist and tropical. Only in certain isolated areas did the environment favor grasses over other plants. Then the environment changed, and so did the kind of plant cover found on the major continents. The evolution of C4 photosynthesis, which makes plants that use it well adapted to CO2 levels below 1000 ppm, and a change of climate to warmer and drier across large swathes of continents, favored grasses even more over shrubs and trees. Today, even though many decry the rising CO2 level—it is more than 400 ppm now—trees and shrubs are struggling and grow more slowly than they did while dinosaurs were around, while grasses do quite well.

Similar cases are found throughout the natural world. About one-third of the book explains what has happened in evolutionary, cellular, and molecular terms. Basically, every biological entity undergoes many small DNA mutations in various cells yearly. Some are damaging and cause the cell to die. Some affect how a cell grows and it becomes cancerous, which can cause the entire animal to die a few weeks or months later. Most seem to be neutral, in that they don't change the protein a gene makes or the way a regulatory sequence works. Finally, some improve the lot of that cell; as it divides, whatever it is doing (making digestive enzymes, making muscle move, releasing a hormone) might be done a bit better so that daughter cells attain that advantage. In a multicellular animal or plant (a metazoan) a mutation must arise in a germ cell, one that will become an egg or sperm, for the trait to enter the next generation. 

The author argues that small mutations such as SNPs (Single Nucleotide Polymorphisms) occur with great frequency. Some mutations can affect larger things. A SNP in just the right place can disable a regulatory sequence, so that a key protein is no longer made. Sometimes an error in DNA copying causes a whole gene to be duplicated. Then if you have copy A and copy B of that gene, and copy B is the next one to incur a SNP or other mutation that changes its function (usually decreasing it), the organism can get along fine as long as copy A works well. Then further changes to copy B might occur until it is sufficiently modified that it might take on another function. However, let us be clear that this doesn't happen all in one organism, but over several generations. In prokaryotes (bacteria and archaea), where the entire organism is a single cell, it is easier to see how this can lead to rapid evolution. In eukaryotes (protozoa and all metazoa, including almost everything big enough to see), a mutation, beneficial or not, must pass through the bottleneck of reproduction, occurring in a germ cell, or it will not affect the next generation. I think this is not made clear enough in the text. The author deals almost exclusively with single-celled organisms.

I'll step aside from the book's content for a moment. The statistics of metazoan reproduction are such a steep hill for new mutations to climb that it would seem that their evolution must almost come to a complete halt. But there is a "third sex" that transmits genetic information horizontally between organisms, including across species boundaries: viruses, retroviruses in particular. Although some retroviruses (such as HIV) cause disease, others do not. Let's call one of these apparently harmless viruses Friendly Human Virus, or FHV. You'd never notice an infection by FHV, it is so low-level. For a period of time the infected cells would produce FHV particles, and in the process they would incorporate the FHV genome into the cell's DNA. Not all infected cells die. About 8% of human DNA consists of hundreds of "endogenous retroviruses", stored more-or-less intact in our "noncoding DNA" (it used to be called "junk DNA"). Some of the FHV particles your body sheds will include copies of some of your own DNA that the new virus particles picked up during their manufacture, which is a rather sloppy process. When someone is infected with FHV that came from you, cells in that person's body get some of your DNA incorporated into their genomes. The "Viral 8%" is part of a "library" of potentially useful genes that may get activated by other mutations later on. Contrast this 8% with the amount of your own DNA that is actually used to make proteins (2%) and regulatory sequences including ribozymes (another 2%).

There is a lot of terminology in the chapters that form the "meat" of the author's argument. It's OK, it's all well described and defined. By the middle of the book a reader can understand how certain kinds of innovation in evolutionary traits occur over and over, until other factors in the environment one change or another something favorable, something that will spread in a population.

The second half of the book discusses similar concepts as they relate to culture. Culture is not only a human thing, although until a generation or two ago, everyone thought only humans had culture. Consider certain small British birds with bills that can puncture the heavy foil lid of a milk bottle. For many years the milkman left milk bottles on people's porches once or twice weekly. At some point, a bird managed to cut its way into a milk bottle to get a beak-full of milk. Birds observe one another, and when another bird saw the feat, it tried it. Soon, the practice spread throughout the British Isles. Milk is now dispensed in a different way, which thwarts the birds. This is an example that seems to have spread rapidly, but the details are interesting. A little records-gathering has shown that the practice was confined to a small area for a few years, and then spread rapidly after that delay. I haven't learned if it happened more than once, but the author of Beauties posits that every time an innovation is researched in detail, it is found to have occurred several or many times, but only the most recent is usually remembered. He discusses the use of citrus fruits to combat scurvy: it was discovered several times during a period of two centuries before finally "taking hold" in the British Navy, to the point that British sailors are still called Limeys.

In general (but see below), the book is a great pleasure to read. There is a lot to think about, a lot to learn. Evolution has more going on than I'd have thought.

As promised, here is an example of what I consider the most beautiful species of snail, the Splendid Jewel Snail, Liguus fasciatus splendidus. The next picture has a few examples of other subspecies of jewel snails.

These are found primarily in Florida, on the trees and shrubs of "hammocks" (the local pronunciation of "hummocks", elevated, shrubby places in the Everglades).

I have a quibble. On page 181 the author discusses writing systems that were studied in detail by Mark Changizi and colleagues, including Latin, Arabic, Hebrew, Greek, Cyrillic, Chinese and Cherokee. They sorted the characters in a script according to the number of strokes. For example, "O" and "I" have one stroke (when written without serifs), while "M" and "W" have four. Analyzed this way, there are great similarities among writing systems, and he states, "Most characters can be written with three strokes, some with one or two, but none has more than four, regardless of the writing system." I think Dr. Wagner missed something. This is ridiculous if one includes the logographic scripts, primarily Chinese, Japanese and Hangul (Korean). The image at right is scanned from the spine of my Japanese wife's "big dictionary". It reads "Complete Kanji Dictionary Ocean", where "ocean" is an emphatic modifier of "complete"; the corpus deals with more than 80,000 logographs. From top down, the number of strokes are 17, 13, 13, and 10. If one wishes to separately treat the portions that don't touch, dividing a single logogram into its root and "the rest", many of those still have more than four strokes each. Hangul characters usually have fewer strokes than Chinese, but seldom fewer than 5 or 6. I dug around among other languages of Asia. A "swirly" script like Tamil may have letters with few strokes in the formal sense, but some single strokes swirl around so much they may as well be three or four, to which another stroke or two are added. I don't know how one even counts strokes in Sanskrit! And then there's classical Mayan. The characters are very complex, and quite variable depending on the writer. Dozens of strokes are typical. A key concept when looking at a Mayan stela: the carved glyphs are intended to appear a though they were written with a brush in a paper codex (of which few survive).  Probably 95% of the world's scripts follow the "4-or-less" tendency, but it is not universal.

Secondly, as to the structure of the book. The endnotes occupy 38 pages, and more than half the space is devoted to long notes that could have been incorporated into the main body of text, which is 240 pages. Such asides take off from the main text in a way that it's often necessary to go back to the original page and re-read what came before the superscript, to get the thread of the discussion. Bad practice. Dear authors, don't put "asides" in endnotes, just keep them in the main text or leave them out. If something is worth saying, that's where to say it. Reserve endnotes for citations or very (very!) brief elucidations.

A well loved river in these parts

kw: book reviews, nonfiction, rivers, americana, culture, history, north american history

A friend thought it might be time that I learned more about the loveliest river in this area, so he gave me The Brandywine by Henry Seidel Canby, a book in the series "Rivers of America", edited primarily by Stephen Vincent Benét. The book was originally published in 1941; I read a paperback edition of 1969. The pen illustrations within are by Andrew Wyeth, and include sketch versions of paintings I've seen in the Brandywine River Museum and the Sanderson Museum. I live within a couple of miles of the Brandywine River, and I cross it via one bridge or another several times weekly. I also spend hours at a time along its banks in the gunpowder yards, so I guess it is high time!

Dr. Canby was born along the Brandywine in 1878, and though he spent many years as a professor at Yale, he returned to Wilmington frequently. We see through him this small, though significant river as it was between 75 and 130 years ago. Through both personal knowledge and wide reading he can trace the history and culture of the area as none other. In his childhood, though mills for making flour, textiles and gunpowder abounded, much of the Brandywine was still in a rather unspoiled state.

The forbidding geology had a lot to do with this; it was easier to build roads around the middle gorge than to try to cross it. If I recall correctly, Canby wrote that there were seven bridges crossing the river between Forks of the Brandywine in Pennsylvania and its confluence with the Christina River in Wilmington, a linear distance of about 14.5 miles, but more than 20 river miles. In that distance it descends more than 210 feet, a slope that averages roughly 10 feet per mile, but in the middle reaches it drops 33-34 feet per mile, making it one of the most favorable mill streams in the middle Atlantic region. It also means that what Canby calls "the gorge of the Brandywine" has some of the steepest terrain in northern Delaware and southern Chester County, Pennsylvania.

The author writes of the river as a lover of his beloved. He quotes other writers at some length, sometimes deploring their over-sentimentality, though he reflects it himself, just in the more restrained manner of a Yalie in all his dignity. It is a river worthy of much sentiment! During the days on which I volunteer in the yards at the Hagley Museum, situated in the steepest part of the gorge, I find the idle times are anything but onerous, being filled with visual delights backdropped by the rustle and grumble of the river.

It would not do justice to the book to simply catalog its 14 chapters. They are quite comprehensive. Rather, three items struck my fancy. Firstly, that the iconic "log cabin" was introduced by settlers along the Brandywine in the late 1600's, but did not spread beyond the area until nearly 1800. Elsewhere, and earlier here also, the vertical-log palisade was used where defense was needed, and various sorts of European structures otherwise, though they were usually quite unsuitable, particularly when badly constructed (the usual case). A log cabin is much easier for non-professionals to build into a sound and minimally drafty dwelling. Had Abraham Lincoln been born 5 or 10 years earlier, he would not have been born in a log cabin!

Secondly, there were no "Indian wars" along the river. Violent relations with native peoples were practically unknown here, and the great wars of legend took place many miles to the west and mainly after the Civil War. The Lenape and other "Delaware Indians" did find themselves exploited, but tended to complain through legal channels, and when they'd had enough most of them moved elsewhere of their own accord, primarily because of failure of the shad runs rather than violence. Nobody at the time understood clearly that all the mill dams were choking off the migration of the shad.

Thirdly, as already mentioned, in 1940 there were but 7 bridges along the lower Brandywine, and much of the river was comparatively unspoiled. Today fishermen are advised not to eat fish caught in the Brandywine anywhere south of the Forks, and by my count the bridges number 23: 17 road bridges, 3 foot bridges (one half collapsed) and 3 railroad trestles. There are also 9 mill dams still in existence, though only the 3 at Hagley are still in use to keep millraces filled. Compared to many mid-Atlantic rivers, though, the Brandywine still has significant unspoiled stretches. The existence of Brandywine Creek State Park protects one stretch of nearly 5 miles, and Hagley has kept another mile or so in a condition similar to that of 1921 when the mills closed.

I didn't yet  mention the Battle of the Brandywine, George Washington's failed attempt to keep the British from taking Philadelphia. Several good books about the battle had been published by 1940, so Canby gives a well-attested sketch of the engagements, but designedly leaves the details to others. The view from miles above: neither commander knew the area, nor had anyone with good local knowledge on staff; the farmers thereabouts were Quakers and were determined to help neither side of the conflict; scouts sent hither and yon brought conflicting reports; and the British were luckier in finding fords north of the Forks about which Washington was ignorant (as they also had been a day earlier), so they could flank the Colonials and get ahead of them. Thus, the British wintered in Philadelphia and the Colonial army in Valley Forge.

There is much, much more to the book, though it is less than 300 pages. To learn more of the river's geography, history of settlement, business growth, literature and art, and its role in American industrialization, you'll find this book a valuable and very entertaining resource.

Growing up fast

kw: observations, culture, personal growth

Every generation, people say, "Kids sure grow up fast these days." Sometimes it is even true.

This forenoon I listened to a dialog on the radio, about guns and firearm education. One man spoke of growing up in Virginia. He had sex education in sixth grade, and a "hunter safety" class in seventh grade. His colleague expressed her amazement that 13-year-old kids were taught to handle guns, since they can't legally buy them prior to age 18. The man defended the practice, saying that many parents took their kids, both boys and girls, out shooting from pretty early ages. I agree with this: if there is a gun in the house, and if a youngster is strong enough to pull the trigger, he or she ought to be taught how to safely handle the firearm. In many places I've lived, there are firearms in at least half the homes.

In this picture taken about 1932, my father and his favorite cousin were photographed by the cousin's father just as they were going out into the field to do some "plinking" (shooting at tin cans), probably under the father's supervision, but maybe not. My father was ten years old at the time, and his cousin, holding the pistol, was nine.

This was the same year my father first drove a car, with some help from his dad. Kids (at least boys) his age were expected to be able to take a turn with the tractor. With that in mind, I began to teach my son to drive when he was twelve. We have only stick shift autos, and it takes a bit longer to learn to use them. But mainly, I wanted him to have a few years of experience before he took the official driver training course and got his license. I think it worked out; he is a good driver (now 22).

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.

Is there a better place?

kw: observations, culture

A friend of mine who is much enamored of various conspiracy theories has decided to move out of the United States. He was asking my advice about Belize, I guess because it is still connected to Britain. I directed him to The World Factbook, a service of the CIA. Whether he will give the CIA any credence is another story, of course.

Besides its ties to the U.K., Belize has an economy that breaks down thus:

• 29% Agriculture
• 17% Industry
• 54% Services

That is encouraging, a service economy. However, there is one big red flag. Belize shares with Guatemala the distinction of being a source of human trafficking (sexual and forced-labor slavery), and the government isn't doing quite enough to take this scourge off the world's radar screens. I told him Costa Rica might be a bit more salutary environment: Also a service economy and the most stable democratic government in Central America. It didn't occur to me to ask if he speaks Spanish.

When we had time to quilt

kw: musings, culture, pastimes

I've never observed a quilting bee, but my grandmother was a great fan of them. With the help of a gaggle of friends, she made quilts for all my brothers and me (we have no sisters), in this double-wedding-ring design, but with a white rather than green background. This image came from a Google Products ad.

Born in 1899, she was 55 before she ever saw a television set. When a woman had leisure time, she was expected to occupy herself with handicrafts, usually sewing. Such tasks, and indeed any tasks that did not require one to be home-bound, were turned into social occasions. The quilting bee was (and for many it still is) the cream of one's social life.

Piecing a top can be a solitary activity, but it doesn't have to be. My wife was in a quilting group when we lived in Oklahoma. She and several others would sit in a loose group, each piecing together their sections (usually squares). In my grandmother's day, it was all hand stitching. More recently, machine piecing and assembling is more common, but it still lends itself to cameraderie; they just have to talk louder over the sounds of the sewing machines. As I understand it, piecing is putting together the tiny pieces into larger units, which are then assembled to make the quilt top.

Once the top is assembled, the quilting step is the greatest fun. The assembled top is attached to padding and a sheet backing, mounted on a quilting frame, then the quilting patterns are stitched in. While machine quilting has become more common, the intricate patterns of traditional quilts are still best produced by hand, by a half-dozen or so skilled women, stitching, gossiping, and enjoying one another's presence. (To be fair, I understand there are men who participate in quilting bees, and all-male quilting bees. I'd enjoy that if I had any hand control at all. No way can I make twelve stitches per inch!).

As this close-up shows, a traditional quilting pattern is lovely. It's function is to hold the quilt to the batting and backing; without it the batting will wad up.

It also shows that one cannot produce the double-wedding-ring pattern based on pieced squares. I can think of two ways to put it together, one using alternating circles and smaller white squares, plus dual-arc edge sections; another using congruent shapes with two in-arcs and two out-arcs each, plus a set which are full circles, to be put along two edges. Either way, this is a more challenging pattern than almost any other.

I love quilts. I grew up sleeping under antique quilts. Most quilts are rather thin. When we lived in South Dakota, my wife and I made a thick comforter with a quilted top (much less elaborate than nearly any other quilt, as you might imagine). It is overly warm in this area.

I've obtained dozens of photos of quilts, which I use in my "photo show" screen saver. The endless imagination of quilters everywhere amazes me. It it the premier folk art form.