Saturday, December 29, 2018

A new Russian spidering tactic

kw: blogs, blogging, spider scanning

I checked stats when I finished the prior post. It appears that a different sort of spider scanning method is in use in Russia:

The spike of ~120 hits on the left came through the UAE. The cluster of smaller spikes on the right, from Russia, total half of all activity for the past week, concentrated in about 30 hours; nearly 300 hits so far.

This may be still going on. If I log in again in a couple of hours, there may be another spike or two showing.

Maybe some day one of the scanners will drop a comment to tell me what they find so interesting!

A Quattrocentennial worth noting

kw: book reviews, nonfiction, bibles, bible translations, history

A lovely book has recently come into my hands, A Visual History of the King James Bible: The Dramatic Story of the World's Best-Known Translation by Donald L. Brake with Shelly Beach. I come to this book late. It was published in 2011, on the 400th anniversary of the publication of the Bible commissioned by James I of England. Curiously, although this translation never received written royal authorization, it is frequently called the Authorized Version. Thus, the frontispiece of the folio printings during the first decades of issuance (and many later printings of all sizes) contain the words "Appointed to be Read in Churches", rather than "Authorized…" etc. Therefore, in Visual History it is never called the Authorized Version but is uniformly the King James Version or King James Bible.

The book is indeed a visual history, replete with portraits of many important figures in the history leading up to the translation work of 1604-1608, and for some time thereafter; and even more pictures of many historical Bibles and Bible pages. Dr. Brake is a Bible collector, with access to many rare volumes in addition to his own sizable collection.

The first complete Bibles printed in English were produced under the direction of John Wycliffe in the late 1300's, during the height of literary production written in Middle English, the language of Geoffrey Chaucer. This image from Wikimedia Commons shows the first verse of the Gospel of John, following the end of an introduction. If you note that the word "the" is in alternate spellings that look like "ye" and "yi", and that a word which looks like "at" is actually "with", you can read it, haltingly.

By the time of the conference at Hampton Court in 1604, during which a Puritan minister challenged King James I to support the production of a new translation (and, to everyone's surprise, the king agreed), there were several competing versions of the Bible in English, in particular the Bishop's Bible, the Geneva Bible and the Great Bible of Coverdale.

The English language was in flux, transforming from late Middle English into what we call Shakespearean English. The actual vocabulary and grammar used by the translators to produce the translation of 1608 dated to the generation before Shakespeare. This was for reasons similar to the love many people today have for the King James Bible's sonorous phrasing: it sounds "old" and thus "dignified". Also, since many of the translators were rather elderly (several died before the work was complete), it was the language of their childhood. Actual Shakespearean English was thought by them in the same vein that people of my generation think of the kind of English spoken by Millennials today. We and our grandchildren can easily converse together, but we sometimes use expressions that evoke a quizzical look from "the kids"…and they from us. I was interested to learn that the antique pronouns "thee" and "thou" and so forth were already falling out of use in 1604, but were retained for the same set of reasons.

Technical matters are also discussed, including the size of the final printed books of various editions, as shown in this illustration from page 74. Books are produced in various sizes by printing different sized pages on a folio sheet, which can be folded in at least five ways.

The typeface of Bibles before the late 1700's was nearly always blackletter (as in the image above), with its calligraphic look. But although the early printings of the King James Bible used blackletter for the text, they used a Roman typeface for explanatory notes and certain other apparatuses. Modern typefaces are nearly all either Roman—or similar "serif" faces—or Swiss—or similar "sans serif" faces.

The largest technical section involves the rules for translation, which are explained in some detail. The scholars wanted to be sure they got it right. However, they made last-minute changes in translating certain expressions. Even though the translation was considered complete in 1608, late changes continued for years. In addition, the way large books were printed, such that a changed word could often be replaced in the impression plate between one print run and the next, meant that the "1611" printing, which really went on for three years, led to numerous variations from book to book. This, plus printers' errors, that would be changed whenever they were found, led to an amazing consequence: While nobody knows how many "first edition" copies were printed, of the 150 or so that presently are known, none is identical in every respect to any of the others.

This poses a bit of a problem for those who consider the King James Version, or KJV, to be inspired as a translation. There is no letter-perfect copy of the "original text"! Numerous re-compilations of the text were made. When you buy a modern reprinting of the "1611 version", it is from one of these. However, the King James Bible one commonly finds at any Christian bookstore is a reprint of the third revision of 1769. It is the Bible that was coming into common use when the Constitution of the U.S. was crafted. The English text of the KJV was revised in 1629, 1675, and 1769.

In a late chapter the author takes up the matter of inspiration. The KJV is loved for many reasons, but there are two groups who revere it far more, to a point that I sometimes characterize as idolatry. Some believe the English translation itself is literally inspired, separately from the Hebrew and Greek originals. I believe the paragraph above disposes of such a notion. Others believe that, for the New Testament in particular, the Greek text used, commonly called the Textus Receptus, or Received Text, is exactly the text God wants to be used when translating into English. This is in spite of the fact that the text prepared by Erasmus, to which they usually refer, was secondary to a text by Beza that was the Textus Receptus of the translators in 1604-1608. The Beza text was favored because some of the text by Erasmus had actually been translated into Greek from the Latin Vulgate, because Erasmus could not get access to Greek texts for all the Bible books! But there is a further consideration.

The primary sources of both "flavors" of the Textus Receptus are Byzantine-era Greek manuscripts dating from the Ninth Century or later. They are both considered "near-majority" texts. I have a modern reprint of the Beza text that came with an appendix containing notes on the changes needed to convert it to a true Majority Text, that is, one that uses the version of each word or phrase as found in the majority of Byzantine manuscripts. There are thousands of such manuscripts, and literal criticism (criticism of the letters and words) is a serious discipline in its own right. Starting in the 1700's a number of older manuscripts were discovered, which fall into two categories names Alexandrian and Western. They are considered to be closer to the Koiné Greek of the First Century, though the Western manuscripts contain some passages in a more paraphrased form.

Over the past couple of centuries it has become clear that, whereas Greek fell out of use in favor of Latin in Europe, and in favor of Coptic in Egypt, it remained the common language of the Byzantine Empire in the East. Thus, the Greek New Testament, and the Greek Septuagint translation of the Old Testament, were used for centuries in the East. As a result there are many more Greek manuscripts from that region still in existence. However, the Greek language changed over the centuries. Byzantine Greek of the 800's or 900's was as different from Koiné Greek as modern English is from Middle English: Go back to the image of the Wycliffe Bible page above. You can figure it out, but it really is a different language from modern English. For the same reason, hardly anyone reads Chaucer "in the original", but in a translation. The Byzantine texts are copies of a translated Greek text, not copies of Koiné Greek texts. This is a significant reason behind the production of the text of Novum Testamentum Graece, currently in its Fifth edition by United Bible Society, which relies more upon the Alexandrine manuscripts. It is considered closer to a genuine Koiné text than any other.

The words of Dr. Brake are most relevant here:
Christians and Bible scholars throughout history agree that insofar as our English translations render the meaning of the Word of God as intended by the original authors in a language we can understand, they are inspired. (p. 244)
That is, the focus should not be on whether the written words in our hands are inspired, but on whether we are inspired by the Holy Spirit when we read them. As I heard frequently when I was a young Christian, "The Bible is the only book whose Author is present whenever we read it."

Sunday, December 23, 2018

Voices from all directions

kw: book reviews, science fiction, space fiction, short stories, anthologies

Good collections of science fiction short stories are hard to find these days. I cut my SF-reading teeth on anthologies, much more than novels, in the 1960's. I don't know whether a lot fewer short stories are being written—it does seem that there are fewer SF periodicals than before—or that there are just fewer collections being published. Thus, I glommed onto a new collection of stories by Jack McDevitt instantly.

A Voice in the Night, which closes with a story of that title, contains 24 stories, mostly written during the past decade, but a few dating back as far as 1986. A few of the stories take us into alternatives to the Conan Doyle world of Sherlock Holmes, a few are straight Campbellian problem-solving romps, and many are various sorts of space opera with the author's particular twist. Or two.

The general milieu of a McDevitt space opera is a universe in which humans are the only spacefaring species, or even in which no other planet found in the past 10 millennia has even had bacterial life. But there are a few that are closer to a Star Trek universe, crammed with aliens, though in those stories, I note that nobody has FTL, and the only contact is via radio. Interspecies conversations take decades to unfold, and tend to be rather local!

McDevitt's stories have new ideas aplenty, and a couple have a different take on the viewpoint God might have. But I realize, in every case, to discuss the idea would be a spoiler, and I'd prefer for anyone reading this to have the joy/shock of getting into these stories for yourself. So that's it, folks. I loved the stories, I read them all-too-quickly, and I hope I find other collections, by this author and others, that are as compelling.

Spider scan report for today

kw: blogs, blogging, spider scanning

I logged onto Blogger a few minutes ago, to see that a spidering event came just a few hours ago. The Audience report is quite revealing:

Of the 143 hits counted for "today", 141 are revealed here. The 120 hits by the Spider came through (not necessarily from) the UAE, via FireFox on a Unix system. The other 23 hits are the normal traffic for an ordinary day.

Tuesday, December 18, 2018

His job really is for the birds

kw: book reviews, nonfiction, tower of london, ravens, ravenmaster

This publicity photo from the London Daily Mail shows Christopher Skaipe, the Ravenmaster of the Tower of London, with one of his charges. He writes in The Ravenmaster: My Life With the Ravens at the Tower of London that if you value your fingers, you'll forbear any attempt at excess familiarity with a raven who doesn't know you. Where a crow could give you a painful peck, even draw a bit of blood, a raven can remove a finger joint.

The Yeomen Warders of the Tower are chosen from military men with an unblemished career of at least 22 years. After he retired from 24 years of distinguished service, begun when he was in his teens, the author was told of opportunities to work at the Tower. To his surprise, after some backing-and-forthing, he was taken on. A few years later he was mentored in raven care by the then Ravenmaster, Rocky Stones. In 2011 he became the sixth Ravenmaster.

"Oh!", you might say, "Isn't raven keeping at the Tower a very ancient tradition?" There are legends aplenty surrounding the Tower's famous ravens, in particular how, should they all depart or die, England will suffer catastrophe. The actual practice of caring for the ravens may have begun in the time of Charles II, in about 1650. The Yeomen Warders, who might have been surreptitiously feeding and protecting the ravens, took upon themselves a more formal caring role, but the "job" of Ravenmaster dates to 1946.

The Tower, formally Her Majesty's Royal Palace and Fortress the Tower of London, began as a stout fortress begun in about 1078 by William I ("the Conqueror"). The original White Tower remains, and two rings of structures have been added in the centuries since. It is a place literally swirling with eerie, bloody, fascinating legends.

The birds themselves are legendary. Charles II is said to have decreed that no fewer than six ravens be kept. A bit of judicious wing-trimming ensures that they can fly from danger when needed, but will find it too exhausting to go far beyond the walls. Apparently, the meaning of "judicious" has varied over the years, and at least a couple of birds, over-zealously trimmed, fell to their deaths before more recent Ravenmasters "got it right". Ravenmaster Skaipe has had much to do with "getting it right", not only about the appropriate balance of freedom and restriction for the birds, but about their night dwellings, which they usually enter quite readily. They know of the foxes of the area, and that their Ravenmaster has a great responsibility, keeping ravens and foxes quite separate. Nonetheless, one of the ravens, 11-year-old Merlina, frequently flies and climbs to the top of the White Tower and spends the night there.

These birds have at least as much personality as the people around them. Merlina is a loner, Munin has a love-hate relationship with Skaipe, Erin has a "hobby" of picking a quarrel with one of the others, they each have their own way of stealing food from unfortunate humans in the vicinity, and so forth.

A raven is a big bird. At first it is hard to tell a raven from a crow. This poster from KidWings (the web site is mainly about owls) shows the differences. A crucial bit of missing data: a typical raven weighs 2.5 times as much as a typical crow or rook. Think of an all-black red-tailed hawk; they are that size.

So, what does a Ravenmaster feed the birds? Though they are excellent hunters and can fend for themselves, they do enjoy treats in the form of dog biscuits soaked in blood (In the book, the type of blood is not mentioned. I suppose pig or beef blood from a butcher will do). Also, the Ravenmaster prepares food for them twice daily, so they won't feel the need to hunt perpetually. It won't do for the public to see two of them entrap a pigeon and gobble it down, from center to skin, in the middle of the Green.

Each chapter illuminates a different facet of life, literally, with the birds. The author believes he has the best job on Earth. I reckon he is right about that.

Saturday, December 15, 2018

Learning to love killer whales

kw: book reviews, nonfiction, natural history, orcas, killer whales, sociology

Prior to about 1965, the public perception of killer whales was of a rapacious beast, "the ocean's greatest predator", more to be feared than the great white shark. By about 1970, a few ambitious, large, ocean-focused aquariums, "oceanariums", had obtained juvenile killer whales, and soon SeaWorld began the famous "Shamu Adventure" shows that made killer whales into crowd favorites.

So far as I know, the first whales put on display in an oceanarium were two pilot whales at Marineland of the Pacific, beginning in 1962. Later they also obtained killer whales. I used to visit Marineland after moving to California in 1967, and I remember the pilot whales, but killer whales came later. I was more interested in the giant pacific octopus on display, an amazing animal. I have seen a killer whale show only once, at San Diego, some 20 years ago.

It was also about 1970 that the term "orca" was pushed into popularity by some that thought "killer whale" was too scary a moniker. I wonder if they understood that orca is one of the Latin words for "demon"? Linnaeus first classified the species as Delphinus orca, or "demon dolphin." Later the genus was changed to Orcinus, so now the scientific name means "demon from hell"! It is no coincidence that classicist J.R.R. Tolkien used the term "orc" for the demonic forces of Sauron in The Lord of the Rings.

After killer whales/orcas went on display, and millions got to see them in action, public perception changed, in just a decade, from fearing and hating them to loving them. In the process, the men who started the process, by capturing young whales and putting them on display, and whose work led to public love for killer whales, and then by extension, to all whales, became public pariahs. The original spearhead of killer whale capture, Ken Griffin, became the most hated, when we actually owe him a great debt of gratitude. Without his work and his obsession, would we still hate orcas?

Jason M. Colby is just the right author to produce a book about the decade during which this shift of opinion occurred, and its aftermath. His father, John Colby, was a whale-catcher during the early days of capturing young killer whales for display and scientific study. He has written Orca: How We Came to Know and Love the Ocean's Greatest Predator. Although I used the tag "natural history" above, this book records mainly unnatural history for orcas.

Prior to the work of John Colby, Ken Griffin and their colleagues (and competitors), the killer whale, AKA grampus or blackfish, was considered a global species that feasted on baleen whales, while also devouring huge numbers of Chinook salmon, fur seals, and shoals of herring. Fishermen hated them as competitors and potential human predators and usually shot them on sight. Since the 1970's we have gained a truer picture of killer whale life and society.

Killer whales are big enough to take on great white sharks, were they so inclined. Great whites grow to about 20 feet (maximum verified, 22 ft), and can weigh 2-2.5 tons. A 22-foot killer whale is just getting into adulthood; they grow to 26 feet (maximum 32 ft), and can weigh 6-9 tons. One population of killer whales eats primarily blue sharks, which are half the length and 1/10 the weight of great white sharks.

Killer whales are very social, living in stable family groups and multi-family clans. A clan, also called a Pod, has a home range and a food preference. In particular, in the Pacific Northwest, one Pod eats only salmon, another eats primarily seals, and another eats other fish including sharks. They inhabit a sonic world. They use echolocation to find prey and a large range of whistles, squeals and other sounds to communicate. The typical sounds made by one Pod differ from those of a different Pod. They have dialects! Where ranges overlap, it seems that many of the whales are bilingual, able to communicate with members of a different Pod.

Reading Orca, and its sad chronicle of whale capture and killing, I began to think of a whale capture expedition in more personal terms. What if humans were to be taken for display in alien zoos and study by alien scientists? Of course, the "alien abduction" fears of many folks reflect this. So just consider:
A gregarious extended family is on an outing, when some kind of net surrounds them. They are held for a time while smaller beings move about nearby and study them. More nets are deployed, which segregate certain individuals, primarily those that weigh between 60 and 120 pounds, ages 8-14. These are taken away, not to be seen again. The larger and smaller ones are released.
That is how alien abduction would actually occur, no midnight force beams, etc. That is what happened to numerous families of killer whales during the heyday of "whale shows" at oceanariums. However, in a typical capture event, some whales died (not always; Ken Griffin very rarely had a whale die during capture). The nets could tangle a young one, holding it underwater until it drowned, for example. Sadly, few whales in captivity lived more than a few months or a year. It took time for the captors to learn to take care of them.

Ignorance is deadly. Most of the whales captured were used to eating salmon or seals. They spurned the buckets of herring they were offered. Death by starvation was frequent until curators learned better, and also learned techniques to induce newly-caught whales to eat herring, the only food they could afford to obtain in massive quantities…also, it's hard to feed seals to captive whales, and if the public were to see the whales eating "cute" fur seals, the popularity of the shows would plummet.

It is still possible to see performing killer whales. But one by one, the shows are ending. The whales in captivity cannot be returned to the wild. Most now living were born in captivity and do now know the dialect of any wild whale Pods. One or two of the currently captive population are pregnant, meaning that SeaWorld and others will have to take care of killer whales for the next 50 years.

Enough of my ramblings. Jason Colby tells, and tells well, the story of orcas and their shift from mythological demon to beloved "sea Panda". Neither perception is accurate. But along the way, the scientific study of orcas and orca Pods became necessary, and much more is known about these amazing animals. I hope further good and popular books are written about their natural history.

Saturday, December 08, 2018

Eat 'em and weep

kw: book reviews, nonfiction, food safety, research

Three stories about writing style:

Story 1: In one of his memoirs, prolific author Isaac Asimov writes of the article he wrote titled "The Endochronic Properties of Resublimated Thiotimoline". It was a spoof, written for a purpose: he had been a published author of popular hard science fiction since he was 19, and he was wondering if he could write in the stodgy, hyper-objective style he would need to use for his doctoral dissertation in Chemistry at Columbia University. The article was as stodgy and hyper-objective as he could devise. He published it in Astounding, figuring that would be sufficient cover. His dissertation passed muster, but unbeknownst to him, his professors had read the article also. When they called him in to announce their (favorable) decision on his degree, the chair of his dissertation committee said, "Greetings, Dr. Asimov! Please tell us more about Thiotimoline."

Story 2: I worked a little more than two years as a machinist in the Physics shop at Cal Tech. We were building a precision radio telescope antenna; it was 34 feet across (10m), and had to be accurate within a few thousandths of an inch (100µ). During the final shaping of the parabola, the assembled dish was mounted on a rotating air bearing 8 feet across (2.4m). It spun slowly, as a specially constructed device cut into the aluminum honeycomb surface, a couple of mm per cut, as it was advanced up a specially-shaped track. Each cut took a full work day. I had to babysit it while the master machinists worked on other things, every day for a few weeks. Because machining uses hearing more than sight, I could move about the room, a huge space in which the mirror for the Palomar Telescope had been polished, which had later been half-filled with a synchrotron, a kind of atom-smasher. I found a cabinet filled with draft copies of PhD dissertations, based on research done using that synchrotron in the 1960's. This is all background: I have the kind of mind such that I can read, with some enjoyment, stodgy, hyper-objective dissertations, which is what I did for most of those few weeks.

Story 3: My brother had been a working artist, primarily a calligrapher and calligraphy instructor, for more than 20 years. The art market was slowly shrinking in the late 1990's, so he decided to return to school, get a Doctor's degree, and, he hoped, become a museum curator or professor. He first completed a Master's in Art History. However, he also was a published author, of nonfiction books, with a very readable writing style. Not having published his own "Thiotimoline" article, he had nothing he could use to convince a dissertation committee that he could write in a style appropriate to a history dissertation. So the History Department declined to admit him to a PhD program. One of them told him privately that the professors were embarrassed that their writing was so bad by comparison to his. Fortunately, a different department requested that he apply, and he was admitted. He received a PhD at age 50 and is now a professor.

I find in the book Did You Just Eat That: Two Scientists Explore Double-Dipping, the Five-Second Rule, and Other Food Myths in the Lab, two scientists who are moving in the other direction. Paul Dawson and Brian Sheldon studied various food myths with their students at Clemson University (Dr. Sheldon is now at N.C. State U). They studied myths about the 5-second rule, Beer Pong, restaurant menus, jet-air hand dryers, and several other things. Being professors, having written their own stodgy, hyper-objective dissertations, they are moving into the public arena. This is not unusual…but this book is unusual, in a good way.

This book is unique in my experience, being a mix of about 2/3 very refreshing text for the general reader, and 1/3 stodgy, hyper-objective reporting of their experiments. I have read many popular books in which the results of scientific experiments are discussed. This is the first such book in which every experiment is described in the kind of detail you'd find in a technical research report. The authors are kind enough to warn us about this in their Introduction, and to set off the stodgy stuff with "Science Stuff Ahead"; they give permission to skip these sections, to anyone who finds them too stultifying. Thus, for example, a few sentences from their chapter about the germs found on restaurant menus:
Swab-samplers (made by 3M Swabs, 3M Company) were used for menu sampling… The restaurant menus sampled fell into three general sizes of around 603, 768, and 1,207 cm². … Back in the laboratory, sample tubes containing the swab and sterile 0.1 percent peptone water were vigorously shaken by hand...
From the descriptions, and sufficient budget, and an army of willing students, you could reproduce each experiment exactly. That is why the writing is the way it is. Of course, I can read this stuff just fine, but most folks can't; the MEGO factor can be huge!

Let's cut to the chase. Is the 5-second rule true? ("If you pick up dropped food in less than five seconds it is still safe to eat.") Is it? How would you define "safe"? The outcome of the experiment, in which several kinds of food were dropped onto tile, wood, and carpet inoculated with a harmless variety of Salmonella, the most common cause of food poisoning, was that "safe" really just means "maybe a little bit safer". In general, if you can grab that grape in one second, it will have fewer bacteria on it than if it takes you 4 seconds, and if you wait, say, half a minute, there will be even more. But the number of bacteria transferred was never Zero. However, by this measure, carpet was "safer" than tile or wood. That is the opposite of what I'd have expected.

Consider this, though, based on other experiments: How many bacteria get on your food from your own hands? How thoroughly and carefully do you wash before handling food? Prior to washing, after almost any amount of daily activity, our hands are as dirty as the floor we are walking on, whether or not we wear shoes indoors.

Rather than be a spoiler about the results in this book, I will instead invoke a forensic principle, known for at least a century, as it applies to the transfer of germs (bacteria, fungi, viruses, and parasites) to and from our food and everything it touches: When two surfaces come into contact, material from each surface is transferred to the other. Numerous criminals have been convicted in part because, not only were their fingerprints found "at the scene", but, if they brushed against the wall, tiny flakes of paint from that wall got on their clothing.

To sum up, if anything touches food, we must assume it will contaminate the food unless steps were taken ahead of time to remove all contaminants. So, if you're going to enjoy Beer Pong, make sure you have really good medical insurance!

Wednesday, December 05, 2018

Animal personality comes out of hiding

kw: book reviews, nonfiction, animals, animal behavior, animal psychology

The rat-runner's motto:
Given any combination of feeding, temperature, and light level, the rat will do what the rat wants to do.
There is a word I'd like to abolish from the scientific dictionary: Anthropomorphize. In common understanding, to anthropomorphize is to talk about some thing or animal as though it were human. We do this all the time: "My phone thinks it knows better than I do," or "My cat loves to have his belly rubbed." But in a scientific article, to speak of any animal as having emotions, feelings, or intentions; indeed, to speak about an animal in any way other than as a piece of automatic machinery that is operating according to (never-to-be-properly-defined) "instinct", was forbidden for decades, upon pain of losing tenure and being blackballed from the hallowed halls of getting published in "good" journals.

John A. Shivik is one of many researchers who are doing away with this blinkered perspective. In his new book, Mousy Cats and Sheepish Coyotes: The Science of Animal Personalities, he explains his own shift of viewpoint and presents many examples of animals that have been proven to have personalities, from familiar dogs, cats, coyotes, horses, and cougars to mosquito fish, spiders, and even protozoans. Yes, an amoeba can have a personality! No brain, but the tiny critters have their preferences.

Here is an example of a familiar sight. The kittens all look the same. They are a purebred litter, bred under controlled circumstances so there's no chance of multiple fathers here. It looks like they are all ready for a nap, but Roger, there, has a different idea. I suspect that seconds later he scampered off. Maybe you've been to the SPCA to adopt a puppy. One comes right to you, and her litter mate hangs back looking shy (Me, I'd pick the shy one, as long as she was friendly when I went over to her).

In Mousy Cats the author explains in some detail how the anti-humanizing trend became a straitjacket for biological researchers. He tells us of his own experiences with coyotes—including one much more wolf-like than he wished!—and other animals; even more, he tells of the work of a growing number of researchers who work with all kinds of animals to demonstrate their differences in personality and how they shape the lives of the individual animals and their species' survival.

We might step back and ask, "Why does there need to be such a wide array of personalities, not only among people but among animals? Why doesn't evolution, or God, or something just produce the 'perfect' animal?" Nature isn't static. The average rainfall where I live is a very solid 3 inches per month (sometimes manifested as 3 feet of snow). But a few years ago the precipitation for the year was not 36 inches, as expected, but about 25. The governor issued orders against lawn watering and washing cars. And then this Spring we had an entire year's rainfall in two months; mold grew in unusual places, such as the rafters in my attic.

More to the point with animals, a litter of coyote pups with a bold, calm disposition will do well when there are plenty of prey to eat and few dangers, but if a pack of wolves moves into the neighborhood, they'd better beware. Wolves kill coyotes, and it's better to be more timid. A litter of coyote pups with a variety of styles of personality, some more bold and adventuresome, and some more retiring and watchful, are more likely to have at least one or two that survive the present environment and go on to gain a mate and have offspring of their own. Sometimes, the bold ones can safely adventure here and there, finding more prey and growing up faster than their more retiring litter mates. During such times they'll have more offspring. Sometimes, all the bold ones are killed off by wolves, and the shy ones manage to avoid that fate. The pendulum never stops swinging.

Varied and changing environments are behind the evolution of varied personalities. You look at a bunch of orb-weaver spiders; my favorite is the Golden Garden Spider. They all look the same. They spin webs that look a lot alike. Scientists have gathered spiders by the dozens to test if they have different personalities. They might take 60 of a particular species and raise them in individual terrariums. How do you test the startle response of a spider? To be simple, you sneak behind it and poke its rear with a pencil eraser! Nearly all the spiders run off the web and hide. How long will it be before each one comes out of hiding? How long before they are back on the web? The researchers will wait a day or two, so the spiders are hungry, and then drop a small cricket into each web. How long does it take for each spider to dash out and attack the cricket? It should come as no surprise that the spiders who take the longest to "recover" from being poked by a pencil eraser also take the longest, and are most cautious, when approaching and attacking the cricket, even when they are famished.

Well, if spiders have personalities, however rudimentary, it follows that any more complex animal ought to have one as well. Indeed, whether we keep pets or not, we all know somebody's cat or dog or cockatiel or whatever, if not our own. We know that each is a unique individual. The researchers that the book highlights are proving it, scientifically. It is about time the scientists caught up with what we all knew all along.

So I repeat what I've said before: It's not that animals are like us, the important point is that we are like them. We have personalities because they have personalities.

A spate of Russian spidering

kw: blogs, blogging, spider scanning

Before getting to a book review, it's good to see what activity has been in the past week. Here we see someone in Russia having a new and different "scanning party":

Here it seems a less automatic process was used: grab a couple dozen posts, look them over for an hour or two, then use about 8 focused searches over a day's time. I wonder what other sites or blogs have seen a similar phenomenon…

Wednesday, November 28, 2018

How we have better veggies

kw: book reviews, nonfiction, biographies, scientists, botanists, adventurers, agriculture

Had your kale lately? How about some quinoa in your soup? Do you like navel oranges, mangoes, or avocados? Have you been to Washington, DC (or several other cities in the region) in the springtime to see the cherry trees in bloom? Thank David Fairchild. His life and adventures are shown in The Food Explorer: The True Adventures of the Globe-Trotting Botanist Who Transformed What America Eats by Daniel Stone.

As a young scientist in the 1890's, David Fairchild caught the interest of a wealthy, globe-trotting dilettante and raconteur, Barbour Lathrop. The rich man claimed to have circled the world many times (the number varied with the telling, usually around 20-40), but his life was otherwise aimless.

Fairchild had met Alfred Russell Wallace, who entranced him with tales of his travels in Malaysia and Indonesia, particularly Java, and the strange and wonderful plants and animals he'd encountered in the tropics. For a Kansas boy, it seemed a faraway planet. A few years later he spoke of it to Lathrop—when he could get a word in edgewise—and Lathrop remembered it; later on he visited Fairchild with an offer to sponsor a plant-collecting trip to Java. Fairchild was at the time in the employ of the infant Department of Agriculture; he eventually quit his job in favor of globetrotting plant collecting, but retained ties to the Department so as to have somewhere to send his discoveries.

Eventually, Lathrop and Fairchild traveled together for several years, giving more purpose to Lathrop's life, and affording Fairchild the opportunity to gather new species and new varieties of plants, in hopes that American farmers and orchardists could enrich the variety of foods on offer.

I didn't know that all the citrus fruits we enjoy, in such amazing variety, were all bred from just four progenitor species: citron, pomelo, mandarin, and papeda (a bitter fruit, but one parent of the Key lime). Nor that there are hundreds of varieties of avocado—yet only a few that can be shipped—or mango—ditto. I'd heard of Meyer lemons, and even had a dwarf Meyer lemon tree in a container for many years, but in this book I read about Frank Meyer, hired by Fairchild to scour China for plant varieties, including new citrus hybrids.

Every good story has a nemesis. The best man at Fairchild's wedding, his boyhood friend Charles Marlatt, serves the rôle here. He was an entomologist, fighting crop pests, particularly those that came from elsewhere. When Fairchild arranged to have Japanese Yoshido flowering cherry trees brought to Washington, 1910, Marlatt found them infested with at least 8 pathogenic insects and a fungus or two. The entire shipload (2,000 young, mature trees!) was burned on orders of President Taft. The Japanese were very apologetic, and prepared a new shipment of trees, grown in "virgin soil" and carefully tended, that were brought in 1912, 3,000 this time, and planted around the Tidal Basin, along the Mall, and extras sent to nearby cities. The real "damage" incurred from Marlatt, in Fairchild's eyes, came with legislation such as various Quarantine Acts. They restricted plant exploration by requiring so much paperwork and inspection that most of the plant explorers that were following in Fairchild's footsteps went on to other pursuits.

However, there is a certain amount of right on both sides of the introduce-versus-ban dichotomy. After all, Fairchild introduced Kudzu, grew it in his own yard, then found he had to go to a lot of trouble to exterminate it! Too bad he didn't get it all. It is a scourge in the southern half of the U.S. But more good than bad has come of plant exploration and introduction. We need both Fairchild (and Meyer et al) and Marlatt.

Kudos to Daniel Stone for reminding us of David Fairchild and others, who may have been famous in their generation, but are nearly forgotten. Remember him the next time you enjoy a mango.

Sunday, November 25, 2018

Spiders hiding their tracks

kw: blogging, spider scanning

In the past 24 hours, 210 hits have been registered that I consider spider scans:
The 133 from "Unknown Region" match the 133 that originated in Linux systems. Linux offers more tools for hiding identity. The 77 from Russia apparently match the 77 that used IE on Windows, but I can't all that a definite match. The "real" traffic, hopefully of people with some scant interest in reading the blog, is around 25. I hope y'all aren't just bumping into me by accident and skipping out in a heartbeat!

Anyway, Cheers to all, and I hope the 5 Americans who passed this way had a Happy Thanksgiving.

Friday, November 23, 2018

Removing the straitjacket of non-causation in statistics

kw: book reviews, nonfiction, statistics, probability, causation, mathematics

In 1926, during the height of the eugenics movement in the U.S., a researcher who has been nearly forgotten studied the relationship between the intelligence of children and that of parents. This is the core debate, even today, regarding the "nature-nurture" dichotomy. Which is more important, upbringing or inheritance?

Step back a minute, and consider, with the current popularity of "big data", how this might be tackled. It is no longer difficult to gather enormous amounts of data regarding the IQ of numerous children, adults, and societal indicators such as neighborhood of residence. Do all the math you might wish, with regressions and correlation diagrams, and what might you find? No doubt some kind of correlation will show up, perhaps very obviously. But what does it mean? What has "caused" the greater intelligence of some children, and the lesser intelligence of others?

The word "cause" was forbidden in statistical monographs for decades. For many researchers even today, the mantra (I chose that word with malice aforethought) is, "Correlation does not imply causation." While this is indeed true, even a tautology, it is not all there is to it. We naturally think of nearly everything in cause-and-effect terms, and work done in the past couple of generations now makes it possible for researchers to discuss causes without losing tenure, grants, etc.

For the young researcher, Barbara Burks, the mantra was nonsense. She sought causes. To this end, she gave IQ tests to every member of 204 households that included foster children, and 105 households without foster children. For 1926, this was pretty big data. The choice of studying both foster children and natural children along with the adults was clever. Even more clever was the little diagram she used to analyze her results:

The arrows imply causation. Here, the "X" factor that might influence both the level of intelligence of the child, and the social status of the household, was thought to be the "heritage", including genetic inheritance, of the family. The parents, in whatever measure they benefit (or not) from "heritage", will have their own X factor, which could have been added as Y, off to the left perhaps.

Note that two of the arrows have heads at both ends. This indicates feedback effects between the social status and the intelligence of all members of the family (I imagine a family of "ordinary" intelligence having a very, very bright kid, and this leading to an improvement in social standing, for example).

Such a diagram embodies a "causal model", in the terminology of Judea Pearl, in The Book of Why: The New Science of Cause and Effect. Such a diagram, and mathematical processes invented by Pearl and his students, provide what is missing in non-causal statistics: the understanding that some things really do cause other things. By the way, Ms Burks's conclusion: genetics provides 35% of the observed differences in the intelligence of children. This was a disappointment to eugenicists, including Ms Burks. In particular, Louis Terman, an inventor of the Stanford-Binet IQ test, also famous for his "genius" studies, rejected it outright. He was quite certain that genetics were behind "nearly all" the differences in IQ. One might imagine him, upon seeing her results and conclusions, huffing, "Impossible!"

This reminds me of the first of Arthur Clarke's laws: "When a distinguished but elderly scientist states that something is possible, he is almost certainly right. When he states that something is impossible, he is very probably wrong." Dr. Pearl writes of his own Odyssey of discovery. He did not come to causal reasoning easily. But now he and his students have developed "causal calculus", which is introduced in The Book of Why, by Judea Pearl and Dana MacKenzie.

I must confess, though my long career as a scientific programmer led me into statistical work again and again, I never became comfortable with the formulas of probability. When I see the term P(Y|X), I have to think a moment to get my head around, "The Probability of Y occurring (or existing), given the occurrence (or existence) of X". In non-causal terms, you can freely substitute "daybreak" and "rooster crowing" for X and Y, either way: "The probability of daybreak, given that the rooster crowed" and "The probability of a rooster crowing, given that day is breaking." Hold that thought.

Dr. Pearl has added the "do" operator, which implies an intervention, so that P(Y|do(X)) means "The probability of Y occurring, given that the intervention X was made, compared to X not being done". This is the reasoning behind the randomized controlled trial (RCT) in medicine, but it was not stated in a formula before. Indeed, in older medical journals the authors use all kinds of locutions and verbal gymnastics to avoid saying, "Medicine X caused a Z% reduction in death rate due to disease Y". Many still do so.

Thus far, I can follow along. Dr. Pearl freely ignores the folklore that each mathematical expression used in a book reduces its audience by half. Now, I like math, but it would take a great deal of study for me to become conversant with causal calculus. In an example called "DO-CALCULUS AT WORK" on page 236, we find expressions such as
Σt P(c|do(s),do(t))P(t|do(s))
This is the second of seven formulas in a derivation. At that point I realized I probably ought to devote my few remaining years to something besides learning how to not only parse such statements, but to create and perform them!

Dr. Pearl's work has great benefits for those researchers who can wrap their minds around these concepts and formalisms. For example, the decades-long struggle to determine to what extent smoking causes lung cancer, the subject of a major chapter, was undertaken in the face of determined and well-funded opposition to the concept, but might have been shortened to a year or a few years if causal language had been allowed. This stricture was as if the scientists studying smoking and cancer, those who were not in the pay of the tobacco companies, tied both hands behind their backs and had to perform their work with their toes and tongues. Now causal language is out of the closet.

An early chapter discusses the Ladder of Causation, from Association (what we observe), to Intervention (what we do to see what happens), to Counterfactuals (what we imagine might happen if X were not so). It appears that only humans can perform counterfactual reasoning, such as, "Will the day break if we get rid of all the roosters?" or, as a song says, "What if we gave a War and nobody came?"

We can't always figure out what is a cause and what is an effect. But where we can, the language of causation helps us model an event, such as by the use of a diagram such as the one above. Also, Do-Calculus now provides a mathematical way to treat cause and effect in a meaningful and quantitative  way. It adds power to Design of Experiments logic, so that a researcher is more likely to correctly determine the appropriate set of causative factors and winkle out just how important each is, in producing the effect being studied.

As difficult as the reading was, due only to my unfamiliarity with the jargon and formulas, reading the book was very enjoyable. The winding path Dr. Pearl took to get past the hamstrung statistical reasoning of half a century ago, on through Bayesian analysis, and on to develop causal reasoning in a formal way, with the appropriate formalisms of the mathematical language of Do-Calculus, make for a quest saga every bit as gripping as the search for a hidden city.

Monday, November 12, 2018

The warmest and fuzziest -- with big claws!

kw: book reviews, nonfiction, animals, animal behavior, pets, wildlife

It takes extraordinary experiences to set the stage for a wild animal to become bonded to a person. In the case of a bobcat, soon to be named Trooper, these experiences included being the only survivor of his family's massacre by coyotes and getting stuck in a patch of cholla; for Johnson, they included a life that led to particular love for wild places and wildlife, and a temperament that just matched the bob-kitten's need. Basically, Johnson found the dying kitten, extracted him from the cholla (a most dangerous cactus), and took him to a veterinarian who was able to meet his medical needs and, even more, knew just how to prepare the kitten and Johnson for a life together in and around the home Johnson and his wife had created. Thus begins Trooper: The Bobcat Who Came in from the Wild by Forrest Bryant Johnson.

Years later, when a self-styled animal activist accused Johnson of "imprisoning" the cat, he was able to show her that Trooper came and went as he pleased and was never caged except when he needed to be taken to see the vet. Trooper loved the vet, just not the car ride. He also preferred to sleep snuggled against Johnson's arm.

At the risk of spoiling, although Trooper was a gentle companion and friendly to people, he kept enough of his wild nature to kill a coyote that began to stalk him and other animals around the Johnson mini-ranch. It was a collaboration: Johnson and neighbors first killed all the coyotes but one of a small pack that "moved into the neighborhood" and began preying on pets and even stalking children. Trooper finished off the last one.

In the years between, Trooper and Johnson learned from each other. Johnson ruminates, somewhat ruefully, that he knew Trooper thought of him as a rather inept cat. Not for Trooper the notion of being a "person". The book is full of stories of cat and man, and the man's wife, grown daughter and other family members. Of the time his wife good-naturedly tried to hire a "home-call" grooming service to "bathe" Trooper, and the way Trooper so thoroughly intimidated the groomer, without harming him in the slightest, that the groomer simply turned and left. Of the time a great horned owl knocked itself silly against a window, and Trooper brought it inside, not to eat, but perhaps hoping for a new kind of playmate; it was a job and a half getting the irate owl back out the door! Of the time the alarm service kept phoning Johnson that there was an intruder tripping the light beam in the house's hallway, but nobody was ever found. What was found? Trooper and another (ordinary) cat that had come to live there, jumping off furniture and interrupting the beam; the alarm company removed that particular sensor.

There are still many people who say animals are totally instinctual and cannot think, or plan, or feel pain. Such people have never owned a pet, never watched it plan, perhaps for days, how to attack a particular kind of prey or enemy. They've never thought through the fact that animals seem to easily learn a number of our spoken words, but we learn hardly any of theirs, or none at all. Even the most inbred, bred-for-looks-not-for-smarts Pomeranian pup or Persian cat shows these attributes. Johnson found that a bobcat, that must live by its wits, had quite a lot going on in that big, fuzzy head of his.

This book gets my Heart-Warming, Heartstring-Tugging, Drippy-Nose Award for the year!

Saturday, November 10, 2018

Our data are doomed

kw: book reviews, nonfiction, internet, internet security

I have read the Schneier on Security blog on and off almost since I began this blog. As far as gurus of internet security go, he is IT. So when I ran across Schneier's latest book, I nabbed it, in part to see whether it would be a collection of blog posts (it isn't). His writing is great, his ideas are spot-on, and the subject is rather depressing.

Click Here to Kill Everybody: Security and Survival in a Hyper-connected World, by Bruce Schneier, is scary as hell, and the author isn't selling anything…not to us at least. He is indeed trying to "sell" policy ideas to the U.S. government, and in part this book is aimed at getting us to put pressure on our representatives to pay more attention to this issue.

The Internet is rapidly becoming the Internet of Things (IoT), in which to say, everything in the home that would have been bought after a certain date is not just a toaster, light bulb, or easy chair, but a computer that cooks toast and Pop-Tarts (and remembers), a computer that talks to the light switch and learns your schedule and can set mood lighting at your request, or a computer that offers you a comfy seat and records your weight and heartbeat and maybe massages you (it may also inform your doctor of your day-to-day state of health). Almost any new car is not just a computer, but a collection of computers that control a transportation machine, more or less at your demand, keep track of its own maintenance schedule, record where you go and your driving habits; in the future it will know your mood, not only from your driving habits but from your temperature, smell, and perhaps level of noise you make (do you yell at other drivers when they annoy you...or at the radio?).

What the car, light bulb, and chair may know about us is one thing. Because they all connect via the Internet, or the coming, enhanced Internet that he calls Internet+, anybody with a modicum of hacking skills can know what they know. Your phone already knows your buying habits and perhaps banking habits. Who else would you be just tickled about if they knew also? Nobody? I thought so. Well, what will you do about it? What CAN you do about it?

If you believe the book's current explanation of the state of Internet security, the answer is, "Nearly nothing." Firstly, most people will be unwilling to go to the least trouble to "do something about it." Secondly, for those few who would be willing, there is precious little they can do. And that, my friends, is the message of Click Here.

The title is intended as click bait, but its message is not entirely hype. The book begins with three scenarios, and returns to them from time to time.

  1. Control of an auto from ten miles away, via an Internet-connected laptop. This was first done in 2015.
  2. Shutdown of a power plant in  Kiev, presumably by Russian hackers, in 2016.
  3. A hacker took control of 150,000 printers on insecure networks in 2017, and had them print taunting messages. This is a 'near-white-hat' attack. I wonder how many of the printers' owners took steps to secure their equipment?

Now consider item #3. Suppose someone hacks into a 3D printer, and has it print a booby trap to injure or kill the owner, when next he/she turns on the light in the room where it is kept? Suppose a 3D bio-printer is hacked to produce a super-flu like the 1918 bug that killed about 4% of the human population that year? How about every insecure 3D bio-printer? This extended scenario is behind the title of the book.

The author thinks only government can deal with this effectively. No other entity has the scope to do so. But at the moment, every powerful player in the Cyber arena has a vested interest in an Internet that is not too secure:

  • The NSA and other agencies want access to anything, anywhere, with little fuss.
  • Businesses would rather spend to make new products than to add security to existing ones. Neither do they have incentive to design security into their new products.
  • To the biggest presences on the Internet, from Google, Yahoo, Facebook, Instagram, Alibaba, Dianping..., all have as their primary product YOU, the user, and the information you post or reveal by your posting habits. They want to sell this stuff, not secure it.

Not only that, the Internet is the most prolific espionage tool to be developed since the microdot camera. When new vulnerabilities in common software are discovered, say by someone at NSA, they don't inform the software company. No, they add the knowledge to their "virtual arms locker", as a took to be used offensively, until someone more civic-minded or someone at the company stumbles across it and it gets fixed.

So, nobody with any power has much interest in better security. Tools to help make security better have languished on the shelf for decades, unused. Schneier explains why.

If you want your own end-to-end encryption, perhaps you can get Tor, but be aware that all the world's governments keep tabs on Tor users because so many of them are criminals. That in itself argues that we all ought to have such tools available by default. In the U.S., the Second Amendment assures that, if we want to own a gun for our protection, we can do so. That way, it is not presently so that "only criminals and cops have guns." But on the Internet, and even more, the nascent Internet+, you can't find a gun anyway, so only the criminals have guns, and most of the cops have at best rather inferior ones.

Will this get better? The author thinks so. He is optimistic enough to think it can get better in just a decade or two. Maybe. It probably won't get better, at least from a governmental intervention standpoint, until a Scenario #3 leads to a few dozen, or thousand, or even million, deaths. That's what it takes to get major policies created or changed. Good luck, y'all…keep your head low.

Sunday, November 04, 2018

Spiders around the world

kw: blogs, blogging, spider scanning

Oh, this is cute:

The one-hour spike on 11/1/18 is 99 hits; the one a half day later is 37 hits. The former, just before midnight my time, is probably from Turkey, and the other from Ukraine.

The low hump on 11/3/18 mostly represents interest in a post on making pumpkins pies. It got a lot of hits over several hours' time. It is a pity I don't get stats on locations hitting particular posts. I'd be interested to see if the pie-making post was checked out by anyone overseas. I took pains to include Celsius temperatures, but I didn't convert cups to ml. Oh, well. My cup measures have both fl.oz. and ml scales, and I suspect people everywhere will know how to convert. But I don't think pumpkin pie is of much interest outside the U.S. But whatever pie someone might want to make, the pie crust recipe and instructions produce a crust that is without peer.

Saturday, November 03, 2018

Pumpkin Pie Season at my place

kw: photo essays, pies, pie crust, how to

Grab a cuppa, this is long…

Above are the ingredients and equipment needed to make two pumpkin pies, using the crust recipe from the 1962 edition of Betty Crocker's New Good and Easy Cookbook, published by Golden Press. It is the one my Mom used to teach me to cook and bake; also the recipe from the side of a can of "Libby's 100% Pure Pumpkin". I have ground up my own pumpkin in the past, but it is a lot of trouble, when a good commercial product is so affordable.

The crust recipe for "1-2-3 Pastries" has these ingredients, per single-crust pie:
  • 1 cup + 2 tbsp. unbleached flour (2 tbsp. = 1 fl. oz.)
  •  cup vegetable oil (I use canola oil)
  • 2 tbsp cold water
The recipe includes a bit of salt but I leave that out. I double these amounts for two pies (2c+2oz flour, c oil, 2 oz water).

I put the flour in a glass bowl and shape a hollow in it using a fork:

Pour the oil in the hollow and fold in:

When fully mixed it will be a little crumbly:

Sprinkle the water over the mix and fold in thoroughly. Press the dough together and let it sit to homogenize while preparing to roll the crusts.

The crusts are rolled between sheets of waxed paper. To make the lower sheet of waxed paper stick to the table, get it very clean and then moisten it well:

Put a piece of waxed paper on the wet table, shiny side up (it'll curl upward). Take half of the dough and shape it into a ball in your hands, and then press it onto the waxed paper.

Put a second piece of waxed paper on top, shiny side down, and press with your hand (at this point I wipe my hands with a paper towel). Then roll it. I roll it in all directions to get it as round as possible.

Here it is, ready to be put in the pan:

Slowly peel off the top sheet of waxed paper. Dry all around with a paper towel, then lift the front edge partway and dry underneath.

Slip the pie pan in there and gently lift the pie crust. Then invert it onto the pan:

This process is just a fiddly bit of gradually pulling the edges up and getting nearly all the air out fron under the crust. I got the wrong camera angle; near my left hand is a bit of crust pulled up to let air out as I maneuver the rest into place:

Gather the overlapping stuff around the edge into a rim that you press into a raised rim. The pie recipe will not fit inside without this step:

While rolling the second crust I got a photo of a useful step: rolling around the edge with the end of the roller on the table, to give it a slight taper. You can leave this step out, for a little more thickness at the rim.

 Here are the two crusts ready for filling:

Here is the filling recipe:
These cans for two pies used to have 30 ounces of pumpkin. That made pies that were just a bit deeper, but somewhat harder to carry over to the oven. The finished filling is very goopy and slops out of the crust if you wiggle even a little. So you'll have the ingredients in text form, in the order I use:

  • 4 large eggs, beaten in a big bowl
  • 1 can (29 oz.) pumpkin
  • 1½ cups sugar with spices mixed in:
    • 2 tsp ground cinnamon
    • 1 tsp ground ginger
    • ½ tsp ground cloves
  • 2 cans Evaporated Milk

This shows the 4 eggs ready to beat (not whip! this isn't an omelette), and the spices sitting on the sugar ready to stir in. I stir them in and then add after I add the pumpkin and mix it with the eggs. Before any of that I heat the oven to 425°F (~220°C).

Here I am stirring the eggs.

In goes the pumpkin:

After stirring in the sugar-spice mix, I add the evaporated milk, half a can at a time:

I use a big plastic ladle to spoon alternately into the two pie shells. At the end, I eyeball what is half and drag that into one shell, then use a rubber spatula to get the rest into the other.

Two pie shells, loaded and ready to cook. I first move them to the countertop next to the oven.

Then I put them in the oven. I hold them so that when I put the pie on the oven grate I don't get a burn.

The recipe says to lower the temperature after 15 minutes, but with two pies I use 20 minutes. I kept the oven open longer, so it takes longer to re-heat. So I lower it to 350°F (175°C) and cook for 45 minutes. Then I check it, which is what I am doing here, by poking the tip of a knife into the center. If nothing sticks to the knife, they are done. If only a tiny bit sticks, I give then another 5 minutes, otherwise I give them another 10 minutes and re-check.

Here they are, all done, pulled out of the oven, sitting on racks. You can see that they began to crack around the edge, which is a good sign that the filling is cooked and properly stiff.

I support cookie sheets with whatever is handy (pill bottles, cup cozies…) to keep dust off while they cool for an hour or so, no more than two hours. They'll still be warm if you serve them right away. Otherwise, refrigerate them.

I cover them to put in the refrigerator. The first layer is waxed paper. I cut a piece a little longer than the width of the pie, and fold it in half, then half again, then fold a triangle as shown here. One more fold is coming.

Here is the piece, folded four times so the arc is 1/16th. I am holding it where I plan to cut. I cut a slight arc that crosses both edges of the triangle at a right angle.

Unfolded, that yields a circle. Put this on top of the pie so it won't stick to plastic wrap.

Both pies are covered (one cover is not pressed on yet), ready to wrap in plastic wrap and refrigerate.

The Libby's recipe makes a great-tasting pie, better than if you use "pumpkin pie spice", and this kind of crust is the flakiest I've ever encountered. It is also much lighter than a crust made with lard or another solid fat. Enjoy!

Learning of life as never before

kw: book reviews, nonfiction, natural history, geological history, life, evolution

Hmm, let's see, will this do?

Probably not. The little blob represents an amoeba. When did amoebas first appear on Earth? Probably around 800 million years ago. Amoebas are quite advanced. Life began with pre-bacteria (or pre-archaea) cells some time between 3,500 and 4,200 million years ago, so eons of evolutionary progress occurred before protozoans such as amoebas came into being. On the scale of this diagram, there would be another 35-40 things strung out to the left, for about two feet, all looking a lot like the period at the end of this sentence, or maybe a tiny oval of similar size.

So, just how has life progressed since it first appeared on earth? To find out, read a wonderful new book by Dr. Peter Ward and Joe Kirschvink, A New History of Life: The Radical New Discoveries About the Origins and Evolution of Life on Earth. Geology has not stood still since I studied it in the 1970's and early 1980's. Neither has biology, nor genetics. In fact, our understanding of DNA and genetics has advanced more in the past decade than in all of prior history…and we realize that we still know something like 1% (or a lot less) of what we thought we would know by now.

Geological history and biological history go together. Only the first era of Earth, called the Hadean, during which there were no solid rocks, was without life. A period called Late Heavy Bombardment (LHB) ended the Hadean Eon and partially overlapped the first appearance of living cells. Life may have arisen a few times, only to be melted out of existence when a rocky body about the size of Texas would cause most of the crust to melt, again. So what we call "the origin of Earthly life" actually began just after the last successful total extinction event. The remaining history of Earth and of Earthly biology is divided into eras marked by partial extinction events. Five (plus one, shown below, in my accounting) are major, in that more than 50% of all living species were eliminated. Others caused many more extinctions in a short time than the background rate, but less than 50% at a blow.

To be clear: "Event" is a comparative term. When referring to geological time, anything that happens in less than a million years, if it is more than 50-100 million years in the past, can be called an event. So let us set a time scale, primarily of these extinction "events", based on what is currently known:
  • 4,570 ma ("ma" means "millions of years ago") - Completion of Earth's accretion, and beginning of the Hadean Eon, during which the entire planet was molten, and which ended when solid crustal rocks began to form.
  • 4,100 to 3,600 ma - Late Heavy Bombardment, when most of the craters on the Moon, Mercury and Mars were formed. One relic on Earth is possibly the Nastapoka Arc in Hudson's Bay in Canada. Anything smaller has been eroded away. The first glimmers of life, and earliest putative fossils, date from the end of this era. There are also chemical signals in rocks aged 3,800 ma, that indicate photosynthetic life existed at that time. The Archean Eon is considered to have begun 4,000 ma. The Last Total Extinction.
  • 2,450 ma - Oxidation Catastrophe. During the Archean Eon life originated and soon became photosynthetic. For a billion years or more oxygen was immediately taken up by reduced minerals such green iron oxide (Ferrous Oxide, FeO2) and pyrite (FeS2), which produced red iron oxide (Ferric Oxide, Fe03) and iron sulfates such as FeSO4 and Fe2(SO4)3. Once all the reduced minerals had been oxidized, oxygen began to accumulate in the atmosphere, killing nearly everything. Those living things that evolved the ability to survive in the presence of oxygen, and later, to even use oxygen for producing cellular energy through respiration, took over the earth during the ensuing Proterozoic Eon. This was probably the nearest thing to a total extinction since the series of total extinctions at the end of the Hadean Eon. Great Extinction #1.
  • 2,400-2,100 ma - Huronian Glaciation, probably the first "snowball earth" period, unless it was "only" a near-snowball, a "slushball" with a narrow equatorial unfrozen belt. A Significant Extinction Event.
  • ~1,650 ma (maybe 2,000 ma) - Origin of Eukaryotes, large, complex cells and later on multicellular life composed of such cells; to be discussed later.
  • 780 (720?)-635 ma - Three better-studied Snowball Earth extinctions of the Cryogenian Era, in the late Proterozoic Eon. Each would have made most of Earth unlivable for all but the hardiest creatures. Three Extinction Events, each lasting several million years.
  • 542 ma - End-Ediacaran Extinction, A Significant Extinction Event. Early soft-bodied, multicellular creatures, and a few with hard parts, abruptly vanished. Possibly caused when predators arose that could eat the Ediacaran animals. The period that followed is the Cambrian Period, the first period of the Paleozoic Era of the Phanerozoic Eon, which is still going on.
The appearance of hard-shelled fossils just before the Cambrian Period makes it easier to distinguish changes in the fauna, particularly extinction events.

  • 488 ma - late Cambrian Extinction Event (AKA SPICE, for Steptoean Positive Carbon Isotope Excursion, a technical designation indicating a dramatic chemical change in the atmosphere and ocean).
  • 450-440 ma - Ordovician-Silurian events, a series of global cooling events, possibly ice ages, that wiped out 70% of species. Great Extinction #2.
  • 375-360 ma - Late Devonian volcanism. Over a few million years, half of all animal and plant genera became extinct, and perhaps 75% or more of all species. Great Extinction #3.
  • 252 ma - End Permian Mass Extinction, the greatest of the "Big 5", which actually starts with #2 in this list. A confluence of several causes, including inconceivably enormous amounts of lava that erupted to form the Siberian Traps ("trap" is a kind of volcanic rock). At least 90% of all species wiped out. Great Extinction #4.
  • 201 ma - End Triassic Mass Extinction, triggered when a less intense extinction caused by trap volcanism was augmented by an asteroid impact. At least 50% of species became extinct. Great Extinction #5.
  • 65 ma - End Cretaceous Mass Extinction, primarily caused by an asteroid impact, but trap volcanism was also occurring around this time in India (Deccan Traps). Wiped out most of the dinosaurs, leaving only birds, and also the pterosaurs and marine reptiles such as the plesiosaurs. The most famous of the "Big 4", Great Extinction #6.
  • 2.5-0 ma - The ongoing Pleistocene-Holocene Mass Extinction. Initially a result of the ice ages that began when North and South America became connected at the isthmus of Panama, it is not yet clear whether this is, or will, rank with the "Big 5". What was begun by continental glaciation is apparently continuing due to human interference with the biosphere, possibly including causing a big boost in carbon dioxide. A Significant Extinction Event. If we outdo ourselves, it could become #7.
This is the framework within which life on Earth has developed and evolved. According to this Wikipedia analysis, these are the most significant of at least 25 extinction events. While Earth nurtures life, and may be a nearly unique planet in doing so, it is still a dangerous place. Just ask the more than 99% of all species that are no longer living here. In spite of that, there are between 5 million and 15 million species of Eukaryotic life in existence, and anywhere between a few million and a billion kinds (the word "species" is harder to apply) of Prokaryotic life.

Now it is time for terminology about the kinds of living cells.

  • Prokaryote is meant to convey "prior to the nucleus", where "kary" refers to the nucleus in cells that have them. There are two major domains:
    • Archaea, which until recently were considered to be bacteria. But they have an odd mix of primitive and advanced features that bacteria don't have at all. For example, their ribosomes, which translate DNA codes into proteins, are complex and very similar to those of Eukaryotes. Bacteria have simpler ones.
    • Bacteria include all other prokaryotes, including all known pathogenic prokaryotes. Some (including me) consider Bacteria a younger offshoot of Archaea, and others consider it the other way around.
  • Eukaryote means "good nucleus". The cells are much larger, and contain mitochondria, which are prokaryote-sized energy-producing organelles that are considered to be descended from prokaryotes that were engulfed by a larger one but, rather than being digested, kept, "enslaved", and eventually became an internal part of all eukaryotic cells. Alternatively, the smaller prokaryote may have begun as an endoparasite to a larger species, that developed into an endosymbiont. Anyway, every cell in your body (except red blood cells) contains from hundreds to thousands of these little organelles, and you'd die in a matter of seconds if they were somehow killed off.

The authors draw on new discoveries in every area of geological and biological sciences imaginable. The various eons, eras, periods and so forth, delineated in the outline above, had an array of living creatures, both plant, animal, fungal, and prokaryotic, that differed significantly from those in any other. For example, before about 120 ma, were you to visit in your pocket time machine, you could not go about smelling the flowers because the few that had existed for the prior 30-40 million years didn't have nectar or perfume yet. There weren't any bees to attract. Jump back to the middle Cambrian, say, 520 ma, and there was nothing living on land except some bacterial crusts here and there. The main sea-bottom creatures were scuttling shrimp-like and isopod-like things including trilobites, also mollusks and clam-like brachiopods. Tentacled things such as ammonites weren't yet present, but there were numerous creatures we would probably not recognize, scuttling and swimming about.

The kinds of living things that existed, and the transitions from one kind of biosphere to another afforded by the various cataclysms, form the main subject of the book. I am overwhelmed by the sheer mass of information the authors packed into some 360 pages. Even many of the end notes,  those that weren't just strings of references, made fascinating reading.

To pick one significant learning from the book as a whole: several of the extinction events are classified as "greenhouse events". Certain periods were characterized by temperatures beyond tropical. Given that the Sun was several percent less bright half a billion years ago, and 40% dimmer around 3,000 ma, carbon dioxide alone could not produce global temperatures that would have exceeded 35°C (95°F) nearly everywhere, day and night. Methane eruptions, possibly from warming of methane clathrates in the shallower seabeds, were involved.

Certain geologic cycles, such as the formation or breakup of a supercontinent such as Pangaea or Rhodinia, cause large excursions in the level of carbon dioxide in the atmosphere. While that level was around 280 ppm a century or so ago, and is 400 ppm today, it was 1000 ppm or higher, sometimes much higher, during much of prehistory. A period of warming when carbon dioxide rises can trigger methane release. Methane doesn't last more than a few years in the atmosphere, because it can be oxidized. But sometimes, oxygen has been low at the same time as high carbon dioxide and methane, and then the methane lasts much longer and accumulates. The Triassic contained one such ultra-hot period.

And a fun fact: The present oxygen content of the atmosphere is 21%. At certain earlier times it was as high as 35%, which had several effects: the amount of nitrogen was the same as ever, so air pressure was ~15% higher; the extra oxygen provided extra energy to animals, and could in particular penetrate more deeply into the semi-passive respiratory systems of insects; and these two things led to some insects getting very large, such as a dragonfly with a meter-wide wingspan. The atmosphere was smokier, though, because of great forest fires. But the oxygen level was kept high by the rapid burial of organic debris that didn't get much chance to rot during that period. So...a dragonfly as big as a crow. Wow!

You don't have to specialize in geology or biology to enjoy this book. It is intended for us all, and the authors are very good at explaining what their jargon means.

(I won't go into detail about a few copy-editing errors I ran across. That's for a private letter. But I must comment that good proofreading and copy-editing are becoming less common. Authors out there, and editors, you can't just rely on a spell-checker. How else to account for the word "Cambria" where "cambium" was meant? The former is the historic name of Wales, and the latter is the living tissue in a tree.)