Hawking's swan song

kw: book reviews, nonfiction, essays, science, the future

When the deepest and most powerful thinker of the Twentieth Century, Stephen Hawking, passed away just one year ago, I was saddened, but grateful that he had lived as long as he did. He, who endured the great curse of a terrible disease, was very lucky to have achieved a certain stature by the time he became so severely disabled. Having a body that others must tend to, because he could not, he was free to live a life of the mind, which he certainly did, and yet he was always a persistent and preternaturally clear communicator, with a love of both teaching and dialogue.

He was working on a last book when he died. With a little tidying up by good friends and editors, it was released a few months later. So this past week Brief Answers to the Big Questions worked its way to the top of my reading stack. What a joy to spend a few days in the presence of such a clear-headed thinker!

After a foreword by Eddie Redmayne, who portrayed Hawking in The Theory of Everything, and an introduction by Hawking's good friend Kip Thorne, ten big, big questions are addressed. Naturally, "Is there a God?" comes first. He was asked that question frequently, sometimes to an irritating extent. I won't dig into his answer, but mention two things that impressed me. I'd had the idea in recent years that he was trying to disprove God's existence. He explains that, for science to be theory of nature, it must confine its explanations to natural effects and forces. If it is possible to develop a theory that fully explains the origin of the universe, then that is a complete natural theory. He does not express hostility toward God. Secondly, he mentions Laplace, who replied to Napoleon's question about the "author of the universe" by saying, "Sire, I have no need of that hypothesis", and he explains that, while we often take that for an anti-God statement, it was, rather, Laplace's way of saying that supernatural causes did not need to be added to his useful scientific methods, for they were sufficient. I'll mention just a few things I found interesting in other chapters; it would be presumptive to try to riff upon them all.

In "What is inside a black hole?" he tells us of the deep connection between the theory of black holes and that of the Big Bang, because both involve a singularity, that is, a location in space-time where our theories cannot probe, because phenomena such as density and the dilation of the flow of time reach infinite values…perhaps. To solve one would be to solve the other.

He discusses, "Will artificial intelligence outsmart us?" he comes at the answer from a few angles, without digging much into how soon such a thing might eventuate. It is clear that the techniques called "artificial intelligence" today, while quite capable and useful, are various expressions of massive data manipulation to winkle out the answers to questions that are posed. He mentions Moore's Law, which has been bent entirely out of shape, compared to how Dr. Moore posed it: that the density of transistors that could be fitted onto a unit area of silicon seemed to be doubling every 18 months. We know that law must come to an end because there are atoms, whose very name "a-tomos" is Greek for "can't be cut". Since a transistor has to have a few layers to operate, and each layer has to have at least a few atoms, the limit to Moore's Law, as stated, will be reached before the size of a transistor has shrunk to perhaps 20 atoms. That will still take a while, as today's CPU transistors still have millions of atoms. But other effects seem to be limiting things; it appears that the Law stalled out about ten years ago. Hawking does not go into certain issues that might be necessary for a machine intelligence to become "more like a human", before becoming "more than human", such as whether intelligence has to be embodied, not just because it is running on a physical substrate of some kind, but because it gets sensory input from thousands or millions of sensors, the way our brains receive input from the tens of millions of sensors of many kinds in our own bodies.

Here and there are side questions and very short answers. I was tickled by one in the "AI" chapter:

Q: Why are we so worried about artificial intelligence? Surely humans are always able to pull the plug?
A: People asked a computer, "Is there a God" And the computer said, "There is now," and fused the plug.

His view is similar to mine, that such an event is far in the future, though he perhaps thought it to be "far" in the sense of a few decades, while I tend to believe it is more like centuries.

His answer to another side question surprised me, and made me wonder if he blundered. Asked what is the biggest threat to the future of Earth, he dwelt on global warming, because it is more immediate than the threat of asteroid impact. He warns that it could lead to Earth getting a "climate like that of Venus with a temperature of 250°C (482°F)." The temperature of the near-surface environment on Venus is about 460°C (over 860°F). If Venus were moved to Earth's orbit, the difference in sunlight intensity would allow it to "cool off" to 350°C (~660°F). Apparently, the differences in the possible carbon dioxide composition of our atmosphere would reduce the effect by another 100°C. Maybe. By my own calculations, raising carbon dioxide from the current 400 ppm to Eocene levels of around 2,000 ppm would result in temperatures like that of the Eocene thermal maximum, about 8°C warmer than now. The secular increase in the sun's brightness since the Eocene, 55 million years ago, was less than 0.4%. I think that Hawking relied on material about global warming that I consider to be little better than propaganda.

On a more positive note, he believed we must colonize other places in space, first the "nearby" planets and their satellites in our own solar system, and eventually those of other stars. He does not believe that science will become a kind of static thing, as portrayed in Star Trek. Scientific progress shows no signs of slowing down, though it is evident that the "low hanging fruit" seems to have all been picked, and the "gentleman scientist" of the Enlightenment period is necessarily being replaced by ever-larger consortia of scientists working together.

By his own example, a heady mix of individual effort on his part, and intense collaboration with others such as Kip Thorne, Dr. Hawking showed a way for science to continue far into the future. And he urges us to re-emphasize the need for science education and popularization. Wouldn't it be something if the science lectures of the Enlightenment period could be resumed, and achieve similar levels of popular success? Scientists such as Humphrey Davy and Michael Faraday were like rock stars in their generation, largely because of popular lecture tours. We need more rock star scientists!

Women writers who can really write

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

Science fiction has always been experimental. While fiction in general is a frequent avenue to try out ideas, "mainstream" fiction just doesn't lend itself to truly outlandish thinking the way SciFi does. The wonderful collection The Future is Female, edited by Lisa Yaszek, contains stories written by 25 female writers, and though the editor emphasizes feminism as a theme, the point of the stories is seldom feminism as such. These writers present strong, talented women, frequently among equally strong, talented men, who are in the main not intimidated nor subjugated by them. For women writing prior to 1940 (the first three stories), that is no mean feat, because of the heavy patriarchy of Western society of the time. And…not all the protagonists are women. The last story, "Nine Lives" by Ursula K. Le Guin, is focused on the interactions of mainly male characters; it explores the way a multi-clone is accustomed to live, and how he fares when the rest of the clone (his clone-mates you could say) all die in a sudden accident.

The stories were written from 1928 to 1969. I don't know if there is a companion volume or two in the works that would feature later stories. I would find that of great interest.

One of my all-time favorite SciFi stories is included, "Ararat", by Zenna Henderson. Her "People" series feature women and men with special powers (actually, shipwrecked aliens who look entirely human) who live on an equal footing among themselves, but are in hiding from the rest of the human race because of prejudice against their seemingly magical abilities. This is a common enough theme, but Ms Henderson explored it in a way much more intimate and moving than any other writer.

Another story I love more than most is "All Cats are Gray" by Andrew North (a pseudonym for Andre Norton). Here a mysterious woman is able to see a nearly invisible monster because she is color blind. I hope that is not too much of a spoiler.

There is less for me to riff upon here, because I am mostly on the outside looking in through a window. My main insight into female experience is the little I've gleaned from nearly 45 years of marriage. My wife is foreign born and raised, so I have the extra handicap of seldom knowing whether her unique viewpoint is because she is female, or arises from a different culture I know only in part. So I leave you with the stories: get the book, enjoy the book, and particularly if you are male, learn from it!

The religion of false peace

kw: book reviews, nonfiction, religion, islam, muslims

A friend suggested that I read Muslim: What You Need to Know about the World's Fastest Growing Religion, by Hank Hanegraaf. It led to a shift in my attitude, in two directions. We'll get to that…

Muslim examines Islam from a Biblical Christian perspective, and a sympathetic treatment of Jewish concerns. I recommend that every Christian and Jew read it. For one thing, "The peoples of the Book" are stated targets for Muslim abuse, conquest, and annihilation. But even the more, you may not be a Christian or a Jew, but if you are not a Muslim, the intention of the Muslim world is to bring all the earth under Sharia law. (Note, I leave out the apostrophes in words derived from Arabic. I can seldom remember where most of them go). Thus I recommend this book to every non-Muslim.

The author discusses the person of Muhammad, his character, and his principal actions; the Quran and how it originated; Sharia law; the principle of the Caliphate; and how the beliefs and practices of Islam square with the Bible.

To me Chapter 3 is crucial, "Sharia is State, and State is Sharia". I confess that I had fallen prey to the misleading propaganda of Islamists, and of President Obama (whom I now consider to be much more a friend of Muhammad than a "Christian"). I thought that "radical Islam" was an aberration, not supported by the Quran. I thought that the things Muslims believed were comparatively innocuous, and no threat to the rest of the world. In each case I was wrong.

Mr. Hanegraaf presents extensive quotes from the Quran, backed up by many quotes from the hadith (historical writings about Muhammad and the Quran, with many interpretations of Quran passages).

• He shows that Islam is far from peaceable, that Jihad is definitely commanded against all non-Muslims. Contrary to many English-language apologetical articles stating that Jihad is primarily an "inner struggle", the great majority of jihadist texts in all Muslim literature, and particularly the Quran, explicitly demand the military subjugation of everyone, particularly Jews and Christians, and requires that any who will not submit by quoting "There is no God but Allah, and Muhammad is his Prophet" and paying a poll tax must be killed.
• He shows that Islam is not just a religion, it is a political system that is entirely theocratic. The statement "Sharia is state and state is Sharia" encompasses it. No "right thinking" Muslim will submit to any other legal system except as a temporary measure to gain favor until that system can be overthrown.
• He presents several passages, and indicates that many more exist, in which Muhammad is given permission by Allah to engage in behaviors that other Muslims were forbidden, or that most people find abhorrent. Chief among these is his marriage, in his fifties, to a six-year-old girl, and his consummation of the relationship only three years later. Others permit slavery, particularly the taking of women as sex slaves.
• The Sunni-Shia schism is outlined in an Appendix. It is rooted in the murder of Muhammad by either one or two of his wives. It is known that Muhammad was poisoned. But who did it? According to Sunni tradition, it was a Jewish woman: Muhammad led the slaughter of some Jews, and he himself killed the husband of the most beautiful of the women. Then he raped the woman and later made her his wife. She poisoned a bowl of broth, after which Muhammad suffered greatly for about three years and then died. But according to Shia tradition, two wives conspired together, and one of them was Ashia, the "baby bride" mentioned above.
• He compares the compilation of Biblical books with that of the Quran. Thousands of early copies of Bible manuscripts exist, but none of the originals. The discipline of Literal Criticism compares all the copies of each passage so as to determine which variation is closest to the original. Interestingly, I have a book that details all the important variations in New Testament manuscripts, and none impinges on the meaning of critical doctrines of the Christian faith. As to the Quran, Caliph Uthman ordered a massive project to gather all copies of the Quran. Once his scholars had put together a definitive copy, he had all other manuscripts burned. All copies since then have been from this "official" document. This is behind the contention of Muslims that the Quran is pure, that no variations exist. Apparently, though, from other sources I've read, a number of manuscripts that were never sent to Uthman do exist. But there is no Literal Criticism for the Quran, nor could there be.

A second turn in my thinking was a welling up of enormous pity for Muslims. I think we all have heard stories of how safe it is to go about in Saudi Arabia or one of the Emirates, for example. This is generally true, though a colleague of mine was beheaded on the street in Riyadh because he wore shorts to exercise, running in public. The reason for such peacefulness is Sharia law, which is terrifying. The beheading just mentioned was carried out on the spot, by a Saudi who saw my friend running by; he just whipped out his sword and did the deed. The populace in these countries is totally subjugated by such draconian laws and practices.

In its way, Islam can be a paradise…for a man. It is much more likely to be a hell on earth for a woman. Women who want the high extremity of "protection" that Islam offers are OK with it. But the slightest infraction can be met with beating, by her husband, and if continued, her life is at risk.

I am reminded of Medieval Cathlocism, which was similarly totalitarian. In a similar fashion, the leaders lived in luxury and the populace was kept in utter subjection to their whims. The church leaders and the royalty cynically ignored the tenets of the religion that they used (and abused) to subjugate the population, but they delighted in the willing submission of many, who truly believed the religion. If anything, Islam is even more onerous, and their leaders, equally cynical.

These are just a few things I learned from reading Muslim. I suspect Muslims don't like any of them to be known by a non-Muslim. The matters discussed in the book are not hearsay. Every item is backed up by quotes from the Quran and the pertinent hadith. A few times there are citations from the biography by Sahih, but those are always backed up by references from the Quran.

What does all this mean to a non-Muslim? If you happen to live in an Islamic country, it means that, while your life may not be in danger today, one day when the political circumstances allow, your life may depend on your willingness to accept Sharia, say the "Muhammad prayer" and pay a poll tax for non-Muslims. Do or die. Countries that are currently non-Muslim may become so in the future. This is the intent of the leadership of every Islamic country, every mosque. They will not rest until no religion but Islam is to be found anywhere on Earth.

Don't take my word for it. Read Muslim for yourself.

Critical thinking - needed now more than ever!

kw: book reviews, nonfiction, critical thinking, psychology, sociology

As I write this, a Kangaroo Court is being conducted in a Congressional committee, to hear "testimony" from a convicted perjurer. Such testimony is intended to, at the very least, embarrass the President of the United States; hopefully, to convince a larger segment of the public that said President is a liar, bigot, and general bad guy; even possibly ("Please, please!", you can almost hear them begging), to gather material that will allow Articles of Impeachment to be drawn up. P.T. Barnum would be proud (Google the two words Barnum and sucker).

So, mini-quiz:

1. Do you know what verse in the Bible states, "Money is the root of all evil."?
2. Do you believe the Moon landings of 1969-1972 were faked?
3. Do you expect part of California to "fall into the ocean"?

My analysis (feel free to disagree):

1. First Timothy 6:10 states, in the King James Version, "For the love of money is the root of all evil: which while some coveted after, they have erred from the faith, and pierced themselves through with many sorrows." Note that it is "love of money" not just "money". The New International Version, usually more accurate in colloquial English, renders the first phrase, "For the love of money is a root of all kinds of evil." Here it is "all kinds of evil", not just "all evil." Big difference.
2. If you believe NASA faked the Moon landings, you're in good company if you're British (52% of Britons think so), but only 7% of Americans think the landings were faked. U.S. Government hype about the Moon program is definitely worth taking with a grain of salt, but in my view, it would be harder to fake than to actually do it!
3. This was a popular belief 40-50 years ago, when everyone was waiting for a "big one" earthquake on the San Andreas Fault. In the half-century since, there have been several "nearly big one" earthquakes, which seem to have relieved the geological strain…for now. But, the S.A. Fault moves sideways, not up and down. The western side is creeping northward. If you wait long enough (40 million years), Los Angeles and San Francisco will be "sister cities", right across the Fault from one another. After a further 100 million years or so, the L.A. area will begin to descend beneath Alaska somewhere along the Aleutian Trench. That's when it will "fall" into the ocean.

Item #1 above is in the "everybody knows" category, at least for Americans brought up in a nominally Christian environment. But what most of "everybody" knows, isn't what was really written by the apostle Paul. Item #2 is a "grand conspiracy" belief. Those who believe it, can't be convinced into not believing it. And #3 takes advantage of general ignorance of geology (which direction the fault moves) and our small time horizon. It isn't just that we only live a century or less; most of us get impatient waiting for the microwave oven to heat a cup of water to make instant coffee! Even H.G. Wells's Time Machine only takes the fellow 800,000 years into the future (except for one scene, at an unknown remove, when the Sun is becoming a red giant).

When I was in college, I took a course in the English department, but it really belonged in the Philosophy department. We read articles in lots of journals of all kinds. We were to figure out what was the bias of the article, and by reading editorials or other articles in the same journal, what was the bias of the journal as a whole. So, the Wall Street Journal was, and still is, quite conservative, while Commonweal was and is liberal, bordering on progressive, and with a Roman Catholic viewpoint. There were five or six others. Near the end of the course we were to read editorials from several local and near-local newspapers, plus the New York Times. It was obvious to all of us that, without exception, the papers were exclusively left-wing. This was in the 1960's! Looking back and comparing with editorials in the local papers now, those would be considered hide-bound conservative (Jack Kennedy was fondly looked upon as a liberal, but today would be to the right of nearly everyone in Congress).

This points up two things. Firstly, I don't think any American college still has such a course in Critical Thinking. That wasn't its title, but it should have been. Secondly, baselines have shifted. Creeping leftism is one kind of "moving goal posts" trend. The fallacy of Moving Goal Posts is one matter taken up by the authors of The Skeptic's Guide to the Universe: How to Know What's Really Real in a World Increasingly Full of Fake, Dr. Steven Novella with Bob Novella, Cara Santa Maria, Jay Novella, and Evan Bernstein.

The authors, three brothers and two associates, are a core group of SGU (see book title), which produces podcasts and other materials on behalf of the New England Skeptical Society. They call themselves and their colleagues "rogue skeptics." Skeptic's Guide first discusses the many ways we can fool ourselves or be fooled by others, presents case studies from their experiences, and shows how to determine (to some degree; nothing is perfect) the veracity of the things we see and hear and read in the media. They have taken on a tall order, and the size of the book (nearly 500 pages) attests to that.

I began to read, with a niggling thought in the back of my mind, "I wonder if they'll make a full-on assault on faith?" I was relieved to find that they do not. They do criticize (rightly) young-earth creationism, anti-evolution beliefs, and the kind of "easy-believism" that attributes favorable coincidences to divine favor. In those areas, I happen to agree with them. Dr. Novella is a physician and educator. He reserved much greater disdain and his best ammunition for anti-vaccination activists and the "AIDS is not from HIV" folks, and most kinds of "alternative" medicine. As to religion, I would not call him an Atheist; that term has been taken over by evangelical anti-theists. I'd call him an honest non-theist. (Hey, Doc, I mean that as a compliment!)

Is it possible to be a Christian skeptic? Particularly for me, a Christian mystic. Let's define terms here: "mystic" means someone who has spiritual experiences; and "skeptic" means someone who withholds belief in claims not properly supported by evidence. The first half of the book points out all the ways that our "experiences" could be fallacious. Well and good. The experiences of me and my fellow believers may not make sense to the SGU folks. They'd say we have false premises. I say we have repeated and reliable experiences and based upon them, we are either crazy, or we are children of God, who know our God by direct experience. However, it is worth taking note that we have finite capacity, which does lead to our brain taking many short cuts with our perceptions. We need to be humble, which is mentioned frequently throughout the book.

So, I am a mystic, but I am also a scientist. I am a retired IT/IS computer scientist, who wrote software for geologists, biologists, chemists and physicists for 40 years. In retirement I work for a natural history museum (part time), where I use my knowledge of the workings of evolution and natural selection daily. I understand Deep Time (millions and billions of years) in a way not many people are equipped to comprehend. As a scientist, I am a skeptic. I am actually quite impressed by an argument the authors make, against the notion of "supernatural" events. If something happens, and it had a physical effect, particularly one that can be measured, it is by definition part of nature. Thus, if there is an entity that we call God, who—as theists believe, by definition—intervenes in the workings of humankind and particularly His believers, that God is part of nature. The Judaeo-Christian understanding of the creator takes that a step further, to say that "real nature", including God, is a lot bigger than the "nature" that human scientists have so far been studying.

I had a colleague at an engineering company where I worked in about 1975, who told me of his belief that God was a "super technologist". Maybe he was right. If what I believe about God is correct, I expect to have the chance to ask Him.

Back to the book. We are bombarded more than ever with "fake news". It is getting easier to fake. Even a century or more ago, some things could be faked. Have you heard of "retouching"? I have a photo from 1914 of a family reunion. I scanned it for my online family tree. In the scan, the oblique light of the scanner made the retouching more evident; I hadn't noticed it before. The photographer actually painted, right on the 8x10 inch print, to make certain of the faces more attractive, particularly one older man who had huge jowls, which are retouched to look more like a more ordinary elderly face. Photoshop was about 75 years in the future! Now such photo-editing can be done very easily and is undetectable without specialized software.

There's one spot in the book where I noticed the authors let an error (made by others) slip past them. On p.88, writing about altering perceptions by the way a fact is presented:

Another example is a survey showing that "62 percent of people disagreed with allowing 'public condemnation of democracy,' but only 46 percent of people agreed that it is right to 'forbid public condemnation of democracy.'" These are, again, the same outcome.

Actually, 62+46=108. Either there is a typo there, in the production of this book, or the source contained the typo. Considering the language used in the two statements, I suspect the latter figure was intended to be 38 percent. Now, this does little more than emphasize that I am a pretty good proof-reader. The point they are making is valid. If I say to you, "This chemotherapy is successful 2/3 of the time", it causes quite a different feeling than "1/3 of those who use this chemotherapy find it ineffective."

And I do want to say a word about selective attention. We can't pay attention to everything, so we are, by nature (natural selection, in which I do believe), fitted to discard nearly everything that enters our senses (90%? 99%? anyway, nearly all). Although we have a visual cortex with as many neurons as the entire brain of a gorilla, and it slurps up a 120-megapixel stereo image (about 8 mpx of color info), about 20 times per second, we must discard most of that. There isn't time or space to form lasting memories of everything. We actually "notice" a small number of "things" per minute, but there are upwards of 800 minutes in a waking day. By the end of the day, most of our "minute-memories" are long gone, and we remember only a few. Weeks later, we aren't sure which day we had eggs for breakfast, and which day we had Lucky Charms or Rice Krispies. We will, however, remember the fight we had with our spouse or the scare we got when a semi nearly ran us off the road…but we may not recall just which day it was. Instead, we'll remember what our spouse was wearing or the tree alongside the road that we narrowly missed.

Now, I could go into the techniques for avoiding being faked out by fake news. The book contains so many of them, you'd have to be the kind of specialist that the "rogue skeptics" are, to effectively use more than a handful. So I'll just mention a couple of things.

First, for many things we might encounter, when a viewpoint is presented, we need to ask, "Who benefits?" This principle is behind the phrase "conflict of interest." We are all prone to that! Secondly, when there are conflicting views of an event, it is useful to ask, "Who has the power?" or "Who is paying for this?"

When someone, for example, wishes to run for President, so as to move American toward Socialism, and that same someone has become filthy rich by taking advantage of Capitalism, I just have to say, "Well, his initials are B.S., and that's what he is feeding us!" But, who benefits? Socialism requires totalitarianism. Under the dictum of Marx, "From each according to his ability; to each according to his need," who gets to choose what "his ability" ought to be, and who gets to choose what "his need" is? In every Socialist nation that has been set up, the totalitarians benefit, a whole lot, at the expense of everybody else. Look at the fine suits the current (and I hope outgoing) President of Venezuela wears in his news conferences, compared to the rags worn by the people the Venezuelan troops are gunning down in the streets because they have the temerity to ask for "more". Every "Socialist experiment" has devolved into a kleptocracy.

So, for today's Kangaroo Court, who benefits? Why would Mr. Cohen volunteer to "tell all" to a Congressional committee? There must be a very lucrative book deal in it (as soon as he gets out of prison for perjury). Also, to me this smacks of revenge. That is another kind of benefit, to lots of people. And I would not be at all surprised if there are large behind-the-scenes kickbacks (suitably laundered) from some Congresspersons who are hoping for that "smoking gun" they need to proceed with an impeachment.

My default mode is to get news from numerous sources. It's just kinda hard to get anything but "leftie special", when 90+% of the media are leftists, and I don't have cable so I can't watch The Blaze or Fox. Luckily I can get conservative news from at least one radio station around here, to counterbalance the "radio Leningrad" I hear from the rest of them.

So, Dr. Novella has become a favorite author of mine, at least among the non-theists. The writing in the book is top-notch, and the thinking is clear, or at least a whole lot more clear than almost anything I see in the newspapers these days.

P.S. P.T. Barnum didn't actually say, "There's a sucker born every minute." An associate of his said he built his business on fooling suckers, "…because there's one born every minute." The geek in me just has to add: Today in America, there are 7.3 births each minute, and in Barnum's time it was pretty similar (more births per person though the population was smaller). So, it seems, 6/7 of us aren't suckers! Somehow that seems optimistic…

Nature's got rhythm - it slows down entropy

kw: book reviews, nonfiction, natural history, mathematics, synchronicity, sync

When you view this video, most of the language you hear is Malay. In parts of Asia, and in the Great Smoky Mountains in the U.S., certain species of firefly synchronize their flashing. Why? You'll get part of the answer from reading Sync: How Order Emerges from Chaos in the Universe, Nature, and Daily Life, by Steven Strogatz.

As a professor of applied mathematics, Dr. Strogatz has studied sync for most of his career. As a freshly-minted college graduate, he chanced to get a book by Art Winfree (deceased), who became a mentor to him and kick-started his lifelong fascination with synchronicity (sync), and how it is found throughout nature, both in living and nonliving systems.

When our brain forms a lasting memory, a scattering of neurons that reach from end to end of the brain will pulse in sync for a moment. For some reason, memories we aren't destined to hang onto cause a less wide-ranging burst of activity. What little we so far know about this is discussed in Chapter 10, "The Human Side of Sync". The synced fireflies seen in the video above, and theories for the phenomenon, are discussed in the opening chapter, "Fireflies and the Inevitability of Sync." We respond strongly to sync, as evidenced by our love of dance, singing together, and applauding of cheering together. "The Wave" in a sports arena is a traveling sync phenomenon. I've experienced The Wave running around a stadium six or seven times before fading out.

Our "body clock", circadian rhythm, seems to be rooted in a clock that resides in every cell of our body. It typically runs on a 25-hour cycle and is reset by daylight. Experiments with people spending months in "time free" areas like caves or specially built rooms, who were given no clues about what day or time it was (and who frequently went rather crazy), elucidated this chart:

Our body temperature follows a pretty strict daily curve usually peaking at or just below the proverbial 98.6° (actually chosen because it is exactly 37°C, though that is a tad warm) about sundown, and dipping as much as 1.5°F (0.8°C) to a low a few hours before sunrise. BTW, my daily high is seldom above 98°F.

This chart gives support to the siesta habit in some cultures (not only Latino), and to the big spike in "inattentive driving" accidents during the Zombie Zone after midnight.

This chart is averaged. Some people's cycle runs later, some earlier. A friend of mine cannot sleep past 3:00 AM, so he must hit the sack between 7:00 and 8:00 PM to get a full night's rest. Teenagers are frequently "owls", needing to sleep until at least 9:00 AM, even though most high schools start their day more than an hour earlier (taking care of the parents' work day requirements); so our kids are sleepy in class and learn less. This is in part why homeschoolers learn better, on average. Their parents start the learning day later.

Nonliving systems also synchronize. A few centuries ago, Christian Huygens, recuperating from illness, noticed that two clocks hanging on his bedroom wall were ticking in sync. Here, they were in exactly opposite phases: one would tick when the other went tock. There is an episode of  Mythbusters focused on putting hundreds of metronomes on a platform sitting on rollers, showing that, if set to (nearly) the same frequency, they gradually all sync up and tick together. A pair of tiny moons in orbit around Saturn was found to be sharing an orbit in which one almost catches up with the other, then both shift—one a little inward and the other a little outward—so that they move apart and swap velocities so that the formerly slow one will begin to get ahead until it was the one catching up. The two moonlets never touch. I find them similar to Huygens's clocks.

What is going on here? It seems that nature loves sync. A few decades ago I read an essay, based on a physics professor's lecture, called "Nature's Hangups". It illustrated a number of the things that happen in nature to keep everything from just falling to a center and eliminating itself in a big "whooomph". Sync had a lot to do with it. Near the end of Sync, the same principle is mentioned, using an eloquent image of complex systems taking advantage of entropy to form local pockets of decreased entropy, things that we call living beings, crystals, and solar systems. Sync describes the formation of "time crystals", the regular pulse of a natural system, analogous to the regular array of atoms of molecules in a mineral crystal.

Phenomena as disparate as our heartbeat, the swirling of flocks of starlings or schools of fishes, the aforementioned synced fireflies, seizures induced by repetitive flashes (I've been knocked out cold by a rising sweep of bright flashes), and the Kirkwood Gaps in the asteroid belt (orbits in sync with Jupiter), all have related mathematical descriptions, revealing an underlying tendency in nature to sync things up. In later chapters, starting with 7, "Synchronized Chaos", we find that even wildly gyrating "chaotic" systems (in the mathematical sense) can synchronize themselves, which may lead to improved ways to encrypt communications.

Dr. Strogatz is a mathematician. He is also one of the great explainers of recent generations. He manages to discuss and describe many highly mathematical subjects, and make them at least conceptually understandable, without using a single equation. Sync is literally keeping you alive, and his book tells how.

The man in the box is missing

kw: book reviews, nonfiction, artificial intelligence, algorithms, surveillance

Google is spying on you. So are Facebook, Twitter, and nearly every web site that you use. Never mind the NSA and the CIA and their ilk (another 15 of them, just in the US!). Here's the rub, though. Amongst the many "likes" and other clicks you make daily; and if you like to write, as I do, amongst hundreds to thousands of words you generate; and amongst the photos and links and other "stuff" you might send out into the ether, daily: Is there someone who can digest it all, winnow it, and produce a comprehensive picture of just who you are?

Not a someone, but a something. Namely, an algorithm; strictly speaking, in each such case (Google, etc.) a veritable forest of algorithms that analyze (gather, group, parse, summarize, mathematically rotate in n-space) all the data we generate for them and give to them.

What is an algorithm? It is a recipe. A cookbook is filled with descriptions of algorithms that a cook will follow to produce this or that dish. A computer program contains, in specialized language, recipes that the computer will follow to "cook" data to produce "dishes".

Early electronic computers were used to produce tables for predicting the flight of a mortar shell, which made it easier to aim accurately. The ballistics table was the "dish". These days, the "dish" is more likely to be something that an advertiser will use to influence you to buy something, or a political party will use to influence how you vote, or a "nonprofit" group will use to gain your support. Does any of that worry you?

David Sumpter, a professor and applied mathematician, worried about these things, and he had the tools and the standing to do some digging around. How much of this is true, and how effective are these techniques? His intellectual and mathematical journey and the conclusions he drew are described in Outnumbered: From Facebook and Google to fake news and filter-bubbles — the Algorithms that control our lives.

He describes what he found, and, to cut to the chase, while the power of the algorithms is amazing, the results are slender. The algorithms are not much danger. Even the more powerful algorithms we can expect in the next generation or two are unlikely to be much danger, in and of themselves. The true danger is that powerful people believe their results, even when it can be shown that the best algorithm is no more accurate than the informed opinion of an intelligent expert.

Why is that so? I must back up here: we in the computer field rather loosely talk about "putting the intelligence" into a program. But that does not make the program "artificially intelligent." In every case, we embody some aspect of human intelligence in an algorithm that a computer can perform very fast. For example, I know how to perform a Fourier Series analysis, to analyze the frequencies in some kind of signal, such as a snippet of a song or a portion of a digital photo. It takes a lot of calculations (millions of them to analyze 1/100th of a second of audio). Computers can do those calculations so fast that audio spectrum analyzers that run on a smart phone can produce a sound spectrum  in real time (I use one to "see" bird songs). No computer "invented" the Fourier Series analysis, a human did. So, why is it that a knowledgeable person can still outperform a mechanical "understanding" of social cues? Two things: (1) The human mind works in ways that nobody yet has a clue about; and (2) We instantly recognize similarities, which computers don't do well, while computers instantly find tiny differences, which we have a hard time at. (Just by-the-bye, I made a 40-year career exploiting the synergy of mind and machine.)

So the problem with letting algorithms "do stuff" is that they don't do it any better than we do. This isn't likely to change much in the next few decades. Further, because the data used to "train" the "deep learning" systems in use today (such as for Google Translate) contain lots of human bias, those biases will be reflected in the results produced by the systems. For example, suppose we use the trillions of sentences in Twitter to train a natural-language understanding-and-response system. Is it possible to pre-filter out the trolls, the "hate speech", the bigotry and sexism and this-and-that-phobic utterances? If we don't, the trained system will exhibit the biases and bigotry of the data that went into it. This is a malicious example of "garbage in garbage out."

For most of us, we experience the results of all that spying and calculation in the ads we see online, and even the kinds of results we get from doing a search. I have learned to search for anything meaningful in an Incognito (or inPrivate) window. My wife and I had this experience: a handle on an end table was getting loose. We found that the threads on its screws were getting stripped, probably from being bumped rather hard at some point. We looked online for handle hardware, from various sources. We found something we liked, and ordered handles enough to fix both end tables. Guess what? I got lots of ads for handles, in Google, Facebook, and nearly everywhere else that had banner ads! I got them for a month. I thought of writing to Google, "Dudes, I bought a set of handles the same day. Y'all are way, way too late!" But what's the use? Until they think to check online purchase information, they can't know it.

I did three little experiments. First, in a Firefox Private window, I went to www.google.com and began typing "how to peel", and then I recorded the auto-complete results:

• a mango
• butternut squash
• garlic
• pearl onions
• a kiwi
• an orange
• ginger eggs
• a banana
• tomatoes

When I did the same thing, logged into my Gmail account (on another tab), the first result was

• a pineapple

followed by the next 8 items above, from "mango" to "banana". Yesterday, I happened to look up YouTube videos about peeling pineapples. No surprise there.

Then I did the same process, starting with "best books for". The auto-complete list was:

• young adults
• teens
• 3 year olds
• men
• toddlers
• 2 year olds
• 4 year olds
• men 2018
• babies

When I did the same thing "as myself", I got exactly the same list. Did you notice, as I did, the glaring omission of women or girls? That is funny, because my wife and I use the same account credentials and the same email accounts. Maybe females don't search online for books (but I'd be surprised...)

Then again, in private, I entered the search term "genealogical". The results list, first page, was:

• the definition
• genealogical.com
• www.dictionary.com/browse/genealogical
• www.thefreedictionary.com/genealogical
• delgensoc.org
• [2 "top stories"]
• "How genealogical sleuthing led to suspect in Warwicks joggers death" - The Providence Journal
• "Genealogical Society learns about creating digital family histories" - Community Journal
• www.archive.gov/research/alic/reference/genealogy.html
• www.archive.gov/research/genealogy
• www.ngsgenealogy.org
• - not detailed
• www.newyorkfamilyhistory.org

The page also included a photo-ad from ancestry.com for its software and service. After that, logged in again as myself, I entered "genealogical", with these results:

• [3 ads]
• www.myheritage.com/Genealogy
• www.geneticsdigest.com
• www.genealogy.com
• the definition
• genealogical.com
• en.wikipedia.org/wiki/Genealogy

and then the rest as above, from www.dictionary.com through the rest except the newyorkfamilyhistory one. The photo-ad for ancestry.com was the same. Are these differences significant? Not usually.

The book ends on a slightly melancholy note. Dr. Sumpter found he'd become something of a wet blanket at parties, because when people started grumbling about what Google and FB and others were doing, he had the real info, which was less flashy. Sure, if an algorithm can sell 0.1% more fribble widgets, and if the market for fribble widgets is usually a few million, that 0.1% could be a few thousand more of them being sold. But people want something to be a little scared about. There's nothing scary about fractions of a percent. Even filter-bubbles turn out to be a toothless bugaboo. Nothing pops a bubble quicker than outside info from a source that isn't trying to change your mind, but is just presenting the facts as seen from elsewhere. All of us have more than one source of information. Sooner or later, any bubble we've been in will come up against "real life" from another angle.

I have to tell this story, a bittersweet one. In 1980 the first Chinese students were allowed to come to American colleges. A few years later some Chinese nationals who had relatives in the US were allowed to visit them. A Chinese friend of ours, a man in his seventies, was visited by his sister. For a few days, she said a lot about how good the Chinese system was, how Communism was better than Democracy, and so forth. I understand, of course, that in China, speaking any other way could get a person in trouble. Our friend and his wife didn't argue with her. They just took her along the next time they went to the grocery store, at a Walmart. The dear lady saw the rows and rows of fresh produce, the bread, and everything else, and began to cry. I must have been rather hard for her to return to China a few weeks later.

Will artificial intelligence make the algorithms work any better? Many of them are already being called AI, but it is hyped. It is just the rapid application of human intelligence. Anyway, we may be in a waning cycle of hype about artificial intelligence. Computer software is in no danger of replacing us any time soon. Before there were electronic computers, people had cleverly devised mechanical aids of many kinds to speed up the processes we needed. Napier's Bones were devised in the 1600's to simplify multiplication and division. Slide rules (I still have a few) preceded the pocket calculator by a few generations, and could also perform trigonometric and logarithmic calculations. I have an old copy of Machinery's Handbook, which contains "log tables", in case you need greater accuracy than a slide rule can produce. The first mainframe computer I used was no more accurate than the table of logarithms, it was just faster.

So far, all these things are tools. The algorithms used on our social data are tools used by marketers and propagandists. If we keep ourselves aware of these facts, we'll have better sales resistance, and "fake news" resistance. And we'll also be able to turn the tools back on themselves to our own benefit: sometimes the ads they show us are for something that we really can use, and we didn't even need to go looking for it!

Snowflake specs

kw: observations, convolution, novelty glasses

Someone gave me a pair of "Snowflake Glasses" as a gag gift. Here is how they look. It is kind of intriguing. There are apparently many of these with different light effects.

 I could see that, whatever they did, it would be a diffraction phenomenon. The purple color hints that they use an Ozalid process to make these. That makes sense, because it is capable of very high resolution, and is used for cheap microfilm. I didn't try these while there were Christmas lights up, so when I did, I first looked at the sodium-mercury street light. A very pretty snowflake! You can see a dimmer one radiating from the reflection on the right.

I noticed a little red-green fringing, which I would expect from a diffraction effect. So I decided to try a more broad-spectrum light, as seen next.

This is the light on a neighbor's house. It shines at a side yard. The color fringing is more evident. Each wavelength is diffracted a different amount, with red moving furthest because its wavelength is the longest.

I just had to see what the pattern looked like under a microscope. That's next.

 Diffraction bends light both ways, so only three pattern orientations are needed to make the hexagonal star. This pattern is called a convolution. It is the mathematical inverse of the star pattern that we see when we look through it. The oval with "snow090" is an identifier. The ovals are spaced far apart, so they don't diffract enough light to be visible, and they do it at a very low angle.

The total pattern is made up of tiles that look like they are about 2"x2" in this image. They are small enough that several of them "fit" in the beam of light that enters the pupil of your eye. Thus, no matter what portion of the specs you look through, you see the intended snowflake.

I am not sure of the magnification here. I was using my inspection microscope at 20x, but this is cropped from the middle of a bigger image, so perhaps it is around 50x.

Just for the record, it would be possible to produce such glasses that select just a few light colors (red, green and blue, for example) and diffract them separately so that they all make the same size snowflake, and there are no color fringes. But it has to be done using a different method, and the cost would be much greater. These are intended for looking at Christmas lights, which are single-color.

Animals you never knew about

kw: book reviews, nonfiction, animals

Bestiaries of the past combined natural history, legend, speculation and moral instruction. Based on better science, and including rich commentary instead of crude moralizing, Caspar Henderson has produced The Book of Barely Imagined Beings: A 21st Century Bestiary.

He goes through the alphabet, sometimes in a surprising way, including two "X" chapters. I am endlessly fascinated by natural history, but I'll keep this shorter by just touching on three special animals, and where his riffs upon them take us.

Barrel Sponges include the Giant Barrel Sponge, Xestospongia muta, which can live more than 2,000 years. Sponges were apparently the first animals to reach sizes larger than a few aggregated cells. They are most sophisticated than they look. There are apparently several (perhaps six) kinds of cells with semi-specialized functions, but no tissues as we would consider them. A small sponge can be forced through a sieve and thoroughly disaggregated to loose cells. It will re-form itself as it originally was.

Henderson discusses the concepts of multicellularity at some length, including some ways it goes wrong, as was seen with the Elephant Man, Joseph Merrick, who suffered the continuous growth of portions of his body. It is still quite mysterious how an animal body, whether sponge or starfish or surfer, keeps its parts proportional. From there the riff goes on to the development of life, once the Bacteria and Archaea split, and creatures that we call Eukaryotes, composed of large, nucleated cells were split off from the Archaea (or descended from one of them by engulfing some bacteria and keeping them as "pets" that are now termed mitochondria and chloroplasts). Every visible creature is a Eukaryote, but they (we) are outnumbered (trillions-to-one) and even greatly outweighed by non-Eukaryotes.

Nautilus, a genus of cephalopod (an order that includes octopus, squid, cuttlefish and others). They and their kind, the Ammonites, were the primary predators in the pre-Dinosaur-age oceans. Today, these are rare and getting more rare. Cephalopods have two kinds of appendages, arms and tentacles. A nautilus has 90 slender arms, without suckers on them. An octopus also has only arms, eight of them, but the arms are well equipped with suckers along their entire length. Squids, cuttlefish and some others have both arms and tentacles. The two tentacles are longer than the arms and have a pad at the end with suckers on it, and only there.

I show this image a little bigger than the others to make the eye more visible. Other cephalopods have eyes with lenses, but this eye has a small pupil with no lens. It is like a "pinhole camera", and it makes a very blurry image. That seems to be enough, along with the animal's tactile and chemical senses, to track down its prey and avoid predators.

Venus Girdle (see video below of Cestum veneris) is a surprisingly lovely type of salp. Salps and other "comb jellies" look kind of like jellyfish, but are in a different phylum, the Ctenophora (ten-o-fore-uh); jellyfish, corals and sea anemones are in the phylum Cnidaria. The "comb" of a comb jelly refers to the rows of cilia that it uses for locomotion. Ctenophores are the largest animals to move about primarily using cilia.

Taking off more from the name Venus (goddess of "love", that is, lust), than from the animal itself, Henderson spends a page or so on sex, and the indications that nearly all animals seem to enjoy it. (I would except those females of species in which the male's "member" actually pierces or spears the female's body to deposit its load somewhere inside!). Comb jellies reproduce very fast, so perhaps the Venus association is actually rather apropos. Where their predators are eliminated, they can rapidly take over an ecosystem and turn a large chunk of ocean into a teeming mass of gooey critters.

One other animal has a rather sideways association with sex in its name, Gonodactylus, the Mantis Shrimp. The scientific name arose when the naturalist who described it thought the paired forelimbs, when held at the ready, looked a lot like a pair of testicles, so the name means "gonad hand". However, those "hands" can move faster than any part of any other animal, when the mantis shrimp clobbers its prey, or even causes cavitation (a kind of shock wave) in the water to stun nearby prey. But I was much taken by the description of their eyes. Humans and most primates have three-color vision. The millions of colors we can see are a mix of the sensations caused by light received by three kinds of cells. Mantis shrimp have around ten different color sensitive cells. In the very brightly-colored and visually confusing environment of a coral reef, they can more clearly distinguish color differences that help them pick out what they need to see.

A book like this is great fun to read, and it is equally great fun to learn of the myriads (millions!) of different animals with which we share this planet.

A coder's memoir

kw: book reviews, nonfiction, computer programming, coding, memoirs, philosophy

David Auerbach coded for some twenty years, twelve of that professionally, including a few years each at Microsoft and Google. Now he is apparently more of globetrotting professional speaker. His memoir Bitwise: A Life in Code is less about what coding is—though he doesn't skimp on that—and much more about the ways we are being changed to interact better with computers. It seems that inducing computers to interact as we do has proven just too hard. To this I agree; I've been hearing promises of "Artificial Intelligence" and "Mechanical Brains" for my entire life. Immense breakthroughs are always "just another ten years" away. It will probably always be so!

I almost never include a book's cover in a review, but this time I just couldn't resist showing you this:

I wonder how many readers or even reviewers of this book noticed that the green letters are phosphorescent? Panel 1: white light; Panel 2: UV light turned on; Panel 3: Room lights and UV light off (a little light scattered in from the next room). I noticed this when I had been reading the book in bed, and saw the green glow after turning off the bedside lamp.

In the title, the special characters are from a scripting language I never learned; it has been so long since I saw them that I don't recall which one. The author tells us he first coded in Logo, a coding script that is easy for children to learn; he began using it at age seven. By the time he began getting paid for writing code his language of choice was C++.

When he worked for Microsoft, he spent a period in a behind-the-scenes battle with AOL, modifying code that took advantage of AOL's Messenger Service so that Microsoft IM users could send and receive messages on both platforms, expanding their contact base without everyone having multiple accounts. Later, working for Google, he had various projects, including some of the ongoing tweaks to the Page Rank algorithms. Search Engine Optimization is an attempt to get a page a higher ranking than it might ordinarily merit, by taking advantage of the way Google ranks pages. Some techniques are rather innocuous, but others are rather predatory, and so Google has a number of coders who continually revise the ranking code to flatten the playing field. It is an arms race. It always will be. As a result, the original "Page Rank" method is dramatically out of date.

The author pretty much disposes of the nuts and bolts of his career in the first part of the book. Part II digs around in the differences between the symbols, labels, and names used by humans, and the way labels are assigned in computer code. Every such "tag" we use is invested with meaning to us and by us. Words such as red, blue, orange and magenta have meaning for us. Usually the meanings of colors don't carry much emotional freight. In data, they would just be numbers. (The most common color coding, often called just "rgb" for red-green-blue, assigns the triplet 255,0,0 to the brightest red and 0,0,255 to the brightest blue. Magenta, being an equal mix of red and blue, is stored as 255,0,255). Other words carry much more meaning.

Suppose we have a group of words such as Baha'i, Zoroastrianism, Christianity, and Islam. Since there are a few hundred religious labels (and let's ignore sub-labels such as Baptist or Sunni), in a database, these might just be referred to by numbers such as 12, 497, 44, and 112. To a computer, these are no more meaningful than the color numbers. But to us, they can carry meaning that people fight and die for. Can you imagine a computer giving its "life" in favor of a practice such as water baptism, or the holiness of a shrine in Kyoto? Such things have occurred among humans!

Part III explores further the implications of about 40 years of "home computing" (and, I suppose, 80 years of programmable machinery starting with the Mark I). Twenty years ago I remember talking with a representative of a disk drive manufacturer. He joked that if his company invented a disk with infinite capacity, perhaps called the "god drive", the government would order two of them. I responded, "So would Sears and J.C. Penney". Now that we can buy multi-trillion-byte disk drives for under $100, and both Google and the NSA (and who knows how many others) have warehouses full of disk servers holding billions of times that much, the term "big data" seems rather pale. We are already in an era of "enormous data", with every likelihood that data storage capacities will continue to explode. Not just the government tracks us. So do a multitude of corporations, Google just being the most visible.

In such an environment, what are we, with our little 3-pound brain and its 100-billion-neuron capacity (via a thousand trillion synapses)? Parts II and III of the book show clearly that the dream of genuine human-level AI remains a dream, and a distant one. Each of our neurons exhibits behavior that requires a very fast multicore processor to emulate. That processor may include a few billion transistors, because the neuron is no transistor. So, to duplicate one human brain's activities in real time would require a 100-billion-computer network, attached to one of Google's data warehouses.

Not only that (the author touches on this, but doesn't dwell), our brain is embodied, attached to millions of sensors of many kinds. Just by the way, not long ago I figured out that the human visual cortex weighs as much as the entire brain of a chimpanzee or gorilla. Among mammals, humans have the most powerful visual engine, by far. Thus, we recognize millions of kinds of items, particularly faces, with ease. The facial recognition software Google and others use still regularly mistakes certain hubcaps and clocks for human faces, and entirely misses most faces that are turned more than 45 degrees from face-on.

What has been the result of a couple of generations of ubiquitous computing, and a generation of "social media" interaction? Simply put, we are getting better at doing things to make it easier for computers to "understand" us. This is not entirely by our choice. When FaceBook added more responses to the "Like" button, they added just five. I am still waiting for a Dislike option. "Angry" doesn't usually suffice; it is a different feeling. However, I realize that they are constraining our choices so they won't have, say, 120 possible responses (yes, we do have something more than a hundred kinds of emotional responses). Six will do, thank you so much, said the FB guru. Six is easier to analyze (and to sell to advertisers). So what do I do? I comment at least as much as I "Like" or "Love", etc. Comments are for people, and as far as I am concerned, my FB friends are still people…the last I checked, anyway.

The upshot is that the latter 2/3 of this book provide the best argument I have seen against the prospect of human-level AI for at least a generation, or two or three, if ever. We really need to consider whether it is really what we want, anyway. I built a 40-year coding career on producing computer products that did things that are hard for people but easy for computers, and making the interface work well enough that the people could also do things people do better, sharing the work appropriately with the machine.

I like the philosophical attitude that David Auerbach brings to the subject.  He made me think about a number of things in ways I hadn't thought before. I got a lot more out of this book than I might have had it been more of a chronicle of all the coding projects and languages he'd been involved with. A book to be savored!

Spiders via Spain

kw: blogs, blogging, spider scanning

In the eleventh hour (~2300 EST) yesterday, about 100 hits occurred:

This time they came via Spain. Who knows where they actually originated?

I wonder if blogs that are much more popular are getting even more webspider attention (maybe much more), but the bloggers don't see it among the larger number of genuine hits.

It has also occurred to me that Google runs spidering operations all the time, but they don't need to run spiders against Blogger, do they, since they already know everything we do…

Genetics – Messier than you ever dreamed

kw: book reviews, nonfiction, biographies, short biographies, genetics, domains of life, trees of life, horizontal gene transfer

The Tangled Tree: A Radical New History of Life by David Quammen took me a week to read, and it was a week well spent. From the Acknowledgements section, it apparently took the author four years to research and write, and that was time well spent.

I have read articles and portions of books about the subjects of Tangled Tree, but I hadn't put it all together. One one level it is a biography of the work of Carl Woese. On another it is a record of the tremendous advances in our understanding the breadth of living things and our increasing understanding of just how complex evolutionary history and genetic inheritance really is. Certainly, there is a great deal more to learn.

Triggered by an offhand remark by Francis Crick, early in his career Carl Woese sought to create and to use tools to discern the sequences of chemical units in genetic polymers. He wanted to use genetic material to look deep into time, to find the relatedness of all life and its deep history. He settled on a group of RNA molecules that are strongly conserved and thus ubiquitous in all cells, the 16s RNA unit of the prokaryotic ribosome and the 18s RNA unit of the eukaryotic ribosome. They have the virtue, from this viewpoint, of changing very slowly, so deep relatedness between many organisms can be determined.

The first breakthrough came in 1977, when Woese produced a kind of RNA fingerprint for certain methane-producing microbes. His colleague Ralph Wolfe remembers him saying, "These things aren't even bacteria." Study of several other methanogens confirmed that impression. Then other special microbes were found that were also "not bacteria" and are now grouped with them in this new domain. After a few names were applied and rejected, the new domain of living things is now dubbed Archaea. They differ in several significant ways from Bacteria. Many thought Woese ought to get a Nobel Prize for this discovery. He thought so also; he was never one to even profess humility! Somehow, he didn't get one.

The book presents a tangled web of its own, discussing Woese's many collaborators and students, some of which became opponents, at least in his own mind. By 2000, when the first quasi-complete draft of the sequence of the human genome was presented, molecular biology had advanced so rapidly that Woese never fully understood what was going on, and was kind of left in the dust. The book gently presents his increasing paranoia as discovery after discovery was made by former students and colleagues. A core issue was the shape of the "tree of life".

The family tree of organisms has deep origins, and has been used in more ways than I thought were possible. Darwin included a sketchy tree in The Origin of Species. Trees became expressions of theory and political platforms within the biological community. But such trees got into trouble when certain further developments ensued. Two are key.

Firstly, beginning in 1967, ten years before Woese's discovery of the Archaea, Lynn Margulis (then Sagan) published her first paper about endosymbionts, as they are now called. In brief, these are the mitochondria (energy producing organelles) in all eukaryotic cells, and the chloroplasts (energy conversion—from light plus carbon dioxide to energy plus oxygen—organelles) in plant cells. It took Mrs. Margulis and her colleagues and sympathizers decades to make us all clear that these organelles started out as bacteria that took up residence in slightly larger cells, which then grew even larger, over the eons, and became more and more complex, to become all the Eukaryotes, or critters big enough to see without a microscope (and a great many that are still pretty tiny). You are a Eukaryote. Without a few thousand mitochondria in every cell in your body, you would die. Very fast. Or, rather, you could not exist at all.

A quick aside before going on. I used the work Prokaryote above. It refers to everything that is not a Eukaryote. In particular (so far!), it refers to Bacteria and Archaea, because they don't have a nucleus (the "Kary-" bit refers to the nucleus). Woese hated the term. But it is just too convenient a way to refer to the non-eukaryotic microbes that actually dominate all life on Earth.

Secondly, in the late 1990's, genome sequencing had produced enough data that researchers were able to determine that everywhere they looked (initially only among prokaryotic microbes), they saw DNA sequences that came from other organisms. Horizontal Gene Transfer (HGT) was soon understood to be very common among the Prokaryotes, including across the "domain boundary" between Bacteria and Archaea. Initially, HGT was studied as a mechanism by which pathogens quickly acquire, and share, antibiotic resistance. Now it is understood to be so widespread that some think there is really only one "bacterial species" with a couple of dozen semi-stable forms that we used to call species; and only one "archaean species", similarly. Or maybe they are all just one big mess of microbial soup! Stay tuned…

By the "mid oughts" (prior to 2010), it was becoming clear that Eukaryotes also contain substantial amounts of DNA that were acquired via various mechanisms of HGT. To date, it seems that 8% of human DNA is the complete genomes of hundreds or thousands of retroviruses. Viruses, particularly retroviruses, are one way that HGT operates in Eukaryotes.

There are shorter sequences that are still a puzzle, and many of them tend to be present in multiple copies. One sequence of middling size is apparently found three million times in the DNA of every cell in your body, and mine! Nobody yet knows why, or whether it does anything. If it does do something, it must do a lot of it! Nobody yet knows where they come from, except from "some other critter". The result is a "tree" of life that resembles a web, a network, anything but a tree. It is hard to even use the term "tree of life" in any meaningful way any more.

A typical human body contains about 37 trillion eukaryotic cells, of a few hundred varieties that make up the tissues of the body. That same body is inhabited, without and particularly within, by more than 100 trillion prokaryotic cells, of several thousand "species" of Bacteria and Archaea. They are not just passive. Certain ones enable you to eat certain foods. The prokaryotic "glove" of organisms on our skin actually prevent many pathogens from attaching and attacking us. A similar "glove" lines our digestive tract. There is so much still to learn about all this! One consequence is this: our cells and their nuclei (where the DNA is) are pretty robust, and keep inside and outside separate. But disease and various insults to our body's integrity can allow DNA from outside some of our cells to get inside, and sometimes to be incorporated. That is another variety of HGT.

Carl Woese didn't like his work being eclipsed. He had the misfortune of making a great discovery that was soon just one of many astonishing discoveries, and he sort of got nudged aside. Though he was awarded many prizes and much praised, without a Nobel Prize, it seems he could never be satisfied. Yet he is remembered as a core figure in the great revelations about the way genetics works, that dominated biology in the late 20^th and early 21^st Centuries.

Tragedies that ring the continents

kw: book reviews, nonfiction, climate change, sea level, flooding

I approached Rising: Dispatches from the New American Shore, by Elizabeth Rush, with a skeptical attitude. The book, though filled with stories of people facing tragedy, was actually a pleasant surprise. Ms Rush is a thoughtful, energetic, and compassionate writer. She is definitely not pushing the über-leftist anti-everybody-who-doesn't-agree-with-hyped-climate-propaganda agenda. She visited a lot of people who live along the coasts of the Unites States, particularly those who had recurring flooding problems before "climate change" was "a thing"; she did her best to winkle out the factors that are increasing their suffering; and she tells their stories.

She introduces her subject by describing her first visit to Jacob's Point, Rhode Island, soon after she moved nearby a few years ago. She spoke to long-term residents and others who had know the area and described for her the impact of rising sea level on the marshes. A marsh by the seaside has a way to grow vertically as sediment is brought in by natural processes. Many marsh plants send roots uphill and upwards also, moving away from encroaching salt water. Building a road alongside a marsh blocks this inflow, and gives the migrating root structure nowhere to go. Even without filling a marsh, we can kill it this way.

I knew already, though, that the biggest factor causing "rising sea level" along much of the American coastline, particularly the East Coast, is that the land is sinking. The dissected appearance of the coastline, particularly in New England, is diagnostic of sinking land. Why is it sinking? The technical term is isostasy, or recovery from a past distortion. In this case, the cause is glacial rebound of the northern North American continent because a few miles of ice that were there during the most recent ice age are no longer there. In mid-continent, centered roughly on western Ontario and northern Minnesota, land is rising. How fast? Something less than a centimeter per year, or about 3/4 meter (2.5 ft) per century. Then, why is the land sinking along the East Coast? The ice was a lot thinner there. The ice pushing down the center of the continent caused the edges to rise. Now, as the center rises, the edges are going down.

This doesn't mean that rising global temperatures caused by the the greenhouse effect aren't making the ocean get a little deeper. It just means that this is a minor effect, but it is troublesome because it adds to an existing problem. So let's look at the subject of the first chapter, Isle de Jean Charles, Louisiana. First, images of the area southeast of Houma, including this island community:

These were taken from Google Earth. The panel on the left is from 1990; on the right, from 2015. One must look closely to see that many of the scattered bits of land in the various lagoons that line the southern coast, seen in the 1990 panel, are missing in the 2015 panel. A more prominent feature of both panels is a dark green area...except it has moved over the 25 year span. In 1990, the area north of Isle de Jean Charles was a salt marsh, and looks very dark green. Further to the northwest, west of Chauvin, is what looks like an ordinary piece of coastal land. It was marshy, but upland and more of a fresh water marsh. By 2015, the salt marsh north of Jean Charles is all under water, and the land west of Chauvin is now salt marsh. The difference in water level from one picture to the next is just a couple of feet. That is all it takes.

This picture shows Jean Charles and some surrounding territory, in the same time periods:

In this case, the 1990 imagery at this resolution is grayscale only. But it shows what we need to see: the longish island was significantly larger, and there were more bits of land scattered throughout the bays 25+ years ago. Take note of the small roadway that crossed from left to right in 1990, that had mostly vanished by 2015, and the larger one to its north, that appears impassible now. Prior to 1970 or so, the island had 4-5 times the land area compared to today. I wish I could have located a satellite image from late 2018, after the exceptional hurricane season. In Rising I read that Isle de Jean Charles now hardly exists outside the narrow strip bounded by the levee system. Most of the residents have already moved inland. The residents are native Americans, and have been enabled, financially, to move due to persistent activism by tribal leaders to obtain Federal aid. Prior to the early 2000's, they were ignored by both state and Federal aid agencies.

This is not all passive changes in water level. Higher water means that hurricanes and other storms can wash away more soil, and the channelization of the Mississippi River over the past century has resulted in very little replenishment. This area is part of the river's delta system. It is worth noting just a few things. The major problem in the area, climate or not, is the channelization of the Mississippi River, that cut off sediment replenishment; secondarily, there is subsidence that every delta system experiences as soil slowly compacts due to gravity pressing out water that it contained when it was first deposited.

All around the US, the author tells of her visits to places in Maine, Staten Island, both northern and southern Florida, and the San Francisco Bay. In some places, the land is subsiding due to compaction, as in Louisiana and S.F. Bay; in others such as Maine, glacial rebound is dragging the land underwater, a few inches per decade. In all these areas, however, governmental inaction coupled with over-development has been the greatest and most tragic force behind the destruction of coastal wetlands and the coastal landscape in general. Two stories of human blindness and greed known to me come to mind:

1) The Rapid City Flood of 1972.

When South Dakota was first settled, by people came in wagon trains up the flood plain in the valley of Rapid Creek. They took note of debris in the trees partway up the valley walls. When they were ready to stop for the night, they would carry everything of value, particularly food, and drive the animals, up to terraces and ledges above this flood line. When they settled Rapid City, they settled on those terraces, which are geomorphological remnants of earlier levels of the flood plain in the distant past. I lived in a house on such a terrace from 1982-86. It is 50 feet above the flood plain.

Later residents with less wisdom built homes and businesses further down, some even right on the flood plain. They installed a "flood control basin", Canyon Lake, upstream. It was designed inadequately, and a big rainstorm that dropped 11 inches of rain in 12 hours caused the flood control dam to burst. Water coursed through the town, destroying hundreds of homes and businesses, killing more than 270 people, and stacking up automobiles from a few car lots like clams on a shelly beach, downstream of town.

When we moved to Rapid City in 1978, areas on the flood plain outside town (now the town had laws against building on the flood plain within city limits) had already been rebuilt with mobile home developments. They are sitting in the crosshairs of the next flood.

2) Newport Beach "view homes", throughout the Twentieth Century.

I was taking an Engineering Geology course in 1971, and we learned about landslides and other earth-engineering matters. The professor, Dr. Martin Stout, is a person I greatly admire. He showed us the sand hills of Newport Beach, and described this scenario:

• An early developer noticed that these hillsides had a great view of the ocean.
• The development company persuaded the city or county government to issue permits to build ocean view homes.
• To get the best view, on each rather steep lot, a cut was made to flatten the land, and the sandy dirt so removed was dumped and leveled so as to extend the flat area beach-ward.
• Each home was built mostly out on this fill dirt, sometimes with pillars installed into the soil to "stabilize" it.
• On such a hillside (there were several), a few dozen such houses were built, sold, and occupied by people who love an ocean view and will pay for the privilege.
• Things rock along fine for a few years.
• An extra-rainy season occurs. The sandy soil gets soft and the houses start falling down, each into the back yard of the one below.
• The homeowners below sue the owners of the homes now in their back yard, for trespass or whatever their lawyer suggests.
• The city or county steps in, condemns all the dwellings involved, and has the homes bulldozed. 
• The land is graded back to an even hillside. Ground cover plants are planted.
• Five to ten years pass. Everyone on the city council or county council that currently has jurisdiction has been replaced with "new faces."
• A development company persuades them to issue permits to build ocean view homes.

On some of these hills, this had happened three times by 1971. When people are this shortsighted, how much hand-holding can we do? And there weren't even any hurricanes!

Genuine sea level change is real, but it is not happening nearly as rapidly as the natural cycles I've mentioned, such as glacial rebound and subsoil compaction. Governmental regulations of the past actually made things worse for people who received aid to deal with a flooded house: They were required to use the money to rebuild the house exactly where it stood before. Only recently have rules in some places been changed to allow people to take their payout and move further uphill or inland to rebuild there.

Here is the actual magnitude of climatic sea level change: 

• Sea water has a moderate coefficient of volumetric thermal expansion, approximately 0.00025 for temperatures between 0°C and 5°C, the temperature of the oceans deeper than a few tens of meters.
• Unlike fresh water, sea water does not get less dense in the lower degree or two before it freezes. It keeps getting more dense.
• The average depth of the oceans is about 3,700 m.
• Multiply this by 0.00025, to get 0.925. That means, if the entire ocean becomes one degree warmer (Celsius), it will get nearly one meter deeper.
• The best figure I can find is that the average ocean temperature has risen 0.2°C in the past century. That means the oceans are 0.185 m (about 7 inches) deeper due to thermal expansion.

The wild card is melting of ice caps. Contrary to what many vocal critics worry about, melting of the the Arctic ice cap cannot contribute to sea level rise because that ice is floating already. The major ice cap that can cause trouble is Antarctica. If it all melts, the seas will get roughly 60m deeper, or 200 feet. That would be catastrophic. The secondary ice cap is Greenland. It has about a tenth as much ice, so melting it entirely would mean a 6m, or 20 ft, rise in the oceans. Less catastrophic, but still catastrophic. I cannot find a good estimate of how many people would be displaced by a 6m rise; the reports are all over the place. It is somewhere between 1/20 and 1/5 of the human race, between 400 million and 1.5 billion.

I have no way to know how likely this is. There was a report just this week that the deep ocean is actually cooling, due to delayed effects of the "Little Ice Age" of the 1700's and early 1800's. Some portions of the Antarctic ice cap are also being strengthened rather than weakened, as this cold pulse works its way down through the miles of ice. But other portions of both Antarctica and Greenland are softening.

What is Ms Rush's conclusion? Humans are to blame for the human tragedies, it is true. But local matters are bigger and more damaging than global effects. It is hard for people to think in terms of centuries, or to plan for the ages. She writes of a "five generation window": most of us knew our grandparents and we may know their stories, and we expect to know our grandchildren and tell them our stories, and maybe some of our own grandparents' stories also. For most of us, that is about a one-century window. But we see evidence everywhere that most decision makers do not plan beyond their next promotion, or the next election, or sometimes the next paycheck. At least 1/3 of Americans have less than $5,000 in any kind of retirement savings account, and 1/5 of them have nothing...zero. zip, nada. I can understand for the 12% that live below the "poverty line", saving isn't feasible. But for the rest, who could save but don't, their "golden years"...not so golden.

We need a national consciousness like the wisdom of the people in those wagon trains, looking for signs of old floods to inform them of safe places to spend the night or locate their new homes.

A lot of things time isn't

kw: book reviews, nonfiction, physics, time

Just over two years ago I reviewed an earlier book by Carlo Rovelli, Seven Lessons On Physics. That was a fun and interesting read, so I was happy to find a new book of his, The Order of Time. It is equally fun and interesting.

Let's first get to the bottom line: Nobody yet knows just what time IS. So of necessity, a lot of this book is about things that time is NOT. Understanding how time works, and perhaps to approach knowing what it is, constitutes Dr. Rovelli's life's work.

Now that we can make comparatively affordable (cheaper than an automobile) instruments that "measure time" to incredible accuracy, it is possible to obtain two of them, place one on the tabletop, and the other on the floor…Then, within perhaps a half hour, the one on the tabletop will show a slight positive difference in "what time it is", to the nearest picosecond or so. You can then switch their places. After a while, the one that is now on the tabletop will have caught up with the other, that is now running slower, and then will pass it by, so to speak. Why? The force of gravity is just a tiny bit greater at floor level than at tabletop level, and gravity slows time.

You can also take one of the "clocks" for a joyride, and when you return, it will have recorded the passage of a little less time than the one that remained behind. Motion slows time.

While we are at it, the equivalence of gravity and acceleration that underpins the General Theory of Relativity by Einstein indicates that acceleration also slows time. It's a bit harder to measure, since we don't have a simple way to divorce acceleration from velocity of motion. Even driving around with a hyper-precise clock, we don't know how to distinguish the change in what it measures that is due to the acceleration from that which is due to the speed(s) traveled.

The fact that time flows differently because of one's velocity, and one's position relative to a large mass, results in the necessity for the satellites used in the GPS system to correct the time their very precise clocks record. Otherwise, in just a day, your navigation device would be misplacing your calculated location by a few kilometers. These corrections, for both the speed of the satellite and its elevation (~22,000 km) above Earth, are sufficiently accurate that your device can know its location within a 5-to-10-meter radius, and a military-grade (and much more costly) device can determine its location within a centimeter or so. The radio signals that the satellites send travel about a foot (0.3m) in a nanosecond. Centimeter-level precision implies time accuracy of ~10 picoseconds, or trillionths of a second.

Back to the book. We have a number of practical and customary definitions of time, that allow us to go about our day-to-day work. Part I of the book draws us to realize that, to a physicist, time is changeable. Physics equations that include time and rate terms work in either direction. There is no "past", "future", or "present". Even the notion of Entropy, which is a physicist's description of the direction of time, is actually based on the "blurring" of our perceptions.

We may think we have pretty sharp vision. Indeed, since our visual cortex is nearly as large as the entire brain of a chimpanzee, our general vision is better than any other animal's (the very acute vision of a hawk is in a very small part of the bird's visual field). But how sharp is sharp? Human visual acuity ranges from 1/20 to 1/60 of a degree of arc. That means, if you hold something in your hand at "reading distance" of about 16 inches (40 cm), you'll be able to distinguish features on its surface as small as 1/60 inch, or perhaps 1/200 inch apart (0.4 to 0.13 mm). But we know we need a microscope to see "small stuff" like pollen grains (10-100 times smaller) or bacteria (even smaller). Special microscopes are needed to "see" atoms, which are smaller than a millionth of a millimeter.

So, we cannot see the molecules moving in a glass of water, but their motion gives the water its temperature. What we measure as a temperature of, say 20°C or 68°F, represents a certain average velocity of the molecules in the water. We don't see that. But the basic concept of entropy can be considered this way: moving energy through a system tends to make it less ordered. Thus, ice is very ordered, because the water molecules are in fixed relationships to one another. When ice melts, the molecules come "unglued" and can move about. Even a small glass of water contains, not just millions or billions, but billions of trillions of them. So there are a lot of ways for those molecules to be arranged, but they all look the same to us. In the glass full of ice, there was only one arrangement. We can't distinguish the motion; to us the glass of water just sits there. That is the blurring of our perception.

In the second part of the book the author describes a world without time; where there are no "things", just events. Not only do you and I not understand this, neither does he. Some very smart scientists have developed mathematical formulas that describe events with no time element. That doesn't mean we have any way to experience utter timelessness.

In Part III, he claims that "Time is Ignorance" (a chapter title). We can say that "Time is nature's way of keeping everything from happening at once", or "Time is a dimension" (as Relativity states). Whatever time "really is", we have our perceptions, which include a flow and direction of time, because that's what we need to survive. We evolved to perceive successions of events as time. We are pretty far from really knowing much more than that.

The spiders continue

kw: blogs, blogging, spider scanning

Just a couple of days ago I remarked on a different tack being taken by a spider scanning operation in Russia. They are continuing:


A closeup look at that last spike, containing 19 hits, shows that 11 of them came within one minute, and 8 of them in the minute following. So it is not someone typing! A spike of ~20-40 hits that take a minute or so to accomplish happens every hour or two.


Anyway, the 200 or so hits not from Russia, plus perhaps 7-10 from Russia (Google only shows top ten), constitute normal traffic to this blog.

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!