Sunday, January 20, 2019

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 As a result, the original "Page Rank" method is dramatically out of date.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…

Monday, January 14, 2019

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 20th and early 21st Centuries.

Monday, January 07, 2019

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.

Tuesday, January 01, 2019

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.

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, D.C.in 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!