Monday, October 15, 2018

Enjoying whale science

kw: book reviews, nonfiction, whales, science, paleontology, natural history

Almost a year ago, I went with several colleagues from the Delaware Museum of Natural History (DNMH) to look at the skeleton of a humpback whale on the shore of Delaware Bay. It had been a juvenile whale, about 35 feet long, that washed ashore dead near a popular fishing pier. It was towed by the state Department of Natural Resources to a more sheltered spot on a wildlife refuge, to rot in peace. Here are some of the crew having a look. The skull is to the right.

We were mainly there just to see it. The director and a curator were along, though, and they decided to see if the museum could get permission to collect at least the skull. Early this year they applied for the appropriate permit, which was approved. They decided to bring the skull, several vertebrae, and a flipper if they could excavate it from the sand. A large shed was put up in the museum's back yard.

Just about a month ago a few folks went to gather it. The skull weighed about 250 pounds, so it took a few people to lift it onto a flatbed truck. Anyway, they got it safely retrieved, along with several vertebrae and the flipper they could get to. The skull was put in the shed, where I took this picture. You can see that the remaining skin, seen in the photo above, had been eroded and eaten away, leaving just the not-too-smelly bones.

This isn't stamp collecting. This skull is about as big an object as the museum is capable of storing and preparing for exhibit…and exhibiting. A new plan for the exhibit halls is in the works anyway, so they'll tinker with it to find a way to include this, possibly as a touchable piece. It will need a bit of degreasing before it is fit to touch, though! Whale bones such as these are full of fats and oils, even after more than a year in an exposed location.

Reading Spying on Whales: The Past, Present, and Future of Earth's Most Awesome Creatures, by Nick Pyenson, I learned that the Smithsonian Museum's National Museum of Natural History (NMNH) has a series of warehouses on the outskirts of Washington, DC, where research collections and other materials not on exhibit are kept. That includes thousands of whale specimens, including hundreds of skulls.

The DMNH skull is rather small compared to some. The skull of a mature blue whale can be more than 25 feet long, and each lower jaw bone weighs about a ton. It takes a lot of muscle to hold such a pair of jaw bones in place during lunge feeding, but a 100-to-150-ton animal has the muscle to do it.

Dr. Pyenson is a paleontologist at NMNH, specializing in fossil marine mammals. To understand the past of whales, he has spent a lot of time with people who work with living (or recently living, in the case of whalers) whales. He is the kind of scientist I like most, one who gets out of his stovepipe and works with others in allied, and not-so-allied, fields.

True to the title of the book, it is in thirds, for past, present and future. Whales as we know them arose rather recently, roughly 5 million years ago. Fully aquatic whales, similar in shape to modern species but smaller ("only" the size of a minivan or school bus), have been around for something like 35-45 million years. Earlier semi-aquatic "whale ancestors" date to 45-55 million years ago. The earliest "whale", called Pakicetus, was kind of like a big dog that could wade and swim. A significant portion of the author's study is aimed at finding how whales grew to the awesome sizes of the largest ones that exist today. A few species regularly exceed 80 feet in length (24m), topped by the blue whale; the largest blue whale ever measured was 109 feet (33m) long.

A tentative scenario for producing really enormous whales is the combination of a globe-girdling Southern Ocean, but a closure of the Atlantic-Pacific communication that existed until 4-5 million years ago, until the uplift of Panama. Currents and wind patterns cause localized upwellings of nutrients, which in turn cause stupendous accumulations of small prey animals such as krill and herring. Large whales migrate long distances to feed on these bountiful feasts in their seasons. A really big whale has to eat a lot. Being big, though, it can travel more efficiently than a smaller animal, so crossing the Earth to get between areas for feeding and breeding is more possible. There are other factors the author enumerates.

The author's life is at the extreme end of being a naturalist, for which he has to (gets to) travel as far as the whales do, and to all the places where whale fossils or whale remains can be found. He tells amazing stories of field seasons in Chile and Norway and Alaska. He got to try his hand at putting a suction-cup tag on a whale in Alaska. Live and learn: he broke the tagging pole, but got the tag on. Such tags stay on for just a few hours or for a few days, then slip off. Then begins the fun of locating the tag, which fortunately is sending "Here I am!" radio signals. Only then can the scientists download the data and pictures the tag has accumulated, to see what the whale has been doing. He also tells of the astonishing find of a series of four strandings that happened a few million years ago, probably caused by red tide or a similar toxic phenomenon. Dozens of complete whale skeletons were found it a special place in Chile, of sizes ranging up to 30+ feet (9+m). That is as large as whales became at that time. But a single, complete skeleton is usually the find of a lifetime. He and his colleagues were blown away to find acres and acres of them!

Whales today exist as about 80 species, from smaller dolphins and porpoises—roughly human size—through the "usual" 40-70-foot sizes we associate with sperm whales, humpback whales and gray whales, to the really big blue and finback whales. About 8-10 times as many fossil species are known.

What of the future of whales? A generation ago their future was in doubt. Already by the early 1900's, it is thought that 90% of all whales had already been caught and killed, but the catch continued until the 1970's, when a series of international laws were enacted. Some whaling still occurs (and it gave the author a chance to dissect some very fragile portions of whale anatomy). But the chapter "Shifting Baselines" reveals a great problem when a trend goes on longer than a human lifetime. The "good old days" that senior whalers now living remember actually represent a much-depleted ocean. Nobody living remembers a time like the 1600's when whales outnumbered ocean-going ships.

I remember when I was trying to get a multi-level marketing business going, and two women came to one of my presentations, apparently drawn by the "anti pollution" portion of my advertising. But they didn't want to sell my products. They really wanted to "Save the Whales." Considering that this was 1970 or so, the whales they wanted to save consisted of about 3% of the whales that once roamed the seas.

Today a few species have rebounded, but there are still probably no more than 10,000 (some say 20,000) blue whales remaining, and there may be more than one million sperm whales. As Captain Ahab could attest, they are harder to catch than a blue whale. But there were probably at least half a million blue whales 200 years ago, and several million to perhaps 10 million sperm whales. Those are just two of around 80 species.

How will climate change affect the whales? It seems that in recent years some Pacific gray whales (the only remaining gray whale species) have made their way through the Northwest Passage to the Atlantic, something not possible for the past 2-3 million years. However, human shipping is starting to take advantage of the same passage, and ship-whale collisions usually go very badly for the whale.

I could rhapsodize on and on. I really enjoyed this book.

Tuesday, October 09, 2018

A different take on robots and cyborgs

kw: book reviews, science fiction, robots, cyborgs

Murderbot is a cyborg with a conscience. Strangely, the transport-controlling "bot" he calls ART (for Asshole Research Transport) seems to have one also. Maybe ART is part human, as is Murderbot, which is what he calls himself, in preference to an Alphanumeric designation that is never stated. He also uses the term "murderbot" more generically, to refer to all SecUnits; the term isn't explained in Artificial Condition: The Murderbot Diaries by Martha Wells, but it's pretty clear that it means Security Unit.

Unless I missed something, there are three levels of mechanical and part-mechanical entities in Artificial Condition, in addition to non-mechanical humans:

  • Bots, which are probably wholly mechanical, though this isn't always clear in the book. They have various amounts of AI. ART, in particular, is an extremely capable and extremely powerful entity, built into the Research Transport (something like a self-driving Space Shuttle). ART may be part human; that is left ambiguous.
  • SecUnits and their ilk, that exist for specific tasks. They are very dangerous, and have "Governor" units built in to keep them from "going rogue". They have a minor but important human component, including brain, face, and some other portions.
  • Augmented humans, more human, less mechanical, but typically stronger and faster and more capable in chosen ways, than they were before augmentation.
Certain entities may be more like the SecUnit, such as ComfortUnits, AKA SexBots. A ComfortUnit that plays in the story has a Governer circuit also. I guess you'd want a mechanical sex partner that was stronger than you are (so you couldn't hurt it) to be "governed" from hurting you.

As for the plot, I'll just provide a glance at the setup. Murderbot is rogue, having hacked his Governor circuitry, and is thus operating on his own. He is trying to find out if he was truly the SecUnit that "went rogue" some years earlier and killed a lot of people, or, indeed, if the deaths were even due to a rogue SecUnit at all. Parts of his memory were "wiped" so he has to do on-the-spot research. As cover, he poses as an augmented human and has himself hired by a trio of scientists who want to go to the same moon, to retrieve data that was stolen from them. He is to be a bodyguard. ART runs the Research transport vehicle that takes him to a waystation near that moon.

With the help of ART, he takes better care of the scientists than they expected. He and ART have a fraught but useful relationship.

I was most fascinated by the interior life of Murderbot (of course, as imagined by the author). Though this is a small book, it takes an important step in a direction that Isaac Asimov was going with his Robot stories. Does the inclusion of a human brain in a massively powerful cyborg endow it with a conscience? In at least this case, perhaps it does. I don't know if Ms Wells plans more little books (150pp, more or less), to become a Murderbot series. I'd welcome it.

Monday, October 08, 2018

Striking a balance between error and perfection

kw: book reviews, nonfiction, genetics, heredity, inheritance

"Heredity" and "inheritance" were once near-synonyms. Both referred to the physical goods an heir would receive upon the death of his (rarely her) parents or other testator. Carl Zimmer begins She Has Her Mother's Laugh: The Powers, Perversions, and Potential of Heredity by teasing out the history of these words, how they have changed through time. He takes off from there, producing the most amazing book I have read so far this year.

This book is quite a tome, at 600+ pages, and only the author's skill in writing terse, yet gripping prose, kept it from being twice as long. It is more than a review of genes, genetics and their history. We get a behind-the-scenes look at many of the players in the developments that became the modern cluster of "genetic sciences." I was particularly intrigued to learn that Gregor Mendel didn't just grow peas as a hobby, and then keep a diligent diary about it. Throughout Europe there had been "in the air" a rapidly growing interest in selective breeding, and he and his abbot decided on a research program to determine ways of improving the practice.

In five parts, the book draws together nearly twenty big themes, and how each was discovered and, effectively, turned into an engineering discipline. "Genetic engineering" has gone on since the first farmers selected only the grains that were biggest and most easily grown for their seed stock, and since the aurochs was gradually transformed into domestic cattle in a similar, but slower, fashion.

I remember reading a couple of years ago that we pass on to our descendants between 50 and 100 mutations, variations from the genetic baggage we received from our parents. Zimmer brings out something I had not taken thought to calculate: Each of our germ cells—ova for females, sperm for males—has some mutations that differ from every other germ cell. They share many, but each has some unique ones that arose when the individual germ cell was produced from the stem cell. Throughout our body, the total number of mutations may be dozens of quadrillions!

That means that we are all mosaics. A tortoiseshell or calico cat (such as my cat shown here) is a visible mosaic. Each colored patch grew from a single cell in the embryo. In a calico cat, with large patches, the differentiation occurred early, when there were comparatively few cells to develop into the entire cat's coat. In a tortoiseshell cat, with smaller patches, which also tend to be more stripey, it occurred later. A "brindle" cat can be thought of as a tortoiseshell cat whose coat colors are much more finely divided, perhaps just a few hairs each.

"Coat" (skin) color in humans is sometimes visibly mosaicked; a friend of my son in college looked like she had been splattered with gray-brown paint. But in every multi-celled creature, every time a new cell is formed by cell division, either during early development or from a stem cell, there is an opportunity for a DNA copy error of some kind to occur. When that occurs the new cell is genetically a little different from its "sister cells". But, the production of the stem cells also produces variants, so that all the descendants of such stem cells have the new variation. I have a number of brown spots on my skin (on average, people have 25 over their bodies, some less, some more, and some much more). Each grew from a single cell with a different expression of melanin. A key point of this section: Cancer is a mosaic expression.

We are all mosaics, of numerous characteristics, nearly all of them invisible. I find this astounding. Yet it shows the balance between perfect copying and occasional errors that characterize growth and development. For the DNA in a cell to be copied perfectly requires a stupendous level of accuracy, a level not seen outside computer technology. The human genome contains about 3 billion base pairs, meaning that when the DNA is "unzipped" for copying, there are 6 billion bases to be copied.

In a business context, you may have heard of Six Sigma Methodology (6σ), which aims to produce products and services with no more than 3.2 defects per million. There is a dirty secret to 6σ: a "process deviation" of 1.5σ is allowed, so the stated defect rate is actually 4.5σ. True 6σ is actually about one defect per billion. DNA copying, to be perfect "most of the time", requires less than one defect per 6 billion, or a production-perfection level of at least 6.28σ…with no "process deviation".

The perfection of copying computer files is about at this level, but only because of parity bits added to 8-bit bytes, which are actually stored as 10 bits, and checksums for larger chunks, which allow a lot of error correction, and detection of many errors that could not be corrected, so the software doing the copying can try again. Did you know that, when you get a hard disk failure, it is only reported to you after the software has tried 50 times without success to make a copy that passed all the checksum tests and other error-detection codes? Programs like CHKDSK look for portions of the hard disk that cannot yield perfect copies and marks them so the software will no longer try to store data there. The cellular mechanisms for DNA copying include methods that are similar in philosophy, though much different in implementation.

So, more often than not, when one of your cells (or a cell in a cat, horse, tree or blade of grass) divides, the result is a perfect copy. Some percent of the time, a small copy error occurs. Some smaller percent of the time, a larger error occurs, like getting a snippet of DNA turned around or copied twice…and there are other kinds of errors. Some errors are bad enough that the new cell cannot function and so it dies.

But there is another level of "error tolerance", in the DNA-to-protein code. Each amino acid has more than one code associated with it. Some important ones have as many as six, among the 64 3-letter codes that represent the 20 amino acids plus START and STOP. So certain small errors make no difference at all in the protein produced. Such "silent mutations" accumulate, and form the "DNA clock" used to determine how closely related one species is from another, and how long ago the two species split from a common ancestor.

Once in a while a mutation that is not silent actually makes the cell or the organism function better. Such beneficial mutations also accumulate, and over time can lead to new species. Non-silent mutations that are not beneficial may lead the cell or the organism to die, and are thus instantly weeded out, or they may handicap it to some extent, making it less likely to reproduce. This combination of a steady, but low, error rate, and an environmental filter on what is and is not beneficial, is the mechanism of natural selection.

So, back to the thesis of the book, at least in its earlier parts, we find that genetics includes a certain tension between near-perfect copying and the weeding out of most, but not all, copying errors. If copying were perfect, nothing would change (this is the Creationist view). But if copying had been perfect from the first dog, the first apple tree, or the first human, every member of each "kind" would be exactly the same, without variation. You and I would look identical (unless you're female, then you and every other woman would look identical). There would be no moles or other kinds of pigmented spots on our bodies. There would be no mosaicking.

On the other hand, if copying were too sloppy, a large fraction of pregnancies would terminate early in miscarriage, a huge load of birth defects would occur, and everything would die out. Actually, with a little luck, natural selection would drive the surviving creatures in the direction of more perfect copying, until a balance, such as the present balance, were achieved.

The later parts of the book present the several stages of "genetic engineering", including stories of the triumphs and disasters along the way. We are friends of a family named Gelsinger, and a cousin of theirs was Jesse Gelsinger, the young man who died at age 19 of a huge allergic response to the virus that was being used in an experimental genetic therapy for his chronic condition. That particular kind of "gene therapy" came to an end then and there.

Now there is Cas9/CRISPR, and some allied methods (some natural) called "Gene Drives" (only one of them makes use of CRISPR). If these methods fulfill their promise, DNA will become as editable as a Microsoft Word document. Carl Zimmer is guardedly optimistic about the possibilities, but this is the source of the word "Perversions" in the book's title. The genie is already out of the bottle. Not everyone who works with these new technologies is righteous. None is wise enough to think through the implications. After all, less than a generation has passed since Jesse Gelsinger died, and he died primarily because the researchers had not expected allergies to be a problem. Well, Duh! A good friend of mine is most likely to die of taking a breath at the wrong time, in the presence of people eating peanuts. A woman we knew well some years ago came into our house after we had sprayed an insecticide in a back bedroom. She almost collapsed, and had to be half-carried out of the house to fresher air. We could visit her, but not the reverse, thereafter.

Will the new genetic tools somehow "get out" and wind up blasting the biosphere with the biological equivalent of that (so far imaginary) nemesis of nanotechnology, Gray Goo? Maybe. It cannot be ruled out! However, the hope I see, and I think that our author sees, is that there is so much variety in nature, so much variation in the 7 billion of us also, that any biological Gray Goo will not affect everyone. One of his correspondents told him that there have been gene drives unleashed in natural ways in the past, but that the biosphere has eventually deactivated them all.

I have just skated on the surface of a couple of the ideas in Her Mother's Laugh. This book contains more ideas per column-inch than I know what to do with. A tour de force.

Thursday, October 04, 2018

The purported enemy we cannot live without

kw: book reviews, nonfiction, business, debunking, polemics

Whether you are reading this on a laptop or desktop computer, or on a tablet or a phone, that "device" is probably a cornerstone of your life, and it probably cost between two and twenty times the amount of pay you receive for an hour's work. The iPhone 10 or iPhone X currently retails for $999, about twice as much as a pretty good laptop computer, which is close to 40 times the hourly pay for someone with median income in the U.S. Most of the 200+ million iPhones sold in the past year cost between $500 and $800. The amount of money that changed hands was roughly $150 billion.

Why do people pay so much for an item the size of an open wallet? In a word: Value. These "devices" do, not just something people want, but a very great many things most people want, and they want it very much. So they pay.

Now look around the room you are in. If you were to count, from paper clips to furniture, the room you are in probably contains hundreds to thousands of items. Every one of those items was bought at some time, either by you or a housemate or family member, or by someone who gave it to you. In the basement room I am sitting in to write this, I have many books. Probably more than 1,000. There are nearly 30 cookbooks, for example. This computer is accompanied by two printers, a couple of scanners, several reams of paper, a big desk, and a router. A closet holds an oscilloscope and other electronics I use less frequently. On a bench behind me there are two microscopes and a great many things needed to use them effectively. Every one of these things was bought, mostly by me, at some time. The only things in the room that I did not buy is the mineral specimens on a display shelf, minerals I collected. Of course, I bought a lot of gasoline for those rock collecting trips, and I bought rock hammers and chisels, bags, etc., etc.

Every one of those purchased items, except for a very few "loss leaders", yielded a profit to the seller. Why was there a profit? Simply put, incentive. The chance to make a profit is the reason for the existence of any and every business.

Ask yourself this: If you were to go into business selling left-handed fribble widgets, and the materials to make them cost $10 each, but people are only willing to pay $8 each, why would you run such a business? You need a lot of cash to back you up, so you could effectively pay $2 each for people to take a widget off your hands! But if people were willing to buy them for $12, and no matter how many you make, you'd have a never-ending clientele willing to pay $12 each, and then you could really do business. Each widget you sell, you have a 20% capital profit. Assuming they don't take long to manufacture, so there is little time cost, that's pretty good.

But really, why do you need profit? Why not sell them for $10? The biggest reason is, you need to pay yourself for your work. You need the income to buy food, clothing, other things you want, and perhaps pay a mortgage and car payment. You have bills to pay for electricity, water and so forth. There might be a machine you could buy that helps you make widgets faster (though the materials still cost the same). Making more widgets in less time, you can earn more money, but you'll need some of that to pay off the loan you have to take out to buy the widget making machine. So, for a while you have to operate on a thin margin. Maybe net profit for a while is only 5%. But later, you'll have more income each day. Then you can get better clothing and eat out more often.

That is why there is business. To make money for people so they can buy things they don't make for themselves. Now consider, what if instead of widgets you want to make jumbo jets, and compete with the companies that make the Boeing 787 or the Airbus A380. It takes thousands of workers to run such a company. It is not just business, it is Big Business.

Does all business need to be Big Business? No. For every big company there are thousands of small ones. But many people are suspicious of Big Business. Folks complain about all kinds of things, from the high pay of executives to the "cookie cutter" nature of many products that seem like all the others. When my father ran a manufacturing company, he said the profit margin was close to zero; less than 1%. That is long term net profit, after materials, salaries, dividend payments on stock, taxes and utility bills, plus upkeep of machinery. The upkeep was the biggest uncertainty. In most years, there was a profit figure more like 4%, but the company saved it all, because every few years a big, expensive machine would need repair or restoration or replacement, and it would use up most of those savings. The profit figure in such a year might be negative 15%, but they amortized it (spread the cost out over all the years since the last time) to avoid panicking the stockholders. This company was on the boundary between small and big, with about 500 employees. It didn't need to grow any bigger; it fit its market pretty well.

If a company wants to grow, it needs a bigger profit margin. Growing companies have to get the money to grow from somewhere, and there is ultimately nowhere to get it but from current sales. You may borrow to invest in the needed equipment or facilities, but you have to pay it back…with money from current sales. I came across a good quote about profit:
"Any business arrangement that is not profitable to the other person will in the end prove unprofitable for you. The bargain that yields mutual satisfaction is the only one that is apt to be repeated." —B. C. Forbes
Considering that everything you own was sold at a profit, it is odd that so many people are so down on business. In recent years (30+) there has been an increasing attitude that big business is bad in almost every way. Article after article, and many books, are published on this theme, that big business is a big problem.

Well, no doubt some problems are there. But some of the things we hear about and read about are not quite so dire. In 2009 Michael Medved published The 5 Big Lies about American Business: Combating Smears Against the Free-market Economy in an attempt to set the record straight. I recently heard about this book, and bought the e-book. The quote above is from that book.

For me this was an experiment. I wanted to know how much different reading an e-book might be from the paper books I love, my exclusive fare before this. It was actually a great convenience. Since I always have my phone with me (a $150 t-Mobile REVVL, not an iPhone), I could open the book and read whenever I had free time. I have been reading another book at the same time (not finished yet), but that book stays at home, usually by my bedside, and it is big. In another few days I'll finish that book and review it then.

What are the big lies? Putting them more briefly than the author:

  1. The current downturn means capitalism is dying
  2. When the rich get richer the poor get poorer
  3. Executives are overpaid and corrupt
  4. Big business is bad, small business is good
  5. Government is more fair and reliable than business

Let me state at the outset: If you believe #5 is true, stop reading now and go start a business. You might learn something. You can't possibly have had any meaningful experience of either government or business. The Law of Government Spending is, "Nobody spends someone else's money as carefully as they spend their own."

I don't intend to rehash these 5 points. It is well worth reading the book to get the appropriate impact. I do want to address #2. In some cases, the rich really are corrupt and wasteful. But most of the rich got that way by making value where there was none. They did indeed gather a lot of riches, but the people that worked for their companies, the supplier companies they paid for intermediate products or materials, and the people who were able to pay less for their product than the competing one they had been buying before, all were richer than before.

Key learning: Business is not just about moving money around, from one set of pockets to another. Business is about creating or adding value. There is a centuries-old debate about the source of value. People say, "Oh, Gold has value intrinsically. It is valuable just because it is gold." Others say, "Gold has value because people want it." Both are right. Gold is useful and so has intrinsic value. It is also beautiful, so people want it as an ornament. There is a third reason: "Gold has a certain intrinsic value, but when it is in the ground, it isn't worth much because it takes a lot of work to mine it and refine it, and it takes more work to make things out of gold that people will pay for, such as jewelry, or special kinds of wire for electronics, or coins and medallions. Most 'value' comes from labor." This is also right. Much of the value of gold, or anything else "of value" is from the labor of those who mined, refined, produced, or manufactured it. Business creates value.

I'll also touch on #3. Is "income disparity" a bad thing? Some kinds of work, anyone can do. The classic is "digging ditches". When I was a kid, parents would say, "Get a good education. You don't want to become a ditch digger." I never saw anyone digging a ditch by hand (yes, there were backhoes in the 1950's). But we got the point. "Minimum wage" jobs are those that need little or no skill. I made my living for more than half my life as a software coder. That is a skill that is less common, and really good coders (Ahem! Yes, I was really good) are well paid because a lot of code needs to be written, it has to be high in quality, and there are not nearly as many coders as there are unskilled workers. My dad was a business executive. He was paid more per hour or month or whatever than I ever was. He had skills that were less common than mine. Not only that, a good executive or manager doesn't just do work, but facilitates the work of others so they are productive and more work gets done.

Side note: I often eat fast food, including Wendy's. The Wendy's nearest us recently went out of business and was closed. A Starbucks came in a few weeks later. There are other Wendy's places I can go to, and do you know what? I went to the nearby one because it was convenient, and it was "good enough". But compared to the others, the servers were second-rate and slow, and the parking lot was in serious disrepair. At least it was clean; one can always look into the kitchen to see that, and I'd also check the tables and floors. But it didn't do enough business to stay in business. The other Wendy's places I go to now are busier than it ever was. The difference? Management.

Back to #3. Why did the president of DuPont (Mrs. Kuhlman) earn a million dollars per month during my last few years there? Even assuming that she worked a 60-hour week (maybe she worked more), was her time worth upwards of $3,500 per hour? Could she really produce more "value" for DuPont in one hour than I could in a month? The board of directors evidently thought she could. I do know that the company was better run under her, and more profitable, than it had been under the prior two presidents (those between the legendary Mr. Woolard and her). But really, here is who I think is worth $3,500 per hour: the guy who goes in with a screwdriver and disarms a terrorist's bomb. Anybody else, I wouldn't pay more than about a tenth of that, company presidents included. But Medved's writing on this point had me about half convinced that CEO's really are worth their pay. Let's call it a draw.

And…I'll leave it all right there. Do you fear, suspect, or loathe business, especially Big Business? Remember the jumbo jets. You aren't going overseas on your vacation without one. Small business can do a lot, but it can't do everything. There's a place for businesses of all sizes. And that's as it should be. The book is a great read.

Monday, September 24, 2018

Fun with the fishes

kw: book reviews, nonfiction, fish, ichthyology

These two little fish, a lanternfish above and a bristlemouth below, may be the most abundant animals on earth. They live about a kilometer deep in the sea, and there are probably a few million billion (that is, about 5,000,000,000,000,000) of each in the sea. That is, around a million of each of these little fish per living human. That is about equal to the total number of termites on (and in) land. This picture shows them around half size, so they are much larger than termites. If there are 1,000 pounds of termites per person, there are close to 1,000 tons of just these two fish, per person. According to this article, one genus of bristlemouth is the most abundant, edging out the lanternfish.

Other fish aren't quite so abundant. Oh, there are a lot of fish in the sea, but not nearly as many as there were before industrial fishing began in the 1800's. Small, bony, bad-tasting fish like bristlemouths haven't been affected, but many, many other kinds of (tasty) fish are only about 1/10th as abundant as they were 100-200 years ago. Further, many kinds of less-tasty ones are destroyed as bycatch, caught in the nets and trawls and discarded dying or dead.

This Gulper Eel is in the running as "ugliest fish", but I think it rather charming. It's a sure bet that Gulper Eels like each other, at least around breeding time, no matter what we might think of them. Fish in general are fascinating. While I like going to a zoo to see the mammals and birds, I adore aquariums. They are just a bit more scarce, and cost more to run, yet are incredibly popular in spite of higher admission fees.

Eye of the Shoal: A Fishwatcher's Guide to Life, the Ocean, and Everything, by Helen Scales, just touches the surface of the huge variety of fish stories that could be told. She tells us a bit about how many major groups of fish there are and what they are like, and discusses ten fish-related subjects, in an enjoyable, readable way. And I must mention the illustrator, Aaron John Gregory.

Ask anyone, "What does a fish look like?", and you'll probably get a description that is pretty much like this yellow perch. You can catch these lovely, pan-size fish in many lakes and streams throughout North America. You could make a checklist: Longish oval shape, a fin or two on top and bottom and sides, scales, forked tail, and so forth. Ninety percent of all species of fish are kind of like that, and are called Teleosts ("perfect bone") or "ray-finned" fish.

But some fish don't have bones. Think sharks, skates, and rays. Their skeleton is composed of cartilage, like the easily broken stuff that gives your nose its shape. Some don't have scales, such as eels (well, actually, they have very tiny scales) and adult swordfish. Some fish, though they have bones, don't have jaws. Lampreys and hagfish are the best known (but maybe you never heard of them). Some fish have few bones; a spine but little else, such as puffer fish.

And by the way, fishes of the most common genus of puffer fish, Tetraodon, contain extremely poisonous tetrodotoxin in parts of their bodies, making them the most dangerous fish to eat. Even with strict licensing of sashimi chefs in Japan, every year a few people die from eating puffer fish called fugu that weren't quite prepared right.

For most of us, our main exposure to fish outside of a public aquarium is in the kitchen or restaurant. Most people enjoy eating fish, and the local grocery store usually has a fish counter where you can buy salmon, perch, tilapia, and perhaps trout, bream, and maybe catfish…plus various non-fish such as clams, shrimp and mussels. About 3/4 of the world's people get most of their protein from fish, which is why so many species of popular fish are seriously overfished.

There is a chapter near the end of the book that discusses this problem, and the lack of any useful solutions. Fish farming can make a certain amount of difference, but probably not enough. Along with all the other dangers we cause because of the sheer number of people on Earth, we are eating our way to eventual starvation for many.

I can't end this without one more picture, this time of the biggest fish it is safe to approach, the Mola Mola sunfish. This one is a "mere" 10 feet "tall" (fin tip to fin tip); they get as large as 14 feet and weigh up to 2.5 tons. Ocean sunfish are curious about people and not aggressive.

With some 20,000 species, fish are the most abundant vertebrates. This book just whets the appetite for learning more and more about them.

Tuesday, September 18, 2018

A Canadian has a look

kw: blogs, blogging, spider scanning

Well, well, well, it seems while I was writing the prior post, someone in Canada (or spoofing a Canadian address) snarfed up 245 items:

Amusing, no? The blips to the left are normal traffic, a hit or two hourly. This had to be a spider; fingers can't fly fast enough.

We really are much different

kw: book reviews, nonfiction, anthropology, paleontology, human origins, surveys

This is one of the most familiar images related to human history, and one of the most misleading. Most of us used to think of human evolution as this kind of regular progression from a chimp-like ape to modern human; others denied it was possible.

Let me be clear, I am an evangelical Christian. My view is definitely not in line with the "young earth special creation" theology that is a most vocal viewpoint, but not the most widespread one. Most Christians, if they think about it at all, accept some form of evolution and assume God intervened somehow, to create the human spirit. So let me just say that I understand evolutionary science very well, and I accept natural selection as the best biological explanation for all the life on Earth. Whether life, and humans in particular, arose biologically is really up to God, and He has so far declined to express a public opinion.

Accepting for the nonce a biological origin for human life, we must learn a better way to understand the process. I have read a few times from various authors that evolution does not proceed in a straight line from less advanced to more advanced, but that the "tree of life" is rather like a branching bush, and the fossils and archaeological material we are able to gather give us a glimpse here and there about our biological and social history.

This is a better image. The red circles represent fossils that have been found, except perhaps for the rightmost, which represents "us". The leaf at far left represents the first "non chimp" species that arose some 6-7 million years ago. The number of hominid (Genus Homo) and hominin (related genera such as Australopithecus) species described so far exceeds 20, not just the 10 that are highlighted here. But in time we may find that the number of species in and around the "human line", over the past few million years, might be something closer to the 130 or so leaves in this diagram.

In Masters of the Planet: The Search for Our Human Origins, Ian Tattersall probably discusses every one of the species so far known that either led to the origin of humans, or were related species that our ancestors would have occasionally encountered. It is becoming clear from the fossil record that there were usually several species of hominin in existence at any one time. The fact that many of us can now get a genetic test to determine how many of our genes are actually Neanderthal or even Denisovan, attests that there was indeed contact between early human and human-related creatures. For a Euro-American such as myself, the Neanderthal contribution is about 3%.

A major, major theme of Dr. Tattersall's is that in our behavior, and particularly the complex language skills that underlie our symbolic mode of thinking, we differ dramatically from other apes and from the related and ancestor species for which sufficient anthropological information can be discerned. We literally cannot imagine a non-symbolic inner life. I was speaking to my French professor many years ago, about the "breakthrough" experienced by French students when they first dream in French. At some point she asked, "Don't you ever dream without words?" I said I didn't think that is possible. At least, it never happens for me; some parts of a dream may be "observation", but if another person is present in the dream, there is always speech. Even the more, I told her, I have an inner dialog running at all times, and frequently, when I close my eyes, I can hear it.

The chapters of the book follow a rough time sequence, outlining hominin development from "bipedal apes" through more and more modern body types, plus a number of variations. There were always a few various, related species present simultaneously. For example, just under two million years ago, when the "Turkana boy" lived, that youngster represented a gracile (slender) body style very similar to ours, though his bones were thicker-walled indicating great strength. Another species present around that time was a more robust hominid: Homo ergaster, if that name still applies. This name, by the way, is being used for a kind of grab-bag of fossils that almost surely represent several species. There are also fossils that overlap this era that are termed "hyper-robust". So the Turkana boy was kind of like a basketball player, with others which lived at the same time that would be more at home among the Philadelphia Eagles (and might be able to carry two of them down the field!), plus some of more middling robustness…truck driver types?

The success of the species that led to us, and related species, was by no means assured. There had to be a compelling reason for upright stance, for example, because the grasslands that began to develop a few million years ago were dangerous places. Social organization must have been the key attribute that allowed a weak, hairless biped, that couldn't yet run the way we can, to traverse open country and not be eaten posthaste.

The last four chapters cover in detail the transition from "archaic human" to "anatomically modern" humans, and finally to "behaviorally modern" people. The last step is the hardest. Homo sapiens of the Cro-Magnon variety had a big brain, but so did their Neanderthal cousins and perhaps another 2-3 species. But starting about 80,000 years ago, and culminating some 60,000 years ago, that brain began to work a lot differently. Cultural artifacts show the difference. The first decorated objects are 75,000-77,000 years old. Paintings in caves as old as 41,000 years have been found. Furthermore, when African humans entered Eurasia, probably along the north edge of the Sinai peninsula, they soon spread to all corners of the earth, including areas the Neanderthals apparently considered too cold for them, and into Australia, which no other hominids seem to have entered.

Dr. Tattersall discusses how and whether this change was something waiting to happen because of other characteristics that had developed, called exaptations by evolutionary scientists. It is hard to imagine that the sudden symbolic flourishing arose by a series of closely spaced special mutations. Brain functions that arose for other reasons must have facilitated the development of language.

We don't yet know very much about it. How much more we might learn, it is hard to say. On one hand, we are "naked apes" (per the 1967 book by Desmond Morris). On the other, we have a symbolic inner life that no other creature has been shown to have, and we have ultra-complex social organizations that are different not just in size but in kind from anything found elsewhere among other animals.

The last chapter focuses on speech, using the opening phrase from the Gospel of John, "In the beginning was the word." It really is words that make us what we are. Cute Geico commercials aside, Neanderthals and all other hominids didn't speak as we do. None of their cultural artifacts show evidence of the kind of symbolic thought that we take for granted. They were clever and capable, and functioned quite well for tens of thousands of years, and their extinction is still a bit mysterious (no, our ancestors probably didn't eat them; more likely, they ate everything else and left nothing for them).

Lest we fall prey to hubris, just because we can think symbolically, doesn't mean that we all are great thinkers. People are lazy, and most folks prefer to avoid thinking too much. Not everyone reports a continuous inner voice. There is a reason that many jobs such as factory assembly line work are called "mindless": It isn't hard to learn the task, and in very little time a person is doing it over and over without noticing much of anything along the way. The fact that so many such tasks are now being performed by industrial robots shows how mindless they are. No robot has yet achieved the smarts of the average cockroach.

I'll wind this up. The book is fascinating, it conveys a ton of information, and it sets a foundation for anyone reading it to evaluate future discoveries by hominid paleontologists. It is a must, even if you happen to believe in "young earth special creation." It is never wrong to learn the stories the rocks tell.

Monday, September 17, 2018

The spiders are getting more clever

kw: blogs, blogging, spider scanning

Have a look at what I noticed today, which apparently happened yesterday:

The "Overview" for the week shows a spike of 166 hits late yesterday. The pageview map is seemingly empty. The details show why: the "Unknown Region" is not mappable. Recent spidering spikes have come from the Ukraine, France and Spain. I suspect they are all spoofed from the same source, as is this one.

I also note that Chrome use is greater than ever (for the spider perhaps?), and that Linux has outpaced Windows, at least for the time being.

Tuesday, September 11, 2018

Premature advice about gene tuning

kw: book reviews, nonfiction, health, diet, genetics, epigenetics, self help

The title concerns me a little: Dirty Genes: A Breakthrough Program to Treat the Root Cause of Illness and Optimize Your Health. The author is Dr. Ben Lynch, a naturopath who for about a decade has been studying the effects of genetics and epigenetics on chronic disease, and susceptibility to disease in general. He developed a "Clean Genes Protocol" people can use who want to improve their health.

So, what is a "dirty gene", and how can dirty genes be "cleaned"? The reason we are all different from one another is that there are very slight genetic variations in all genes. There are numerous variants of every gene. The variants for a particular gene are called alleles. The differences among alleles are mostly in the small numbers of SNPs that each gene contains. We'll look at SNPs later on.

We can use eye color as an example. When I was young I learned the Mendelian explanation of inheritance for brown eyes and blue eyes. Somewhere in the genome is a gene with a few common alleles (variants) that controls eye color; call it BrownEye. One allele makes eyes brown by coding for a protein that produces the brown pigment; call it BrownEye+. Another allele makes eyes blue because it codes for the same protein in a form that won't operate correctly, so the pigment is not made, and the natural blue iridescence of the iris is seen instead; call it BrownEye-. These two sentences explain why brown eyes are considered dominant: We all have two copies of each gene. If someone has two copies of the same allele, of course their eye color will be the expected color, brown if the two copies are BrownEye+ and blue if the two copies are BrownEye-. What happens when someone has one copy of each allele? The BrownEye- allele produces a "broken" protein that can't produce pigment, but the BrownEye+ allele produces a working protein, so the pigment is made anyway; thus, that person will have brown eyes. Caution: this is very simplified. More than one gene is involved, and there are several kinds of "brown", plus "green" and "hazel" eye colors.

I don't know what it is that is different between these two alleles of BrownEye. There are several kinds of mutations, changes in our DNA, and we each accumulate a few hundred new mutations in the DNA of every cell in our bodies in our lifetime. The average rate is about 65 "per generation", based on a statement in this Wikipedia article. I presume that a "generation" is the 20-40 (average 33) years between our birth and the age at which we typically reproduce. We continue to accumulate mutations after that, but none of those are going to be found in our descendants.

Remember, we have two copies of our entire genome in each cell. By far the most common mutation—which can be caused by cosmic rays, environmental toxins, and the "stumbling" that the DNA copying machinery does on occasion—is the SNP. This means that, at the age we usually reproduce, each egg or sperm cell in your gonads will differ in about 33 locations from the DNA you were born with, and 90% of those will be SNPs.

Dirty Genes is all about SNPs, considering those that cause our DNA to operate different from the "optimal genome" (my term) to be "dirty"; the author doesn't say what kind of SNP is "dirty", not in any useful way. I think he is really writing about alleles, but there can be many more than the two I posited above, even for something "simple" like eye color.

With this lead-up, we can get a bit more practical. Getting your whole genome sequenced now costs something over $1,000, compared to the few billion dollars spent to produce the first total sequence. If you were to get your whole genome sequenced, and that of one of your parents or siblings, you would find on average about 10 million SNP differences between the two of you, scattered somewhat clumpily throughout each genome.

A SNP is a "single nucleotide polymorphism". A nucleotide is a 3-codon (3-"letter") sequence such as AGC. If in a particular place you have AGC and your father has ACC, that "G" is the SNP. This may or may not cause trouble for one of you. The following diagram will help:

Each copy of your genome contains 3 billion codons. You have two copies, and each has its own SNPs. Divide 6 billion by 10 million to get 600: There is on average one SNP each 600 codons. However, they are a little more concentrated in the non-coding and non-regulatory regions of the DNA, but I have not been able to find out the quantitative difference. So we'll assume no concentration for the moment. (Illustration credit: MansiG123 - Own work, CC BY-SA 4.0)

The coding DNA, the DNA that is used to make proteins, totals about 1.2% of the whole. So it contains at most 1.2% (probably somewhat less) of all the SNPs, or 120,000.

Regulatory DNA, that performs functions such as controlling the rate a particular gene produces protein, totals about 8% of the whole. So the number of SNPs found there adds up to another 800,000. The number of SNPs that can potentially "do something" is thus a little under one million. This squares with a statement by the author that we all have "a million" SNPs. But he doesn't explain it like I just did.

Now look at the diagram. We have to consider the section headed "coding region" to actually refer to coding DNA and regulatory DNA, or 9.2% of all our DNA. The "transfer table" used to convert DNA codons to amino acids in proteins has 64 codes. Three of these are used for start or stop (I think there are 2 "stop" codons). For the rest, 61/20 (there are 20 amino acids) is just over 3, and it means that the average amino acid has 3 codes that will request it in a pending protein synthesis.

A SNP that codes for the same amino acid as the DNA without that SNP is considered a "Synonymous" mutation. The protein isn't changed. So we can put 66% on the "Synonymous" box above, and 33% (or 34%) on the "Non-Synonymous" box. Below that, "Missense" means that the amino acid in the "different" protein will allow it to operate, but perhaps differently, while "Nonsense" means either that the "different" amino acid in that location will cause the protein to fold wrong and not work at all, or that the codon is a premature "stop" and the protein is cut short. "Nonsense" is more rare than "Missense", but I don't know by how much.

It comes down to this: About 300,000 of the SNPs in your DNA make it operate differently from whatever might be considered "optimal" or "standard". Since the actual distribution of SNPs is biased toward non-coding DNA, the number will be less. We have something over 20,000 coding "genes", maybe as many as 23,000. Each of them, then, contains a few SNPs; the average is about 14. So looking back at our BrownEye gene, the broken pigment that produces blue eyes is probably due to only one of the SNPs.

I infer that a "dirty gene" is one that has a Missense or Nonsense SNP, as compared to the "optimal" gene. Dr. Lynch is concerned with a combination of diet, exercise and other habits that support the proper operation of genes, as much as is possible based on the SNPs they contain.

The second genetic theme in the book is the methylation process that our cells use to actually accomplish gene regulation. Methylation is not yet well understood. It accounts for changes in gene expression; in particular, for example, the thousands of genes in a liver cell that are not needed for liver function are deactivated by being "coated" with methyl groups so they cannot be "reached" by the protein-producing machinery. Various levels of methyl "coating" are used for more fine regulation, such as the timing of certain proteins when they are needed or need to be temporarily slowed down or shut down. This is controlled by many of the "things" (we can't call them genes I suppose) that the regulatory 8% of your genome contains.

SIDEBAR: Hmm, I have seen the term "regulatory sequence" in a number of articles, and two abbreviations that may be synonyms: "regseq" and "refseq". These are both also used as software abbreviations, though, so I'll temporarily use "RS" for any of the "things" in the regulatory DNA.

The author's explanation of SNPs and "dirty genes" is directed quite differently from the above. I guess I expect more intelligence in those who read this, compared to his expectation for those who read his book.

Now I have to pan it. Ten years is a long time, and Dr. Lynch has given this a lot of effort, but he is up against a huge and hugely complex subject. What I think he has really done is to take the menu of recommendations that naturopaths have used for decades and give it a "new and improved" explanation with new buzz words. But certain fundamental knowledge is dramatically lacking. I'll pick one example that struck me early on.

No matter who you are, the Clean Genes Protocol begins with eliminating certain foods. Among them is gluten. This in spite that it is well known that only 1% of people suffer celiac disease, and thus cannot eat gluten. My former supervisor is one such, so I am familiar with it. Curiously, every time but one that gluten is mentioned in the book, it is a forbidden food. That one time, he throws a sop, telling us that one of his sons isn't bothered by gluten, but that he and the other son are very bothered by it. The term "celiac" is nowhere found in the book. That is shocking. Inexcusable.

A second example: The SNPs in a gene called the "methylation master gene", called MTHFR, are stated as a cause of Down Syndrome, along with a laundry list of lesser problems. Down Syndrome is caused by a very different kind of mutation, an extra Chromosome 21. I suppose you could call that 120 million SNPs. This is beyond belief!

I was only on page 24 when I saw that. I didn't read in detail much farther. I began to go through some of the recommendations—and found the gluten bungle—to see if it all might still make sense. It does not.

Compared to the recommendations of most naturopaths, the advice is actually a bit watered down. Though it is a fairly big book, he is trying to simplify the actual advice. But the reasons he gives for the recommendations do not make sense. "Dirty genes" is a catchy term. Maybe some day someone will define it more appropriately. But what is being "cleaned" from these "dirty genes"? Methyl groups. And you know, that is actually true, for the most part. The trouble is, this all has limited application. It is nowhere near as fine tuned as he claims.

The book is repackaged naturopathy with a shiny, new explanation for why things work or don't work, but the explanation doesn't explain enough. Our knowledge of the genome, the RS package (the "regulome"?), the proteome (all our proteins), and the saccharome (the different types of cellular sugars and simple carbohydrates, that outnumber proteins 20:1 or more), is very, very early and incomplete. Furthermore, instead of producing steps tuned to each individual's needs, the book's advice contains far too many broad brush recommendations will cause the majority of people to refrain from doing or eating things that don't matter, or that are perhaps better for them than not. In this case, a little knowledge can be quite a danger, indeed.

Sunday, September 09, 2018

Dinos as you have never known them

kw: book reviews, nonfiction, science, paleontology, palaeontology, dinosaurs, mesozoic era

For at least a little while my hunger to know "everything" about dinosaurs has been satisfied! I just read The Rise and Fall of the Dinosaurs: A New History of a Lost World by Steve Brusatte. What an amazing book, and it is not enormous as you might expect: a mere 404 pages, index included.

I used to think of the earliest dinosaurs as Dimetrodons or something similar, but they were not ancestral to dinosaurs. Note the splayed legs, like a lizard or crocodile. Dinosaurs had legs under the body like a mammal or bird. These were Synapsids, and one small branch of that order that survived the great Permian extinction went on to give rise to mammals, while a different order altogether became the proto-dinosaurs.

The drawing of a Coelophysis (pronounced "seal-off-a-sis") shown here, from the opening of Chapter 2 of Rise and Fall, represents an early dinosaur, but not the earliest. These critters lived somewhat late in the Triassic, and gave rise to birds, which are the survivors of dinosaurs. That robin, cardinal or jay out in the yard? Just your everyday dinosaur!

Note how the hind legs of Coelophysis are attached to the body similarly to the legs of a chicken. Of course, the forelegs do not have the range of motion of the wings that came along much later.

A note on geologic time. Three big Eras divide up the last 541 million years:

  1. Paleozoic (Old Life) Era, from 541-252 million years ago
  2. Mesozoic (Middle Life) Era, from 252-66 million years ago
  3. Phanerozoic (Recent Life) Era, since 66 million years ago

Each era has a few Periods. The last period of the Paleozoic Era is called the Permian, and ended with a terrible ecological catastrophe, probably caused by enormous and long-lasting eruptions of lava in the middle of Asia. More than 90% of all species went extinct, and more than 99% of all living things died. Among those that survived were some synapsids (the mammal ancestors) and a few groups of "saurians" (lizardlike animals) two groups of which became the dinosaurs about 10 million years after the end-Permian extinction event.

The three periods after the Permian, that make up the Mesozoic Era, are the Triassic, the Jurassic, and the Cretaceous. Dinosaurs were present from early in the Triassic until another disaster caused by the crash of a mountain-size asteroid killed off at least 70% of all species (on land at least) and more than 90% of all land-based living things. Certain smaller dinosaurs, the birds, survived into the Phanerozoic and from them all the 10,000 or more species of bird we see around us today have evolved.

That isn't really a summary of the book, just an introduction to its landscape in time. I have read portions of the book over the past few years because they were published in briefer form as articles in Scientific American, to which I subscribe. Dr. Brusatte is one of the talented young scientists of a generation about half my age, that are discovering new dinosaurs at the rate of about one per week, describing not only the animals but the environments they lived in, and in books such as this, presenting them to the public.

As the author describes, he has been present to witness or participate in some of the scientific revolutions that produced this comprehensive view of the true "Age of Dinosaurs", which is still going on! The first ones evolved about 243 million years ago, and though they did not become dominant until the latest Triassic or very early Jurassic period, they then remained dominant until the asteroid came along to level the playing field.

So, although today we speak of the "Age of Mammals", and the largest creatures now living are indeed mammals, there are about 5,400 species of mammals now in existence, and slightly more than 10,000 species of birds. We cannot count our modern dinosaurs out; they outnumber mammals two-to-one. And, if you ever tangle with an Emu or Cassowary, you'll get a taste of what life was like for mammals when dinosaurs ruled the land. Though our son was nearly four when he met an Emu willing to be hand fed, I suspect he hasn't forgotten this "dinosaur encounter"!

The author devotes two chapters to the development and life of tyrannosaurs. They are the iconic theropods, and theropods are ancestral to birds. The ultra-famous Tyrannosaurus rex probably had feathers, although it may have had just a smattering of them, the way an elephant or rhino has a few tufts of hair. A large animal doesn't need much insulation from the cold. Interestingly, dynamic analysis of specimens of Tyrannosaurus that were of different ages shows that the younger ones were better runners, while their huge elders were not as fast, and operated more by stealth and ambush. It makes me wonder, though, how well stealth works when you're roughly twice the size of an elephant.

I cannot close without mentioning the many micro-biographies of the people—dinosaur hunters, paleo-ecologists, and others—that have over the past centuries pieced together the evidence for the amazing lives and living of the dinosaurs. The book has a larger "cast" than most novels, and introduces them to us in all their variety (and scientists come in all varieties!).

If you read only one book about dinosaurs this year, read this one.

Monday, September 03, 2018

Sometimes the tornado wins big

kw: book reviews, nonfiction, tornadoes, atmospheric science, meteorology, storm chasers, biographies

I've never chased tornadoes, but I have seen a few. The number is small enough to catalog:
  • 1964, August, Cedar Point, Ohio: A squall line spit out seven waterspouts, one after another, that marched out of Sandusky Bay and crossed the Causeway and Chaussee between the amusement park and the city of Sandusky, then dissipated. Waterspouts are seldom stronger than EF0 or EF1.
  • 1985, Summer (July?), Rapid City, South Dakota: 4 tornadoes, all probably EF1, touched down in and around the city. I saw two of them. Looking west out my back door, I saw a funnel forming, ran out to take a picture of it, then found it hard to open the door against the wind. My wife called me to the other side of the house. To the northeast, a tornado was on the ground right across the street, tearing up sorghum in my neighbor's field. It was moving east, and no houses were hit. Driving into town the next day, I saw three buildings. Two were untouched; the third, in between the others, had lost its roof, a metal roof which was curled up behind the building. The barbed-wire fence in front of the buildings was full of fiberglass insulation.
  • 1990, Summer (August?), Stillwater, Oklahoma: I didn't actually see this one, it was wrapped in rain. I was visiting a friend when my wife phoned to say the tornado siren near our home had gone off—would I please come home? I kidded her, "It sounds like I am safer where I am, but I'll come right now." All the stop lights were not functioning, and nobody else was on the road. As I turned onto the main drag that runs north through town, it began to rain so hard there was soon surf in the middle of the street. When it began to hail, I turned into a parking lot up against a large store, to its south. I tuned to a Tulsa station (the local station was off the air), just in time to hear them say, "We have it on radar, it is crossing Perkins at McElroy." I said to myself, "That is where I am!" The store was on the southeast corner of that intersection. The tornado was actually half a block to my north, taking the top floor from a row of two-story apartment buildings and piling up their A/C units in land to the east. It also broke off a dozen or more power poles around ten feet above ground level, so it was a "skimmer", not quite on the ground yet. I saw all this after the sky cleared, about two minutes after the radio announcement. I made it home safely.
  • 1994, June, near Colby, Kansas: We were on our way to Denver from Stillwater. Our son was 7 at the time. Highway I-70 had just hooked northwest, several miles west of Grinnell. Perhaps 10-15 miles ahead we saw a squall line dropping a tornado, which traveled across the road and then dissipated. Another soon followed, and then a third. Then the storm itself broke up. I had slowed down, expecting we might have to stop before getting near the storm. We got to that bit of highway about 15 minutes after the last tornado collapsed and the sky had cleared. There was about a half mile of wet highway, with some torn-up ground on both sides. These were probably EF1 tornadoes. Though that is "weak" compared to the monster EF4 and EF5 storms, an EF1 can still roll a car around until there is too little room left inside for you to stay alive.
What is the tornado scale? The "F" or Fujita Scale was developed by Theodore Fujita in 1971. It was originally a 13-level scale of wind speeds, derived by the formula (V = wind speed in mph):
V = 14.1(F+2)1.5
Dr. Fujita didn't expect F numbers greater than 5 to ever be used. So far, none has. This formula produces this table of the minimum wind speed for each F number:

  • F0 = 40 mph
  • F1 = 73 mph
  • F2 = 113 mph
  • F3 = 158 mph
  • F4 = 207 mph
  • F5 = 261 mph
  • F6 = 319 mph

The "EF" or Enhanced Fujita scale replaced the "F" scale in 2007, with the threshold velocities changed to account for improved research into the kinds of damage caused by various wind speeds. The six thresholds (there is no EF6 or higher) are 65, 85, 110, 135, 165, 200. There is no corresponding formula, but a geometrical analysis indicates to me that a theoretical EF6 region should begin at about 235 or 240 mph and EF7 at about 285-290. This is important for what follows. But let it be said, an EF5 tornado can rip the slab of a house right out of the ground, and even pull some basements up, so there is little point in assigning larger numbers without measurement. When a tornado leaves nothing behind but plowed ground, you're already off the charts!

The Man Who Caught the Storm: The Life of Legendary Tornado Chaser Tim Samaras, by Brantley Hargrove, is a very exciting, fascinating, and ultimately rather sad, biography of Tim Samaras. The author is an excellent journalist, who dug into his subject to the point that he participated in several storm chases with friends of Tim, and witnessed some awesome tornadoes in the process.

Tim Samaras exemplifies the self-educated genius. Classroom study was not for him. With his parents' encouragement, he began taking apart various appliances and electronic devices from an early age. Sometimes he could get them back together. By the time he needed paying work, he was such a valuable instrument inventor and repairman that he was hired in spite of having no college. He cut his professional teeth designing and running instrument packages that could, for example, measure the blast force of two tons of ANFO, the explosive that Timothy McVeigh used to destroy the Murrah Building in Oklahoma City in 1995 (an explosion I felt from 75 miles away).

Tim was also a weather fanatic, and took to storm chasing very early on, teaching himself the meteorological knowledge he needed to forecast where a storm would produce a tornado—or a row of them—and how powerful they were likely to be. From 1999-2001 he developed the HITPR, the first instrument package to survive a direct hit by a tornado core and record the central pressure and temperature profile. He called it "the turtle"; its shape was designed to hug the ground better and better as the wind grew stronger. Its first success came in 2003 in Manchester, SD.

Other successes followed, in spite that the funding he was able to attract was rather poor compared to some other "professional" groups. He continued to get measurements nobody else could get, right up until the end. This was in part due to his superior forecasting abilities, knowing which way a storm was likely to turn, so he could deploy one or more turtles (or successors thereof) and get out of there alive. In one case, the tornado core hit his device 15 seconds after he had turned it on!

His son Paul became a leading photographer and videographer for his work. Thus it was, that when his on-the-spot forecast was not spot-on, May 31, 2013, near El Reno, OK, he, his son, and a close friend, meteorologist Carl Young, were killed by an EF5 tornado. Its official wind speed, measured by others with radar near the time of his death, was 295 mph. The highest wind speed measured for the El Reno tornado was about 305 mph, the second tornado in history to exceed 300 mph. Here is where my estimates above are meaningful: if there is any meaning to the extrapolation I made, this was really an EF7 tornado, and by the older scale, nearly an F6. At the time Tim was killed, its "core" was 2.3 miles wide. The core is defined as the area within which wind speeds exceed 110 mph, at least for tornadoes EF2 and stronger. To people on the ground and comparatively nearby, who survived, it looked like an upside-down mountain, stuck in the Earth. To anyone closer than about a mile away from its outer edge, it seemed to fill from horizon to horizon, and hang overhead like a rippling cliff.

The following image, clipped from a YouTube video by Dan Robinson, shows the tornado from several miles away. Its visible funnel is "only" about a mile wide at this point, but the smaller funnel to the right is a suction vortex that shows the actual width of the whole storm. This vortex, if I read the book right, was itself moving around and around the core at around 100 mph, and had its own winds in the 150+ mph range. Thus the outer edge of that vortex—or one like it—would be the source of the extreme winds that approached and probably exceeded 300 mph.

Largely due to the work of self-educated engineer Tim Samaras, meteorologists and physicists are puzzling out the workings of these storms that produce most violent winds on Earth. RIP Tim Samaras and Paul Samaras and Carl Young. I am sorry you are gone. May your legacy continue. And much thanks to Brantley Hargrove for bringing their story to us, particularly folks who may never see a tornado for themselves.

Sunday, September 02, 2018


kw: book reviews, fiction, social experimentation

Suppose, having committed a minor crime, then a few more (not so minor), you are arrested, and you are presented with a choice: either a year or two of jail time, or a social program titled "Transition". You and your spouse (both must participate) will live in the home of a Mentor couple who will retrain your life skills, with full expectation that you and said spouse will emerge as contributing members of society, rather than a drain upon it.

That is the premise of The Transition by Luke Kennard. The protagonist, Karl, has sort of stumbled into a life of credit card fraud to make ends meet. When the personal Ponzi scheme falls apart, he takes the chance to avoid overt jail time by committing himself and his wife Genevieve to The Transition.

I could summarize the plot, but why try? The pendulum-swing of society has produced a generation some call the Millennials. A certain proportion of them are heedless, unambitious, and were "raised" to expect things to work out, even as society has swayed so as to stack the deck against them. Allow me to say that the majority of Millennials are quite a bit more savvy than either Karl or Genevieve (though Genevieve is portrayed as having more street smarts). But I can think of a number of young adults who might actually benefit from The Transition, were it to operate as advertised.

Of course, what is the point of writing a big novel if things work as advertised? There is a subversive element, graduates and non-graduates of Transition, and of course Karl gets involved. It seems he finds a streak of ambition hidden within, and his ambition is to bring the system down. Do you think it can work? Look at the title I chose for this post for your answer!

Friday, August 31, 2018

Poetry Postscript

kw: continuation reviews, nonfiction, poems, poetry, reading

Speak of a mental block! In yesterday's review I utterly forgot to mention a most valuable bit of the author's advice. First among several points he makes is one I was taught when a child: Read a poem the first time, aloud, as if it were not a poem. Do not sing-song the rhythm, but read it sentence by sentence. Indeed, the author of How to Read Poetry Like a Professor (Thomas C. Foster) says in a few places that the unit of thought and feeling in a poem is not the line, but the sentence. For some poems, it can be hard to determine where a sentence ends, but it is usually no problem. Try it out with this, presented not in poetic lines, but as though it were prose:
If you must love me, let it be for nought except for love's sake only. Do not say, "I love her for her smile—her look—her way of speaking gently; for a trick of thought that falls in well with mine, and doubtless brought a sense of pleasant ease on such a day." For these things in themselves, Belovèd, may be changed, or change for you; and love, so wrought, may be unwrought so. Neither love me for your own dear pity's wiping my cheeks dry; a creature might forget to weep, who bore your comfort long, and lose your love thereby! But love me for love's sake, that evermore you may love on, through love's eternity.
There you go, five sentences, though if you replace the semicolons with full stops it comes to seven. I took slight liberties with this, to update certain grammar elements and punctuation marks, for the poet preferred a comma-dash (,—) to a semicolon, for example. Doing so, I did not disturb the meter.

Perhaps you know enough of poetry to recognize the meter when read aloud, that it is iambic pentameter, the rhythm de rigueur for sonnets. Can you then tease out the fourteen lines? Yet there are not fourteen thoughts here, just five. The discipline of putting such emotions into sonnet form induce the poet to compress the expression. Here is a scan of the page I 'translated':

A very few people might recognize this as one of the Sonnets From the Portuguese by Elizabeth Barrett Browning. The book is the 1902 edition. The 44 sonnets therein are among the great classics of English-language literature. I daresay, if you've never read them before, that reading this sonnet first in the sentence-by-sentence way, you will enjoy it more than you might have had you first read the scan, and you may find it enjoyable to get a copy of the book (it is still reprinted). Or, if you like lighter fare, perhaps you could instead get When We Were Very Young by A.A. Milne, who is best known for Winnie-The-Pooh. Milne wrote some of the most recitable poems I know (also still in print; my copy is the 1945 edition, my very first book).

Thursday, August 30, 2018

Making poetry accessible

kw: book reviews, nonfiction, poems, poetry, reading

While we lived in Oklahoma, from 1986 to 1995, we were members of the Stillwater Gem and Mineral Society. For part of 1994 I edited their monthly journal, The Rockhound Gazette. In the July 1994 issue I placed a little ditty I had written, shown here. About the end of the year, much to my surprise, the regular editor, Ruby Lingelbach, presented me with a plaque and award letter! She had entered the "poem" in some sort of contest at a conference of the Rocky Mountain Federation of Mineralogical Societies. It won first place.

So, can I call myself a "prize winning poet"? Just maybe!

For the aficionado, the meter is Trochaic Heptameter followed by an unaccented syllable, a 15-syllable line. That is rare for "ordinary" poetry, but is a meter useful in song. In fact, were I to add an appropriate chorus after the second and fourth verses, it could be sung to "O! Susanna".

You're not an aficionado? No worries. You can get a bit of grounding in such matters in How to Read Poetry Like a Professor: A Quippy and Sonorous Guide to Verse, by Thomas C. Foster.

Now, maybe you don't want to read poetry "like a professor". After all, when I read a poem, I don't really want it to be hanged, drawn and quartered and dragged to the four winds. I just want to enjoy it. I suspect most folks are the same.

Frequently, knowing a bit can help us enjoy a poem more. In this book, should it interest you, you can indeed learn a few things about drawing out more of the meaning the poet put in there. The author covers a lot of ground, from the way a poem strikes both eye and ear (much poetry is intended to be heard), to the various structures the poem or the lines might have – including whether there are rhymes; and the matters of symbols and symbolism. Although, on that latter point, it is well to remember what Sigmund Freud said about symbols in psychology, "Sometimes a cigar is just a cigar."

I am glad I had a few years of classical education before starting public school, even though the level of poetical understanding I got was rather basic. So I know that the word "iamb" is a trochee, and "trochee" is an iamb; that is, both are two-syllable "feet", but an iamb trips along with the emphasis on the second syllable while the trochee resembles a heartbeat, "LUB dub". The other two sorts of common poetic feet actually sound their meaning: "dactylic" is emphasized like "pówdery", while "anapest" is emphasized like "underfóot".

I have often said that a poem needs structure, and if it has "neither rhyme nor reason [rhythm]", it isn't poetry. The author shows how some "free verse" isn't as free as we might think, having structure just as rigid as a sonnet (with its 14 lines of 10 syllables in primarily iambic meter, in 8- and 6-line sections). However, he concedes that there is a huge amount of "bad" verse of any kind we might imagine, and for free verse in particular, it frequently differs from plain prose only in having the lines broken off short. So I continue in my belief that, if it can't be chanted or sung, it is probably not a poem.

However, read the book and judge for yourself. Perhaps if you tend to avoid poetry, you'll find it more enjoyable in the future. A fun read, this book!

Friday, August 24, 2018

Stories rocks tell

kw: book reviews, nonfiction, geology, geologists

I was in college 14 years, educated mainly in geology. Funny thing: graduate school ruined geology for me as a profession. So I returned to rockhounding as a hobby, and earned my keep by writing software for geologists and other sciences; I had enough classwork in the "hard" sciences to get majors or minors in them all. But reading the writing of Professor Donald R. Prothero made me nostalgic for what might have been. However, I judge that Dr. Prothero is quite a bit more talented than I in big-picture geology, and the long shelf of his books on the subject attests to that. The oldest book of his currently on sale, a major textbook, Interpreting the Stratigraphic Record, published in 1990, still sells for about $128.

Today's book, however, is much more accessible (and less costly!) than the text: The Story of the Earth in 25 Rocks: Tales of Important Geological Puzzles and the People Who Solved Them. (That's not the longest title I've seen, but it is close.) We can take the word "Rocks" in the title rather loosely, since one chapter is on the San Andreas Fault, all 800 miles of it, and another is the first stratigraphic sequence and the first geologic map, produced by William Smith in England in the early 1800's. However, actual rocks aplenty are dealt with, from tiny zircons used to determine the ages of ancient rocks to meteorites, coal and the tin oxide mineral Cassiterite that led to the "tin can" and "tinfoil", before aluminum (aluminium to the English) became cheap enough to replace tin.

This is the story of the earth, after all. The stories of the rocks are secondary to the earth processes they reveal. The San Andreas fault, seen here where it crosses Carrizo Plain National Monument about 100 miles north of Los Angeles, is flanked by rocks that can be matched up across it. Except "across" is a flexible term: the rocks found on the left (SW) side in this photo from Wikipedia match up with rocks found on the right (NE) side about 200 miles further south, northeast of San Diego. The chapter on transform faults, near the end of the book, which uses the San Andreas as its poster child, reveals how such faults fit into the puzzle of large-scale tectonic movements that we now call Plate Tectonics. Other chapters use other rocks and rock phenomena (such as magnetism) to bring together other pieces of this biggest of earthly puzzles.

Going to the opposite end of the size spectrum, the tiny crystals in this photomicrograph, of a field of view just 2 mm wide, are zircon crystals, extracted by dissolving a piece of granite pegmatite (granite with large crystals) with hydrofluoric acid. The image is from this publication by Thomas E. Krogh et. al. on ResearchGate.

Zircons are very valuable geologically because they often contain most of the uranium found in granite and similar igneous rocks, and their robust structure keeps all the daughter elements from uranium's breakdown, so that measurements of the ratio of uranium to lead can tell you the age of the zircon, and thus of the rock it came from. Beware, though: zircon crystals are also found in sedimentary rocks, and do not tell you the age of those rocks, but the age of the rocks in which they first formed. As long as you know this, they are still useful. You just need to know what you are doing.

Just by-the-by, the oldest piece of rock found on Earth is a tiny zircon crystal with an age of 4.4 billion years. The half-lives of U-238 and U-235 are 4.5 and 0.7 billion years, respectively. The final product of U-238 is Pb-206, and that of U-235 is Pb-207. Thus, since the time that ancient crystal was formed, nearly half its U-238 turned to Pb-206, and all but 1.3% of the U-235 turned to Pb-207. A zircon that contains more atoms of lead than of uranium is going to be very old.

The overarching theme of the book is the gradual development of the foundational "sphere" of Earth System science (Geosphere, Hydrosphere, Atmosphere, Biosphere, in decreasing order of mass). When I was a child the development of mountain ranges was explained as the wrinkling of a thin "skin" (Earth's crust) as the planet shrank while it cooled. The analogy was made to an uneaten apple that gets wrinkly as it dries out. When I first took an Earth Science course in high school, there was talk of orogeny (mountain building) as being a side product of geosynclines, based primarily on vertical motions. I do recall someone remarking that the coastlines of Africa and South America seemed to match, and I first heard of "continental drift" at that time, maybe just before 1960. Only after I became a geology major (my third major) in 1970 did I learn of plate tectonics, in which the continents don't just "drift" but are moved along by a "conveyor belt" system, riding in the midst of enormous basaltic plates, driven by a combination of sea-floor spreading at diverging plate boundaries and subduction at converging plate boundaries. Now the analogy is a pot full of thick syrup with a sugary crust on top, heated from the bottom so it convects slowly, moving chunks of the crust about.

At one point or another, every chapter of this book ties back to the plate tectonic system. And why not? It is the whole-Earth process that literally creates geology. To see a planet without tectonic motions, look at Mars. The early loss of that planet's water and 99.4% of its atmosphere pretty much halted major erosion, so that we see a 3-4-billion-year-old landscape with two major kinds of features: one very big canyon (and a few smaller ones), formed as the last of the waters dried up, and a few enormous volcanoes, three times the height of Mount Everest. Oh, and there is a scattering of impact craters gathered over the past few billion years; though there are many, they are much less abundant than craters on the Moon, because Mars did have an eroding atmosphere and hydrosphere for its first billion years or so.

At present, back here on Earth, the Himalayas, the Sierras, the Andes and a few other ranges are growing, the Rockies and Urals are at a standstill, and other ranges such as the Appalachians are eroding away. New features replace old features. This will continue, though at a slightly decreased rate, until the Sun becomes a red giant, and perhaps longer. In another 4.5 billion years, half the present amount of uranium will be gone, and only 8% of the present amount of the radioactive isotope of potassium (K-40) will remain. Crank these figures backward, and we find that radiogenic heating was six times as great as it is now about 4 billion years ago (4Ga in geologist-speak). So plate tectonics rocked along quite a lot faster when Earth was young.

I was rather charmed to notice that most of the photos in the book are credited to Wikimedia Commons. It is now possible to write a book like this one without spending months writing letters to people who might have photos of things you want to illustrate, and permission to use them. However, there are a few other signs of rapid production that caused me a bit of concern. No author should be without a good copy editor, as these three examples (only a few of a dozen or so) attest:

  • Page 80, first paragraph: discussing Lord Kelvin's estimate of 100 million years as "the time since the Cambrian", it is stated that this is off by "a factor of almost 50". The Cambrian era began a little more than 500 million years ago, so a factor of 5 would then be the correct one. However, looking up what Kelvin actually wrote, I find that he considered 100 million years to be the age since the Earth cooled from a molten state. Here, the actual factor should indeed be something like 45. So the mention of the Cambrian is the actual error. One's copy editor must know something about the science, not just English usage.
  • Page 130, Figure 12.4, a photo of the 4.4 Ga zircon I mentioned above, called a "microphotograph." No, it is a photomicrograph. A microphotograph is what you find in microfilm, where a page of text is rendered to a size of about 1 cm, or even in a "spy dot", in which the page is reduced to 1 mm. A photograph of something through a microscope is a photomicrograph. The error is common, but should not be found in a book by a scientist of this stature.
  • Page 221, last paragraph: discussing the news reporter's adage, "If it bleeds, it leads", except in this instance, the word is spelled "ledes". That's one of several dramatic misspellings I found.

OK, I just had to scratch that itch.

Of most importance is the content. This book is a must-read by anyone with the slightest curiosity about the "solid" Earth, about rocks, about how mountains are formed, or about earthquakes. Dr. Prothero is an engaging writer, thoroughly fun to read, who imparts a great lot of information quite painlessly. We need more such teachers among us.