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!