Thursday, May 18, 2017

Inside the diagnosis

kw: book reviews, nonfiction, medicine, diagnostic procedures

It has been said that one human brain is more complex than all the rest of the universe…minus the other brains. Add a body to that brain, and the total human person is complex indeed. Thus, for a physician to correctly diagnose a troublesome condition is akin to a detective gathering clues in the mean streets of an immense, universal city. It is no coincidence that both the author of the Sherlock Holmes stories, and the man who inspired Holmes, were doctors.

Some diseases are simple enough; red, puffy eyelids leaking pus clearly indicate conjunctivitis, or pink eye. That is one of a handful of diseases anybody can diagnose. Most others, not so much. As Stuart B. Mushlin, M.D. tells us in Playing the Ponies and Other Medical Mysteries Solved, a syndrome such as POEMS is indicated when five factors are all present: Polyneuropathy, Organomegaly, Endocrine abnormalities, Monoclonal protein abnormality, and Skin changes. It is a blood disorder that is, fortunately, treatable, but is fatal without treatment.

Dr. Mushlin enjoys a good tussle with the facts of a difficult case. That is a trait he shares with my uncle and his father, who were legendary diagnosticians. In the chapter "The CPC", he describes two cases brought before a Clinical Pathologic Conference. Here, a doctor is presented with all the facts of a case, one from the recent past, and must then discuss before the group his diagnosis and the thought processes that led to it, and suggest treatment. Then the pathologist will either praise or pillory the presenter while describing the actual history and final diagnosis and treatment. It is a great educational setting, in which doctors of all levels of experience learn in ways no textbook can convey.

In this book we learn the great humility a physician must have. Knowing how to listen is a greater asset than encyclopedic knowledge of all diseases (though that helps!). Being willing to take a step back and think again, looking for that evanescent "other factor", can be the key to discerning a subtle syndrome.

I enjoy reading books by doctors. They usually write well. In Dr. Mushlin's case, he clearly enjoys writing, and it came through in my own enjoyment of the reading. I love a joyful teacher. Oh, and the "ponies"? That's about what one of his patients did with the insurance payoff!

Wednesday, May 17, 2017

The new normal arrives about twice per generation

kw: book reviews, nonfiction, ecology, limnology, great lakes

My family moved to a suburb of Cleveland, Ohio in 1961. One of the first things we did was ride a tour boat up the Cuyahoga River. The tour operator proudly showed how the thoroughly channeled, and very twisty, river had been scooped out here (and cemented in) and patched there (and cemented in) so that ore boats could just barely be eased around corners and bends that sometimes exceeded 180 degrees. He showed off more than 100 bridges across the Cuyahoga that had various ways of turning, tilting and lifting out of the way when a ship came through.

He also, almost casually, mentioned that the oily sludge atop the river was about four inches thick. We could smell it; it was the backdrop to the whole cruise. I remember Dad leaning over to us, sotto voce, "This could burn!" Eight years later it did burn. What none of us learned until much later was that the June,1969 Cuyahoga River fire, which motivated the legislation that became the Clean Water Act, was only the latest of thirteen fires over 101 years. Yes, the Cuyahoga River first caught fire in 1868.

The Great Lakes, Superior, Michigan, Huron, Erie, and Ontario, are really a sort of "northern ocean". When I tell people I have lived on all four coasts of the U.S., it takes most of them a while to realize that the "third coast" is the Gulf Coast. Only one has thought it through and asked which of the Great Lakes I'd resided at.

In The Death and Life of the Great Lakes, Dan Egan chronicles the repeated environmental insults that these "unassailable" lakes have endured. The century-long "fire season" was not the first. Canals linking the lakes to the sea were first constructed in 1783, 85 years before the first fire on the Cuyahoga. The most famous, the Erie Canal, links the Hudson River to the Niagara River above the falls, near Buffalo, New York. It allows barge traffic to bypass the rapid-strewn St. Lawrence River and Niagara Falls, to get to Lake Erie.

Prior to 1825, when the Erie Canal opened, the great lakes were ecologically isolated, mainly by gravity. The rapids along the St. Lawrence River prevent even mighty salmon from reaching Lake Ontario, and Niagara Falls effectively blockades upstream motion by downstream species. Once canal and lock systems were completed, allowing large ships to be lifted as much as 600 feet to reach Lake Superior, they could bring cargo in and out. Their unintended cargo was devastating to the lakes. Some creatures such as the sea lamprey could swim up the canals and through the locks on their own. Others, such as shellfish, traveled as larvae in the ballast water that all ships carry to keep their balance.

Take a close look at these museum specimens. The small shells are about 12-15 mm long, smaller than one of my thumbnails. They are Zebra Mussels, Dreissena polymorpha (Pallas, 1771). They are native to the Ukraine and southern Russia. Looking carefully you can see the stripes and zigzag lines that give them their name. The specimen on the right is attached to the shell of another, native freshwater bivalve.

In 1988, two zebra mussel shells were found in Lake St. Clair, between Lake Erie and Lake Huron. Soon, they were to be found throughout the great lakes. At first, it was thought that they would not infest the deepest part of the lakes because they are not found deeper than about 30 meters. Then a second, related species the Quagga Mussel, Dreissena bugensis Andrusov, 1897, was found. They live deeper down, all the way to the bottom of the deepest part of Lake Superior, 406 m (1,332 ft). (A quagga is an extinct relative of the zebra.)

The portion of this museum tray outlined in blue shows the specimens of zebra mussel in the collection of the Delaware Museum of Natural History. The few older specimens are from Crimea. All the newer ones are from Europe and the U.S., primarily the great lakes.

The list of insults to the great lakes' ecology is long, and it is likely that Dan Egan hasn't covered each and every one. But he has covered all the critical ones:

  • After lampreys came, most of the lake trout died out. An effective poison was developed to "control" lamprey populations, but it was too late for the trout. An east coast herring had also sneaked in, and here they were called alewives. They had boom-bust cycles that left millions or billions dead on the beaches.
  • Two species of salmon were introduced purposely to prey on alewives and also to provide sport fishermen some excitement. Nothing fights like a salmon.
  • Zebra and quagga mussels are just two of the invasive shellfish. Others are less troublesome, but there are dozens of them. A fish from Russia, the roundhead goby, also made its way over, and they prey on these mussels.
  • Another species related to lake trout can prey on gobies. It has become established and, while it doesn't have the fight of a salmon, is a fun catch and good eating.
  • The aforementioned fires, and not only on the Cuyahoga River.
  • Prior to the introduction of second- and third-level sewage treatment, when we lived there, Cleveland's "sewage treatment system" consisted of a big pipe five miles long that discharged right into the lake. Cleveland was not alone. Only when there was an offshore breeze was it sort of safe to swim off the beaches of Cedar Point. Onshore breezes could bring undigested turds ashore.
  • The Chicago Ship Canal siphons some of Lake Michigan into the Mississippi River watershed, also carrying away Chicago's sewage. St. Louis fought several lawsuits before Chicago was forced to quite literally clean up its act.
  • Envious eyes are frequently cast on "all that water", particularly during droughts, which by definition, happen about half the time in any particular place! A city, county or state gets used to fully using the available water in good years, then goes crying for alternatives to fill the gap when things are more "normal". Climate change may make the great lakes even wetter, but the extremes from driest to wettest are likely to be greater than now, and it will just establish a new baseline.
  • Dredging and blasting for ship channels between Huron and Erie has led the level of Lake Huron to decrease by a couple of feet. The "new" channel bottom is softer than the old, and eroding fast. The drawdown will certainly increase.

As long as the stewardship of such resources is in the hands of people who have to run for election every two to four to six years, things can't get much better. Political decision makers have a short memory.

This book is as fascinating as any novel. Sometimes I found myself saying, "What??" Each generation finds a new way to make things worse. The lakes are resilient. They can recover, slowly, to a new ecological balance, if allowed to do so. But we don't have much capacity to leave things alone.

Sunday, May 14, 2017

A hard read, but a necessary one

kw: book reviews, sociology, race relations, polemics

After I finished reading this book, I gave myself a couple of days to think it over. Professor and minister Michael Eric Dyson confronts whiteness and white privilege in a way nobody else has dared to do, in Tears We Cannot Stop: A Sermon to White America. And, being about as white as they come, of course I knew it is directed at me. This is the only way to properly receive a sermon. If you are there to hear (or read) it, God has arranged it: It is for you.

So I thought it over. I remembered a few things.

I remembered a lovely young woman I took on just one date. This was in the Los Angeles area, in 1967, and I couldn't tell if she was Hispanic or what. When I picked her up, though, I saw that her father was black, though he stayed in another room, probably hoping he would not be seen. It didn't matter to me. She and I had a nice time. On the way to take her home in Altadena, it was raining a little and I was stopped for speeding. The policeman was matter-of-fact, I was very quietly polite, and he decided not to ticket me. As we drove off, though, I did notice she was looking at me like I was from Mars. The reason didn't occur to me until decades later…

What did occur to me was to wonder what might happen if I continued to date her and my parents met her. Mom from Arkansas. Dad from Missouri, whose sweet mother called Brazil nuts "Nigger toes". Sheesh! They had got all up in arms when I dated a Catholic girl. What about a "black" one (even if she didn't look particularly black)?

Twenty years later: I remembered living next door to a black family, a couple a few years older than we were, in Oklahoma. They were living "north of the tracks", in our neighborhood because they couldn't stomach the "black culture" at the other end of town. But it had a long reach. Their two boys, both in their twenties, were into gang culture, and their daughter was a cocaine addict who stole from us a couple of times. Still, we hung out with them once in a while, though some of our neighbors would kid us about eating too much watermelon.

I thought about other things, but it is better to think about Dr. Dyson and what he has to say. In plain fact, according to his own experience, and experiences of his family, all very well-educated people, America is still two nations, one white, one black. Hispanics and other "people of color" are largely ignored outside of their own enclaves, and don't seem to belong to either nation. But Black America is an occupied country. Plain and simple.

When I am stopped while driving, I always know what I did wrong. I stay in my car. The policeman is calm and matter-of-fact, and whether I get a ticket or not, the encounter lasts no more than ten minutes. When a visibly black person is stopped, it is a different world. The driver has seldom violated any law he or she knows about: more than half the time the stop is for DWB, "Driving While Black". The policeman is at best stern, usually loud, and issues sharp commands. The driver, and sometimes all the people in the car, is frequently told to get out of the car, hands up, and to "assume the position", with hands on the hood, legs spread. All too often, a ticket is issued for some trumped-up reason the driver knows is false. The car is frequently searched, and if even a trace of marijuana is found, everyone gets at the very least a night in jail. It easily escalates from there. All the car's occupants are praying, "Lord, let me go home alive." In about 250 cases in 2016, somebody whose only offense at the time was "being black while breathing" wound up dead. One is bad enough; five per week is appalling!

Dr. Dyson is a skilled preacher. He goes straight for the heart. It is the heart of America that is sick, particularly White America. We don't have to be racist to get racist results. We benefit from a system that was rigged in our favor generations ago, and the "civil rights movement" has hardly made a dent in that. Sure, in most places the "white sheets" are no longer seen, but the "white environment" still eases the way for the non-colored, and holds back all the rest, with varying degrees of rigor.

Where does the rubber hit the road? What is the bottom line? Dr. Dyson's book is in the form of a worship service, but I suspect you've never been to a service this soul-searching. But you ought to. It is like eating your vegetables; it is good for you. If you say you don't see "white privilege", it is just a kind of institutional blindness. Let the book open your eyes. But what to do? The "Benediction" part of the "church service" is subtitled "R.E.S.P.O.N.S.I.V.E." It would rankle you if I spell out these ten words. Read the book and see. These are actionable items, and they directly touch on the responsibility every so-called "white" person has for the state of our two-country national culture.

I'll keep to myself the things I can do or have done, because to do otherwise would be grandstanding. I am humbled by Dr. Dyson's honesty.

I use the term "polemic" in the keywords advisedly; a sermon is polemical. The "sermon" in this book is a polemic in the most positive sense.

Thursday, May 11, 2017

Presenting CWWN v11 - The Present Testimony (4)

kw: book summaries, watchman nee, christian ministry

This volume of The Collected Works of Watchman Nee contains the last part of the letters and articles by Watchman Nee published in The Present Testimony from October 1933 to August 1934. The articles include parts five through seven of "The New Covenant"; classic teaching by Nee such as "The Meekest Man", about the life and labors of Moses, "Living by Faith", about how God prepares us for a life that is steady in spite of circumstance, and "A Shallow Life", where he expounds the Parable of the Soils (which begins, "The sower went forth to sow") in a most searching and personal way.

A great portion of Watchman Nee's teaching is devoted to training young Christian workers, both those who might become elders and those who might engage in apostolic (missionary) work. After reading "Ministering to the House or to God?", a young and eager Christian might be forgiven for thinking he or she can never come up to the standard. And, of course, that is the point. Only Christ can minister to His church; our most pressing responsibility is to learn to "live Christ", based on Galatians 2:20, "It is no longer I who live, but Christ lives in me."

The closing portion of the book is "Questions Related to the Workers", not from The Present Testimony, but the contents of a talk delivered in January 1934. This was not a Q&A session, but is instead full answers to the ten most frequent and most crucial questions he had heard over and over from young workers. I consider this message an excellent "warm up" for reading his book, The Character of the Lord's Worker, published in 1948 and the subject of a (much) later portion of this series of posts.

The volume concludes with a Table of Contents for all 36 issues of The Present Testimony.

Wednesday, May 10, 2017

Russian spiders redux

kw: blogs, blogging, spider scanning

When I was setting up a new post yesterday I noticed that someone(s) in Russia is/are at it again:

The new activity began about 10:00 AM EDT on May 7. That would be 5:00 PM Moscow time or (more likely) 9:00 PM in Novosibirsk…and also 2:00 AM on May 8 in Kamchatka. Hmm. The time zone where it was midnight is VLAT, in Vladivostok. It is entirely possible that a timed trigger was set for 0000 hours somewhere near there.

Last I checked, Russia is still my primary "customer". I expect them to subside again in a day or two. Oh, well. As I've said before, this is an annoyance, because with the (now usual) American spider logging about 200 hits per day, scattered throughout my blog, and the occasional Russian activity that reaches several hundred per day, I don't have much idea how many genuine readers this blog has. Even though I write primarily for my own enjoyment, it is still nice to be noticed.

Tuesday, May 09, 2017

A snail family and a photo experiment

kw: species summaries, natural history, natural science, museums, research, photographs, digital darkroom

A few weeks ago I finished a project to clean up the data for all of the specimen lots of freshwater snails at the Delaware Museum of Natural History. We loaded almost 10,000 data records to the new database product, and linked them to the InvertEBase site (the link opens the Collections page; we are #3). Then I began working my way through the land snails (called terrestrial gastropods in most literature, and they include tree snails). The Curator and I decided to work taxonomic family by family, or in groups of related families, working with about 1,000-2,000 records at a time.

The two great groups of terrestrial gastropods are the Pulmonates (infraclass Pulmonata of class Gastropoda) and the Operculates (in class Caenogastropoda along with many freshwater and marine species). "Pulmonate" means they have a lung; "Operculate" means they have a small, separate shell with which they can block the aperture of their main shell when they pull inside, and this allows them to survive periods of dryness and also blocks most predators.

The majority of land snail families are Pulmonates, so we began with the family Ellobiidae and two related families, Carychiidae and Amphibolidae. Digging into current taxonomic research, I found that the family Carychiidae is now a subfamily of Ellobiidae, and is now named Carychiinae. I also found that, while a few species in family Amphibolidae are terrestrial, most are marine, and our collection contained only marine species. Nonetheless, having extracted the records, I proceeded with both families, dealing with 75 lots of Amphibolidae and 1,236 lots of Ellobiidae.

It is instructive to survey the family Ellobiidae, which tend to have a certain appearance no matter what environment they inhabit. Some genera are all terrestrial, some are all marine, a few genera are estuarine (adapted to brackish water), and others contain species found in various habitats.

We'll first look at Ellobium chinense (Pfeiffer, 1856). Lawrence Pfeiffer originally described the species under the name Auricula chinense, thus the parentheses around his citation, indicating the reclassification of the genus.

These are medium-sized, up to 3 cm long and 1.4 cm wide, and rather ovate or cigar-shaped. In the closeup below notice the small lump on the inner lip of the aperture. The apertures of nearly all species in this family are variously decorated, probably depending on the kinds of predators these snails encounter.

The genus Ellobium is primarily Asian, and this species occurs in Japan.

Here we have another strictly terrestrial species, Pythia pantherina (A. Adams, 1851). Though the genus of this species has been changed to Pythia, I don't have information what its earlier name was. (Scarabus) on the older label indicates a subgenus, now no longer used.

Shells of this genus have the most elaborate dentition in the aperture, which indicates they have more severe predation at the aperture, probably by birds. Such a wiggly aperture allows the soft-bodied snail to emerge and crawl about, but prohibits entry to all but the slenderest of bird beaks. Other predators have other ways in: see the shell at lower left in the closeup, with two tiny pinholes in its lower left area (I didn't notice them until I looked at the closeup). They are from a predatory drilling snail, which uses its abrasive radula (sort of like a tongue with tiny teeth) to scrape a hole through the shell. It then injects a nerve poison. The animal inside relaxes, and enough of it extrudes through the wiggly aperture that the predator can either dismember it in place or pull it out to be consumed.

The genus Pythia is found throughout the Indo-Pacific region, typically on mangrove roots above the high tide line, and a little further inland. These specimens, six of the eleven in this lot, are from the Sulu Archipelago of the Philippines.

The third species of interest is Auriculastra subula (Quoy & Gaimard, 1832); the genus was formerly Auricula. These are quite small, seldom exceeding 1 cm in length.

The closeup below shows a single tooth in the aperture on the inner lip, simlar to the Ellobium specimens above. This is an estuarine species, found on mangroves in tidal marshes. It is not fully marine and cannot tolerate ocean water for any length of time.

The genus Auriculastra occurs throughout the Indo-Pacific and South Pacific. These are from Fiji. They show more wear than the prior two species, indicating that they get roughed up in the sandy lagoons, probably during the frequent storms.

The fourth and final species is Ovatella algerica (Bourguignat, 1864), originally called Alexia algerica. These are very small, just a bit bigger than those called "minute", seldom exceeding 0.6 cm in length. Note, however that like the others they have the ovate/cigar shape characteristic of the family.

The closeup shows that they also have small teeth, in this case two of them, partially blocking the aperture. These are 8 of the 20 in this lot. The original label also shows a better example for future shell collectors than the other three: the town, the beach ("Quarry Beach" in Las Palmas), and the country, plus the month and year of collecting. Is lacks only the collector's name. I am not sure why an earlier version of the database placed these in Argentina, but I am glad it has been corrected ("Argentina" on the oldest label is in someone else's handwriting. The handwritten correction on the older DMNH label is from the 1990's.)

These species are found near-shore Europe and north Africa. Their habitats are fully marine to salt marsh. The Canary Islands are offshore from north-western Africa.

The photographic experiment I mention in the title is a matter of spacing for the sake of good focus. The typical way to photograph museum mollusk specimens is to arrange the specimens on black velvet, velveteen, or (as in 3 of the 4 cases above) on black felt, and then to arrange the labels and the scale indicator around them. But even the small shells of these Ovatella specimens have a significant thickness when being photographed close-up. One may either focus on the upper surface of one of the shells, or on the labels, with the consequence that the other will be a little out of focus. One way around that is to use a lens aperture of f/8 or f/11 for greater depth of field. I tried something different.

I cut a number of small pieces of corrugated cardboard, either 3/4" x 2" (2x5 cm) or 1/2" x 1.5" (1.3x3.5 cm). I put these under the labels to bring them up to a plane close to the tops of the shells. In the case of the Ellobium specimens above, it took three thicknesses of cardboard, and you can see the spacers under the smallest label in that photo and the first photo of the Pythia specimens. It worked very well! Everything I want to see is in good focus, using f/4 to f/5. I was also using a +2 closeup lens on my camera's 18-105 mm zoom lens.

With the camera back fixed at 24" (60 cm) above the table top, I used focal lengths of 36 mm and 105 mm. I used a spot focus just below the top of a central shell in each group for the autofocus to work with, and I am pleased with the results.

Each of the original images was cropped, and the color levels clipped to remove the grayness the camera allowed in the black background, and the gamma and saturation were adjusted so the colors in the image matched the colors of the shells. The images above are all re-sized to 1620x1080 pixels, so you can click on them to get images that fill most screens. I also used just a little bit of Unsharp Masking to emphasize the shell decorations, also to make the images look more "eyeball true". My Nikon camera under-sharpens its images, which I like. I usually prefer its usual, softer look, but when I want to sharpen back to "normal", UM is the most versatile way of doing so.

Finally, although felt is cheaper than velvet, the clean, smooth blackness of genuine velvet makes for much better final images, as can be seen by comparing the first two images with the other six.

Saturday, May 06, 2017

Not a book for the squeamish

kw: book reviews, nonfiction, science, biology, microbiology, microbiome, microbes

Anyone who pays attention to at least a little news of science should know by now that 9/10 of the cells in our bodies are bacterial cells, primarily in the gut (intestines plus stomach). The human colon in particular is packed with them. They are tiny, but 80-100 trillion bacterial cells take up a volume of about one pint, or ½L, and weigh a pound or so (half a kilo). They comprise a significant percentage of our feces. They multiply rapidly enough that their numbers don't diminish.

But there are numerous bacteria on our skins also, in the millions. As Ed Yong writes near the end of I Contain Multitudes: The Microbes Within Us and a Grander View of Life, shaking someone's hand is to exchange microbes with them. Certain germophobes who know this will not shake hands. One man I know keeps a bottle of Purell in his pocket and uses it frequently. But maybe the situation is not quite so dire as folks like him think it is.

Numerous experiments that produced germ-free mice, rats, and other animals have shown that the animals cannot develop normally, and have shorter lives, compared to their "dirtier" species-mates. Bacteria and viruses were around for something like two billion years before larger organisms arose, starting with protozoans ("protists" to most systematic biologists now). Symbiosis between critters of a whole range of sizes has been the rule for the ensuing 1.5-2 billion years.

When a human child is born "naturally", that is, through the vagina, it picks up a cocktail of symbiotic bacteria—hundreds to thousands of species—that immediately begin to cover the infant's skin and fill its innards. And this is good! The mother's milk contains hundreds of special compounds that the infant itself cannot digest, but that feed the bacteria within, ensuring that the baby's development will be normal and its immune system will operate properly. As long as the mother is not desperately infected during delivery, the "Mom germs" are good germs, and the immune system takes them for "our guys". Babies delivered by C-section and/or fed only "formula" (germ-free cocktails that rather badly imitate the nutritional composition of human milk) are not going to develop as they would have, nor have as robust an immune system.

This is ubiquitous throughout the animal kingdom. The "body" of any animal, from a nematode 1mm long to an elephant or whale, is covered and filled with enormous numbers of microbes, and most of those are at worst neutral, and usually beneficial. There are foods animals (us included) cannot digest without them. There are amino acids a vegetarian cannot get in sufficient abundance from food, but effective amounts are supplied by internal microbes. Microbes ensure the survival of pandas, which would otherwise starve on a bamboo-only diet.

There are five kinds of microbes:

  1. The smallest are viruses, and are typically a few tens to a few hundreds of nanometers in size. Most viruses in our environment, and in us, prey on bacteria, or form symbioses with them so they can be properly symbiotic with us. Such "bacteriophages" are probably mis-named. "Bacteriophage" means "bacteria eater", and while many of them do invade bacteria and destroy them, others live with the bacteria, within them, and cause them to produce biomolecules that are useful to the bacteria or to their animal hosts.
  2. Bacteria are the next largest, from half a micron to several microns in size. Now that genetic tools can be used to take a proper census, it is found that there are hundreds to thousands more species of bacteria than we ever thought, when we were confined to knowledge of those that could be cultured in the lab and peered at with microscopes. But the concept of "species" is a little slippery with bacteria. They have a "sideways sex" operation called conjugation, by which even rather widely unrelated kinds can exchange genetic material. This is how antibiotic resistance can spread not just through a population of, for example, Salmonella, but through the whole microbiome of which they are a part. Bacteria are also called "prokaryotes", meaning their genetic material is not found in a nucleus, but is spread throughout the cell.
  3. Archaea are similar in size range to bacteria but are a different kingdom, very different. Many of them are extremophiles, living best at temperatures near or even above the boiling point of water, or in very salty water. Their relationships and history with animals is very poorly known. These are also prokaryotes.
  4. Fungi range from the very tiny, slightly larger than bacteria, to enormous. The ones of interest in the context of this book are primarily single-celled for most of their life cycle, but they have a nucleated cell, and are thus called "eukaryotes". Nearly all life big enough to see without a microscope is composed of eukaryotic cells.
  5. Protists, or protozoa, are eukaryotes that used to be considered either one-celled plants if they had chlorophyll, or one-celled animals if they didn't. All can move about, so they seem to be on the boundary between plant and animal kingdoms, and are now considered a kingdom of their own. The critters that help both cattle and termites digest cellulose are protists. They could not live without them.

The book discusses numerous research programs aimed at finding out just how widespread these mutualisms are. Mutualism is often a better word then symbiosis, because the latter implies a more positive, almost meaningfully positive, relationship. A deeper look shows that animal bodies all have systems for keeping their "inner critters" where they will do good, and keeping them out of the circulatory system or the bodies of cells, where they are more likely to do harm. Indeed, septicemia is a serious failure of such systems, in which bacteria are allowed into tissues or blood, and can quickly lead to death. When we do die, whatever our cause of death, it results in these systems collapsing, and our bodies are invaded and devoured by our inner symbionts, unless we are soon embalmed.

As a result of much recent research, it is becoming apparent that pathological behavior is comparatively rare, and is usually short-lived (ending in either death or cure), while mutualistic relationships are life-long, numerous, and range from innocuous to very beneficial for us.

Some bacteria have become very general in application, across entire phyla. The best example is Wolbachia, which can strongly influence the reproductive behavior of insects. It also tailors their internal microbiome, allowing some microbes and disallowing others. It is found in specimens of more than half the species of insect in which it has been sought. It has the potential to be a great friend to us: research going on as we speak is aimed at using a strain of Wolbachia as a symbiont in Aedes mosquitos, making it impossible for them to harbor the dengue virus, while also giving Wolbachia-carrying female mosquitoes a reproductive edge. This incredibly painful disease infects millions annually. What a blessing if dengue could be wiped out! Early tests show that this might come to pass in as little as a decade or two. Research is also going on to work a similar miracle with mosquitoes that carry malaria.

Mr. Yong strove in his writing to avoid sounding like a pro-germ cheerleader. Our understanding is growing rapidly, and must remain balanced. We have for a century or so treated all bacteria as evil denizens to be extinguished at every opportunity. We need a more nuanced response. Widespread use of antibiotics can make the microbiome in many of us quite dysfunctional, leading to further problems, that we try to cure with more medicines. A fecal microbe transplant (FMT) might have done the job right the first time. So far, the only condition that FMT is known to usually cure is infection with Clostridium difficile (C-diff). And why does someone get C-diff to start with? Aggressive treatment with antibiotic, which cleans out the gut, allowing the C-diff bacteria a fertile field to colonize. As FMT and other probiotic methods become better understood, it may be that we will one day cure many of our ills by taking a microbe-laden pill that is designed to scoot through our stomach and release its payload in the intestine, where it might re-formulate the mix of critters in there to drive out the problem microbes and strengthen the immune system, all at once.

I have touched on just a tiny few of the matters raised in the book. It is well worth the read. Unless, of course, you are such a germophobe that the very idea gives you the willies! Then, maybe it would be best to make the book a gift for your physician, with strict instructions not to tell you what goes into your treatment in the future.

Friday, April 28, 2017

How (living) things move

kw: book reviews, nonfiction, biomechanics

We take motion for granted. For most of our lives, from about the age of one until we are in our dotage, we walk, trot, jog, run, and jump; we also creep, crawl, sidle, and shimmy. Most of us dance in one way or another. Familiar pets also move about, as do animals in general. That is what defines animals: the ability to move with intention and comparative rapidity.

How many of us give any thought to how we move? Eadweard Muybridge was one who did more; he set up groups of cameras, either in a line or in a cluster, and set them to trigger in sequence while someone, or himself, walked or ran or performed some motion of interest.

This sequence of photos, from three different angles, of a woman performing an underhand serve in lawn tennis, was captured in 1887.

The word "biomechanics" has been around since the 1860's, possibly coined by Sir Norman Lockyer for a series of articles in Nature. But it remained a niche discipline for a century, until the late 1960's and the great expansion of cross-discipline work among scientists, the "breaking down of the stovepipes", so that physicists and mechanical engineers and biologists could collaborate more freely.

For the book Exploring Biomechanics: Animals in Motion, author R. McNeill Alexander could have taken various approaches. He chose a functional arrangement: beginning with a discussion of muscles and their mechanisms—and noting that non-muscular mechanisms of motion would be discussed as he came to them—he gathered his material into chapters on

  • Running and walking
  • Jumping, climbing and crawling
  • Gliding and soaring
  • Powered flight (such as flapping)
  • Floating (in water)
  • Swimming
  • Non-muscle motions, primarily of microbes and protozoans

I was particularly intrigued by "Floating". I had not thought of that as a biomechanical area. But it turns out there are several ways that sea creatures keep from sinking into the abyss, other than to just keep swimming (Of course, one way is to live in water shallow enough that one can safely rest on the bottom). I knew that bony fishes usually have gas-filled swim bladders, and I also knew that deep-sea squid such as the giant squid have lots of ammonia in their tissues to reduce their density (and that's why if you have a grilled giant squid steak at the Explorer's Club it will taste like soap!). There are several other passive flotation methods. None is perfect, but each serves a purpose for a certain group of animals. The most extreme to my mind is the semi-cohesive, fatty "jelly" of a jellyfish. I didn't realize that 95-99+% of a jellyfish is nonliving, low-density jelly, surrounded by a layer of living tissue only one or two cells thick!

A lot of biomechanics has to do with ratios. The ratio of limb length to body size tells a lot about lifestyle: short legs on a long body (think dachshund or mole) are good for tunnel running or tunnel digging; long legs and a flexible backbone are for speed (such as the ongoing contest between antelope and cheetah); long, slender wings are good for soaring but not so good for speed runs; the short, wide wings of a hawk give it speed and maneuverability; and on and on.

In an epilog "What we want to know next" the author emphasizes that most past study of animal flight was based on our understanding of airplanes. Helicopters and gyrocopters are a better model, because in birds, bats, and insects, the flight surfaces are dynamic elements, not static. The details of their dynamic motion allow greater efficiency than any static wing can hope to accomplish. But dynamic aerodynamics is an infant field. In fact, as much as we may know already, we are nearer the threshold of biomechanical studies than we are to the finish line.

Monday, April 17, 2017

The making of a most beloved detective

kw: book reviews, biography, novelists, short story writers

It would be too much to say that Arthur Conan Doyle saved my life, but during one terrible year, he did indeed save my sanity. More on this anon.

I am pretty sure I have read every story and novel featuring Sherlock Holmes, many of them several times. I have a one-volume edition of the stories that were published in The Strand. Thus, although I almost never read a biography, I could not pass up Arthur and Sherlock: Conan Doyle and the Creation of Holmes by Michael Sims.

The book focuses on the first 33 years of the life of Arthur Conan Doyle, culminating with the year before he "killed Holmes off", though this is not mentioned; the text climaxes with Conan Doyle's dedication of the collection The Adventures of Sherlock Holmes to his teacher, Joseph Bell, the inspiration for Holmes.

I hadn't known that Arthur Conan Doyle used both middle and last names as his surname. I find this is sometimes done in Britain, so Mr. Sims, while usually referring to him as Arthur, also calls him Conan Doyle. Never "Doyle".

The back-story illustrates that nobody really springs fully-formed into maturity, particularly in a creative career such as writing. We find that Conan Doyle began writing for publication while still in medical school. I suppose the curriculum was not nearly so rigorous as that in modern medical colleges. He had his first story published in 1879. His writing mainly spent time going 'round and 'round the circuit of being sent out and returned with a "No thanks". But his works were published from time to time during the eight years before he first created Holmes.

The first Holmes novel, A Study in Scarlet, was published in 1887, but the great detective did not immediately become popular. That took a few years. The bulk of the early Holmes stories were published in The Strand between 1891 and 1893, when "The Final Problem" culminated in Holmes's apparent death along with his nemesis, James Moriarty, in a waterfall.

The Strand collection signaled success to Conan Doyle. He had quit his medical practice to write full time. I find that Joe Bells' assessment of himself and his student, in the light of Sherlock Holmes, brings light to the reality that Conan Doyle himself, having learned all he could of Dr. Bell's deductive method, practiced it himself as a diagnostician, and then brought it to its ideal fruition, taking it beyond what either himself or Bell could do. I do recall noticing as I re-read my favorite Holmes adventures in recent years, that while Holmes is portrayed as making startling deductions about Watson and a few other people they meet, the solving of crimes owed much more to gathering clues, and frequently to staking out a suspect. Holmes thus exceeded Messrs. Lestrade and Gregson in persistence more than analysis. He gathered more "stuff" to be analyzed.

Conan Doyle freely acknowledged his literary debt to prior writers such as Poe and Gaboriau. He sought their influence while avoiding raw imitation. In the public imagination, his Holmes exceeded their creations, which are less remembered.

I was hoping that this book would delve into the rest of Conan Doyle's life, but of course, the ten-year hiatus in Holmes stories from 1893-1904 puts a cap on such an idea. Holmes had been created, had run a popular career, and had apparently died in Switzerland. Finis. So the stories and books that began with The Return of Sherlock Holmes are never mentioned. Neither are the Dr. Challenger stories, The Lost World, the Poison Belt, and The Land of Mist. But here my life intersected with Conan Doyle's world-building in a most salutary way.

In the 1959-60 school year I attended a College Preparatory school, which was suggested by a family friend who had a son there. I hated it. The school contained grades 7-12, which is a formula for rampant bullying, for one thing. It was run along the lines of a British academy. We wore suit and tie daily, no exceptions. I had passed some kind of entrance exam with a very high score, but did not do well academically. High IQ is mainly based on a good memory and lots of reading. I had the social skills of a potato.

A study period each morning and afternoon were included in the long school day. I had the freedom to spend them in the school library. Soon I discovered a complete set of Conan Doyle's books. I had already read nearly all the Sherlock Holmes stories, in various books belonging to my parents. But this collection had everything, all of his fiction. That includes the three Professor Challenger stories, which provided just the right kind of escape for me at a critical period in my life. Naturally, I read each of them at least twice, plus everything else, Holmes and all, at least once through. I found that I connected better with Professor Challenger. He didn't set as high a standard of emulation as did Sherlock Holmes. To this day, when I read a Holmes story, I take it slowly. I read a Challenger story at a more rapid clip.

The life of Conan Doyle is a cipher to nearly everyone, even the most avid readers of the Holmes stories who can quote which odd clue occurred in which story and whatnot. I like Holmes even better now, knowing the men whose accomplishments underwrote his own.

Monday, April 10, 2017

Putting America-based Jihad in perspective

kw: book reviews, nonfiction, sociology, terrorism

For those of us who were adults in 2001, the 9/11 attack that destroyed the World Trade Center towers was a before-and-after moment. For those of us a generation or two older, it is remembered as keenly as the assassination of President Kennedy in 1963. A certain few events, lesser in scope, perhaps, but serious enough, can loom as large for many people who were close enough to be affected.

In my case, the Oklahoma City bombing just 22 years ago affected me in two ways. I was in Stillwater, 70 road miles but 52 straight-line miles away. I was outside on a fine Spring day and I heard it and felt it. Initially, I thought it was a somewhat large explosion within Stillwater, such as a natural gas explosion demolishing a house. Then I heard radio reports of what it really was, although they were garbled at first. I had to be in OKC the next day, so I drove by, as close as I could get. Seeing how the front of that enormous building had simply been removed was a gut-hit experience.

Such an event happening today would immediately bring Islamic terrorists to mind. But Timothy McVeigh was no Muslim. He did not claim any religious motive at all in the things he wrote about the attack. He professed that he sought vengeance for Federal hypocrisy.

America has a long history of terrorism upon its territory; see this Wikipedia article, for example. Probably the most famous terrorism campaign prior to 2001 was the long history of the KKK, primarily active from 1865-1877 (more than 3,000 victims), but with scattered bombings, lynchings, riots and smaller massacres reaching into the 1970's.

Today Americans are worried about terrorism at home and abroad, wondering whether this country is in danger of "Islamofascist takeover" for example. No doubt, the past 16+ years have taken their toll on the American psyche, but fortunately, most of the worrisome incidents have happened in other countries. Yet people worry, "Is it time to arm myself? To get shooting lessons for the whole family?" and "What do we do if someone comes for US?"

Into this ferment author Peter Bergen offers his new book United Stated of Jihad: Investigating America's Homegrown Terrorists. Although Mr. Bergen deals at some length with events throughout the Middle East and around the world, his focus is on American citizens and legal residents. He studied the case histories of more than 300 such people. Some of them, such as the Tsarnaev brothers, committed terrorism within the USA. Some managed to "join jihad" by going to Somalia, Yemen, Syria and other places where they could learn to be a muhajid (colloquially, a Muslim guerrilla fighter) and fight (and usually die) alongside member of ISIS or other groups. A goodly number of them were caught before they could do anything, and quite a number started attacks that failed, such as the "underwear bomber".

America's law enforcement and military leaders have been trying to learn, mostly the hard way, what makes a terrorist's mind tick. You can look at any sort of situational arc, and find the entire range of responses to it. For example, long before 9/11 there was the phenomenon of someone "going postal", named for the killing of 14 in a post office in Edmond, OK by Patrick Sherrill. While this was a revenge killing rather than a specifically terrorist action, it is otherwise similar. He had a grievance of long standing and, in the parlance of the day, "snapped" and went on a rampage.

As we often hear, many people have chronic grievances, but most tend to blow off steam by singing along with "Take this Job and Shove it" or frequenting "happy hour" or taking on a vigorous sport such as Rugby. An example in the book struck me very memorably, for it exemplifies the spectrum of response. It is used to illustrate the difference between "affective" violence and "predatory" violence. Rather than quote, I'll paraphrase:
You are in a bar at happy hour and get just tipsy enough to spill a drink on the guy next to you. Nine times out of ten, he'll say, "Hey, buy me a drink and we can forget about it." One time out of ten he'll take a swing, or offer to "settle it outside", and the violence that ensues is "affective". That is, he gets mad, you get mad, and the two of you have it out. But in a very few cases, a guy who says, "...we can forget about it" will surreptitiously keep an eye on you, follow you home, drive around the block a time of two, get into your house by a back door or window, and slit your throat. That is "predatory" violence. It is the source of the proverb, "Beware the wrath of a patient man."
Going postal is similar. The kind of psychopathic mind that "snaps" in that way doesn't really "snap." It calculates and when the cost/benefit ratio is favorable, watch out! True mayhem takes planning.

As it happens, getting into the mind of someone who shows signs of radicalization (by Islam or any other ideology, including conspiracy theories) has not proven fruitful. Gathering behavioral signals works better. All too many of the 300 talked to a few or even several friends in ways the friends thought worrisome, for example. A method now known as MOSAIC does a fair job of gleaning the signal from the noise. It was developed by Gavin de Becker, the author of The Gift of Fear, which I read a few years before I began blogging.

I won't take up space by listing the steps and so forth. Take a look, for example at the online Mosaic Threat Assessment method that de Becker maintains. It uses indicators that are not specific to any religion or ideology, but are behavioral, and while it can indeed yield a better sense of someone's level of potential for jihad, it can also help you determine if your chronically angry spouse or co-worker is a threat to you. Note: the site contains instructions to help you ensure that "someone" won't find out you are checking out a threat. If such a person is a genuine threat, that's helpful!

Circling back to the core of the book's message: While the threat of jihad in America is real, it is over-hyped. International terrorist organizations such as ISIS know how to keep the 24-hour news business humming, and take full advantage of the premise, "There is no such thing as bad attention". But how much threat is there, really? Not every plot is foiled. Some come "out of the blue", or so it seems. We would have to educate all 200 million adult Americans in MOSAIC-style assessment to catch nearly every case. So some risks always remain. How much? Left to ourselves we are poor judges of risk. I like this example:
On the beach one day, someone yelled "Shark!" Most folks ran up the beach and jumped in their car. About half of them lit up a smoke. Many started the engine and drove off.
What is the real risk here?

  • Is there really a shark? Maybe...perhaps probably.
  • A dangerous shark? Maybe...I've bumped into "sand sharks" four or five times. Most shark species don't bite anything bigger than they are.
  • A few people per year genuinely die of shark bite.
  • In America, almost 40,000 die yearly in auto accidents. Driving ten miles puts you at about the same risk of dying as the chance you'll die of shark bite in your lifetime.
  • In America, about 400,000 die yearly because they smoke/smoked. I don't know how to figure out how many ciggies equal the risk of dying of shark bite. Probably less than a pack!
  • If the person screams "Shark!" with real, curdling terror in their voice, the chances you'll die by being crushed in the rushing crowd are much greater than the chance that a deaf guy over there who stayed in the water will actually get bitten.

Final thought. The number of people who died in America in massacres and similar events that were not connected to jihad is greater than the number who died of events such as the Boston Marathon bombing or the Fort Hood shootings. And if we contemplate single events: if you happen to be murdered, by far the most likely culprit is a relative of yours, someone who is not a Muslim or any other kind of religious fanatic.

Terrorism in America began while the colonies were a-borning. Twenty or fifty years into the future, will Islamic terror still be at the forefront? Maybe. Maybe not. Probably not, I think. But acts of terror will go on. Until we find a way to "breed out" the seeds of terror, it will remain some people's chosen revenge.

Friday, March 31, 2017

A collection on which I'll pass

kw: book reviews, short stories, collections, contemporary life

Some wild card choices just don't stack up to others. I won't name the book or the author, who gets enough publicity without my help. Supposedly award winning and all that. There's a lotta awards out there!

The title page blurb said, "One of the most satisfying cover-to-cover short story collections…" I guess some folks are easily satisfied.

Story one got very seamy very quickly, so I jumped to the last paragraph to see if anybody grew or even learned anything useful. Nope. Another story of clueless people who stay clueless.

Story two circles in on itself. A guy fooling himself, and it's a habit he's apparently won't break.

Story three, the narrator, someone with few values and no stomach to stand for those few, is left about where the story started, but perhaps even slower on the uptake.

OK, that's enough. I have better ways to spend my time.

Wednesday, March 29, 2017

Pioneers of celestial measurement

kw: book reviews, nonfiction, science, scientists, astronomy, astrophotography, spectroscopy

Look carefully at the white line across the gray band, where the ink marks are in each section. The ink marks were made by Edward Pickering in 1889, when he noticed the doubling of the Calcium K line (λ=393 nm, near UV) in the upper photo of the spectrum of Mizar. Mizar, also known as Zeta Ursa Majoris, is the brighter of the Mizar-Alcor double star in the "corner" of the handle of the Big Dipper. One needs keen eyes to see that it is double.

Mizar itself was found to be double by comparison of these two spectra photographed a week apart in 1887. It is the first known "spectroscopic binary". Two stars of roughly equal brightness circle each other in about 20½ days. The splitting of the K line (and all the other lines shown if you look closely) is because of the Doppler effect: when one star is moving toward us, and the other is moving away, the wavelength of the light that reaches us is shifted, one toward the blue, the other toward the red end of the spectrum.

This discovery was made possible by the "glass universe" being compiled at Pickering's behest by pioneers of astrophotography and astrospectroscopy whom he had commissioned to photograph the whole sky, over and over, on glass/emulsion plates using telescopes owned by Harvard Observatory.

This immense photographic effort, and the numerous women—and a few men—who made literally hundreds of thousands of discoveries using the plates, are chronicled in The Glass Universe: How the Ladies of the Harvard Observatory Took the Measure of the Stars, by Dava Sobel. I believe I must declare this book the most fascinating I have read so far this year. I have known for many years of "Pickering's Harem", the female "computers" who carried out manual calculations for the Harvard Observatory, and I knew of a few astronomers, names now to conjure with!, such as Annie Cannon, Mina Fleming, Cecelia Payne, and Henrietta Leavitt, whose work in the late 1800's and early 1900's literally opened the heavens by classifying the stars, discerning nebulae, measuring stars' temperatures, and discovering the period-luminosity relationship that became the yardstick for measuring the size of the Universe. This book brings them all to life for us.

Please forgive me a sort of quibble at the outset (not about what the author wrote, however): I read the Large Print edition by Thorndike Press. On the copyright page the publisher put a standard disclaimer for a work of fiction. I contacted Ms Sobel, and she assured me that there is no fiction in this book. I am very glad of that!

There is a common notion that the Harvard computers were given mainly "grunt work" and had little else of value to contribute. Not so! When Edward C. Pickering assumed leadership of the Harvard Observatory in 1877 a number of computers already worked there, most of them female, and he added more and more, eventually hiring more than 80. He always looked for hidden talents and helped the computers develop as far as they could. Williamina ("Mina") Fleming was originally hired as a maid, but he soon found she was a capable computer, and she went on to co-develop the system for classifying stars that we still use, based on the mnemonic "O, Be A Fine Girl, Kiss Me", which sorts the spectral types by temperature from hottest to "coolest" (still hotter than the filament in a light bulb). In this picture, Mrs. Fleming is standing, and the computers of the day, including Annie Cannon just below her, are shown searching photographic plates and calling out their readings to a compatriot seated nearby.

Ms Sobel presents the life stories of a dozen or so of the computers-turned-astronomers and their colleagues, and shows equal interest in the instruments and methods used to make their discoveries. And the entire narrative is wrapped around the philanthropy of two women whose fortunes underwrote much of the work. Firstly, Anna Draper, wife and collaborator of astronomer Henry Draper, came to Pickering after her husband's untimely death in 1883 and offered to support a continuation of the stellar spectroscopy and cataloging work that Henry had begun with her assistance. The support continued until her death in 1914, and her bequest to the Observatory allowed the rest of the Henry Draper Catalog (still in use) to be completed thereafter. Stars with labels such as HD217014 (AKA 51 Pegasi, the star around which the first exoplanet was discovered) are cataloged therein. Secondly, Catherine Bruce funded the production of the Bruce Telescope, a 24-inch-diameter refractor, which was used first at Cambridge, Massachusetts in 1893, then in Peru and finally in South Africa until 1950. This telescope and several of smaller size were used to take the photographs that make up the bulk of the Glass Universe, a four-dimensional archive of the sky from 1885 to 1993!

This is a small segment of one of the glass plates, showing the globular cluster 4 Tucanae. Astrophoto plates are negative images, and were read directly by researchers such as the Harvard computers, one of whom has inked directly on the plate a few arrows and lines to point out certain stars of interest, most likely variable stars.

A technical note: Very early on it was found that the best discernment of star images could be had by exposing a plate until the background skyglow produced a "density 1" gray, which passes 10% of the light when the plate is back lit. Depending on the darkness of the sky at the observing location, and the photographic speed of the plates used, this would usually take an exposure of between 30 and 90 minutes. In one night of observing at a very dark site with fast plates, one might take 20 or more exposures.

A very major part of the work at HAO was to discover variable stars and chart their variation over time. The stars marked in this plate were found by comparing plates taken over several days' or weeks' time. The long- and medium-period variables were typically the most consistent, and this was fortuitous, because Henrietta Leavitt later discovered that the greatest number of these are Cepheid variables whose period of variation is proportional to their brightness at its peak.

Cepheid variables are giant stars with masses 4 to 20 times that of our Sun, and are as much as 100,000 times as bright. This makes them visible over very great distances, up to tens of millions of light-years, using larger telescopes. The Leavitt Law, or Period-Luminosity Relationship, allows measurement of the distance to galaxies within that range of distance. Such measurements led to Edwin Hubble's discovery of the expansion of the Universe.

If you look at a group of bright stars such as the Orion constellation or the Hyades cluster (the horns of Taurus, the Bull), after a while you can notice that a few stars are yellowish or reddish compared to the rest. Orion, in particular, has the star Betelgeuse (and, yes, it is pronounced "beetle juice"), which is visibly rather orange, in one corner. Most of the rest of the stars in Orion are quite bluish.

For stars, blue means very hot, white means "sorta hot", yellow is not as hot, and orange-red is the coolest. To put numbers on it, Rigel, in the corner of Orion opposite Betelgeuse, is a blue-white giant star with a visible-surface temperature of 12,000 K (over 21,000°F), as compared to our Sun, a yellow-white star of temperature about 5,800 K (9,900°F). Betelgeuse, while not the coolest visible star, comes close at a temperature of 3,500 K (5,800°F). The tungsten filament in a (now nearly obsolete) halogen light bulb typically has a temperature of 3,300 K (just below 5,400 °F), so a "piece" of Betelgeuse brought into your living room would look slightly less yellow than a halogen lamp.

The observers and computers at Harvard took advantage of spectroscopy to do much better than just making visual color estimates. The gray and black streaks on this plate image are spectra of stars, photographed with the help of an objective prism. The objective prism for the Bruce Telescope was a thin wedge of glass more than 24 inches in diameter that turned the whole telescope into a multi-stellar spectrograph. It also incorporated a slight curvature in one direction to turn a stellar point of light into a thin streak, so that the spectra would have useful width.

These little streaks may not look like much but they record an amazing amount of information about a star. Much more than the proportion of blue to red light—which are hard to determine from such photos, though it is not impossible—, the spectra include Fraunhofer lines. These are absorption lines caused by elements in the gaseous upper atmosphere of the star. The kinds of lines that are present are a much more sensitive indication of both the composition and the temperature of the star.

If one were to look through a telescope set up in this way, it might look something like this, from a photo taken at the University of Virginia. This shows the Hyades cluster; if you concentrate on the position of the red end of each spectrum you can see the tilted "V" shape of the cluster.

This photo as shown here is too small for Fraunhofer lines to be seen, so I made this clip of just a few of the spectra:

The dark lines are the more prominent Fraunhofer lines. The K line mentioned above is barely visible in one of these spectra at the far right. Its wavelength of 393 nm is just beyond the traditional edge of Ultraviolet (400 nm), but that wavelength is actually visible to most people if the spectrum is bright enough. Each line is characteristic of a particular element. A dark line in the narrow yellow area would indicate Sodium, for example, just as the K line indicates ionized Calcium. The very strong lines for Hydrogen and Helium found in the spectra of the hotter stars of categories O and B led to the discovery that stars are primarily made up of Hydrogen, about ¼ Helium, and all the other elements add up to no more than about 1%.

Annie Cannon and others excelled in looking at the gray streaks, the hundreds to thousands of them that populated each plate, and categorizing each star by temperature and "spectral type" such as G2 (the spectral type of our Sun). Miss Cannon eventually categorized a third of a million stars.

I could go on and on, but this is long enough already. I love a book like this, that tells about the people and the work they did and why it is important. Without the "boring" work of the Harvard computers and astronomers, nearly all female, we would know only a tiny fraction of what we have learned about the Universe.

Follow-up: The Harvard plates are presently being digitized for Digital Access to a Sky Century @ Harvard, or DASCH ("Dash"). Have a look, but beware, there is a large learning curve. If you want to have a turn at stellar classification, check out Stellar Classification Online Public Exploration, or SCOPE., a Citizen Science project. While a few million stars have been classified, the great majority of the billions of stars, just in the Milky Way galaxy, have yet to be classified. Enjoy!

Sunday, March 19, 2017

Can a scientist be well-rounded?

kw: book reviews, nonfiction, science, nature, essay collections

Nearly a month has passed since I reviewed Eiseley, Volume One. Loren Eiseley's writing rewards close reading. If you are an aficionado of the Evelyn Wood speed reading method, you probably won't like Eiseley's essays. But if you can "slow down and smell the roses" you will find much to enjoy in Eiseley: Collected Essays on Evolution, Nature, and the Cosmos, Volume Two.

This book collects all of The Invisible Pyramid, The Night Country, and many selections from The Star Thrower. It is this last that probably engendered a parable about meaning that has circulated for most of my lifetime:
Walking along a lonely beach one windswept day, I saw that many starfish had been thrown onto the sand. I saw in the distance a man stoop, pick up a star, and sling it over the waves back into the sea. As I came up to him I looked around and said, "There must be thousands of starfish. You cannot throw them all back. How can it matter?" He held out a star and said, "It matters to this one," and flung it out to sea.
This is not a quote from Loren Eiseley; when he met a star thrower, he began throwing also, but said nothing to the man. That story is from an essay somewhere amidst Volume One. But, to take last things first, when he gathered essays to publish as The Star Thrower, perhaps he saw himself as one striving to do something "that matters to this one," among any who might read from him. These essays explore the boundary between science and, not just art, but everything else one might call "not science". Musing on the dramatic changes in human life that occurred once speech was attained, he considers the significant costs of our exceptionally large brain:
"His skull has enhanced its youthful globularity; he has lost most of his body hair and what remains grows strangely. He demands, because of his immature emergence into the world, a lengthened and protected childhood. Without prolonged familial attendance he would not survive, yet in him reposes the capacity for great art, inventiveness, and his first mental tool, speech, which creates his humanity. He is without doubt the oddest and most unusual evolutionary product that this planet has yet seen." (p. 357; emphasis mine)
The essay is titled "Science and the Sense of the Holy." Animals other than a very few primates (most especially humans) are divorced from considerations of time, space, and greatness (though not from rank: viz. pecking orders and the "Alpha male" phenomenon). A common house cat is able to anticipate tracking down the mouse she has just discerned beneath the stove in the kitchen. But for her, the next three or five minutes constitutes long-term planning. Your dog may consider you a deity, and thus the joking answer to the question some evangelists pose: "Why do we never see a dog set up an idol and worship it?", "Because dogs live among their gods!" But you dog's planning abilities are slender as compared to those of any toddler.

Eiseley gets to the meat of the matter in the essay "The Illusion of the Two Cultures." He writes here, and had written before, of the dismissive attitude he saw among numerous young scientists, that to pay attention to anything "arty" was quite suspect and to be discouraged, strenuously if necessary. These young Philistines are presumably in it either for glory or a good salary, but have no "sense of science."

Science is the art of the repeatable. The pinnacle of scientific achievement is to produce experimental results, publish them, and to have another scientist, or a laboratory full of them, reproduce the experiment and attain the same results. This is called "confirmation". Phenomena that cannot be repeated cannot be "confirmed" and are not admitted as science. Thus, one of my favorite parables (and less widely known than the one about the starfish), titled Non-repeatable phenomena:
There is a class of activity that is undertaken by nearly every person on Earth. Sometimes it produces great emotional responses—either positive or negative—and sometimes, not. Some people undertake these things alone, and some with one or more others; sometimes with many others. Some use various artifacts and implements, and others are able to obtain great results using only their bodily members. Some may attempt to repeat what others have done, to no effect whatever; others do so with greater and greater effect upon each repetition. There is no way to measure, ahead of time, whether a particular instance will be effective or not, or even perhaps quite negative. What is this activity? Music!
The same could be said of any performance art, of fine art, of "folk art"—which is fine art that hasn't been "discovered" yet—or even telling a story or joke ("Some can tell 'em, and some can't"). Thus, Eiseley gnaws at the great rift between "science" and "the arts" that had arisen in the past couple of centuries, and is growing still. Pointing out the need we all have for awe and beauty (I remember Einstein and his violin), he declares that this rift does disservice to both. It may not be possible to write great operas about the experiments of Edison or Faraday (though I once wrote a somewhat creditable sonnet about photosynthesis). Perhaps no painting can convey the beauty a mathematician sees in a new and succinct proof. But the best scientists everywhere confess that, when an experiment "comes together", they feel a sense of awe or beauty; when an astronomer has discerned a pattern in the dry data gathered from star after star or galaxy after galaxy, the emotional release equals that from hearing the climax of a great symphony as performed by a great orchestra. By the way, check out the audience who paid $100 or more to hear, say, the Berlin Philharmonic perform Beethoven's Ninth Symphony. People whose day job is technical or scientific will be well-represented. Thus Eiseley declares that "the two cultures" so frequently decried by some and touted by others, are an illusion. Without a sense of beauty, awe, and even holiness, few would persist.

I'll leave it to the reader to enjoy the first two-thirds of the volume and discover its delights. See why we are more similar to a slime mold than we may like to think ("The Star Dragon"), or how our attainment of wide-ranging consciousness of past and future has caused us to suffer "the wound of time" ("The Mind in Nature"). You won't be sorry.

Sunday, February 19, 2017

The bones may be dry, but not the writer

kw: book reviews, nonfiction, science, nature, essay collections

Once or twice over the years I stumbled upon an essay by Loren Eiseley. He always had a fresh take on a subject, and his writing has a lyrical quality unlike anyone else from the mid-Twentieth Century on. So when I came across his collected essays in two volumes, I couldn't resist!

I've just finished reading Loren Eiseley, Collected Essays, Vol. 1, edited by William Cronon. This volume and its companion are the 2016 offering of The Library of America Series. Volume 1 contains in three sections the three books The Immense Journey, The Firmament of Time, and The Unexpected Universe, and a fourth section, Uncollected Prose.

In modern terms, Eiseley was primarily a hominin palaeontologist; he studied the bones and grave-related artifacts of ancient humans and their ancestors and related species such as the Australopithecines. He studied human and prehuman evolution. This is in contrast to an anthropologist who studies human artifacts as evidence of culture and technology. Gathering specimens of archaic humans has always been difficult and very few were known in the 1950's to 1970's when Eiseley was most active. As late as the 1990's you could fit all known specimens of non-sapiens hominids and hominins into a footlocker. A small one. In his day a largeish suitcase was probably sufficient.

When writing for scientific publication, he could write prose as concise and acerbic as any. When writing for the public—and it is clear that this is what he most enjoyed—he wrote with heart and imagination and great lyricism. I know no other like him. He could immerse himself in a different viewpoint and somehow the writing drags us in with him. For example, writing of a spider, that was spinning a web in the heat of a street light late into winter:
  "Good Lord," I thought, "she has found herself a kind of minor sun and is going to upset the course of nature."
  I procured a ladder… There she was, the universe running down around her, warmly arranged among her guy ropes attached to the lamp supports—a great black and yellow embodiment of the life force, not giving up to either frost or stepladders. She ignored me and went on tightening and improving her web. … a kind of heroism, a world where even a spider refuses to lie down and die if a rope can still be spun on to a star. (p 111)
He notes that the web was her entire universe, and that she paid attention to nothing that wasn't in direct contact with her web. Then he wonders what we are missing, thinking that all the universe we see is all the universe there is.

He had a kind of sideways take on natural selection. Clearly understanding evolution and evolutionary theory, he points out that the popular image of "survival of the fittest" is quite wrong-headed and actually back-to-front. More than once he described how little lungfish struggle from drying pond to, hopefully, wetter ones, and calls them "fish failures". The genetic pathway their ancestors took made them less fit as a fish, but more fit overall, allowing them to endure where "fishier fish" could not. A species of lungfish or something like it evolved into the earliest amphibian. Those lungfish that still exist aren't much in the way of being fishes, nor of being salamanders, but are a compromise of both.

In the same way, proto-human primates were small, became hairless and rather weak, adopting an upright posture before they had brain enough to be much of a toolmaker. Somehow this "failed ape" survived long enough to develop toolmaking, fire, and broader social groupings, all with a brain not much larger than a chimp's.

But at a later stage, language erupted. To this day we know less about the development of language skills than about the depths of the sea. In several of the essays Eiseley waxes lyrical about what this could have meant. Language effectively brought most physical evolution to a halt, substituting cultural evolution. Human culture effectively shields us from most strictures of natural selection. But as compared to the lungfish, are we closer to the salamander, or still only a little ways beyond the ape? Are we like the lungfish in truth, no more than halfway developed in a direction we cannot discern? Are we still "failed apes" and "not-quite amphibians"…let alone a true "land" animal along the track of that analogy? In one of the last essays in the book Eiseley wonders if, having grasped the fires of the universe, will we survive our own half-formedness and grow to be worthy of the powers to which we aspire?

Indeed. I can hardly wait to dig into the second volume!