Give a dog a voice and she will use it

 kw: book reviews, nonfiction, language, dogs, speech therapy

Meet Stella, subject of the book by Christina Hunger, How Stella Learned to Talk: The Groundbreaking Story of the World's First Talking Dog.

Ms Hunger, a speech therapist who works with pre-verbal toddlers and autistic children, got Stella as a puppy several years ago. She noticed that Stella's gestures and sounds were similar to the things a young child or other non-verbal person will do to communicate.

She frequently uses AAC (Alternative and Augmentative Communication) devices with her clients to enable them to begin speaking when it seems that the usual abilities aren't (yet) working. She bought four recordable "speak-back" buttons and placed them where Stella would go to request to go outside, or play, or eat. It took the dog a few weeks to first try pushing one of the buttons. During those weeks, whenever Christina would take her outside, for example, Christina would say, "Outside" and push the button that also said aloud, "Outside". Similarly for the others. Once Stella figured out what the buttons were for, she began using them.

Over time, Christina and her husband added more buttons, until they decided to attach them to a single board in one place, so Stella could use them in combination if needed (such as "outside" "play") without walking from place to place. It took Stella some time to get used to the new arrangement, but then she took off. The board shown here has 25 word buttons and one with the phrase "love you". That was a year or two ago. I think the number of words Stella can now use has grown beyond 40.

Throughout the book the author makes it clear how much repetition and patience are needed. She also discusses speech therapy issues that are common to Stella and the toddlers she works with, such as the frustration a child (or dog) experiences when she wants to communicate something more clearly. Sometimes Stella has used word combinations to express a thought not on the board, such as "water bad" when the bowl was empty; "empty" hadn't been supplied (this is my illustration, I couldn't find the place in the book where this first occurred, and the book has no index). Little children do the same thing, particularly those with an AAC that they are outgrowing. We learn that children pick up words faster than we expect, so she is always ready to add many words to a child's AAC. AAC devices for children can often use thousands of words. Time will tell how many Stella learns!

Christina's blog is here, and there are dozens of videos on YouTube about Stella's accomplishments.

The Man Who Shaved the Universe

 kw: book reviews, nonfiction, science, astronomy, philosophy of science

I was a developer of scientific software for forty years. One bit of my "Coder's Credo" is, "A complex system that works began as a simple system that works." In practical terms, this meant that I had to first "get the science working", which was usually simple, at least conceptually. The complications that had to be added all derived from the user interface (making the software usable for humans) and the data interface (coupling it to the database or knowledge base). I built my career on a minimalist approach: Add new stuff only when there is a clear advantage.

Millennia ago, the Universe seemed simple compared to the Earth. In the night sky, stars were thought of as distant lamps stuck to a "firmament". The Sun, Moon, and five rather bright "wanderers" (in Greek, πλανόδιοι, which became "planets") were a complication that most folks ignored. But certain curious ones began to theorize; they wanted to figure out how the sky worked.

Fast-forward to a mere 21-22 centuries ago. The prevailing theory of the sky, at least in Europe and north Africa, was a nest of concentric, "crystalline" spheres. The outer sphere held the "fixed stars", and the seven wanderers were each ensconced in its own sphere. Over time, observations of the motions of these "planets" showed something odd: they didn't all march across the face of the "fixed stars" at a steady rate, and some looped back on themselves. Also, the Moon's apparent size changed a little. By about 150 AD, a system of epicycles attached to the spheres had been developed to better model the movements of the planets, including the Moon and Sun.

This illustration from an Arabic document of the 1300's shows the epicycles needed to model the motion of Mercury, shown at four times during a particular year. This image is from Alamy (a commercial site), where its epigraph says,

"Ibn al-Shatir's model for the appearances of Mercury, showing the multiplication of epicycles using the Tusi couple, thus eliminating the Ptolemaic eccentrics and equant."

This shows that Arabian astronomers went beyond Ptolemy. At its height in the first half millennium of the Christian era, about 80 epicycles were needed for a "good" model, and the notion of "crystalline" spheres was politely ignored. Here, I count six epicycles needed to produce motions for Mercury that matched astronomical observations.

We all know that Copernicus tried to simplify the Solar system by recognizing the Sun as its center. However, he also needed epicycles to model planetary motions accurately, because he thought all orbits were perfect circles centered on the Sun…or, at least, the rotational center of a cluster of circular epicycles followed a circle about the Sun.

Leaving behind circles in favor of ellipses, Kepler, using Tycho Brahe's data for positions, produced a greatly simplified model of the Solar system, such as that seen here (this one leaves out Saturn, at twice the distance as Jupiter).

This particular image also shows the orbits of several major asteroids and three comets. Comet Halley's ellipse extends to 35 AU, seven times as far as Jupiter. The orbit that just brushes past Jupiter belongs to Comet Kopff, one we never hear of because it is visible only with a telescope at least 4" in diameter.

The older tradition of natural philosophers, exemplified by Ptolemy, resulted in models of natural phenomena with steadily increasing complexity. Something happened about the time that Ibn al-Shatir began writing his astronomical manuals, that began to turn the study of nature from natural philosophy to science as we know it.

Here I turn to a better authority on science history, Johnjoe McFadden. In his book Life is Simple: How Occam's Razor Set Science Free and Shapes the Universe, Professor McFadden traces the progressive simplification of science and scientific theories, based on a 14^th Century meme we call Occam's Razor. This is expressed in several ways, as it was by William of Ockham in the early 1300's. I like, "Do not multiply entities beyond necessity." This statement does not disallow complexity, it discourages unneeded complexity. Einstein's version is, "Make things as simple as needed, but no simpler," which looks at the matter from the other end.

Either way one looks at it, the principle known as Occam's Razor slices away unnecessary encrustations from scientific models. Before reading Life is Simple, that's about all I knew of the matter. I didn't even know that William, born in Ockham, lived in the early 1300's, about 700 years ago. This was just before the era of Geoffrey Chaucer (Canterbury Tales), who was born just a few years before William of Ockham died. The "English" of the day was Middle English, when the use of "thee" and "thou" and "doest" for "does", still found in the King James Bible, were at their height. But William wrote in Latin, which requires just a tad more translation than Middle English.

Neither did I know how the Razor grew and spread among the literate people of Europe and the Middle East. By the time of Kepler, 300 years later, and Newton, a generation later, simplification of theories was accepted throughout the world of the Enlightenment. The thread of the Razor through history is followed in all its excursions, leading to its dominance today.

It has become the ambition of many scientists to determine a Theory of Everything, which can be expressed on a T-shirt as a single equation that unifies not just the Weak and Strong and Electromagnetic forces, but also Gravity and Quantum Mechanics. Such a theory would not be a theory that "explains" everything, for a corollary to the Razor is, "That which explains everything explains nothing." The prolific clusters of epicycles in cosmology are an example. The more cycles you add, to account for refinements in astronomical observations, the less you actually know about them. The laws of orbital areas derived by Kepler, and the three laws of motion of Newton, as modified by Einstein, allow us to calculate exactly where each planet, moon, asteroid, comet, and artificial satellite is going, for decades or centuries into the future, and where they were at any time in the past. The calculations are tedious, but not difficult, and modern computing machinery shoulders the load of the tedious part.

Sadly, many (most?) modern theorists have gotten bogged down in String Theory. Somehow, these mathematical models require calculations in at least 10 or 11 dimensions (some versions, as many as 26 dimensions). None of the string theories so far proffered can be tested experimentally, and the number of possible string theories is a gigantic number with about 500 digits. And we thought 80 epicycles are too many! At the moment, this is a lot more "hair" than the Razor can manage to tame.

I was quite enthralled by the stories, the history, of how modern science developed once it was freed from the cosmogony of Aristotle and Ptolemy, which somehow became the foundation of Roman Catholic cosmology (for the curious: cosmogony is about "what is there", and cosmology is about "how it goes"). In effect, the Razor removed God's hand from the tiller of the Universe, at least so far as science is concerned. William of Ockham was also far ahead of his time in political understanding, which is probably a consequence of his revolutionary understanding of nature: he insisted that rulers' legitimate power came through the consent of everyone. His understanding of natural rights is an embryo of the Bill of Rights in our Constitution.

While I recommend this book for its historical perspective, I have a few quibbles about statements made by the author when he stepped outside his area of expertise, which is molecular genetics. Those who think my objections are TMI can stop here. What follows touches on three items that surprised me the most:

• On p 271, discussing the Planck Law for the spectrum of a heated blackbody, he writes that such bodies "emit light in a narrow band that depends only on the black body's temperature." Not quite. The actual spectrum of a blackbody (note the absence of a space) covers all wavelengths, and the width-at-half-height of the spectrum is about 2.8:1. For example, for a blackbody at a temperature of 7,250K (~12,600°F), the half-height spectrum ranges from 240 nm to 680 nm. The peak of the spectrum for this temperature is at 400 nm. The location of peak radiation depends on temperature, and the relative shape of the spectrum follows. An analogy about whacking a piano and somehow getting only a single note is quite bogus. The range of "notes" so emitted is strongest over more than an octave (18 half-tones), and there is some resonance from every string on the "piano".
• On p 293, about symmetry, "…time symmetry implies energy conservation, translational symmetry implies conservation of momentum, and Newton's third law, that every action has an equal and opposite reaction, is a consequence of rotational symmetry." About the last phrase: Where did that come from? Newton's third law is equivalent to time symmetry, and has nothing specific to do with rotation.
• On p 327, regarding the Bayesian likelihood of a particular combination of numbers being thrown in ten tosses of a 60-sided die, he states correctly that this is the tenth power of 60, or 60¹⁰, but then he evaluates it as 600 million to one. Hardly! 60¹⁰ = 6.05 x 10¹⁷, or 600 million times about a billion, or 600 quadrillion. Really! Don't any of his editors and readers know enough math to punch this out on a calculator?

That's enough of that. I can't blame him too much. Although I strive to be a generalist, I admit I know woefully little about molecular genetics, at least compared to Prof. McFadden. So, if I ever write a book that happens to wander into that arena, I'll see if he's willing to give it a read, and after he stops laughing, make the odd correction here or there.

Mathematics – behind the scenes of everything

 kw: book reviews, nonfiction, mathematics, applications

After a forty-year career as a scientific programmer, AKA "coder", I can look back to see that I was primarily a working mathematician. The scientists whose methods I embodied in computer code were, of course, having the computer "do the math", but I frequently had to correct their math. They were all brilliant, but one cannot always expect someone whose life has been devoted to chemical engineering or mineralogy or seismic analysis to have kept up their math skills over the prior couple of decades. On the other hand, I greatly enjoyed calculus and other "mid level" math operations, so I was "up" on what they needed and could make sure they used the math properly. I don't claim to understand perhaps 90% of the higher level math in the current literature. But I understand enough that I could make a career of it. 

In all that time, I developed only a few new methods, and published only a single peer-reviewed article, to be found at Science Direct. The abstract is open. Sadly, the article is behind Elsevier's paywall. But the key takeaway is this: I had to develop new methods to numerically solve the very stiff differential equations used by physical chemists studying the conversion of organic grunge (they call it kerogen) into crude oil. Relevant to the current book, I used methods called "convergence acceleration", which were developed before crude oil was a thing. In particular, one method was first used to study stresses in earthen dams, and another was used by Leonard Euler in the mid-1700's, for a project I don't now recall. I borrowed a couple of related methods from a theoretical dissertation by a colleague at my graduate school.

What's the Use?: How Mathematics Shapes Everyday Life, by Ian Stewart, a retired Professor of Mathematics who has at least five times my expertise, is based on a notion first expressed by Eugene Wigner in a 1960 article titled The Unreasonable Effectiveness of Mathematics in the Natural Sciences.

Wigner was not remarking on math's broad effectiveness. That isn't hard to understand. Rather, mathematicians and others who use lots of math find that methods, perhaps derived for specific problems, or perhaps for their theoretical beauty, are found to be useful in realms so remote that it seems miraculous. As the author points out, some say, "The Universe must be made of mathematics!"

The book starts off with a brief historical survey, reaching back far beyond Leonard Euler. However, Euler is responsible for a breakthrough in complex analysis that led to a formula, called Euler's Identity, which displays the essential unity of all mathematics:

The five symbols, here related by two operators (the "+" and the "="), are combined into an astonishing expression. Let's unpack them, from right to left:

• 0, zero: Before the year 1200AD, the zero as a placeholder had been in use for about 500 years, but was not yet accepted as a number, outside of India and China. Only in the 1700's (in Europe) were zero and the negative numbers accepted as numbers, making subtraction, for example, immensely more useful.
• 1, one: The first of the "natural numbers" or "counting numbers" is the original number.
• π, pi (pronounced "pee" in Greek, but most of us say "pie"): This is the ancient symbol for the ratio of the circumference of a circle to its diameter. Millennia of effort to "square the circle" were based on the belief that π is a rational number (one that can be expressed as the ratio of two natural numbers; 335/113 is a useful approximation, but is not exact). Only in the 1700's was it proven that π is an irrational number, which is expressed by a string of digits that never ends and never repeats. Being related to the circle means it is the basis of trigonometry, but that is only the beginning!
• i, the "imaginary" number: This is the square root of minus one. It has no place in any of the hierarchy of "number line" numbers: natural numbers, integers, rational numbers, and irrational numbers, which together constitute the "real" numbers. The combination of a real number and some real-number multiple of i is a complex number. Complex numbers became useful when it was realized that they represent coordinates in the plane.
• e, Euler's number: This was originally the base of natural logarithms, which show up in the solutions to many calculus problems. It is named for Euler, but was actually assigned by John Napier a century earlier, when he developed natural logarithms. Its value is approximately 2.7182818285… e and π are the first two irrational numbers to be proven to be transcendental, which has an esoteric meaning related to polynomial derivations. Many (infinitely many) irrational numbers are the solutions to polynomial equations, but most (more infinitely many!) are not. However, they are hard to find. Natural logarithms and their inverse, exponential expressions, are found everywhere in both calculus and complex analysis.

The hard part, which seems magical to many, is to evaluate e^ix, where x is some real number, and then to show that when x = π, the expression's value is -1. Endnote 50 in What's the Use? is a very short proof that exponentiation with i becomes a rotation, meaning a trigonometric combination: e^ix = Cos(x) - i*Sin(x). When x = π, the Sin part equals 0 and the Cos part = -1. This is the connection to π.

Why is this important? Much trigonometric algebra is much easier to carry out in this form. The operations automatically keep track of all the Sin and Cos functions that are embedded in the exponential expressions. Electrical engineering, frequency analysis, and a host of other disciplines would be either impossible or a great deal more difficult without complex analysis using exponential expressions.

What does this have to do with everyday life? Cell phone communications use digital decomposition and reconstruction of audio signals. Getting the digital signals transmitted efficiently requires some high-powered math. Turning a song into an MP3 file, so it takes up 1/10th or 1/20th the space on your hard drive (or phone memory) is a several-step mathematical exercise. Doing the same with a visual image to produce a JPG file is similar, and the five steps, drawn from five quite diverse realms of mathematics, are described—in brief!—in Chapter 10, "Smile, Please!".

Before getting to that point, however, the author discusses efforts to allot voting districts "fairly", describing several definitions of "fair", along with at least some hints of a proof that no matter what you may call "fair", it can't be done perfectly. He discusses the relationship between a problem involving seven bridges and two islands, that is actually insoluble, but is related to equitable ways to allocate kidneys for transplants, which is soluble. The way encryption works in your web browser (and email, I hope!) and your phone is based on "trap door functions" which are, of course, mathematical in nature. He also shows ways being developed to make much stronger trap doors to cope with the immense computing power that quantum computing just might deliver. Then, we have Einstein's theories of relativity (there are two, Special and General): both are needed to get GPS to function accurately, in addition to several other realms of mathematical operations.

There are 13 chapters showing that math is hidden behind a great deal of what goes on in the world. Civilization is impossible without it. In case this fills you with dread, remember that you don't have to be an automotive engineer to drive a car, but we do need some automotive engineers to have cars to drive. Thus, not all of us have to understand higher math to use our GPS, cell phone, or microwave cooker, but there need to be some pretty bright mathematicians out there to make these things work.

Don't shy away from this book because it is about mathematics. The author's writing is very readable, and he does his best to help us glimpse the way some of these things work. One book won't make much of a dent in your struggles with algebra, or calculus, or whatever. But it will yield an appreciation for the unreasonably diverse ways almost any mathematical development could be used for practical things later on.

Measuring the Non-Spherical Earth

 kw: book reviews, nonfiction, expeditions, science, geography

During the Age of Enlightenment theoretical and mathematical endeavors quickly outstripped the abilities of researchers ("natural philosophers", later called scientists) to apply them to the world around them. One such conundrum was the shape of the Earth. It was known that the Earth is "round" since the Earth's circumference was first measured in about 240 BC, and it was assumed for centuries to be a perfect sphere. One of the first to question this assumption from a scientific point of view was Isaac Newton. After discovering gravity, and considering that the Earth is rotating rapidly, he conjectured that the equatorial radius ought to be a little greater than the polar radius, based on an equilibrium between centripetal force and the self-gravity of the sphere. This describes an oblate ellipsoid.

In ensuing decades, others put forward reasons that the Earth might instead be prolate, that is, that the equatorial radius could be smaller than the polar radius. This may seem esoteric, but it has implications for navigation. Christopher Columbus, knowing along with the rest that the Earth is round, had proved himself wrong about the size of the Earth. "Everyone" knew that Earth was spherical in the 1490's, contrary to what was once taught in school, but Columbus thought the Indies would be "close", that the circumference was some 25,000 km (he didn't use km; this is using modern units) rather than 40,000 km. He thought India ought to be reachable by sailing only a few weeks west from Spain (as a famous poem relates, he was puzzled after 20 days of sailing and finding nothing, but "sailed on" for another 16 days). That 15,000 km error was enough to conceal two large continents, and his accidental discovery of the Americas helped trigger the Enlightenment. It also greatly increased the number of sailing expeditions across the open sea, and when you are at sea, it's essential to know where you are and the direction you need to sail to get where you are going.

If the Earth is not exactly spherical, the distance between latitudes will vary with latitude. The instruments in use prior to the 1900's were able to measure latitude with good accuracy, by sighting from the pole star, for example. Here is a quote from the Wikipedia article Earth's Circumference:

Measured around the Equator, it is 40,075.017 km (24,901.461 mi). Measured around the poles, the circumference is 40,007.863 km (24,859.734 mi).

The difference between the two is just over 67 km. Suppose a navigator calculates a rhumb line (a line to navigate by keeping a specific compass heading) to take his ship from Cadiz, Spain to Barbados. The uncertainties of navigating nearly 6,000 km might take the ship a few km. If the spherical-versus-spheroidal calculation adds another km or so of error, one might miss the island entirely.

As we read in Latitude: The True Story of the World's First Scientific Expedition by Nicholas Crane, the scientific societies of 18th Century Europe, particularly France, became convinced that it was necessarily to make measurements to determine with certainty whether the Earth is an oblate or prolate ellipsoid, and by how much. This illustration is a pictorial representation of the required calculation:

This exaggerated ellipse shows the difference between radii and lines normal (at right angles) to the surface. Latitude is measured by sighting the North Star. Its angle from the horizon is 0° at the equator and 90° (straight up) at the north pole. The green radius line shown is at a 15° angle, which would be 15° latitude on a sphere; the red radius is at 75°.

However, at the point where the green radius intersects the surface, the angle to the North Star is 47°, not 15°. Similarly, at the point where the red radius intersects the surface, the angle is about 85° rather than 75°. The other red line and green line show that to reach a position with the "right" latitude, as measured by the North Star, one must move away from the pole, unless one is at the pole or the equator already. And that means that a degree of latitude is longer on the surface of the Earth in the northerly regions than in the equatorial regions.

It was known that a degree of latitude had a certain length in Europe. However, any difference in the length of a degree (about 67 miles or 111 km in modern terms), measured in southern Europe compared to northern Europe, was too small for the academicians to clearly distinguish. The French Academy of Sciences decided to sponsor an expedition to the equatorial regions of South America, specifically to Ecuador, beginning at Quito, the city nearest the equator. At that time the area was part of the Viceroyalty of Peru, subject to Spain.

There, a team of academicians and technicians and two Spanish officers (and a multitude of helpers) were to accurately measure at least one degree of latitude, from the equator south. They eventually decided to measure three degrees, to obtain a more accurate result. That was to mean traversing more than 200 miles of mountainous terrain with quadrants, telescopes, and other equipment, tons of it.

A team of ten was sent, as the Geodesic Mission to the Equator. Not all returned, and those that did returned nearly ten years later, having suffered privations and disasters beyond what any of them could have imagined. I find it hard to understand how any of them survived. Just measuring a selected star as it crossed the zenith was a torturous trial, with the added complications of dramatic temperature and humidity variations changing the shape of the building to which the telescope was affixed, occasional earthquakes knocking it out of alignment or stopping the pendulum of the "official" clock, and cloudy nights so frequent that taking a single measurement could take a week, or weeks, of trying. One team member was an instrument maker, a former clock maker, who was kept very busy.

The team spend nearly a year to reach Quito, at a time of year that any roads that existed were muddy morasses, and much of the route had no roads. They had started out in May, 1735, and it was the rainy (or "somewhat rainier than usual") season in 1736 when they reached Quito, not all at the same time. The "team", about as badly led as any team in history, split up at one point, and a few took a different route, which delayed them; the opposite of their intention. Almost everything they did went contrary to expectation.

As I read I remembered my sessions of Summer Field Camp. Living in a tent, first in a mountainous area of Nevada, and later in a wilderness basin among glaciers in the Sierras, used up all my tolerance for camping out. And that was just three months. Compared to ten years! I remember that one reason I picked the graduate school I went to, several years later at age 30, was that their field camp was not too far from the city. I wanted to avoid another season of tent living. Wimp! 

The book delineates their many privations, but it also illuminates the significant science they were able to produce in spite of them all. They succeeded in laying out and measuring a baseline in a 7-mile-long valley (that now hosts the Quito airport), and then laying out a succession of triangles, south through about 100 miles of a "corridor" between Andean ranges, to Riobamba, and another 100 miles to some distance beyond Cuenca, where the layout was much more challenging, there being no "corridor".

A couple of years into their expedition, the Mission learned that a second Mission had been commissioned to measure a degree of latitude in northern Europe near the Arctic Circle. Another year later, at which time they had initially thought their task would be complete, they learned that the measurement at the Arctic Circle was a success: the degree measured 0.66% longer than a degree measured near Paris, 57,437 toises versus 57,060. This was decades before the invention of the meter. A French toise is just over 1.949 meters (I had to look this up; the author doesn't tell us), so the two measurements were 111.946 km versus 111.211 km. This in itself proved that the Earth's shape is oblate. However, the Mission pressed on, not just to confirm the finding (which they most decidedly did), but for the sake of many other observations and measurements of natural history, historiography, and geography they performed along the way, including measuring the speed of sound at various elevations (using borrowed cannons).

Near the end of January 1743, after collecting the angular measurements of a couple of hundred triangles over the 200-mile stretch, and doing days and days of pen-and-paper calculations, they obtained their result: one degree of latitude at the equator is 56,573 toises, or 110.262 km. Modern geodesy shows this result to be low by only a quarter of a percent, and the accepted figure today is 110.567 km, or 305 m greater.

Calculating from these figures the ellipsoid for the earth yields an interesting result, that the equator is farther from the center of the Earth than the poles by more than 22 km, and the radius at 28°N, the latitude of Mount Everest, is about 8 km less than the equatorial radius. That means that sea level near the equator is almost as far from the center of the Earth as is the peak of Mt. Everest, which is 8,848 m. In terms of distance from the center of our planet, all the high peaks in the equatorial Andes are "higher" than Mt. Everest, and the highest is Chimborazo, a 6,263 m peak, as measured from local sea level.

The author relates in an endpiece that he sought to tell a story rather than produce biographies, or relate the science in detail. Numerous books do so already. While I might prefer a few more scientific details, it is indeed an enthralling story, a real page-turner. Very enjoyable, if at times horrific in the sufferings of the members of the Geodesic Mission.

Genetic Toolkit reaches a whole new level

kw: book reviews, nonfiction, science, biology, crispr, cas9, cas12, cas13, biographies, nobel prize

For those who are aware of CRISPR, the usual meme is CRISPR/Cas9. "Nine!", you might say, "Are there eight more?" Yes, a whole lot more than that. Reading The Code Breaker: Jennifer Doudna, Gene Editing, and the Future of the Human Race, by Walter Isaacson, I learned of several others. First, a bit of jargon and some overly-brief explanation.

• CRISPR refers to a bacterial anti-viral defense system, and is the acronym for "Clustered Regularly Interspaced Short Palindromic Repeats". From back to front:
• "Palindromic Repeats" are strings of DNA that read the same both ways, such as GTCACCTAATCCACTG.
• "Short" because they are just portions of a virus's DNA sequence, probably just long enough to reliably detect a specific virus.
• "Regularly Interspaced" because they aren't jammed end-to-end but are separated by sequences that serve as delimiters.
• "Clustered" because they occur all grouped together in a bacteria's DNA.
• Cas is short for CRISPR-associated, and refers to enzymes that work with the Repeats, to cut DNA where the Repeat latches on.
• Cas9 is the shortest of the first dozen or so Cas enzymes to be discovered. It is "easiest" (only by comparison!) to work with. It cuts DNA exactly where a specific Repeat attaches.
• Cas12 and Cas13 not only cuts where the Repeat attaches, but goes on to cut up all the DNA in the vicinity.

I have a mental image of CRISPR/Cas9 (CC9 hereafter) at "homing scissors". If you dump a solution containing it, having the sequence in its Palindromic Repeat set to match some DNA in a specific virus, and that virus is present, in pretty short order the DNA of every virus present will be cut at the specified location. 

Gene editing is using CC9 to cut, and some associated chemicals to insert "new stuff" and seal the cut. It can be done with precision.

By contrast, my mental image of CC13, in particular, is an axe murderer with a roomful of victims. Perhaps a more prosaic image is someone splitting logs, going through a wood pile and making "small logs out of big ones". This enzyme complex and related ones such as CC12 form the basis for virus detection; we'll come to that in a moment.

The book is a biography of Jennifer Doudna, primarily a career biography, with just enough of the rest of her life included to produce a feel for her as a person. The author portrays someone most of us would love to work with and for: personable, demanding but not overbearing, not a micromanager yet fully engaged, and a superb team leader.

There are two big turning points in the book. Firstly, well into a career of study and work with RNA, Dr. Doudna and her collaborators, and others in usually-friendly competition with them, sought to take the bacterial CRISPR/CasX system and modify it to work inside non-bacterial cells (specifically, human cells and those of other animals). These parallel efforts bore fruit almost simultaneously, and were reported in professional publications about eight years ago. The series of breakthroughs turned CC9 into a premier gene editing tool. As the author learned at the lab bench, the process is "easy", at least in comparison to earlier genetic engineering tools such as TALENs.

Secondly, the "whack and chop" nature of CC13 makes it useful for virus detection, thus: Put it in solution with nucleic acid that has a fluorescent protein attached. The protein is not fluorescent until the DNA it is connected to is lopped off. If viruses are present that match the Repeat in the CC13 complex, the enzyme first cuts the virus's DNA, then begins cutting everything else it can reach. Do this with a UV light on, and the solution will begin to glow. More recent work has coupled the CC13 (or maybe CC12; I wasn't sure) with a dye so you can use it like a pregnancy "dipstick test". This is the basis for rapid Covid-19 tests.

There is much in the book on the ethics of gene editing. We read of the evolving feelings of Dr. Doudna, beginning with a visceral reaction, "No germline editing!", to a more nuanced view. The views of everyone in the field were rocked by the revelation in 2018 that a Chinese researcher, He Jiankui, had edited a gene in twin embryos to give them resistance to HIV; they were then implanted and brought to term, and the babies were born by C-section. The researcher, who expected acclaim, was instead prosecuted. Should he have been? That's a question we all must now answer, because the horse is out of the barn.

Writers of science fiction have for decades written stories about various aspects of gene editing, from the utopian to the dystopian. The reality is likely to be more prosaic. I recall the novella Mr. Boy by James P. Kelly, in which people regularly get their genes "twanked", either to boost characteristics they want, or to experiment with living in a very different body. We're not just talking temporary sex changes here: the teenage protagonist's best friend spends time as an intelligent Stegosaurus. I reckon that took a lot of twanking! Step back a pace or two, and it isn't hard to imagine parents choosing to give birth to a nascent Barbie or Mr. T, or perhaps Einstein or Venus Williams; upon growing up, if full-body "twanking" has arrived, the Mr. T may decide to become a bicycle racer instead, for example. And skin color might become as variable as that of a squid; perhaps we can get squid skin! "I'm feeling rather orange today; I'm tired of being blue," could become quite literal.

That paragraph is all my own. The author muses on the possibility that germline editing will result in decreased diversity, as though standards of attractiveness were universal. I think there could be a dip early on, followed by a blossoming of imagination. But I do hope that we first work toward eliminating scads of genetic diseases such as Huntington's and Cystic Fibrosis.

When a Nobelist gets "the call" it happens at a time convenient to King Carl Gustaf, which meant before 3:00 am in Berkeley. As usual, the media knew before Jennifer Doudna did, because her pre-Three phone call was from a reporter. She and her dear friend and collaborator Emmanuelle Charpentier were the Nobelists in Chemistry in 2020.

That's enough from me. I note that my last review was two weeks ago. This big (530 page) book rewards thoughtful reading. I'm just a tiny bit sorry to anyone who follows this blog. Read the book!

An inadequate story of life

kw: book reviews, nonfiction, biology, history, taxonomy

You may need to look twice at this photo to see what it is. Just for the sake of suspense, I'll describe it a little further down.

The Story of Life in 10½ Species by Marianne Taylor incorporates a great idea, but its promise is marred by writing of spotty quality and dreadful graphic design. I will list some specific difficulties at the end of this review. First let's get to the concept.

It's practically a tautology that if you gave this book's title to a hundred biologists, the 100 lists of species would have very little overlap, although "Human" would probably be on nearly all the lists. With well over a million species described, and every biologist having some favorites, it's just a given. In this case, probably because Ms Taylor is a science writer rather than a working biologist, her view is broad enough to make quite a good selection. Furthermore, each chapter discusses numerous related species, families, and even orders or phyla, to put each choice in context.

I am not sure, were I given this task, that I would limit my exposure of the plant kingdom to only one, the Cinnamon Fern, Osmundastrum cinnamomeum. However, the author makes a good case that the ferns represent the beginning of plant life, and there is more than glancing mention of later developments in the history of plants, leading to the angiosperms (flowering plants). Each of the chapters is headed by a low-key white (or gray)-on-black photo of the subject: in this chapter, a closeup of the fiddlehead, a nascent fern leaf. Contrary to what is stated in the text, all fern leaves emerge as fiddleheads and then unfurl, not only those which have specialized sexual functions. Such factual errors sprinkle the text, and I will note just a few later on.

Eight chapters discuss various animals, after the subject of Chapter 2, Virus. The chapter's photo is of a norovirus (AKA Norwalk Virus), which looks like a coronavirus, but then so do numerous others, including Polio virus and Influenza virus. Other viruses look like icosahedra (Adenovirus), twisty bits of yarn (Ebola Virus), cigarettes (Tobacco Mosaic Virus), or even moon landers (Bacteriophages). This chapter discusses what it means to call something "living", because viruses are not considered "living" by many biologists: they don't have their own reproductive machinery but must co-opt it from other cells.

The eight animals discussed are, not in order, two birds (the extinct Dusky Seaside Sparrow, shown in the photo above, where you can see it's a bird after a second look; and Darwin's finches, which triggered his thinking about natural selection), a mollusk (Chambered Nautilus), an insect (Lord Howe Island Stick Insect), sponge (the least animal-like animal), a large mammal (giraffe), human (need I say more?), and a reptile (Yangtze River Soft-shelled Turtle, which is nearly extinct).

The extra half species is "artificial life", which is always "just around the corner" but never, it seems, closer than a generation or so. It may always remain so!

Each of the species discussed is from a different taxonomic family, at least, and usually a different order or phylum. The phyla (plural of phylum) represented are Pteridophyta in the Plant kingdom (fern), Vira (virus) in the unnamed semi-living kingdom, and then in the Animal kingdom Mollusca (Nautilus), Porifera (sponge), and Chordata (AKA Vertebrata: all the rest except artificial life). I was sorry not to see any representative of phylum Echinodermata (starfish, crinoid or urchin), a favorite of mine. The entire domain of the prokaryotes, which encompass two kingdoms (Bacteria and Archaea) are mentioned here and there over a few pages. Considering that they out-mass all the rest, they deserve more than that.

Except for the occasional cognitive glitch caused by an error, or by struggling to read black text on dark red or dark purple pages, the book made for interesting reading. I'd have enjoyed it more had I not felt that sometimes she was just parroting Wikipedia articles and didn't otherwise know her subject.

Throughout, the author waxes polemical about the Holocene extinction that is all around us. No surprise that; all my biologist friends would agree, as do I in part. At least she has the grace not to use the over-hyped term "Anthropocene".

I will close by taking the unusual step of listing some (by no means all) difficulties and errors:

• Photos I categorize with "black cat in a coal bin" The photo of the sparrow shown above isn't quite the worst. Also, to the right, is a color photo of a living coelacanth (p. 71) that is nearly as bad. This scan is actually easier to decipher than the printed photo in the book. In my notes I flagged four more "very bad pix".
• Page 13: The word "that" must be removed from the middle of the first sentence for it to make sense.
• Page 16 begins by mentioning "94 chemical elements that occur naturally on the Earth". There are 90. Uranium is #92, but 43 (Technetium) and 61 (Promethium) have no stable isotopes and are not found in nature. Elements 93 (Neptunium) and 94 (Plutonium) happen to exist artificially, and have long enough half lives that they haven't all decayed away, but did not occur on Earth before the invention of the cyclotron.
• Page 58 speaks of age-dating using radioactive decay, but calls radioactive elements "[those that] lose a neutron particle...". Neutron ejection is a very rare mode of radioactive decay. Loss of a helium nucleus (alpha decay) or electron (beta decay), or even a positron (beta-plus decay) are more common.
• Page 64, on albinism, mentions the pinkish eyes of albinos, "[because] the blood supply in the retina is visible". No, it is the blood supply in the iris. Without shining a bright light into the eye, whether albino or not, you won't see the red color of the retina. Continuing, more sparsely:
• Page 95 has illustrations of continental motions, and shows a possible configuration 250 million years in the future. While the text states correctly that the Americas will by then be pasted onto the east side of Asia, the illustration shows them against Africa and Europe.
• There are three places that show an outline map of the Galapagos Islands. In two cases, the colors are OK, but on page 193, light blue on dark purple, against which the black text is very hard to read, is an extremely bad choice, particularly where the text crosses color lines. To give credit where it is due, page 216 has medium green-gray on dark gray with white text, which is a much better choice, and the white text is kept in the dark background.
• The gray-on-black photo of a finch on page 209 is much worse than the pic of the sparrow on page 165.
• Page 246: Clearly the author meant to refer to a preceding page, but the sentence ends abruptly without the reference.

That's enough to show that as a reader I suffered some kind of disruption about every ten pages. I hope someone revisits this subject de novo, has the text and illustrations reviewed by competent scientists, and employs a good copy editor and graphic designer (The "Design and Art Director", Wayne Blades, needs to find other employment!).

We all say we hate it but we all do it

 kw: book reviews, nonfiction, science, mathematics, geometry

…No, my subject is not Sin (but that would be equally true), but Geometry. But before we go on, let me tell a story.

My brother and two close friends took several courses in college together, including a math class that emphasized proofs. I'll conceal identities here, and just represent my brother as Art, and his friends as Bob and Cal. They all did pretty well in their "math proofs" class. Art studied diligently and did well, while Bob struggled mightily to keep a "B" grade, but Cal did the best with the least work. Another fellow student told them one day, "Bob walked into a room and saw a big machine with a large gear on one end. He was told he had to make it run. He looked it over, then put his shoulder against the gear and heaved a great heave, making the gear turn. Art came in next. He nosed around and found a crank that fitted into the gear's shaft. He put it in, and turned the gear. Then Cal came in. He found a cord with a plug, plugged it in, pushed a button, and the machine began to run." When it comes to mathematics courses that require proofs (algebra) or demonstrations (geometry), I am definitely in Bob's league, at best.

Now, when I see a clear geometric demonstration, I can often comprehend it almost instantly. But I could never have produced that demonstration.

These two fellows (one an Arab, one a European), shown in a 15th Century drawing, are having a go at some demonstrations. The Westerner is trying his hand at squaring the circle (which is known to be impossible), while the Arab is, more practically, extending a demonstration of the Pythagorean Theorem.

In a memoir, we read that Abraham Lincoln said of himself that he "nearly mastered the six books of Euclid." In Shape, The Hidden Geometry of Information, Biology, Strategy, Democracy, and Everything Else, by Jordan Ellenberg, we find that Honest Abe struggled for months to square a circle. Of course, he failed, and apparently he never came across a proof or demonstration that doing so is impossible.

All the demonstrations and constructions in Euclid's work must be done with compass and straightedge. The ancient compass was so constructed that once you set the two points you could scribe a circle about one of them, but the two legs collapsed when lifted from the paper; you cannot "set" that kind of compass. Further, the straightedge must have no markings on it; its only use is to draw straight lines through points already marked on the page. It so happens that if you are allowed to make a single mark on the straight edge, effectively turning it into a ruler, you can construct an extended radius, such as what we see in "b" in the illustration above, that has the required length of one side of the square. Otherwise, "No markee, no squaree." This point is not mentioned in Shape, but I suspect that Dr. Ellenberg knows it.

If Euclid were to drop into the office of any modern professor of geometry, he would recognize nearly nothing, except the (probably translated) books on a shelf, nearly out of sight, that he wrote about 2,300 years ago. Much of the "geometry" carried on these days is topology, which isn't about circles, squares or triangles, but about holes. Yes, holes. To a topologist, anything with no holes but with a defined edge is a "circle", including things we'd call squares or triangles. But if you punch a hole in it it's now something else. Most topological work is done in three (or more) dimensions. You may be familiar with the statement, "A topologist has trouble telling the difference between his cup of coffee and the donut he wants to dip into it." Both a cup with a handle, and a donut, are solid shapes with a single hole.

A fun discussion in Chapter 2 involves the title, "How Many Holes Does a Straw Have?" I asked my wife. She said, "One." That is a proper topological answer. If you shorten the straw, and make its wall thicker, it becomes a donut. Distort it some more, also pressing out a cavity (but not a hole!) in one section, and you get a coffee cup. This is easier to do with clay than with paper! But just for fun, the author shows how people defend the answer "Two", because many people would say, "It has a hole in each end"; and even the answer "None", because some would say you started with a flat sheet of paper and rolled it up.

I have to say, I was puzzled that the word "cavity" never appeared in that chapter. Topologically, a cave (source of the word "cavity") has no holes if it has no "other end". In topology, you only have a hole if you can go into one side (or end) and come out the other. So the animal known as Hydra has a cavity, but no holes, while most animals have a single hole called the Alimentary Canal, with a mouth at one end and an anus at the other. So we are donuts. Very lengthy donuts.

Well, that's not where this book is ultimately going. The earlier chapters help us get used to some geometrical ideas, and we soon get to maps. Here are two maps, and they are related:

These maps are the same (but for drawing idiosyncrasies) as on p. 394 of the book. The author calls the second (green) one a "chart", but it is also a map. It is the "first inversion" of the blue map; the green lines represent the relationships between the blue-outlined areas.

Have you ever played Nim? You begin by stacking an arbitrary number of coins in two or more piles. In one version, each player can take either one, two, or three coins, all from one pile. Other versions exist with different "taking" rules. Players alternate taking coins until one coin is left. The player who must then take that last coin loses. The author shows a simple proof that the first player will always lose if the other player makes no mistakes.

These two maps (or "map" and "chart") illustrate something about electoral districts in a state. One method for detecting Gerrymandering (where it isn't obvious, and I'll explain more anon) involves playing Nim with the line segments in the green map until a player can't remove any segment without breaking the map into two pieces. One such game ends after four moves, to look like this:

The green map from before is now a Tree, a connected map with branching but no loops and no holes.

I won't take this further here, except to say this Nim game brings about several possible ways to break up a district made of smaller units into two districts. It is one step in the process of making an electoral map having districts that are "more fair", but then we get into a discussion of what "fair" means.

For example, "proportional representation" is often talked about. To get away from R vs D or L vs R (or X vs Y, which could be sexist), I'll refer to the two "interested" parties as H and O (Lionel fans, take note). Consider a state that has ten districts, and having 60% H voters and 40% O voters. Assume they are all pretty evenly spread throughout the state. How would you draw district boundaries to "ensure" that 6 H and 4 O district representatives will be elected? If you could, would that be "fair"? That would simply guarantee that the H's in the legislature would always win every vote, unless the O's could sometimes convince a couple of H's to vote their way. So, effectively, the O citizens in the state would be without representation.

Gerrymandering, so-called because a proposed district map drawn by one Eldridge Gerry included a district shaped like a lizard, is thought of as unfair mapmaking designed to ensure that a certain party will always win. When you know where the voters live, and voter registration is how you know, you can wiggle the boundaries around to get most opponents into the smallest number of districts, and create many more districts that will just barely elect your own members. The illustration below was cropped from an article titled "The most Gerrymandered districts in America":

Even though the author's passion clearly lies in "dealing with Gerrymandering", he acknowledges that while it is often visible, it is dramatically hard to quantify. The more so because we cannot yet clearly define what "fair" means.

I have an idea: a Federal law that requires one election in four to be automatically reversed the day after the poll results are revealed. To reduce the amount of "gaming the system" that would be indulged in, a pair of fair coins would be flipped on the day in question. This ceremony would be conducted in public, with much publicity. If both coins come up Heads, all elections are reversed. Otherwise, their results stand. Of course, that means that sometimes two Reversal Years might occur in a row, and perhaps even three. It would also happen that five, ten, or more years may pass with no Reversal Years. That's OK. The added uncertainty might not make for better legislating, but it would definitely make it more interesting! I have about as much confidence that such a procedure could become law as I have of the Sun setting in the East tomorrow evening.

Now I want to back up to the idea of the Tree. The author has an interesting statement about trees and related graphs in a footnote on p. 106: "…there's a more general notion than a tree, called a directed acyclic graph…a DAG is like a tree where some branches are allowed to fuse together… Think of a particularly aristocratic family where your parents may share a great-grandparent or two." This isn't as rare as he thinks. Inbreeding happens whenever the "breeding pool" gets too small. 

For example, I have an ancestor, a Quaker, whose parents left Nantucket in the fifth generation after its settlement by ten families. Four generations back, her father could have been descended from eight of the ten families if no marriages between cousins or second cousins occurred, as could her mother. However, her father is descended from only seven, and her mother is descended from six. Between the two, going back to the settlers' generation, the Starbuck couple appears three times, the Coffin couple appears three times, and the Garner couple appears twice. And the couple themselves were second cousins (or a little closer than that, considering). First-cousin marriage is legal in seven U.S. states, and second-cousin marriage is legal in all. First-cousin-once-removed marriage is legal in 42 states. Thus, many family "trees" are really "family directed acyclic graphs". Fortunately the software at sites such as Ancestry.com is written to accommodate relationships of all kinds, perhaps even including the one described in the song "I'm My Own Grandpa."

Also, realistically speaking, when you go back more than a dozen generations or so, you'll find all kinds of links between relatives. Anyone living today who is descended from Charlemagne (crowned in the year 800), is a 38th or 39th or 40th generation descendant. Take a "tree" back 38 generations, and there are theoretically almost 275 billion ancestors. But the population of Europe in 800 AD was around 25-30 million. Think that over…

When I started the book, I had no idea it would go in these directions. It is too much fun to think about all these things. This is an author I'll keep in a tickler file.

Heaviest spidering hit yet

 kw: blogs, blogging, spider scanning

A couple of days ago I reported a sufficient number of hits on my blog, over just two days, to download the whole thing. Apparently the incident wasn't even half over. Here is the world view for the past week:

That's 4,897 hits for the USA. The total for the rest of the world is 97, which makes 4,994 overall. Since a typical week without spider activity totals about 300 hits, about 4,700 hits are anomalous.

As it happens, Google Stats notes about 4,700 hits from Safari on a Mac. So again I suspect a single agent on a single machine, but why there are more than twice as many hits on my blog as there are blog pages is mystifying.

Something new among the spiders

 kw: blogs, blogging, spider scanning

Look what I saw when I checked my blog stats:

This is about 350 hits per hour for most of the past nine hours. Almost all from Safari on Mackintosh computer(s). It looks like it was a full-site scan, because that's about all the posts I have, going back to 2005.

I'd be curious to hear from the spider-wrangler, just what is the purpose of all this?

Dual purpose memoir

kw: book reviews, nonfiction, naturalists, natural history, autism, memoirs

I scour the Science shelves at libraries and bookstores. Naturally, once I saw Diary of a Young Naturalist, by Dara McAnulty, I anticipated a good read. I was not disappointed.

The author has been a naturalist as long as he's been able to get out and into nature. The book is taken from his diary starting in Spring 2018, through Winter 2019, just before his 15th birthday. He writes to re-process a day and its experiences. It is a triumph for him to share all that with us.

This is a memoir with two tracks, as his diary has two tracks. He shows us nature as he sees it, and he shows himself to us, as he experiences himself and the world around. This takes some doing because he is autistic, at least according to the modern definition (It wasn't that long ago that "high-functioning" autistic persons were described as having Asperger's Syndrome, but that term has been swallowed up into "the spectrum", which covers a huge range from classical autism—which depicts those who cannot communicate nor even recognize the difference between people and furniture that inexplicably moves about—, to the highest-functioning end of Asperger's, which grades into the hyper-focus of ADHD).

Both Dara and his brother Lorcan are "on the spectrum," though they experience it differently and behave differently. I'm not certain that his sister Bláthnaid is also autistic, but once or twice he writes of her as though she might be so. Whatever their status, all three children are very, very lucky in having a mother who knows how to nurture them and provides a safe haven for them, and a father who is equally accepting and nurturing. This family picture is from Irish News. Dara is wearing blue.

Dara, in particular, is easily overwhelmed by business/busyness in the human world. It is time-consuming and difficult for him to recover from attending a public function or giving a speech, something he is called on to do more and more often, particularly as his blog has gained popularity and he's become better known among naturalists and environmentalists. Just attending school takes its toll, all the more when he is bullied, as autistic youngsters frequently are. However, the school in their new neighborhood is quite different, he's bullied far less often, and he writes of gathering a number of students to form a club for environmental activism.

In spite of all the troubles he's had, Dara writes with open-hearted charm. There's a freshness akin to what I've enjoyed during conversations with young friends "on the spectrum." Describing his family's last leave-taking of Rathlin Island, which he describes as shaped like a mermaid's tail—they were soon to move farther away from the northern coast—, he says, "There's a Rathlin space inside me, mermaid-shaped, and it needs to be filled again." In this picture, perhaps you can almost see the mermaid, off the picture to the upper right, taking her leave. (Picture from Wikimedia).

Later on, writing of a walk in late September: "The beach is invigorating today. I haven't stretched my legs properly in a few days, and the comfort of walking unloads a little more weight. With every passing day, a little more joy sneaks in – is there a peak, a maximum amount of joy that we're allowed to feel?"

I see I have dwelt mostly on autism. The book is filled with bits of knowledge about birds and other animals. I don't know if I can easily recognize more than a handful of bird species. Dara seems to know dozens, perhaps hundreds, by sight, sound, or even from a single fallen feather. He's much more than a bird watcher, however. He writes of insects, particularly those that inhabit streams and ponds, toads and frogs, and numerous other creatures whose habitats we have, quite frankly, invaded and often ruined.

He has a visceral reaction to things. He feels with his whole body. This can cause surprise at times: he writes of finding a jay feather and handing it to a girl standing nearby. Her mother snatched it away, saying, "Dirty!", at which point Dara screamed. He screamed loud and long, and it took much of his mother's care to calm him down. This was probably when he was younger than ten. He also writes of a later incident: seeing a boy pick up a chestnut, followed by a similar reaction from that boy's mother. But Dara held back and waited. When the mother was distracted, he found a bigger chestnut, sidled up to the boy, told him a bit about chestnut trees, and let the boy whisk the nut into his pocket before the mother could see. That's one-on-one activism, and I hope the youngster keeps his love of nature.

At about 200 pages, the book is just right. Not every day is detailed, perhaps a quarter of them or less. What we do have produces a comforting feeling that at least some young people are "getting it", that they realize we cannot continue to devour the earth, heedless of those with whom we share it.

Back door astronaut

 kw: book reviews, nonfiction, space flight, test pilots, commercial space flight, biographies

Let's cut to the chase. Test Gods: Virgin Galactic and the Making of a Modern Astronaut, by Nicholas Schmidle, is deep and complex, though very readable, bringing to us the story of an extraordinary test pilot, warts and all, and some of the author's story, also warts and all, interwoven with the history of an extraordinary spaceship company.

Marines Pilot Mark Stucky found his way to becoming an astronaut at NASA blocked at every turn, and eventually found his way to the company Scaled Composites, where he test-flew the prototype of SpaceShip Two, an improved replacement for SpaceShip One, being built for Virgin Galactic.

SpaceShip Two crashed in 2014, which set back Virgin's plans by a couple of years. A second version of SpaceShip Two was built. The book opens with a test flight in in 2016 in which SS2 spun out at altitude. The episodes ends with Mark Stucky about to try something. We know it worked because he is still with us, but it isn't until a later chapter that we learn the trick Stucky used to bring the craft under control.

The narrative carries us through the test flight of Dec. 13, 2018, when Stucky and co-pilot Frederick Sturckow flew the craft to an altitude of 51.4 miles, above the 50-mile criterion used in the US for "the edge of space." At that point the two men joined the elect number of astronauts, and also became the first persons to reach this altitude in a piloted craft since the Space Shuttle program was shut down in 2011.

The author was "embedded" in Virgin Galactic from 2014-2018, and his unusual level of access allowed him to write such a book about Mark Stucky, Virgin Galactic, and provide close-up-and-personal insight into Richard Branson, the founder (and main funder) of Virgin Galactic, other company figures, and some of the test pilots. This photo shows Mark Stucky and David Mackay after they piloted SS2 on its first flight past Mach 1 (the December 2018 flight reached Mach 3, and it takes Mach 25 to achieve orbit).

When Stucky and the author met, as I understand from the text, they learned that Stucky had known, and been trained by, the author's father Robert Schmidle, a test pilot and fighter pilot for the Air Force. It turned out that the several of the test pilots at either Scaled or Virgin had known the elder Schmidle and some had been trained by him. Thus, the book is in part about the author himself, learning more of the test pilots' life that his father seldom spoke about.

Test pilots are a special breed. They think their way through crises that make most people freeze. My father knew a fighter pilot during WWII; they are of similar stock. This man in particular had a gunfighter's reflexes; Dad called him "twitchy". Such men do things so far beyond most of us, that the book's title Test Gods is warranted, at least on a secular level.

I really can't say more. It seems that authors like Nick Schmidle are also a special sort, able to take firm grip on our heart strings and make us see through their eyes and feel in our own guts, what they are feeling.

I understand from some searching around that the publication of Test Gods precipitated a falling out between Mark Stucky and Virgin Galactic. Perhaps the book exposed too much. But the cracks were beginning to show long before. When you corral too many alpha males together, fireworks are guaranteed. I credit Mark Stucky's unusual tact with holding things together as long as they held.

A little over a year ago the Virgin Galactic's craft, piloted by a new set of pilots, "reached space" for the fourth time, the first with a full crew of four, including Richard Branson, attaining an altitude of 53.5 miles. Perhaps Branson's dream of taking tourists to the edge of space is soon to be achieved, at a little less than half a million per ticket.

Technical note: SS2, officially named VSS Unity, is launched from a dual-fuselage "mother ship" called White Knight Two, now officially named VSS Eve. The launching craft brings the spaceship to an elevation of about 48,000 feet (nearly 24 miles, almost halfway to the 50-mile criterion), and then releases it to power its way upward to space.

Give it to me straight, Doc

 kw: book reviews, nonfiction, science, publications, research, fraud, bias, negligence, hype, polemics

When I was a chemistry major, taking organic chemistry, we had a lab exercise called The Martius Yellow Competition. It's a famous experiment, designed at Harvard, in which we had to produce seven compounds, one of which was the famous dye Martius Yellow. The dye is protein-specific, making it useful for staining certain cell preparations for microscopy. That also makes it problematic if you get it on you. It stains your skin bright yellow, and the stained skin takes about a month to grow out. A few of my fellow students finished that lab day with big yellow blotches on their hands and even faces.

What is of interest here is that two of the compounds—all are crystalline solids at room temperature—are hard to crystallize. To get one of them to precipitate out of solution, we had to cool the solution on an ice bath and then scratch the bottom of the flask, carefully, with a metal spatula. The other needed exposure to UV light, which we accomplished by putting the flask on a window sill for an hour or so.

Of course, if you already have a little bit of the target material on hand, in crystalline form, you can get a solution to crystallize quickly by seeding it with a bit of dust from crushing a tiny crystal of the same stuff. And here the professor told us a story. One of his mentors was an elderly chemist who had a beard. Once in a while one of his students would be having a hard time getting a solution to crystallize. He would call the professor over for advice or help. The professor would look at the flask, scratching his beard, and then the desired crystals would begin to form! As we heard the story we first thought the old professor must have poor hygiene habits. But No: Then he told us the old fellow knew what to anticipate, and early in the morning of such a day, he would put a bit of solution on his beard and let it dry. The scratching would release a few seed crystals into the air. When any of them fell into the flask in question, it would start the crystallization!

Such playful tricks aside, during my extended education (14 years at four universities and colleges), I learned that some scientists play fast and loose with their "science." Not all published "science" is genuine, and some of it is downright dangerous. I knew professors who were, quite simply, frauds. I don't wish to mention any names, because others have already exposed the worst of them, or their "work" has been superseded anyway. But I learned that there are several ways to get results into print even if you have no useful results to report. It's the fruit of the perverse motivation system called "Publish or Perish".

Thankfully, I don't need to get into detail, because a real scientist, Dr. Stuart Ritchie, has written a great book about how science goes wrong: Science Fictions: How Fraud, Bias, Negligence and Hype Undermine the Search for Truth. Dr. Ritchie is a real scientist, in contrast to myself: I got the degrees, but spent almost half a century writing software for scientists, without doing any science. Much of my value was making sure they got their math right, because I remembered all the calculus they had forgotten. I am particularly adept at statistics, so I know deeply how easily they can be misused to cook up a result almost out of thin air.

As an illustrative aside: I am an amateur radio operator (a Ham). On one occasion the members of a radio club I was part of visited an amateur who specialized in moon-bounce communication. He had a steerable antenna the size of a barn door, fed by a thousand-watt transmitter. It was just barely capable of getting a signal to the Moon and hearing it when it came back. The signal was noisy and barely discernable above background noise. Sometimes a Morse code "dah" would be broken up and sound like two "dits". (The dah is three times as long as the dit). Our host told us that sometimes the signal is so buried in the noise, and you listen so hard, that you can imagine an entire conversation out of random noise.

This is relevant. Many, many published results are based on something called "statistical significance", which has a criterion called the p value, with a "significance threshold" of 0.05. As long as the p value is less than 0.05, the result is considered "significant". It requires backward thinking to understand a p value. It is the probability that the "result" you obtained could have happened completely at random. Sometimes you will hear it said that there's only one chance in twenty, or less, that the conclusion you have drawn is incorrect.

That is not a very strict criterion. If you peruse scientific literature that includes statistical analysis, you are likely to find that most of the papers show results with a p value only a little below the threshold: 0.048, 0.04, 0.045, and so forth. Sometimes a "more robust" result will be reported, with a p value of 0.01 or even 0.005. To me, that is more like it. Because if you have thirty or so publications, all touting a p value just below 0.05, you have to say to yourself, "At least one of these is likely to be false. Maybe more than one." Then you should ask, "How can I find out which?"

The "how" is to replicate the experiment. Some experiments aren't too hard to replicate. What if the new experiment gets a different result? You can't stop there and say "It was wrong." It requires digging deeper, and nailing it down, then finding a journal to publish your counter-article (which can be remarkably hard; see the author's first story). In Science Fictions you'll read about some of the ways one can follow up.

What is more serious is the practice of hiding results that didn't work out, often called Null results. This is called the File Drawer Bias. For some kinds of experiments, particularly in psychology and medicine, there may be five or ten times as many "results" in the file drawer as the ones that were published. Automatically, we have to realize that a quarter to a half of the published reports are probably incorrect. Again, replication might be able to clear the matter up. However, doing experiments takes time and money. Our author reports a partial solution that is being implemented by many funding bodies, both governmental and private: They will only support the experiment if it is pre-registered and the results are guaranteed to be published. Such as system can still be gamed, but it is harder.

All this shows up close to halfway into the book, where the author tackles the issue of Publication Bias. Earlier, he takes on Fraud, as the most dangerous, and paradoxically, often the hardest to deal with in any timely way. A few heartbreaking stories are told, such as a surgeon who claimed he had perfected an artificial trachea to replace one damaged by accident or cancer. All of his patients died, usually after only a few months. Yet he was protected by the institution where he worked because of his fame. But eventually it all blew up. Far too many charlatans get famous enough (based on little substance!), that they are protected this way. And let us not forget the "accepted science" of the late 1700's, which resulted in the physicians for retired President George Washington bleeding him nearly dry because of a bad cold, such that he died.

Fortunately, we are more likely to encounter various kinds of bias. We are all biased. I was fortunate enough to take a class in literary discernment (I don't recall its actual title). We read articles from a great many publications. Some journals that I remember were The Wall Street Journal, Commonweal, National Review, The New Republic, The London Times, and The New York Times. We learned that every writer is biased, as is every editor. We learned to determine the bias of each writer and, from multiple articles, the likely bias of the editorial board for some of the publications. We also learned how to tell if a writer or editor is aware of the bias and has tried to mitigate it to any degree. Hint: Look for the number of modifiers (adjectives and adverbs) and their "flavor" (for example, "The company reached a compromise with the plaintiff" compared to "…reached a risky compromise…" or "…reached a satisfactory compromise…", and also compare to "…barely reached…"). Honest editors remove as many modifiers as possible, keeping only those that bear their weight in meaning.

I don't know how much Negligence is a problem. The stories didn't stick with me. Hype was of greater interest. Who remembers (from 1989) Cold Fusion? Lots of hype. Eventually, a total fizzle. The first story in the "Hype" chapter of Science Fictions tells of a supposed bacterium that used arsenic instead of phosphorus in its biochemistry. It turned out to be a story of contamination in the lab, not novel biochem in the field. It seems to be accepted today for a scientist with any kind of result to issue a press release long before submitting an article for peer review and publication. Perhaps the Snake Oil guy above would fit better alongside this paragraph!

But, seriously, what, oh what, can be done about it? Dr. Ritchie knows science from the inside. His last two chapters plus the Epilogue have suggestions that look workable to me. They primarily deal with incentives. Some of the current incentives seem designed to reward bad science. The simplest example is the Publish or Perish atmosphere in which tenure is only to be had by publishing at a superhuman level. This rewards "salami slicing", in which work that has several results will be published as several small papers rather than one that links them all together.

A family proverb is the "Moses method": To change the system, get everyone into the wilderness and wait 40 years for the older generation to die off. I hope the suggestions of Dr. Ritchie can make great inroads into the mess we are presently in, a lot quicker than 40 years.

Special bonus feature:

I sometimes tell scientists I know my suggestion for getting lots of good science done:

• Do a sketchy experiment to test an outlandish hypothesis. Drag it out until you get some kind of publishable result.
• Publish, with much fanfare.
• Based on the publication, trawl for funding to do more experiments to "confirm" your finding.
• Publish again; two papers if possible. Many more, if you can.
• Produce plenty of fanfare, including "stick in your eye" statements to rile up the establishment.
• Repeat as much as possible or until you can't get more funding.
• Some angered scientists will publish rebuttals. Some may even try to replicate your result.
• Answer every rebuttal, vociferously, in multiple venues if possible.
• Publish a "synthesis" of the entire matter. Be sure to cite all your prior work. Your "citation index" gets you noticed more.

This will get a lot of scientists to work their butts off to prove you wrong. One side effect is likely to be some unexpected, good science. Then, if you want to retain a shred of reputation, publish again, "de-biasing" your results, with more modest conclusions and a bit of mea culpa about the "little bit of overreach" in which you formerly indulged.

And now, back to our regularly scheduled program. It's a great book!

Today's spiders, Russian style

 kw: blogs, blogging, spider scanning

I posted a book review a few hours ago. I just looked at the stats and saw a big spike. Here we see the national "interest" over the past 24 hours (as of 9pm EDT):

Eight arms and nine brains

 kw: book reviews, nonfiction, octopuses, intelligence, philosophy

After reading (and reviewing) Metazoa by Peter Godfrey-Smith, I just had to get his earlier book Other Minds: The Octopus, the Sea, and the Deep Origins of Consciousness.

The author has spent much time at a place near Australia called Octopolis, where as many as a dozen or more octopuses, which are usually solitary, live in rather close association. Near the end of the book he muses about how Octopolis came to be, and mentions in a glancing way a few other reports of these animals living near one another. He has also spent much time "visiting" giant cuttlefish (up to a meter in size) that frequent other areas, also near Australia. These experiences inform his thoughts about "What is it like to be an octopus" and about consciousness in general.

Theories of why we have large brains and consciousness tend to revolve around our sociability. At least among apes, brain size correlates with social environment. So why do octopuses have such large brains? Currently, only at Octopolis are they seen to associate socially, although much of that is fighting. I suppose society has to start somewhere.

The book opens with a quote from William James, which I reproduce here in full:

The demand for continuity has, over large tracts of science, proved itself to possess true prophetic power. We ought therefore ourselves sincerely to try every possible mode of conceiving the dawn of consciousness so that it may not appear equivalent to the irruption into the universe of a new nature, not-existent until then. —William James, The Principles of Psychology, 1890

This exactly accords with my understanding. René Descartes thought that only humans were conscious, leaving him free to unflinchingly torture a dog, claiming the animal's screams were robotic utterances. I titled my review of Metazoa "Is 1% of a mind still a mind?" Let's see if we can figure what proportion of a mind as we know it might reside in the common octopus, Octopus vulgaris.

The nervous system of the common octopus includes half a billion neurons. However, 60% of these reside in eight sub-brains, one near the base of each arm, and the other 40% are in a torus (a donut-shaped mass) that surrounds the esophagus. Thus, the main brain has about 200 million neurons, while each arm's sub-brain has about 37.5 million. We should probably consider the main torus as equivalent to the cortex in vertebrate brains, and the 8 sub-brains, taken together, as equivalent to the cerebellum, which runs the body and, so far as we know, does not contribute to consciousness. The size of the main torus is equivalent to the entire brain of a Norway rat. But if we consider the octopus torus-brain equivalent to the vertebrate cortex, it more closely matches that of an average house cat (250 million) or a less-familiar animal, the rock hyrax (200 million).

Octopuses are mollusks. Of mollusks, octopuses, squids, cuttlefish, and scarcer animals such as the nautilus and sepiolid ("Dumbo octopus") make up the order of cephalopods, which means "head-foot". Among mollusks, all the brains are found among the cephalopods. The largest snails and clams (members of two other orders of mollusks) have brains containing ten to twenty thousand neurons, not millions.

What is the size of the human cortex? We've all heard that we have "about 100 billion nerve cells". The actual number is close to 85 billion, but only 16 billion make up the cortex, where we think consciousness is created, the feeling of what it is to "be a person." Most of the rest are in the cerebellum, which runs the mechanics of our body. If there is a linear relationship at work here, 16÷0.5 = 32: our cortex is 32 times as large as that of an octopus. Does that mean we are 32 times as conscious? Maybe so! Or perhaps self-awareness (which may or may not be the same thing) is a less-than-linear function of brain size, such as a square root. Then we could say we are about 5.5 times as self-aware as an octopus. 

Let's speculate for a moment what it might "be like" to be a honeybee, which has a million neurons. Estimating that half are involved in its sense of self, the little bee may be 1/32,000th as conscious as we are, or perhaps as much as 1/180th. Whatever they think about, it's sure to be a lot slower, and less profound. Beyond that I dare not tread!

Regardless, it is pretty clear from the stories and analyses by Dr. Godfrey-Smith that octopuses are quite self-aware. He tells one story that touched me, of a SCUBA diver who saw an octopus in its den and reached his hand toward it. The octopus reached back and grasped his hand, then came out of the den and began "walking" (they do this on two or four of their arms, with the others coiled or held upward), leading the man on a "tour" of the area that lasted ten minutes. That incident may be the closest a person and an octopus have come to communication on any meaningful level. Far too frequently, the animals are brought into a lab and "tested" with mazes or food choices and so forth. Frequently, they express their frustration by squirting water on the experimenters. Perhaps they prefer not to be treated like the village idiot.

A side thought just occurred to me. The brains of birds and mammals are differently arranged, and the neurons of birds seem to be more efficiently packed and connected. Thus an African gray parrot, with a walnut-sized brain, nonetheless has about 2.5 billion neurons, and can learn to speak and hold conversations with humans. Rather simple conversations, true, but none of us has learned even a single word of "parrot".

As we ponder now we might communicate with residents of a different planet around some other star, we would do well to consider how we can better communicate with parrots, octopuses, and other critters among which we live. 

Do octopuses have a visual language? Their skin is akin to a video screen, and sometimes seems to reflect their thinking. Perhaps much of the time their skin patterns are akin to a visual EEG! I wonder what is on this one's mind.

I really like this author's writing. I've riffed on what he wrote more than reported about it. The best authors stimulate thought!