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!).