A Crack in Creation; Jennifer A. Doudna, Samuel H. Sternberg; 2018; Mariner Books;246 pgs; Notes, index
If you examine the book cover, you will notice that some of the letters are in yellow, the others in white. The letters in yellow are A, C, T, and G… the first letters of the four amino acids that make up DNA. The author's last name is "Dou DNA", but that is just a coincidence. So this is a book about biology. I know a lot more about physics and computing than I do about biology, but oddly, that knowledge was quite helpful. My thanks to Blythe Nilson who corrected some ugly errors in my first draft of this piece.
CRISPR, the underlying technology here, is as important to our future as nuclear power. So you should know something about it. You don't need to know how it works, just what it might be able to do.
Physics and chemistry are closely related. Biology is chemical. And DNA biology is also very computational. DNA's ACGT structure is binary (i.e. base 2) code. You might say "Then why are there four letters, rather than two?" Because nature needed an easy way to copy DNA. The DNA chain is made up of paired letters: A always pairs with T, and G with C (each pairing is a bit). This allows the DNA to be cut in two long pieces, and then each piece is reassembled into a complete DNA chain by re-pairing (or repairing) the chain by adding the appropriate matching letter. One copy of DNA becomes two. This is the chemical basis for reproduction.
Each triplet of these letters code for a particular amino acid, and the sequence of DNA dictates how these amino acids will be built into proteins. Proteins are the true stuff of life.
As I read this book, I was struck by the number of times I could see software analogies in the chemistry. In computing, data and code are two sides of the same coin. The same is true for the molecules of life. They are hardware (a fixed bunch of atoms arranged just so) and software (do this, then do that) all packaged up into a single object.
Enter CRISPR (an acronym for Clustered, Regularly Interspaced, Short Palindromic Repeats), a new technology that is both enormously promising and bloody scary at the same time. CRISPR is not a great name. Even knowing what the letters stand for tells you nothing about what is actually is. The one chapter in the book that describes the CRISPR details is challenging. It is full of acronyms and strange words, making it hard to follow. The rest of the book is much less challenging.
CRISPR was initially just an observation that part of the DNA of the bacteria consists of Repeating Clusters of DNA. The repeated bits read the same forward as backward (Palindromic), were quite Short, and were always the same distance apart (Regularly Interspaced). It soon became apparent that these genes were associated with the bacteria's immune system. What a bacteria fears is a phage (short for bacteriophage), a virus that attacks bacteria. The CRISPR genes contain a length of genetic material in the Regularly Interspaced part. These bits of RNA are actually viral RNA that was taken from a phage in the past, and is now used as a pattern matching template to recognize viral DNA. Associated with CRISPR is an enzyme that, once activated, destroys its DNA/RNA target… in this case, the phage.
Aside: RNA and DNA are chemically very similar and sometimes serve similar purposes. RNA is a single stranded molecule, and DNA is double stranded. RNA uses uracil (U) instead of thymine (T) in its code.
Once the enzyme is released, it zooms down the DNA chain at a rate of 300,000 nucleotides per second, carving it up into amino acid junk! That is fast!
Scientists realized that this mechanism could be used to find, change, and/or disable genes with amazing accuracy. For a software guy like me, I see many analogies to computer code. Each segment of phage DNA/RNA in CRISPR is used as template to find an invading phage and kill it. This is like a parameter to a subroutine or, if you prefer, a kind of microscopic Google search using the DNA segment as the search target. This is hardly surprising since, at its core, genes are a series of zeros and ones that are used to make you and me. In other words, it is all software and software is easy to change (hence the "soft" part).
CRISPR technology has enormous potential for both good and evil. It might be used to cure horrible genetic diseases such Huntingtons, or it could be used to create supermen. It can be used to hunt down one gene with one wrong letter, tag that gene for repair, and then get the mechanisms of body to repair it. Sickle Cell Anemia is one such disease.
When writing software, one generally designs top-down and builds bottom-up. In the software of real life, there is no design, only what works. Software starts with building tools; and then uses those tools to build larger software structures which, in turn are used as tools to build even more complex structures and procedures. And with all these tools lying around, there often comes a realization that the existing tools could be easily repurposed to do something that previously seemed out of reach. I have experienced this many times in my software career. Bio-researchers are discovering all these tools lying around in the cell and are closing in on learning how to use them.
CRISPR opens many doors, some of which we should probably keep locked. Curing an awful disease is obviously a good thing. Changing human germ cells is much scarier. Changes to human germ cells means that the change is passed on to offspring. And that smacks of eugenics, NAZI supermen, designer babies etc., and it raises many ethical questions.
The closing chapters of the book focus on the future and the inherent advantages and dangers that CRISPR embodies.
Biotech like CRISPR gives us god-like powers to manipulate life. Advances in biotech and computing make it possible for us to wield those powers. I do not think it an exaggeration to say that CRISPR is the biotech equivalent of the Manhattan Project. I hope mankind learns to use it wisely, because use it we will.
This is a great book. Interesting details; not overly technical; and a Perry Mason who-dun-it (or more accurately, what-dun-it). First, the crime scene is set; then the possible perps are introduced; followed by the gathering of evidence, a trial, and a courtroom confession, with a somewhat "Orient Express" flavor.
The mystery is "Where did the moon come from?" This is called selenogony. Selene, the moon, is the daughter of Theia in Greek mythology. Before I tuck into my overview, a few fun facts.
George Howard Darwin was an eminent scientist and a great thinker on moon questions. With pen and paper, he did much of the basic number crunching on the moon and the gravitational dynamics that affect it and us. His contributions are overshadowed by those of his famous father Charles. Mind you, he was big on eugenics, so there is that too. Like his dad, he was knighted. Charles Darwin changed many people's thinking from catrastophism (stuff like the Flood) to gradualism (the Grand Canyon was carved slowly over thousands of years). The new "thing" was slow change over many years.
Many will recall the crashing of comet Shoemaker-Levi 9 into Jupiter (an excellent example of catastrophism at work). In addition to discovering the comet, Shoemaker, a geologist by training, did groundbreaking research into cratering (pun intended). He is the first, and still only, person to be buried on the moon.
Another fun fact: It is not possible to fire a bullet into orbit from the surface of the Earth. It will either go on forever, or fall back to Earth. This is true for any planet.
The three possible perps for the origin of the moon were: Fission, Capture, and Co-Accretion.
Fission: The early hot Earth was spinning very fast and flung the moon off (some thought, leaving the Pacific Ocean "hole" behind);
Capture: The moon accreted elsewhere; wandered into Earth's orbit and was ultimately captured into orbit around the Earth;
Co-Accretion: The two planets (the moon is a planet in all but name) formed together out of one accretion disk of material. An accretion disk is a collection of material orbiting something. Over time, gravity flattens the material into a disk shape and, over more time, objects in the disk stick together until larger and larger bodies are formed. Typically one body, a planet, is formed by vacuuming up everything within a certain distance of its orbit. In this example, two bodies accreted.
A fourth option was rarely discussed because it smacked of catastophism, which science had decided they did not like. That option was a huge impact (or Splat). More on this later.
Each theory has its problems. The resolution came after the last Apollo mission.
Aside: Apollo's moon data and samples were the only scientifically useful results that have been produced by manned space travel. The ISS is a boondoggle.
The same moon is visible to everyone on the planet, every where and every night. It was the standard clock for thousands of years. As a clock, it had a problem, of course. The lunar month was not an even divisor of the solar year. This made the seasons crawl about in a most unsettling way.
The fact that we live on a sphere can be determined in several easy ways. The most dramatic is to witness is lunar eclipse. You can plainly see the circular shadow of the Earth on the moon. But to many, the moon was flat, just like the Earth. Aristarchus of Samos was the first to suggest that the Earth both revolved and rotated.
A relevant short joke: "The only thing flat Earthers have to fear is sphere itself."
Kepler struggled with the then-ruling model of the solar system, which consisted of circles within circles, with the Earth at the center. Copernicus suggested that the Sun was at the center. Kepler tried many times to make circles work. Circles were perfect; and god was perfect; so it was a nice fit. Kepler tried circles with an offset center. His model was close. Only 8 minutes of arc off (the size of a quarter at 36 feet). But that 8 minutes meant he was wrong! He persevered until he finally broke with circles and invoked the elipse. Ta da! Kepler's three laws of planetary motion.
And it was about this time that Galileo turned his telescope on the moon… that pesky, mottled, luminous body in the sky. What he saw stunned everyone… shadows crawling across the moon's surface as it went through its 28 Earth-day day. The moon was a sphere too! The moon had mountains. Of course, he next turned his telescope on Jupiter and revealed something even more shocking: that stars (actually moons) were orbiting Jupiter… which was impossible because everything went around the Earth. Enter the Spanish Inquisition, but that is another story.
When George Darwin came along to ask moon origin questions, Newton's gravity was well understood. Especially when it came to where the action is: Tides and tidal forces.
A word about tides: Sailors have tracked the tides forever. They understood that there were three overlapping cycles: The moon revolving around the Earth; the Earth's rotation; and the position of the Sun. There are two high tides every day. This implies two bulges in the planet's oceans. The ocean nearest the moon is attracted more strongly than an ocean on the other side of the world, and so it bulges. The Earth itself is attracted to the moon, and falls toward it all the time. The Earth is attracted more than the ocean furthest from the moon, and this creates a bulge on the opposite side of the Earth. Gravity falls off with the square of the distance; tides fall off with the cube.
Tides (more accurately, tidal forces) are where the action is. Tides can squeeze and compress moons until they are molten. Tides explain why the moon only shows one face to the Earth. Tides can rob angular momentum from one body and transfer it to another. Without tidal forces, the solar system would be boring. In fact, it is tides that cause the moon to slowly move away from the Earth. Darwin knew this, but did not know how old the Earth was. If he had known, he could have used it to calculate when the moon was very close to the Earth, and perhaps divine its origin.
I mentioned Shoemaker and his craters. In modern times, we know of many craters on Earth. Some are volcanic and some were caused by impacts. The moon was covered in craters and the speculation was that they were volcanic. Why? Because impactors come in at many different angles and you would expect to see the crater smeared out in a line (think of a golf ball hitting a sand trap at an oblique angle). Shoemaker showed this was wrong. When an asteroid hits the moon or the Earth, it is travelling at orbital speeds… in the 20,000 mph neck of the woods. Pound for pound, they carry more energy than TNT. When the impact takes place, it is best modeled by a huge explosion. This is why impact craters are round and not smeared in one direction. Simply counting craters (along with some interesting math) gave an initial estimate of the age of the moon to be close to that of the Earth.
We are getting close to the end of the story. When the astronauts returned to the Earth, they brought hundreds of pounds of moon rock, including one that appeared green on the moon. At this point, the arguments get geologically quite detailed. They involve things like the behavior of elements at pressures of 250,000 atmospheres and temperatures of 8,000 Celsius. Suffice to say that under certain temperatures and pressures, some elements are iron-loving and not rock-loving. Under those conditions, they would follow iron into the core of the planet. Under other conditions, those same elements are rock-loving and would stay near the surface. Any theory about the moons origin must explain the various densities of elements at different levels.
It was at this time that the crazy impactor theory re-arose. It had some holes in it, but they could be resolved with more research.
The Fission theory was always wonky because no one could come up with a plausible story that could explain the enormous energies involved. The Earth-Moon system is essentially a double-planet and is unique in the solar system. If fission could happen, it should happen more than once.
The math of Co-Accretion suggests that the Earth should have swallowed the moon before it ever got moon-sized.
And Capture seemed like an impossibly unlikely bank shot in pool. Scientists do not like such "just-so" stories.
But a major impact solved all these problems (with a few open questions). At a conference (the trial, in my Perry Mason analogy) held in Kona, Hawaii, something very rare took place. Something actually happened. Conferences of this ilk are like political debates. Everyone knows what everyone else thinks; they hear what the others think; they say what they think; no one changes their mind; and they all go home. Not this time. The Impactor theory was re-opened as a possibility, and a score card was created for the four theories, the last being a kind of "Orient Express" conspiracy of Co-Accretion and Capture… AKA the Impactor theory. And Impact won! Scientists changed there minds right there and then. The role of Perry Mason was filled by moon scientist William Hartmann.
I knew the who the "perp" was when I bought the book. I grew up during Apollo. The book is a fascinating who-dun-it with whacko characters who discover half the story, and seers that broke the prejudice mold and created a scientific consensus. Well written with just enough hard science so you can follow the arguments.
I wrote an essay about 23.4 degrees (http://www.thegodcon.com/the-god-con/234-more-comments-from-a-space-nerd). Most things in the solar system are spinning, and most of that spinning is at right angles to the plane of the thing's orbit. But not Earth. It is spinning at 23.4 degrees off that angle, and a good thing too. Without it, no seasons on Earth, and no us. That wonky angle is evidence of an off-center impact with Earth of a planet about the size of Mars. A pool shot with English on it. It blew off a huge chunk of the Earth's iron-poor mantle, which ultimately coalesced into our moon; and it knocked the Earth off-axis. This explains why the moon is so iron poor, and why moon rocks and very old Earth rocks are the same age and composition. Tidal forces spread the shattered Earth's crust into a disk much like Saturn's; which quickly glommed into our moon.
Thus, we live on what might be quite rare in the galaxy: a double planet. The moon and the Earth both rotate about a common center of gravity which is about three Earth diameters away from the center of the Earth.
The impactor has appropriately been dubbed Theia, mother of the moon.
Lee Moller is a life-long skeptic and atheist and the author of The God Con.