Teeny-tiny deities

 kw: book reviews, nonfiction, genetics, recombinant dna, gene editing, ethics, morality

When I saw the title of As Gods: A Moral History of the Genetic Age, by Matthew Cobb, I knew I was in for a bit of preachiness. I was right, but it was worth it. Dr. Cobb has been among those in the forefront of genetic research for several decades. His perspective is unique. His moral perspective is also nearly unique, as he reports. Few can keep their integrity: As is usual with us faulty humans, when something gets big, really big, you can ferret out nearly every motive by keeping in mind, "Follow the money." There's enough potential money involved that whole national political attitudes have been shifted, repeatedly. I am politically unwise, so I'll leave it to you to read the gory details; I'll look at the technologies he presents us.

The book traces the history of genetic modification, including the dreams of those who, before the ink was dry on Watson and Crick's publication of the structure of DNA, began to opine rapturously about "rewriting the code of life". The predictions of "what we can do with DNA" exceed even the rhapsodies of those promoting "artificial intelligence". I see these two realms of technology running in parallel, a neck-and-neck race for general godhood on both fronts.

Let's look at the current situation first. The present culmination of all the technologies called "genetic editing" is the precise removal and replacement of a single nucleotide, an advance called Base Editing. It's a step beyond the more familiar CRISPR (more below). Versions of this called Prime Editing and Double-Prime Editing are being worked out at present. These technologies still need to go through a number of medical and regulatory hoops before they can be used for therapies, but they are the most promising to date.

CRISPR, when it appeared a decade ago, and garnered a Nobel Prize for Drs Jennifer Doudna and Emmanuelle Charpentier in 2020, was called "DNA scissors". I describe it a little more here. Once the CRISPR agent latches onto DNA, a CAS protein (CAS9 is best known) cuts both strands, and related molecules add "new stuff" at the break and the knit it back together. In more recent years it has been found that the agent isn't as specific as was first thought, and that multiple trials are often needed to get the result you were after. That makes it too risky to use for editing the human germline (the sex cells that turn into babies). Base and Prime Editing methods need a great deal more research and testing to make sure they are as reliable as we need.

However, these targeted mechanisms are a great deal better than older methods, outlined in the book, including something called TALEN, which I liken to a moderately-well-aimed axe. A TALEN needs less accessory machinery than CRISPR and its descendants, because the aim is to remove the "bad half" of a DNA double strand, and let cellular machinery patch the break with a copy of the opposite, "good" side.

Let us consider, though, that methods such as TALEN and earlier tools are not totally obsolete. A proverb of mine (from the Computer Science arena) is, "Nothing is obsolete if it does something you want done." Nature typically takes the "If it isn't broke, don't fix it" approach; our bodies are full of remnants of older structures that work well enough that evolution hasn't removed or replaced them. Think of the appendix; its function has been largely superseded by the spleen, but is still does a couple of immunological functions well enough that we still have it. It is worthwhile keeping, even though we can live without it (mine is gone, 20 years past). Other animals with a less-developed spleen have a much larger appendix. Irony personified: "appendix" means "added on" or even "useless". It isn't.

"Recombinant DNA" is now considered old hat. The technology is more than forty years old. Millions of diabetics are alive because nearly all the insulin they need is produced by this technology. Before recombinant insulin was economical, an eye doctor prescribed insulin drops for my eye, to heal an injury. It was pork insulin, and I was allergic to it; I almost lost the eye. This is the real "Frankenstein" method, where DNA from one organism is spliced into DNA from another. 

Every time a new genetic technology was developed, it was both hyped and decried. Purple promises abounded in medical literature and the popular press, and accusations of "acting like God" abounded right alongside them. On four occasions, lovingly detailed by our author, the researchers have come together and slowed things down. Though they have never called for a moratorium (the "m" word, to many of the author's colleagues), perhaps at least temporary moratoria ought to have been urged. The researchers may not have gone far enough, but the fact that they went as far as they did, and four times, indicates the moral quandary in which they found themselves. 

One side aspect of CRISPR (I think  I have this right) is the Gene Drive, which produces a kind of non-Mendelian inheritance that can drive a species to extinction, either by eliminating all the males or making them all sterile. The mechanics of XY chromosome systems makes it easier to target males. The appearance of this technology led to the closest thing to a moratorium, but eventually, this did not come about. As it happens, a Gene Drive isn't the magic bullet. Limited tests had some early success followed by reduced effectiveness of the Drive. It isn't 100% effective (is anything?). Thus, there are a few survivors. They sire a population that isn't affected by the Gene Drive, and pretty soon the pest (such as a mosquito) you were trying to eradicate returns in a more resistant form. But suppose you did drive a malaria-bearing mosquito species to extinction, worldwide: How likely is it that another species will take its place? Will the replacement be better, or perhaps worse?

If a Gene Drive were developed that affected the human species, then what? There are some folks, often called "environmental wackos", who think the Earth is better off without humans. If a few of them get their hands on a few million dollars, what's to stop them from producing, and then releasing, such an agent? Could its progress be stopped? "Playing God" works both ways.

I find I haven't said much about AI, though I intended to. Similar noise abounds around AI as a doomsday technology. But I think I don't need to say more at this point. Mark Twain wrote, "The reports of my death are greatly exaggerated." So are the predictions of imminent human extinction by DNA or by AI, and also the utopian fantasies regarding both.

A quote near the end of the book sums up a lot of this very well, as told to the author by Sheila Jasanoff:

I think that the fears, the nightmares, serve their own purpose. They are prods to make people think harder about the things that can go wrong. If the 'hope people' are the warriors, then the 'fear people' are the worriers. I think we might need both of them in society, to keep the one calibrating the other, and in some kind of balance.

Although there are those who really wish to exercise godlike powers, it's ironic that the best anyone can so far do is make tiny changes—one base here, half a dozen there—to a DNA library with several billion. A real God, for those who believe in Him, made all of it, all at once.

__________________

A bit off a quibble as a postscript. A chapter titled "Weapons" describes several kinds of what are called "gain of function" research, and mentions several viruses, including a variant of Smallpox, that were made many times more virulent than the "natural" product. But the author goes out of his way to say that the SARS-Cov-2 virus that causes COVID-19 was not produced this way, stating "there is no evidence of this". He has believed a lie. I do not attribute falsehood to Dr. Cobb, but naivety and foolishness. A very few facts:

• Dr. Fauci is known to have responded to a Federal moratorium on gain-of-function research by going around the regulations to funnel several million dollars to the Wuhan Institute of Virology to carry out such research on coronaviruses. (This is usually called money laundering)
• He and others said for a long time that the virus came from a bat bought at a "wet market", and later that it came from a pangolin. The Wuhan wet market does not have either bats or pangolins for sale, not now, and not in 2019. (Yes, I have sources in China)
• He has more recently said that there may have been a "lab leak".
• One of the doctors at the Wuhan lab published several articles, including in Nature, about gain-of-function research on coronaviruses collected from bats a few years previously.
• Thousands of Wuhan residents took vacations in the US and other Western countries in mid-to-late 2019, before the Chinese government announced anything about a new respiratory disease erupting in the Wuhan area. This "pulse" of Wuhan-resident vacationers was unusual. It was followed by the first "pulse" of COVID-19 cases in the West.

I conclude that there was a lot more involved than a "leak" from the Wuhan lab. It is a near certainty that the first genetically-engineered bioweapon has already been used. In folklore, the "bad gods" such as Loki always seem to get their licks in first, and are just barely overcome. Human gods are no better, and typically far worse.

Singapore Spider ramps it up

 kw: blogs, blogging, spider scanning

Nine days ago I noted a new player in the spider game, Singapore. Today I see they are still at it:

For at least the past week, and probably going back 10-11 days, more than 1,000 hits from Singapore have occurred daily. I wonder if others have noted this.

Singapore is so small its bright blue dot doesn't even show on the map above.

Pestiferousness

 kw: book reviews, nonfiction, science, sociology, pests

Smack in the middle of Pennsylvania, about a half-hour drive from Penn State University, we find Penn's Cave and Wildlife Park. Our whole church had an outing there some years ago, and on the fence of the wildlife park I saw this sign. It raises the point: when a bear and a human find themselves in close proximity, who is the trespasser?

One point made in Pests: How Humans Create Animal Villains by Bethany Brookshire is that humans are the ultimate trespassers. When the bear is "in the woods", supposedly a "natural" setting, of course the person is in the bear's territory. When the bear is enjoying your swimming pool, though, take a moment to consider: if "your" yard and house were "developed" just a couple of years ago, that bear's favorite scratching tree might have been removed to make room to install the swimming pool. A quarter acre or more of forest may have been removed to plant grass for the yard. What else used to live there with the bear?

Pests is not about insects or disease or anything most of us first think of when we hear the word "pest". It is about vertebrates that are called "pests" by some significant number of humans, somewhere. The word "pest" comes from Latin pestis, meaning Plague or pestilence, plus several other meanings including "curse". In the opening chapter the author curses, frequently and eloquently, about a squirrel that destroys her tomatoes, every year without fail. She even tried chicken wire, but the squirrel could reach through, and cherry tomatoes fit through. Chicken wire works for us; we fence far enough from the plants that squirrel limbs aren't long enough to reach.

So, the bailiwick of the book is mammals, from mice to elephants; birds such as pigeons; and reptiles such as snakes. In particular, Burmese pythons in Florida have cross bred with native boas/pythons to produce offspring that are much larger; big enough to tackle humans. Most of us find ourselves pestered by more prosaic critters: mice, voles, squirrels, or rabbits, perhaps rats.

The single biggest problem is the huge range of attitudes about any animal that might be called a pest. For example, we know deer live near our neighborhood, in a few loosely-connected patches of forest totaling 30 acres, and there are forested areas of similar size scattered all through the surrounding several square miles. When we have apples drop in the fall, we'll sometimes see where a deer or two bedded down to munch fallen apples in a protected corner near the tree. We haven't caught any in the act (yet). My wife doesn't like deer that get into the yard, while I am more neutral. A few neighbors try to feed the deer, while others would rather shoot them, except there is no hunting allowed in residential areas even in deer season. 

Similar ranges of attitude exist in my neighborhood for the local squirrels, foxes, raccoons, and hawks. I've seen a Cooper's Hawk land on a squirrel not ten feet from me and flap away with it to feed her nestlings (Cooper's Hawks are mainly bird hawks, but they're not too particular). My wife wishes the hawk would go after the rest of the squirrels in our yard.

Slide halfway around the planet to Kenya. A hungry elephant can consume all of a poor farmer's crop overnight. While it is barely possible to build a fence that elephants can't destroy, it would cost more than what an entire Kenyan town could afford. The author reports that combinations of electrified wires and bees, along with other measures, discourages most elephants. In Kenya, "coexistence" isn't a cool slogan on a bumper sticker, spelled out in bowdlerized religious symbols, it is a necessary wildlife management skill.

Stories abound, but the author's focus is on attitudes. Those who can afford it like to live in more "natural" settings, but then far too many of us get perturbed when "nature" pays a visit. Leave a door ajar, and a sparrow might get inside (dodging a Cooper's Hawk perhaps): you could spend a couple of hours trying to get the terrified bird back outside. Meanwhile, it will have poo'd and peed in a few places; birds don't wait to find a toilet to "drop it". Is that bird a pest? Attitude…

The author points a finger at the Western/Christian cultural undercurrent of "dominion", based on Genesis 1:28. Less than half of English translations of The Bible use "dominion" to translate the Hebrew word, while a larger number use "rule", which is more accurate. A few use "take charge". By domesticating many animals and penning out the rest, the human race has definitely set itself up to "rule" nature. "Pests" are those animals that remind us our rule isn't perfect; we aren't totally sovereign. A little humility is a useful antidote to our hubris.

A big issue is ignorance. There was a joke when I was a child about a city kid on a field trip seeing a pile of discarded milk bottles, who said, "A cow's nest!" That's only slightly exaggerated. Every day children eat eggs but have never seen a chicken, let alone reached under a hen (risking a peck) to feel the warm eggs. Perhaps suburban houses and yards should come with a "Former Owners' Manual", describing the lives of the rabbits, squirrels, voles, mice, raccoons, foxes, perhaps even deer or coyotes (or even pumas) that were displaced to clear the land and build the house. The Manual should include strategies for coping with former residents and their descendants that may still make use of the place. Lacking that, reading this book is a good way to begin to learn.

Singapore Spider!

 kw: blogs, blogging, spider scanning

Over the years I've seen Singapore show up in my stats a time or two. This morning, getting ready to write a review, I noticed a big bump: almost 1,000 hits so far today and 400 yesterday. An ordinary day yields about 50.

This shows 1,326 from Singapore, probably all in the past two days, and 206 from Russia, which has been the source of most spider scanning for years. I suppose it's possible that someone in Russia is using a proxy server in Singapore.

Other stats on the page show that all of the Singapore hits were on Android using Safari. An interesting combination.

I hope the searcher(s) found something worth reading.

Planets outnumber stars

 kw: book reviews, nonfiction, astronomy, astrometry, exoplanets

We have so far detected about 5,000 exoplanets (planets of other stars). Since the first confirmed detection in January 1992, astronomers have developed five methods to detect exoplanets, over most of the range of plausible sizes, and quite a range of orbital periods. That's enough to learn a few things.

In Worlds Without End: Exoplanets, Habitability, and the Future of Humanity, author Chris Impey describes the most common type of planet: Diameter larger than Earth but smaller then Neptune, in an orbit on the warm side of the habitability zone, or inside of it. These are called "super-Earths" and "mini-Neptunes", with the dividing line about twice the diameter of Earth. Neptune weighs just over 17 times as much as Earth, so variations in density increase the range of masses from about 17:1 to perhaps 25:1 (or 20:0.8).

The technology of exoplanet discovery makes up the first of four sections of the book. The other three sections consider habitability, how we might search for life on exoplanets, and the possibilities for us or our machines to visit them.

I hadn't known that there are five ways to detect an exoplanet. In particular, I didn't know that astrometry can be used for that. Astrometry means "star measurement", and in this application, it refers to precise measurements of a star's location or position. While quite a number of exoplanets have been detected by the doppler shift in stellar spectra, using telescopes on Earth's surface, the use of a star's position is many times more delicate, and can only be done from telescopes in space. A bit of figuration will illustrate the difference.

Considering the mass of Earth as a basis, and calling it 1, the mass of Jupiter is 317.8 and that of the Sun is 332,946. The Sun's diameter is 1,392,000 km, the average distance of Earth from the Sun is 149.6 million km, and the average distance between Jupiter and the Sun is 778.3 million km. The orbital velocity of Earth is 29.78 km/sec = 107,200 km/hr and that of Jupiter is 13.1 km/sec = 47,160 km/hr.

The doppler shift caused by the Sun's reaction to the planetary motions is calculated by mass and distance ratios. Thus, for Jupiter, the mass ratio is 317.8/332,946 = 0.000 954 5; so the Sun's velocity is that times 13.1 km/sec = 0.0125 km/sec = 12.5 m/s. It takes a very precise spectroscope to measure the doppler shift caused by this motion, but it has now been done many times. 

The closer Jupiter is to the Sun, the faster it goes, and therefore the faster the Sun goes. Let's put Jupiter in Earth's orbit and check the consequences: 0.000 954 5 x 29.78 = 0.0284 or 28.4 m/s. This is more than twice the earlier figure. This is much easier to detect, and explains why the first exoplanets to be detected were "hot Jupiters" that orbited very close to their host stars. Also, doppler shift is the same from any distance, as long as you can gather enough light to get a good and precise spectrum.

Now we consider hyper-precision astrometry. The diffraction limit of the Hubble Space Telescope in visible wavelengths is around 0.02 milli-arc-seconds (5.5 billionths of a degree). It would be the same for any space telescope of equal size. However, even though star images are enlarged by diffraction to that degree, the position of a star can be measured with greater precision than this. One must magnify star images to cover many pixels of the detector, and the centroid of the star image can be calculated with great precision, in the range of millionths of an arc second (trillionths of a degree). The longer the exposure (the more photons captured), the more precisely this can be done, as the statistics of the "shot noise" of photon detection reduce the errors that would cause.

Specialized orbiting telescopes are being planned that can do this for a number of stars in a field of view. The positions of many stars would be measured again and again over long periods, looking for tiny shifts. How tiny?

For Jupiter again, when the planet moves from one side of its orbit to the other, it moves 1.56 billion km. The Sun moves 1.56 billion × 317.8 / 332,946 = 1.49 million km, or 1.07 times the Sun's diameter! However, this motion requires six years...starting at the right place.

How far away can we detect the shift? One millionth of an arc second has a tangent of 0.000 000 0159; dividing this into 1.49 million km yields 93.6 trillion km. That's almost ten light years (9.9). To reach a reasonable number of stars with this technique requires astrometric measurements with a relative precision from star to star of a ten millionth of an arc second, or smaller if possible. This takes big telescopes and long exposure times. But it has been done!

OK, that's a long discussion of two methods: Doppler Shift (the first method to work) and High Precision Astrometry (the most recent). To round out the methods, the third is the most prolific to date: the Transit method, which measures the little dip in brightness that occurs when a planet passes in front of a star. The fourth is Microlensing, for which stars are watched for brightening that occurs during the period (measured in days) that one passes in front of another and its gravity magnifies the star behind; a small extra glimmer signals that the star in front has a planet. The fifth is Direct Imaging, which works best for large planets farther from their host stars. Each method has a useful range of planetary size and orbital distance, which means we are getting a more and more complete overview of what is out there.

I will give rather short shrift to the latter three sections of the book. They are very interesting, but secondary to my interest in the subject. Only a small percentage of exoplanets so far detected are at a suitable distance from their host stars to have a chance of having liquid water at or near the surface. Thus, the discussion of habitability and life are more speculative. The author does bring up an interesting subject: Could the Earth be detected by any of these methods, from suitably placed stars in "nearby" space, the nearest few hundred light years? Very possibly!

The statistics of what we now know indicate something even more interesting: Nearly every star seems to have at least one planet, and wherever the viewpoint and associated method(s) are favorable we find a few planets, usually 3, 4 or 5. Precision timing of Transits is beginning to reap a harvest of added planets in many of the systems initially found using that method, for example. That means that there are more planets than stars, overall.

Furthermore, the Solar System has, so far discovered, 200 moons, most of them around Jupiter and Saturn. BUT! Although the surface temperature of satellites that distant from the Sun is far too cold to allow liquid water, the interiors of several larger satellites could hold a large liquid ocean, which could then host life. It may be that the greatest number of objects in the Universe that host living beings (microbes, at least) will prove to be satellites of large planets!

That in itself made the book worth reading.

Nonsense in , interestingness out

 kw: ai experiments, generated art, dall-e, nonsense processing

I read that an AI researcher made up a word, "crungus", and used it to prompt a generated art app. He reported that this yielded several pictures of ogre-like monsters. I decided to try the same "word" with DALL-E2. I ran it twice, with these results:

While the program primarily associates the prompt with food, it threw a human-ish character into each set of replies. Most of the foods have a crunchy look, like tempura. It is refreshing, however: no monsters for me.

I should mention that every time I run DALL-E2 I use a freshly-opened Incognito Chrome browser window. OpenAI has history of what I've been doing in its own database, but any cookies DALL-E2 may have dropped get erased when I close the browser.

I made up another nonsense word, "knorb", which yielded this:

It's a pity DELL-E2 doesn't have an "Explain" button, but if its neural net consists of many layers of millions of nodes, who wants to read through an "explanation" anyway? This word somehow triggered images related to tools and mechanical things. Next I chose a word made up by a comedian in a funny article about punctuation, "flabbergasterisk". Here the results were so surprising I ran it a second time:

The first set of returns produced more food. The second set also has a food theme, but I rather like the still life composition of the second one in the second set. As originally conceived, the flabbergasterisk looks like this:

To check DALL-E2's vocabulary, I picked three obscure, but genuine, words. The first was "Limerence":

Limerence is a psychological term defined as involuntary, intense, obsessive desire for another person, without sexual overtones. The three women pictured could be objects of desire, but at least one of the images is a bit suggestive in nature. I don't know what kind of bird is pictured at the left. The next real word was "Omnishambles":

Here the program is in uncharted territory. "Omni" means "everything" and "shambles" means to be in disorder, so the word means "disastrous disorder" (it's how I would describe the Biden Presidency). It isn't a geographical term. The final word is "Velleity":

"Velleity" is a mild wish or inclination without motivation; it doesn't lead to action. One could call it the "wishy" side of "wishy-washy". The flower pictures are nice, but are total non sequiturs. I am not sure how a near-empty jar of rolled oats relates to anything.

It has been a fun exercise.

Finishing on a downstroke

 kw: continuing reviews, story reviews, science fiction, fantasy, anthologies, world science fiction, dystopias, human extinction

Of the four stories remaining in The Best of World SF, Volume 2, edited by Lavie Tidhar, I skipped one, which happens to be a novella. The other three are not up to the standard of the earlier stories in the volume, but are of moderate interest.

"Between the Firmanents" by Neon Yang (Singapore). I got a page or two into this novella, realized it was going into hellish territory, and skipped out. It is fantasy, with no hint of the "science" of SF. The "gods" portrayed are as wicked and lascivious as the old Greek and Roman deities, or perhaps more so.

"Whale Snows Down" by Kim Bo-Young, translated by Sophie Bowman. Told from the viewpoint of deep-sea dwellers such as anglerfish and siphonophores (as this image, from NOAA), it consists mainly of ruminations and conversations among those dwellers regarding the sudden increase, oceans-wide, of "marine snow" (organic detritus from things that die at the surface or in shallower water). The denizens conclude that the humans have finally done themselves in. It's odd: whales are depicted as having gills. Possibly the translator mistranslated a word for "baleen". This is the best of these three.

"The Gardens of Babylon" by Hassan Blasim, translated by Jonathan Wright. This story and the one that follows circle back on themselves, in different ways. Both are fantasy, although somewhat technological fantasy. This one is slightly better written than the other.

"The Farctory" by K.A. Teryna, translated by Alex Shvartsman. "Farctory" is but one of several words that get an inserted letter or two ("cola just to keep the reader off balance. The other imagery follows suit.

The volume ends with a letdown, although there are a couple of interesting ideas here also. Overall, Best, V2 is well worth reading.

Idea stories, a baker's dozen

 kw: continuing reviews, story reviews, science fiction, fantasy, anthologies, world science fiction, utopias, dystopias, robots

Here I limn another thirteen of the stories in The Best of World SF, Volume 2, edited by Lavie Tidhar. It's something more than a third of the volume. As before, I skipped none, and enjoyed nearly all equally.

"To Set at Twilight in a Land of Reeds" by Natalia Theodoridou (Greece). Maintenance robots need maintenance also. I wonder why SF robots are so frequently emotional? 

"The Beast Has Died" by Bef (Mexico), translated by Brian Price. An alternate history, with TV and other technologies in the 1800's, and also a technology for scanning a brain to produce a simulation of a person.

"Twenty About Robots" by Alberto Chimal (Mexico), translated by Fionn Petch. This story is dedicated to the prior author. Each vignette is preceded by a binary number from 0 to 19 (00000 to 10011), but not in any order I could discern. The author stretches the limits of the robot genre. It's becoming clear that the editor loves robot stories.

"The Regression Test" by Wole Talabi (Nigeria). An advanced version of a Turing Test. An uploaded human mind, as it interacts with others, will naturally learn and evolve (in the non-biological sense). The test, by someone intimately familiar with the original person, is to detect a divergence into delusion. As I expected, there is a betrayal awaiting.

"Kakak" by William Tham Wai Liang (Malaysia). "Kakak" means "sister" in Malay. Another story rooted in emotional robots, but here the levels of emotionality vary more.

"Beyond These Stars Other Tribulations of Love" by Usman T. Malik (Pakistan). Caring for an ailing and increasingly demented mother… It's unclear how the protagonist thinks going on a starship (a NAFAL accelerator), with increasing time dilation as the trip proceeds, can help him care for his mother, even though a quantum-entanglement link has been set up between him and a robotic caregiver.

"A Flaw in the Works" by Julie Nováková (Czech Republic), translated by the author. Another story of emotion-laden robots, written for the centennial of R.U.R. by Karel Čapek; those robots had an emotional element also. These robots, in political exile, get the opportunity to make first contact.

"When We Die on Mars" by Cassandra Khaw (Malaysia). The gradual weeding out of more than 100 volunteers for a one-way trip to Mars, to a final twelve (see Note 1 below). This initial crew will establish a basis for others to follow. This seems a lot like Elon Musk's plan.

"The Mighty Slinger" by Tobias S. Buckell (Barbados) and Karen Lord (Grenada). Early in the story, the thought emerged, "Music as a political force". By the end: "Music as a weapon". Concepts that were obvious to the protest singers of the 60's, my musical mentors. If you've never heard "There, but for Fortune" sung by Joan Baez, go right now and do so! Oh, and the title...think David.

"Corialis" by T.L. Huchu (Zimbabwe). If you've seen The Andromeda Strain, or read the book, you may recall the extensive decontamination of the people before they can enter the super-clean laboratory. Preparing to adapt to the microbes of a new planet goes far beyond that (see Note 2 below). The protagonist realizes something more is needed for the humans and the life-forms of Corialis to become fully compatible.

"The Substance of Ideas" by Clelia Farris (Italy), translated by Rachel Cordasco. A different kind of alien world. Here, it seems that certain life-forms store ideas and memories in proteins, so that eating them… well, that's the "substance" the author is talking about. As usual, Murphy's Law intervenes.

"Sleeping Beauties" by Agnieszka Hałas (Poland). Suspended animation, we used to call it. Here it's used to exile an increasing range of "undesirables" to a prison planet. You gotta wonder, is it worth the expense? I could have done without the ending, a scene more sadistic than any I've encountered. This makes other dystopias seem tame.

"Waking Nydra" by Samit Basu (India). Another take on the phrase "sleeping beauty". The elaborate defenses of Nydra's "castle" make the story longer than it needed to be. The mindset of the caste system (the protagonist is clearly considered beneath contempt by the "heroine") underlies it all. A not-so-surprising betrayal rounds it out.

There are but four stories to go. Stay tuned.

Note 1: My first two years of college I was a chemistry major. My sophomore year I took Organic Chemistry, a three-quarter series of classes; the school year was in quarters, rather than semesters. The first day of class the professor (a rather recent PhD from Harvard) said the following:

This class will decide which of you will actually major in chemistry. The testing and work in each quarter will reduce your number by half. At the moment there are 150 of you…149…148 (as two students walked out). About fifteen will pass the final exam at the end of the third quarter.

He was right. I was one of those fifteen, finishing with an A-. I loved those courses.

Note 2: You may know the Central Dogma of Genetics, that DNA is copied to RNA, and the RNA is used to construct proteins, according to a standard coding table. There are 20 amino acids that make up all proteins (on Earth), and there are 64 3-unit codes (the units are A, C, G, and T in DNA, and instead of T, RNA has U), called codons. This allows for some redundancy in the translation, and protects against certain kinds of single-nucleotide mutations.

You probably don't know that there are (so far), 24 variations on the "standard" translation table. They can be considered minor variations; all the variations occur in one or more of 18 of the 64 "positions", leaving 46 untouched.

Some bacteria, most mitochondria, a few protozoa, and even a few small metazoans (multicellular animals) have variant coding schemes. That means the ribosomes, the protein-building "machines" that couple the RNA codons to their corresponding amino acids, are tailored to the appropriate table for the creature in question. It also means that the mitochondria in every cell of your body have the "vertebrate mitochondria" coding table, and some of the bacteria and archaea in your intestines have specific variations.

Now, consider, if we find life on another planet, will it be DNA/RNA/Protein based? Perhaps that is inevitable, but it's not certain. Even if so, will that planet's "standard" code translation table be the same as any of the Earthly ones? That is much less certain! Mathematically crossing 64 with 20, we find about 10⁷⁰ possible tables! If multiples are kept together, the number reduces to about 10⁴⁰. These numbers might be much higher; I may not have thought of everything when I did my bonehead permutation math.

The bottom line: I suspect it's impossible for aliens to eat us, or for us to eat them...or their food animals/plants/whatever. If we want to migrate people to an exoplanet, we'd probably do best to find a totally barren one and terraform it.

Ideas in abundance

 kw: book reviews, story reviews, science fiction, fantasy, anthologies, world science fiction, utopias, dystopias, robots, zombies

By page count I am a bit more than a third of the way through The Best of World SF, Volume 2, edited by Lavie Tidhar. I reviewed stories in the first volume in six posts, beginning with SF from everywhere, almost a year ago. As with that volume, I'll review story by story, 12 in this post, focusing on new ideas.

"The Bahrain Underground Bazaar" by Nadia Afifi (Bahrain). It takes an aging woman a very long time to come to terms with the death wish within. A technological ability to experience a dying person's last moments don't seem to make her journey any easier than ours.

"The Ten-Percent Thief" by Lavanya Lashminarayan (India). With most of the world a slum of poisoned air and water, devoid of nature, a woman risks her life to plant a single flower bulb outside the protected enclave of a city of the rich.

"At Desk 9501" by Frances Ogamba (Nigeria). A technology permits those with the constitution to live extra-long lives to confer some of their lifetime to extend the lives of others who are dying untimely, for a fee of course. The life-givers experience side consequences.

"Milagroso" by Isabel Yap (Philippines). One translation of "milagroso" is "miracle". A producer of technological miracles is confronted with the real thing. Magical reality, in a controlled, subdued way.

"Bring Your Own Spoon" by Saad Z. Hossain (Bangladesh). In a dystopia that is not too different from much of life in Bangladesh, a poor man who is a superb cook is helped by a Djinn to open a restaurant for the dirt-poor, who can pay only with bartered goods. Of course it is illegal, and doesn't last, even with the power of the Djinn. Magical reality with a slightly hopeful ending.

"Blue Grey Blue" by Yukimi Ogawa (Japan). It's ambiguous whether the colors seen are in the world around or the eyes themselves. In this fantasy, eye colors and the colors of the people change with mood and the fortunes of life.

"Your Multicolored Life" by Xing He (China), translated by Andy Dudak. This seems peripherally related to The Prince and the Pauper by Mark Twain, without the happy ending. I would retitle it "The Slave and the Scholar". Two men do indeed change places, and though the circumstance of each is actually improved, it doesn't last.

"The Easthound" by Nalo Hopkinson (Jamaica). A kind of zombie story, where all adults became monsters that destroyed and devoured first each other, and then attempted to do so to their children. Some children survived by killing the remaining "sprouted ones". Then they learned that puberty results not in adulthood, but in "sprouting" as a monster. It's the most dystopian story I have ever read; the extinction of humanity is at most a dozen years in the future.

"Dead Man Awake, Sing to the Sun!" by Pan Haitian (China), translated by Joel Martinsen. Not all who die are fully dead. Some are undead, and the undeadness is spreading, transmitted by a bite. Perhaps the human race is being transformed into a new kind of creature that cannot die all the way dead. Zombie or vampire, or both?

"Salvaging Gods" by Jacques Barcia (Brazil). AI to the max. Manufactured gods, and at least the one limned in this story can perform miracles of the sort that genies (or Djinn) perform in Arabian folk tales. But nothing lasts, for God is flawless, while these gods are flawed.

"The Next Move" by Edmundo Paz Soldán (Bolivia), translated by Jessica Sequeira. An occupying soldier has gone rogue, "saico" (psycho) in the parlance of the story, which has a number of phonetic spellings of colloquialisms. Of course he is eventually "eliminated". Much of the story is his own stream of consciousness.

"The Child of Clay" by Dilman Dila (Uganda). A robot world, in which the strongest motivation is reproduction, by a technology full of mystery. One robot is childless, and in seeking a solution, returns biological life to a barren land. It took a page or two to realize that "rit" and "rits" are pronouns, the pronouns "it" and "its" preceded by an "r" for "robot". I suppose the making of new pronouns arose from the recent "choose your own pronouns" fashion. That's the closest to anything positive to arise from recent "woke" fashions.

By comparison with the best stories I've read in recent anthologies of both science fiction and mainstream fiction published in the US, nearly all of the stories in Best of World SF are better.

AI illustrates Jabberwocky

kw: ai experiments, artificial intelligence, generated art, poems, illustrations

Behold the Jabberwock! The first poem longer than a nursery rhyme that I learned to recite was "Jabberwocky" by Lewis Carroll, the author of Alice's Adventures in Wonderland and other books.

I've been experimenting a lot with DALL-E 2, and I decided to see how it might "illustrate" the poem. First I prompted it with the word Jabberwocky. This is an out-painting of one of the results.

DALL-E's initial response was this panel of four images:

It's interesting that two of the pictures have the creature holding a book or paper, indicating that DALL-E "knows" this is a piece of literature. I like the whimsical blue ones, so I out-painted the second one also. 

Note that each session of out-painting required five or six "generate" actions, each of which consumed a credit. For those new to DALL-E 2, when you sign up you receive 50 free credits, which is enough to help someone become familiar with the way it works. Thereafter, 15 free credits are added to your account each month, but must be used up in the month they are added. If your usage is light, and you have a modicum of patience, that is enough. At any time, credits can be bought in batches of 115 for $15, which comes to just over 13¢ per credit. Thus, generating each of these lovely creatures cost me about 75¢.

I wanted to have DALL-E illustrate the verses of the poem. I decided to get its response to couplet after couplet; each verse is two couplets. DALL-E doesn't keep track of what we do with it so I knew I couldn't get it to produce illustrations with any coherence from one to the next. Therefore, I just generated a single response for each couplet and extracted all the results.

Here they are; enjoy!

’Twas brillig, and the slithy toves

      Did gyre and gimble in the wabe;

All mimsy were the borogoves,

      And the mome raths outgrabe.

“Beware the Jabberwock, my son!

      The jaws that bite, the claws that catch!

Beware the Jubjub bird, and shun

      The frumious Bandersnatch!”

He took his vorpal sword in hand;

      Long time the manxome foe he sought—

So rested he by the Tumtum tree

      And stood awhile in thought.

And, as in uffish thought he stood,

      The Jabberwock, with eyes of flame,

Came whiffling through the tulgey wood,

      And burbled as it came!

One, two! One, two! And through and through

      The vorpal blade went snicker-snack!

He left it dead, and with its head

      He went galumphing back.

“And hast thou slain the Jabberwock?

      Come to my arms, my beamish boy!

O frabjous day! Callooh! Callay!”

      He chortled in his joy.

’Twas brillig, and the slithy toves

      Did gyre and gimble in the wabe:

All mimsy were the borogoves,

      And the mome raths outgrabe.

I did not re-run the last verse. The source for the text of the poem is the Poetry Foundation. It differs slightly from my recitation memory.

Cool stuff about the Universe

 kw: book reviews, nonfiction, astronomy, universe, humor, essays

Can you see the difference between the two lower rows of light-colored ovals? We'll mention the dark blue ones in a moment. The three ovals in the bottom row are "white", meaning they have the color value #FFFFFF or (255,255,255). According to Dr. Jan Scudder, author of The Milky Way Smells of Rum and Raspberries … and Other Amazing Cosmic Facts, that very pale yellow, which she calls "light beige", is the average color of the Universe. The color value is #FFF8E7 or (255,248,231). I used PowerPoint to produce the ovals and to set them on backgrounds of white, black, and sky blue. 

This is found in the second chapter of the book, in which color values are discussed briefly, but one fact is reversed: A footnote on page 9 states that #000000 is white and #FFFFFF is black, but the reverse is true. Zero means "no illumination" and FF (or 255) means "full illumination". Otherwise, the usage of color values is correct, as I verified with the top set of ovals, #0D0ACB (13,10,203), called "a particularly pleasing deep blue"; the little bit of red and green slightly desaturate the dark blue so it doesn't overwhelm the eyes. The pure blue color of computer screens is a bit harsh all by itself:

In this image, the oval on the left has color value #0000C8 (0,0,200) and the one on the right is "full-on blue": $0000FF (0,0,255). Some people's eyes are more sensitive to the slight difference between the leftmost oval and the one in the center. By the way, values prefixed with the hash are hexadecimal, or base 16, in which the letters A through F represent quantities from 10 through 15.

The book consists of 34 essays, enlightening, humorous essays. The fifth chapter, from which the book's title is taken, is "The galactic center tastes of raspberries and smells of rum". The "dense" gas clouds near the center of the milky way are still hard vacuum compared to the air we breather, but are 3,000 times as dense as most interstellar gas. That makes these gas clouds capable of blocking much of the damaging UV that breaks apart most molecules, so that deep within them (they are hundreds to thousands of light years across) molecules such as ethyl formate survive. Ethyl formate is an ester that is found in abundance in raspberries. Also found is another ethyl compound, ethyl alcohol (ethanol), the "kick" in rum, vodka and whiskey. The author also points out that, if we were to somehow gather a few cubic parsecs of this gas and concentrate it by a factor of ten billion billion (ten quintillion), it would be a rather toxic brew. It may have hints of raspberry rum, but would also contain cyanide compounds and formaldehyde, for example. So it would really be more like the smell (don't taste!) of a preserved corpse of someone who died of cyanide-spiked rum, with an odd raspberry note.

I was interested in the chapter titled, "There's a pitch-black exoplanet". A distant planet designated WASP-12b is as dark as fresh asphalt; it reflects only 6% of the light that hits it. The dark patches on the Moon reflect about 7%, so you can look in the sky at a full moon to get the idea. By the way, the lighter parts of the moon are more like fresh, dry dirt, and reflect perhaps 15%, making the overall "brightness" of the moon about 12%. If the moon were papered over so it reflected 90% or more, it would be six or seven times as bright as it is. I wish Dr. Scudder had mentioned this. I take issue with a statement in that same chapter: "You'll never get a reflection off a star". In a close double, a pair of co-orbiting stars that are perhaps as close to one another as Mercury is to the Sun (36 million miles, or 58 million km), one of the stars is frequently much brighter than the other, and the dimmer star does indeed reflect a little of the brighter star's light. This has been observed spectroscopically. It stands to reason that some of the dimmer star's light will also reflect off its partner, but this would be extremely hard to detect.

There's an interesting timeline in "Jupiter's magnetic field will short-circuit your spacecraft, but Venus will just melt it." According to this Wikipedia article, Earth's magnetic field ranges from 0.25 to 0.65 gauss (refrigerator magnets have around 50 gauss at their surfaces). The larger unit, the tesla, is 10,000 gauss. The high-dollar superconducting magnet in an MRI machine has a strength of 3 to 10 tesla. That can pull the wristwatch off your wrist (or right through it!), which is why you daren't wear any metal into the MRI room. Electronic conductors moved through a magnetic field produce an electric field; that's how generators work. Move a typical laptop or smart phone around in space near Jupiter, and it will generate thousands to millions of volts, throwing sparks all about. Venus is less spectacular, but just as deadly to almost anything not make of tungsten. Its surface temperature is 450°C (~840°F), and the atmospheric pressure is 100 times that of Earth. In the timeline, starting with Venera 4 in 1967 and ending with Vega 2 in 1985, every spacecraft that landed or attempted to land on Venus had the same experience: crushed and then melted, after times ranging from 20 to 127 minutes. That's 13 spacecraft (all sent by Russia) that gathered a total of somewhat over 880 minutes (14.7 hours) of experience of Venusian weather. It's been a while since anyone tried to send something to the surface of Venus, but the Russians intend to try again in 2029. They hope for a "lifetime" of 3 hours on the surface. Perhaps special electronics made of diamond instead of silicon can be developed. And don't leave any air pockets inside your craft so it doesn't get crushed.

Another quibble, sorry to say: In the chapter "An Exoplanet we thought was made of diamond might be lava instead", the planet 55 Cancri e (the letter "e" indicates 5th body in the system, or 4th body that isn't a star) is "twice as physically large as the Earth, and eight times more massive, which tells us it's substantially more dense…" As stated, this is nonsense. 2×2×2 = 8, so the sentence would only make sense if the last phrase were "exactly as dense". However, here we find that the diameter isn't twice that of Earth, but 1.88, and this number cubed is 6.64; we also find that the mass is indeed 7.99 that of Earth, so now, we're in business. 7.99/6.64 = 1.2. The same article states the density of 55 Cancri e as 6.66. The average density of Earth is 5.51. Now the numbers work together properly. This error shows the danger in over-simplifying science when writing for the public. The early thought that this planet might be made of diamond was based on an erroneous measurement of the diameter. Diamond has a density of 3.5, or less when it is impure. And diamond doesn't compress well, so even under great pressure inside the planet, it's not going to rise to 6. Iron-rich silicate magma/lava also has a density near 3.5, but is much more compressible.

In spite of occasional minor blunders the book is delightful. I like the author's writing style.

Studying tartan designs

 kw: analytical projects, plaids, tartans, statistical distributions, scale free, lognormal

Guess what this is? It isn't quite what it looks like. It's a printed plaid, a plaid-like pattern printed on white flannel, the backing for a comforter we made many years ago. Until I looked at it closely (microscopically), I thought it was a woven plaid.

Close inspection also reveals that the weave is single-over-under, rather than the over-2-under-2 of most plaid fabrics. Nonetheless, it is an attractive pattern, one of my favorites!

Some time ago I began to wonder about the distribution of stripe widths on plaids. Long ago I wrote, in GWBASIC, a "screen saver" program that produced plaid patterns on the screen. I used a scale free distribution because it is easy to program. It would generate a bunch of width values and then scramble them by sorting against a set of random numbers; it would assign colors and generate a plaid pattern.

I don't know how plaids are designed. The Scottish tartans such as Black Watch or Douglas can be centuries old, and were selected with aesthetics in mind, and an eye for being imposing because they were worn into battle. Today I suppose artistic designers pick the colors and stripe widths in a purely aesthetic way.

I decided to study the statistical distributions found in my own shirts and other fabrics. I figured out how to wrap a shirt around a dictionary to hold it on a scanner, and did so for 17 flannel shirts and two plaid jackets, plus the pattern above which I photographed because the comforter is large and very thick. I have a number of plaid summer shirts, which I may analyze in the future, but they are not included here.

The large variation in stripe widths led me to consider three model distributions: Normal, Lognormal and Scale Free or Log-Log. When graphed with appropriate coordinates, each of these is a straight line, but, for example, a Normal distribution will graph as a curved line on either Log-Log or Lognormal coordinates. First, we need to see the shapes of these distributions:

The Normal distribution is frequently called the Gaussian distribution, because it was first proposed by the mathematician Carl F. Gauss in the early 1800's. When several random variables are added and measured repeatedly, the distribution of the sum tends toward the center-weighted shape shown in orange. A mathematical proof of this additive tendency is called the Central Limit Theorem.

The Lognormal distribution results when an exponential function is taken for a set of values that have a Normal distribution. The Lognormal shape is shown in green. Also, when several random variables are multiplied and measured repeatedly, the distribution of the sum tends toward a Lognormal distribution. The logarithmic form of the Central Limit Theorem describes this tendency. Furthermore, when an area or extended object is fractured or divided into many pieces via a random process (such as dropping a pane of glass), the areas or weights of the pieces closely approximate a Lognormal distribution. I verified this once in the laboratory using a small piece of glass I broke with a light blow of a hammer, and then weighed a couple hundred pieces. The mathematical proof of this is called the Theory of Breakage, which was propounded by A.N. Kolmogoroff in 1941.

The Scale Free distribution results when a series of measurements are taken of the reciprocals of a uniform random distribution. This is also called a Fractal distribution, based on the work of Benoit Mandelbrot in the 1980's. A theoretical continuous Scale Free distribution has no limit in either direction; no largest or smallest member being predicted. Discrete sets of values that have a Scale Free distribution, however, do have a largest and smallest member. While the theoretical, continuous Normal and Lognormal distributions also have no limits, the probabilities of extreme values are vanishingly small (for a Lognormal distribution, "extreme" means either a very large positive value, or a value that is positive, but very, very close to zero).

Each distribution can be rectified (made to approximate a straight line) by sorting all the values and graphing them in order in an appropriate coordinate system. Idealized examples of these three distributions are all shown together in the three coordinate systems that are relevant to this discussion:

These charts each rectify one of the distributions. Firstly, for "Probability Coordinates", the horizontal axis has units of standard deviation and the vertical axis is linear. The sorted values in a Normal distribution (orange) follow a straight line here. Secondly, for "Log-Probability Coordinates", the horizontal axis is the same, while the vertical axis is the logarithm of the values, which straightens out the Lognormal distribution (green). Thirdly, for "Log-Log Coordinates", the horizontal axis is the logarithm of the ordinal number of the sorted values and the vertical axis is the logarithm of the values. This rectifies the Scale Free distribution (blue). Note that in each case, the "other two" distributions display a distinct curvature.

Now, for sets of more realistic distributions, created by appropriate random processes, we see the same three graphs:

The three coordinate systems are the same as those above. A straight line has been added to each graph to emphasize which set of values has been rectified.

How does all this apply to a study of plaids? I gathered data from the scans of the 20 plaids, measuring each one in both directions. This is because the warp and woof of the weave have different pitches, so the plaid designers adjust the number of threads of each color so the resulting plaid will not look distorted. Here is an example of a set of data for one of the plaids. I used rather generic color names, because the widths of the stripes were the meaningful parameter, not the color pattern.

Note that, while the order of the colors is the same in both directions, the number of threads is seldom the same in direction 2 as compared to direction 1. This enlargement of the pattern shows the threads; it takes a careful look to see that the spacing is different between horizontal and vertical. Look at the white square. It has 9 horizontal threads but 6 vertical threads, yet the "square" appears pretty close to a square.

One benefit of the over-2-under-2 weave is that it makes counting threads in wider bands easier, because I could count by 4.

This is a more overall view of the pattern. Although each "unit" of the pattern contains 5 white stripes, 4 black stripes, 2 navy stripes and only 1 gray stripe, gray dominates because its stripe is so wide, with navy blue running a close second.

What did I do with all these numbers? There are a lot of them. A few patterns had 38-40 stripes, and many had quantities in the 20's. Some plaids have mirror symmetry, a smaller number don't.

I copied all the data, sorted each set (each direction for each plaid), and set up both ordinal and probability axes for them all. I charted them in groups to see how they looked. I was looking for rectified distributions. As we see below, with a few of them as an example, the results are not clear-cut. I had been hoping to see a clear indication that the distributions were primarily either Scale Free or (my preference) Lognormal. The reality is a little of both. The graphs that follow pertain to six non-symmetrical patterns.

The overall view is that many of the lines have a downward curvature at the right, but not all. In particular, the yellow line and the gray line mostly hidden behind it (#16), and the lighter blue and lighter green lines in the midst of the scrum (#10), don't curve down.

The downward curvature indicates that most of these are better modeled as Lognormal. The next graph shows that presentation.

Here many of the lines appear straighter, while some either flatten out or curve oppositely (not really "upward"). We also see that the dark red line and the dark blue that accompanies it also flatten out, even though they have a bit of downward curvature in the other graph.

None of the patterns showed a hint of being closer to Normal than to Lognormal or Scale Free, so I didn't pursue that any further.

"Eyeballing" the charts proved unsatisfactory, so I used a mathematical measure of linearity, relevant to either Log-Log or Lognormal coordinates, to more clearly discern the trends.

I saw from this that some of the patterns were more Lognormal in one direction and more Scale Free in the other. I found the following:

• 7 patterns were Lognormal in both directions.
• 4 patterns were mixed, but leaned Lognormal more than Scale Free.
• 2 patterns were mixed, but leaned Scale Free.
• 7 patterns were Log-Log in both directions.

Here we have, from left to right, #3, which is the most Lognormal of them all, #8, which is the most ambiguous, and #6, which is the most Scale Free of them all.

As it happens, #3 and #8 are favorites of mine, and if the red plaid from our comforter were made into a shirt, as a pattern, it would also be a favorite (although my wife doesn't like me to wear red shirts); it is also a mixed-distribution pattern. I care less for #6; I consider it almost ugly. Just to show that Scale Free patterns are also attractive, another of my favorites is shown here, #10, which is more Scale Free in both directions:

A characteristic of Scale Free distributions is a greater number of narrower stripes, and this one shows that. It illustrates that what we like doesn't have a very strong mathematical basis. I had been thinking just the opposite, but I don't mind being proven wrong.

In the future I may scan my plaid summer shirts and analyze them, to see if these tendencies hold up. This has been an enlightening exercise.