Encoding Single Quotes

For men, the softer emotions are always intertwined with power and pride. That was why Karna waited for me to plead with him though he could have stopped my suffering with a single world. That was why he turned on me when I refused to ask for his pity. That was why he incited Dussasan to an action that was against the code of honor by which he lived his life. He knew he would regret it—in his fierce smile there had already been a glint of pain. But was a woman's heart any purer, in the end? That was the final truth I learned. All this time I'd thought myself better than my father, better than all those men who inflicted harm on a thousand innocents in order to punish the one man who had wronged them. I'd thought myself above the cravings that drove him. But I, too, was tainted with them, vengeance encoded into my blood. When the moment came I couldn't resist it, no more than a dog can resist chewing a bone that, splintering, makes his mouth bleed. Already I was storing these lessons inside me. I would use them over the long years of exile to gain what I wanted, no matter what its price. But Krishna, the slippery one, the one who had offered me a different solace, Krishna with his disappointed eyes—what was the lesson he'd tried to teach?

Sound is the most absorbent medium of all, soaking up histories and philosophical systems and physical surroundings and encoding them in something so slight as a single vocal quaver or icy harpsichord interjection.

Sex, one of the most complex of human traits, is unlikely to be encoded by multiple genes. Rather, a single gene, buried rather precariously in the Y chromosome, must be the master regulator of maleness.I Male readers of that last paragraph should take notice: we barely made it.

All the positive associations the subjects had with Coca-Cola—its history, logo, color, design, and fragrance; their own childhood memories of Coke, Coke’s TV and print ads over the years, the sheer, inarguable, inexorable, ineluctable, emotional Coke-ness of the brand—beat back their rational, natural preference for the taste of Pepsi. Why? Because emotions are the way in which our brains encode things of value, and a brand that engages us emotionally—think Apple, Harley-Davidson, and L’Oréal, just for starters—will win every single time.

Some scientists, however, cling to the belief that the only obstacle to mastering common sense is brute force. They feel that a new Manhattan Project, like the program that built the atomic bomb, would surely crack the common-sense problem. The crash program to create this “encyclopedia of thought” is called CYC, started in 1984. It was to be the crowning achievement of AI, the project to encode all the secrets of common sense into a single program. However, after several decades of hard work, the CYC project has failed to live up to its own goals.

The CF gene codes a molecule that channels salt across cellular membranes. The most common mutation is a deletion of three bases of DNA that results in the removal, or deletion, of just one amino acid from the protein (in the language of genes, three bases of DNA encode a single amino acid). This deletion creates a dysfunctional protein that is unable to move chloride-one component of sodium chloride, i.e., common salt-across membranes. The salt in sweat cannot be absorbed back into the body, resulting in the characteristically salty sweat. Nor can the body secrete salt and water into the intestines, resulting in the abdominal symptoms.

Parts of it are surprisingly beautiful. On a vast stretch on chromosome eleven, for instance, there is a causeway dedicated entirely to the sensation of smell. Here, a cluster of 155 closely related genes encodes a series of protein receptors that are professional smell sensors. Each receptor binds to a unique chemical structure, like a key to a lock, and generates a distinctive sensation of smell in the brain—spearmint, lemon, caraway, jasmine, vanilla, ginger, pepper. An elaborate form of gene regulation ensures that only one odor-receptor gene is chosen from this cluster and expressed in a single smell-sensing neuron in the nose, thereby enabling us to discriminate thousands of smells.

Second, the production of RNA Messages was coordinately regulated. When the sugar source was switched to lactose, the bacteria turned on an entire module of genes-several lactose-metabolizing genes-to digest lactose. One of the genes in the module specified a "transporter protein" that allowed lactose to enter the bacterial cell. Another gene encoded an enzyme that was needed to break down lactose into parts. Yet another specified an enzyme to break those chemical parts into subparts. Surprisingly, all the genes dedicated to a particular metabolic pathway were physically present next to each other on the bacterial chromosome-like library books stacked by subject-and they were induced simultaneously in cells. The metabolic alteration produced a profound genetic alteration in a cell. It wasn't just a cutlery switch; the whole dinner service was altered in a single swoop. A functional circuit of genes was switched on and off, as if operated by a common spool or a master switch. Monod called one such gene module an operon. The genesis of proteins was thus perfectly synchronized with the requirements of the environment: supply the correct sugar, and a set of sugar-metabolizing genes would be turned on together.

There were so many different ways in which you were required to provide absolute proof of your identity these days that life could easily become extremely tiresome just from that factor alone, never mind the deeper existential problems of trying to function as a coherent consciousness in an epistemologically ambiguous physical universe. Just look at cash point machines, for instance. Queues of people standing around waiting to have their fingerprints read, their retinas scanned, bits of skin scraped from the nape of the neck and undergoing instant (or nearly instant-a good six or seven seconds in tedious reality) genetic analysis, then having to answer trick questions about members of their family they didn't even remember they had, and about their recorded preferences for tablecloth colours. And that was just to get a bit of spare cash for the weekend. If you were trying to raise a loan for a jetcar, sign a missile treaty or pay an entire restaurant bill things could get really trying. Hence the Ident-i-Eeze. This encoded every single piece of information about you, your body and your life into one all-purpose machine-readable card that you could then carry around in your wallet, and therefore represented technology's greatest triumph to date over both itself and plain common sense.

Indeed, as predicted, when the gene encoding the hemoglobin B chain was later identified and sequenced in sickle-cell patients, there was a single change: one triplet in DNA-GAG-had changed to another-GTG. This resulted in the substitution of one amino acid for another: glutamate was switched to valine. That switch altered the folding of the hemoglobin chain: rather than twisting into its neatly articulated, clasplike structure, the mutant hemoglobin protein accumulated in stringlike clumps within red cells. These clumps grew so large, particularly in the absence of oxygen, that they tugged the membrane of the red cell util the normal disk was warped into a crescent-shaped dysmorphic "sickle cell." Unable to glide smoothly through capillaries and veins, sickled red cells jammed into microscopic clots throughout the body, interrupting blood flow and precipitating the excruciating pain of a sickling crisis. It was a Rube Goldberg disease. A change in the sequence of a gene caused the change in the sequence of a protein; that warped its shape; that shrank a cell; that clogged a vein; that jammed the flow; that racked the body (that genes built). Gene, protein, function, and fate were strung in a chain: one chemical alteration in one base pair in DNA was sufficient to "encode" a radical change in human fate.

It is conceivable that an interplay of genes and epigenes coordinates human embryogenesis. Let us return, yet again, to Morgan's problem: the creation of a multicellular organism from a one-celled embryo. Seconds after fertilization, a quickening begins in the embryo. Proteins reach into the nucleus of the cell and start flicking genetic switches on and off. A dormant spaceship comes to life. Genes are activated and repressed, and these genes, in turn, encode yet other proteins that activate and repress other genes. A single cell divides to form two, then four, and eight cells. An entire layer of cells forms, then hollows out into the outer skin of a ball. Genes that coordinate metabolism, motility, cell fate, and identity fire "on." The boiler room warms us. The lights flicker on in the corridors. The intercom crackles alive. Now a second code stirs to life to ensure that gene expression is locked into place in each cell, enabling each cell to acquire and fix an identity. Chemical marks are selectively added to certain genes and erased from others, modulating the expression of the genes in that cell alone. Methyl groups are inserted and erased, and histones are modified to repress or activate genes. The embryo unfurls step by step. Primordial segements appear, and cells take their positions along various parts of the embryo. New genes are activated that command subroutines to grow limbs and organs, and more chemical marks are appended on the genomes of individual cells. Cells are added to create organs and structures-forelegs, hind legs, muscles, kidneys, bones, eyes. Some cells die a programmed death. Genes that maintain function, metabolism, and repair are turned on. An organism emerges from a cell.

We must consider what we mean when we say that the spiking activity of a neuron 'encodes' information. We normally think of a code as something that conveys information from a sender to a recipient, and this requires that the recipient 'understands' the code. But the spiking activity of every neuron seems to encode information in a slightly different way, a way that depends on that neuron's intrinsic properties. So what sense can a recipient make of the combined input from many neurons that all use different codes? It seems that what matters must be the 'population code' - not the code that is used by single cells, but the average or aggregate signal from a population of neurons. In a now classic paper, Shadlen and Newsome considered how information is communicated among neurons of the cortex - neurons that typically receive between 3,000 and 10,000 synaptic inputs.They argued that, although some neural structures in the brain may convey information in the timing of successive spikes, when many inputs converge on a neuron the information present in the precise timing of spikes is irretrievably lost, and only the information present in the average input rate can be used. They concluded that 'the search for information in temporal patterns, synchrony and specially labeled spikes is unlikely to succeed' and that 'the fundamental signaling units of cortext may be pools on the order of 100 neurons in size.' The phasic firing of vasopressin cells is an extreme demonstration of the implausibility of spike patterning as a way of encoding usable information, but the key message - that the only behaviorally relevant information is that which is collectively encoded by the aggregate activity of a population - may be generally true.

As an anology, consider the word structure. In bacteria, the gene is embedded in the genome in precisely that format, structure, with no breaks, stuffers, interpositions, or interruptions. In the human genome, in contrast, the word is interrupted by intermediate stretches of DNA: s...tru...ct...ur...e. The long stretches of DNA marked by the ellipses (...) do not contain any protein-encoding information. When such an interrupted gene is used to generate a message-i.e., when DNA is used to build RNA-the stuffer frragments are excised from the RNA message, and the RNA is stitched together again with the intervening pieces removed: s...tru...ct...ur...e became simplified to structure. Roberts and Sharp later coined a phrase for the process: gene splicing or RNA splicing (since the RNA message of the gene was "spliced" to removed the stuffer fragments). At first, this split structure of genes seemed puzzling: Why would an animal genome waste such long stretches of DNA splitting genes into bits and pieces, only to stitch them back into a continuous message? But the inner logic of split genes soon became evident: by splitting genes into modules, a cell could generate bewildering combinations of messages out of a single gene. The word s...tru...c...t...ur...e can be spliced to yield cure and true and so forth, thereby creating vast numbers of variant messages-called isoforms-out of a single gene. From g...e...n...om...e you can use splicing to generate gene, gnome, and om. And modular genes also had an evolutionary advantage: the individual modules from different genes could be mixed and matched to build entirely new kinds of genes (c...om...e...t). Wally Gilbert, the Harvard geneticist, created a new word for these modules; he called them exons. The inbetween stuffer fragments were termed introns.

Unlike any other chromosome, the Y is “unpaired”—i.e., it has no sister chromosome and no duplicate copy, leaving every gene on the chromosome to fend for itself. A mutation in any other chromosome can be repaired by copying the intact gene from the other chromosome. But a Y chromosome gene cannot be fixed, repaired, or recopied from another chromosome; it has no backup or guide (there is, however, a unique internal system to repair genes in the Y chromosome). When the Y chromosome is assailed by mutations, it lacks a mechanism to recover information. The Y is thus pockmarked with the potshots and scars of history. It is the most vulnerable spot in the human genome. As a consequence of this constant genetic bombardment, the human Y chromosome began to jettison information millions of years ago. Genes that were truly valuable for survival were likely shuffled to other parts of the genome where they could be stored securely; genes with limited value were made obsolete, retired, or replaced; only the most essential genes were retained (some of these genes were duplicated in the Y chromosome itself—but even this strategy does not solve the problem completely). As information was lost, the Y chromosome itself shrank—whittled down piece by piece by the mirthless cycle of mutation and gene loss. That the Y chromosome is the smallest of all chromosomes is not a coincidence: it is largely a victim of planned obsolescence (in 2014, scientists discovered that a few extremely important genes may be permanently lodged in the Y). In genetic terms, this suggests a peculiar paradox. Sex, one of the most complex of human traits, is unlikely to be encoded by multiple genes. Rather, a single gene, buried rather precariously in the Y chromosome, must be the master regulator of maleness.I Male readers of that last paragraph should take notice: we barely made it.

The tyranny of caste is that we are judged on the very things we cannot change: a chemical in the epidermis, the shape of one’s facial features, the signposts on our bodies of gender and ancestry—superficial differences that have nothing to do with who we are inside. The caste system in America is four hundred years old and will not be dismantled by a single law or any one person, no matter how powerful. We have seen in the years since the civil rights era that laws, like the Voting Rights Act of 1965, can be weakened if there is not the collective will to maintain them. A caste system persists in part because we, each and every one of us, allow it to exist—in large and small ways, in our everyday actions, in how we elevate or demean, embrace or exclude, on the basis of the meaning attached to people’s physical traits. If enough people buy into the lie of natural hierarchy, then it becomes the truth or is assumed to be. Once awakened, we then have a choice. We can be born to the dominant caste but choose not to dominate. We can be born to a subordinated caste but resist the box others force upon us. And all of us can sharpen our powers of discernment to see past the external and to value the character of a person rather than demean those who are already marginalized or worship those born to false pedestals. We need not bristle when those deemed subordinate break free, but rejoice that here may be one more human being who can add their true strengths to humanity. The goal of this work has not been to resolve all of the problems of a millennia-old phenomenon, but to cast a light onto its history, its consequences, and its presence in our everyday lives and to express hopes for its resolution. A housing inspector does not make the repairs on the building he has examined. It is for the owners, meaning each of us, to correct the ruptures we have inherited. The fact is that the bottom caste, though it bears much of the burden of the hierarchy, did not create the caste system, and the bottom caste alone cannot fix it. The challenge has long been that many in the dominant caste, who are in a better position to fix caste inequity, have often been least likely to want to. Caste is a disease, and none of us is immune. It is as if alcoholism is encoded into the country’s DNA, and can never be declared fully cured. It is like a cancer that goes into remission only to return when the immune system of the body politic is weakened.

A single miRNA can influence many of these differently spliced versions simultaneously. Alternatively, a single miRNA can also influence quite unrelated proteins that are encoded by different genes but have similar 3′ UTR sequences. This can make it very difficult to unravel exactly what a miRNA is doing in a cell, as the effects will vary depending on the cell type and the other genes (protein-coding and non-protein-coding) that the cell is expressing at any one time.

All of the patterns we've discussed of course exist in four dimensions rather than three, and the metaphors about braids, cables and trees, shouldn't be taken too literally. The key point is simply that you can be an unchanging pattern in spacetime-the specific details of this pattern are less important for the points we're making. This pattern is part of the mathematical structure that is our Universe, and the relations between different parts of the pattern are encoded in mathematical equations. As we saw in Chapter 8, Everett's quantum mechanics endows you with an even more interesting-but no less mathematical-structure, since a single you (the tree trunk) can split into many branches, each feeling that they're the one and only you--we'll return to this later.

The number of seconds in half-a-day oscillates with a frequency of one million Hertz by a repeating scheme which equals to the natural logarithm constant (i.e., e) raised to the literal power of PI itself; the latter is nothing but a projection from a daily numerical phenomenon exhibiting its influence throughout the whole solar year using a binary temporal balance in two halves of a single day (i.e., a half equals to 43200 seconds) and of a single year (i.e., Equinoxes on March and September). That exact mathematical pattern was encoded into the structure of the Great Pyramid of Giza and was demonstrated through its height while being silent about its lunar foundation which is found in its base rather than its apex.

Perhaps, then, the most surprising consequence of a visionary Theory of Everything is that it implies that on the grand scale the universe, including its origins and evolution, though extremely complicated, is not complex but in fact is surprisingly simple because it can be encoded in a limited number of equations, conceivably even just a single master equation.

How strange it was that the music people favored defined them in so many ways—what they liked, what they rejected, what stuck with them from their school years, what they kept, what they burned into memory, what they let go. How was it that what they heard in a single decade—for most, their second on the planet—encoded a set of remembrances that stayed with them forever? It was simply commercial output, a business after all, nothing more than that—song factories a few years removed from Tin Pan Alley. It wasn’t Beethoven or Mozart, but it was glue—happy and sad, lived and imagined, the soundtrack of youth became the soundtrack of peoples’ lives.

deception has matured considerably in recent years. We now realize that our brains aren’t just hapless and quirky—they’re devious. They intentionally hide information from us, helping us fabricate plausible prosocial motives to act as cover stories for our less savory agendas. As Trivers puts it: “At every single stage [of processing information]—from its biased arrival, to its biased encoding, to organizing it around false logic, to misremembering and then misrepresenting it to others—the mind continually acts to distort information flow in favor of the usual goal of appearing better than one really is.

dApps are like traditional software applications except they live on a decentralized smart contract platform. The primary benefit of these applications is their permissionlessness and censorship resistance. Anyone can use them, and no single body controls them. A separate but related concept is a decentralized autonomous organization (DAO), which has its rules of operation encoded in smart contracts that determine who can execute what behavior or upgrade. It is common for a DAO to have some kind of governance token, which gives an owner some percentage of the vote on future outcomes.

Suppose we wanted to transmit this knowledge, everything we had ever learned, to another world. First we would want to make the representation as compact as possible. By squeezing out redundancies we could compress the number so that it would occupy smaller and smaller spaces. In fact, if we are adept enough we can represent the number in a manner that requires almost no space whatsoever. We simply take the long string of digits and put a decimal point in front of it so that it becomes a fraction between 0 and 1, a mere point on a line. Then we choose a smooth stick and declare one end 0 and the other end 1. Measuring carefully, we make a notch in the stick -- a point on the continuum representing the number. All of our history, our philosophy, our music, our art, our science -- everything we know would be implicit in that single mark. To retrieve the world's knowledge, one would measure the distance of the notch from the end of the stick, then convert the number back into the books, the music, the images. The success of the scheme would depend on the fineness of the mark and the exactness of the measurement. The slightest imprecision would cause whole Libraries of Alexandria to burn. [...] Suppose the medicine men of Otowi had discovered this trick. Suppose, contrary to all evidence, that they had developed a written language, a number system, and tools of enough precision to encode a single book of sacred knowledge into the notch of a prayer stick -- the very book, perhaps, that explains what the symbols on the rock walls mean. And suppose a hiker, exploring one day in the caves above Otowi, found the stick. Could the knowledge be recovered? [...] Aliens trying to decode our records might recognize what seemed to be deliberate patterns in the markings of ink on pages or the fluctuating magnetic fields of computer disks (though, again, if the information had been highly compressed, it would be harder and harder to distinguish from randomness). If they persisted, would they find truths to marvel at, signs of kindred minds? Or would they even recognize the books and tapes as things that might be worth analyzing? One can't go around measuring every notch on every stick.

As Trivers puts it: “At every single stage [of processing information]—from its biased arrival, to its biased encoding, to organizing it around false logic, to misremembering and then misrepresenting it to others—the mind continually acts to distort information flow in favor of the usual goal of appearing better than one really is.

To the extent that genomes can be thought of as compressed encodings of biological structures, they are spectacularly efficient. All the trillions of cells in the human body-not just the tens of billions in the brain-are guided in one way or another by the information contained in 30,000 or so genes. The best high-quality set of pictures of the body- the National Institutes of Health Visible Human Project, a series of high-resolution digital photos of slices taken from volunteer Joseph Paul Jernigan (deceased)-takes up about 60 gigabytes, enough (if left uncompressed) to fill about 100 CD-ROMs-and still not enough detail to capture individual cells. The genome, in contrast, contains only about 3 billion nucleotides, the equivalent (at two bits per nucleotide) of less than two-thirds of a gigabyte, or a single CD-ROM.

The researchers looked deeper into these observations, in hopes of gaining insight into the mechanisms underlying the high evolutionary rate and extraordinary immunologic plasticity of influenza HA. They probed in more detail the precise codons that are used by the virus to encode the influenza HA1 protein. The discriminated between codons on the basis of volatility. Each three-nucleotide codon is related by a single nucleotide change to nine 'mutational neighbours.' Of those nine mutations, some proportion change the codon to a synonymous codon and some change it to a nonsynonymous one, which directs the incorporation of a different amino acid into the protein. More volatile codons are those for which a larger proportion of those nine mutational neighbours encode an amino acid change. The use of particular codons in a gene at a frequency that is disproportionate to their random selection for encoding a chosen amino acid is termed codon bias. Such bias is common and is influenced by many factors, but here the collaborators found strong evidence for codon bias that was particular for and restricted to the amino acids making up the HA1 epitopes. Remarkably, they observed that influenza employs a disproportionate number of volatile codons in its epitope-coding sequences. There was a bias for the use of codons that had the fewest synonymous mutational neighbours. In other words, influenza HA1 appears to have optimized the speed with which it can change amino acids in its epitopes. Amino acid changes can arise from fewer mutational events. The antibody combining regions are optimized to use codons that have a greater likelihood to undergo nonsynonymous single nucleotide substitutions : they are optimized for rapid evolution.

The specific nuclear reaction that is needed to make carbon is a rather improbable one. It requires three nuclei of helium to come together to fuse into a single nucleus of carbon.

Everything that is made of atoms has a density quite close to the density of a single atom given by the mass of an atom divided by its volume.

belief in the ultimate simplicity and unity behind the rules that constrain the Universe leads us to expect that there exists a single unchanging pattern behind the appearances. Under different conditions this single pattern will crystallise into superficially distinct patterns that show up as the four separate forces governing the world around us. It has gradually become clear how this patterning probably works.

Right about here every discussion of quantum epistemology invokes Schrödinger’s cat, a thought experiment that Schrödinger proposed in 1935 to illustrate the bewilderments of quantum superpositions. Put a pellet inside a box, he said, along with a radioactive atom. Arrange things so that the pellet releases poison gas if and only if the atom decays. Radioactive decay is a quantum phenomenon, and hence probabilistic: a radioactive atom has a finite probability of decaying in a certain window of time. In thirty minutes, an atom may have a 50 percent chance of decaying—not 70 percent, not 20 percent, but precisely 50 percent. Now put a cat in the box, and seal it in what Schrödinger called a “diabolical device.” Wait a while. Wait, in fact, a length of time equal to when the atom has a fifty-fifty chance of decaying. Is the cat alive or dead? Quantum mechanics says that the creature is both alive and dead, since the probability of radioactive decay and hence release of poison gas is 50 percent, and the possibility of no decay and a safe atmosphere is also 50 percent. Yet it seems absurd to say that the cat is part alive and part dead. Surely a physical entity must have a real physical property (such as life or death) ? If we peek inside the box, we find that the cat is alive or dead, not some crazy superposition of the two states. Yet surely the act of peeking should not be enough to turn probability into actuality? According to Bohr’s Copenhagen Interpretation, however, this is precisely the case. The wave function of the whole system, consisting of kitty and all the rest, collapses when an observer looks inside. Until then, we have a superposition of states, a mixture of atomic decay and atomic intactness, death and life. Observations, to put it mildly, seem to have a special status in quantum physics. So long as the cat remains unobserved, its wave function encodes equal probabilities of life and death. But then an observation comes along, and bam—the cat’s wave function jumps from a superposition of states to a single observed state. Observation lops off part of the wave function. The part corresponding to living or deceased, but not the other, survives.

But already it seems clear that we don’t inherit from our parents a single “biological self.”33 Instead our genomes encode a wide variety of potential selves, and our social environment—including our perception of that environment—helps to determine which of those selves we become.

This is what we mean, I think, when we say carelessly that a work of art is ‘timeless.’ Not that an artwork encodes some single abiding truth that a priestly class can discern, but rather that it rewards different interpretations as the world changes around it.

Church also figured out how to encode an HTML version of a book, one he’d cowritten, in a single drop of DNA,