Amino Acid Quotes

The only religious opinion I feel sure of is this: self-awareness is not just a bunch of amino acids bumping together.

The clothes you're wearing, the room, the house, the city that you're in. Everything in it started out in the human imagination. Your lives, your personalities, your whole world. All invented. All made up. All the wars, the romances. The masterpieces and the machines. And there's nothing here but a funny little twist of amino acids, playing a marvelous game of pretend.

A heart is made of proteins built by amino acids, animated by electrical impulses.

You see, proteins, as I probably needn't tell you, are immensely complicated groupings of amino acids and certain other specialized compounds, arranged in intricate three-dimensional patterns that are as unstable as sunbeams on a cloudy day. It is this instability that is life, since it is forever changing its position in an effort to maintain its identity--in the manner of a long rod balanced on an acrobat's nose.

Who could ever reckon up the damage done to love and friendship and all hopes of happiness by a surfeit or depletion of this or that neurotransmitter? And who will ever find a morality, an ethics down among the enzymes and amino acids when the general taste is for looking in the other direction?

Just as amino acids can be called the building blocks of life, associations can be called the building blocks of thought.49 In

Your body is made of the same elements that lionesses are built from. Three quarters of you is the same kind of water that beats rocks to rubble, wears stones away. Your DNA translates into the same twenty amino acids that wolf genes code for. When you look in the mirror and feel weak, remember, the air you breathe in fuels forest fires capable of destroying everything they touch. On the days you feel ugly, remember: diamonds are only carbon. You are so much more.

It is one of the striking generalizations of biochemistry—which surprisingly is hardly ever mentioned in the biochemical text-books—that the twenty amino acids and the four bases, are, with minor reservations, the same throughout Nature. As far as I am aware the presently accepted set of twenty amino acids was first drawn up by Watson and myself in the summer of 1953 in response to a letter of Gamow's.

With odds standing at 1 chance in 10164 of finding a functional protein among the possible 150-amino-acid compounds, the probability is 84 orders of magnitude (or powers of ten) smaller than the probability of finding the marked particle in the whole universe. Another way to say that is the probability of finding a functional protein by chance alone is a trillion, trillion, trillion, trillion, trillion, trillion, trillion times smaller than the odds of finding a single specified particle among all the particles in the universe.

Make no mistake: if he rose at all It was as His body; If the cell’s dissolution did not reverse, the molecule reknit, The amino acids rekindle, The Church will fall.

The only religious opinion I feel sure of is this: self-awareness is not just a bunch of amino acids bumping together!

And it turns out that dopamine is made from protein—specifically, from the amino acid known as tyrosine, which is found in both animal and vegetable forms of protein.

... the brain's operations arise fundamentally and inescapably from raw associations. Just as amino acids can be called the building blocks of life, associations can be called the building blocks of thought.

I knew that the little starbursts I called flavor crunchies were actually an amino acid known as tyrosine that formed in aged cheeses like cheddar and Gouda. I also knew that I would definitely continue calling them flavor crunchies.

Originally, the atoms of carbon from which we’re made were floating in the air, part of a carbon dioxide molecule. The only way to recruit these carbon atoms for the molecules necessary to support life—the carbohydrates, amino acids, proteins, and lipids—is by means of photosynthesis. Using sunlight as a catalyst the green cells of plants combine carbon atoms taken from the air with water and elements drawn from the soil to form the simple organic compounds that stand at the base of every food chain. It is more than a figure of speech to say that plants create life out of thin air.

I once read that human beings can live solely on potatoes. A potato contains all the essential amino acids humans need to build proteins, repair cells, and fight diseases. ... You would have to eat about twenty-five potatoes a day to get the recommended amount of protein, however, and you would have calcium deficiencies.

IN 1953, STANLEY Miller, a graduate student at the University of Chicago, took two flasks—one containing a little water to represent a primeval ocean, the other holding a mixture of methane, ammonia, and hydrogen sulphide gases to represent Earth’s early atmosphere—connected them with rubber tubes, and introduced some electrical sparks as a stand-in for lightning. After a few days, the water in the flasks had turned green and yellow in a hearty broth of amino acids, fatty acids, sugars, and other organic compounds. “If God didn’t do it this way,” observed Miller’s delighted supervisor, the Nobel laureate Harold Urey, “He missed a good bet.

The macromolecules of organic life embody information in an intricate structure. A single hemoglobin molecule comprises four chains of polypeptides, two with 141 amino acids and two with 146, in strict linear sequence, bonded and folded together. Atoms of hydrogen, oxygen, carbon, and iron could mingle randomly for the lifetime of the universe and be no more likely to form hemoglobin than the proverbial chimpanzees to type the works of Shakespeare. Their genesis requires energy; they are built up from simpler, less patterned parts, and the law of entropy applies. For earthly life, the energy comes as photons from the sun. The information comes via evolution.

Vegetables, grains, and legumes contain all the amino acids necessary to build muscle from scratch. Like

Pretty much any amino acid arrangement can be hydrolyzed, including those of the recyclable that dares not speak its name. A four-person crew will, over the course of three years, generate somewhere in the neighborhood of a thousand pounds of feces. In the ominous words of sixties space nutritionist Emil Mrak, “The possibility of reuse must be considered.” Sometime

If amino acids can only be made where there is no free oxygen in the atmosphere, and porphyrins can only be made when there is free oxygen, then these things needed by every cell could not have existed together to form the first cell! What’s more, many of these compounds are antagonistic. They will combine and destroy each other—anywhere except within a living cell.

The Murchison meteorite was found to be 4.5 billion years old, and it was studded with amino acids—seventy-four types in all, eight of which are involved in the formation of earthly proteins.

Miller’s experiments with these more challenging inputs has so far produced only one fairly primitive amino acid. At all events, creating amino acids is not really the problem. The problem is proteins.

Classically, cosmetics companies will take highly theoretical, textbookish information about the way that cells work—the components at a molecular level or the behavior of cells in a glass dish—and then pretend it’s the same as the ultimate issue of whether something makes you look nice. “This molecular component,” they say, with a flourish, “is crucial for collagen formation.” And that will be perfectly true (along with many other amino acids which are used by your body to assemble protein in joints, skin, and everywhere else), but there is no reason to believe that anyone is deficient in it or that smearing it on your face will make any difference to your appearance. In general, you don’t absorb things very well through your skin, because its purpose is to be relatively impermeable. When you sit in a bath of baked beans for charity, you do not get fat, nor do you start farting.

Catabolism Catabolism is the metabolic process by which more complex substances (such as proteins) are broken down into simpler ones (such as amino acids), together with the release of energy. This is also known as destructive metabolism. •••

The emerging medical research into treating Long COVID in 2023 was matching my research into treating the long-term effects of altitude sickness that I published in my 2022 books. Amino acids appear to be key in treating both hypoxic conditions.

A small segment of DNA that encodes a gene is transcribed into a snippet of RNA, which then travels to the manufacturing region of the cell. There this “messenger RNA” facilitates the assembly of the proper sequence of amino acids to make a specified protein.

COMPLICATED molecules. About a fifth of our body weight is made up of them. In simplest terms, a protein is a chain of amino acids. About a million different proteins have been identified so far, and nobody knows how many more are to be found. They are all made from just twenty amino acids,

We’d die quite quickly without amino acids, the organic compounds that serve as the building blocks for every protein in the human body. Without them—and in particular the nine essential amino acids that our bodies cannot make on their own—our cells can’t assemble the life-giving enzymes needed for life.

For the reasons stated above, I am convinced that in a large percentage of cases, depression is the result of a neurotransmitter deficiency which is most often due to low stomach acid. In over 50 percent of cases, depression is treatable by supplying (relatively) large quantities of the essential amino acids

The sequence of bases in a DNA molecule correlates with the sequence of amino acids in the proteins that make up the organism’s body, and they got that sequence by structuring the organism’s ancestors—reducing their entropy—into the improbable configurations that allowed them to capture energy and grow and reproduce.

Methionine is also an essential amino acid needed for growth and development. However, when it comes to longevity in life, research has found that rats eating a methionine-restrictive diet lived 43-percent longer than those that consume a diet high in methionine. Methionine is known for its thyroid-suppressing properties like cysteine

the following supplements are recommended specifically for MS. They’ll help reduce pain and protect your myelin sheath as you heal from EBV: EPA & DHA (eicosapentaenoic acid and docosahexaenoic acid): omega-3 fats to help protect and fortify the myelin nerve sheath. Be sure to buy a plant-based (not fish-based) version. L-glutamine: amino acid that removes toxins such as MSG from the brain and protects neurons. Lion’s mane: medicinal mushroom that helps protect the myelin sheath and support neuron function. ALA (alpha lipoic acid): helps repair damaged neurons and neurotransmitters. Also helps mend the myelin nerve sheath. Monolaurin: fatty acid that kills virus cells, bacteria cells, and other bad microbes (e.g., mold) in the brain. Curcumin: component of turmeric that reduces inflammation of the central nervous system and relieves pain. Barley grass juice extract powder: contains micronutrients that feed the central nervous system. Also helps feed brain tissue, neurons, and the myelin nerve sheath.

When the genetic code was solved, in the early 1960s, it turned out to be full of redundancy. Much of the mapping from nucleotides to amino acids seemed arbitrary—not as neatly patterned as any of Gamow’s proposals. Some amino acids correspond to just one codon, others to two, four, or six. Particles called ribosomes ratchet along the RNA strand and translate it, three bases at a time. Some codons are redundant; some actually serve as start signals and stop signals. The redundancy serves exactly the purpose that an information theorist would expect. It provides tolerance for errors. Noise affects biological messages like any other. Errors in DNA—misprints—are mutations.

As Richard Dawkins argues in The Blind Watchmaker, there must have been some kind of cumulative selection process that allowed amino acids to assemble in chunks. Perhaps two or three amino acids linked up for some simple purpose and then after a time bumped into some other similar small cluster and in so doing “discovered” some additional improvement.

To spell collagen, the name of a common type of protein, you need to arrange eight letters in the right order. But to make collagen, you need to arrange 1,055 amino acids in precisely the right sequence. But—and here’s an obvious but crucial point—you don’t make it. It makes itself, spontaneously, without direction, and this is where the unlikelihoods come

The distribution of amino acids is not the same as in animal protein. In particular, plant protein has less of the essential amino acids methionine, lysine, and tryptophan, potentially leading to reduced protein synthesis. Taken together, these two factors tell us that the overall quality of protein derived from plants is significantly lower than that from animal products.

The factor VIII project, both teams knew, would challenge the outer limits of gene-cloning technology. Somatostatin had 14 amino acids; insulin had 51. Factor VIII had 2,350. The leap in size between somatostatin and factor VIII was 160-fold-almost equivalent to the jump in distance between Wilbur Wright's first airborne circle at Kitty Hawk and Lindbergh's journey across the Atlantic.

Through its associated amino acid tryptophan, the 35th Gene Key is connected to the secretion of serotonin within the body. Serotonin is well known as a chemical that induces states of satiation and deep fulfilment. As a result of the interference from the Shadow frequency passing through this codon, serotonin production within the body is inhibited, leaving human beings with a perpetual feeling of hunger.

The Murchison meteorite was found to be 4.5 billion years old, and it was studded with amino acids—seventy-four types in all, eight of which are involved in the formation of earthly proteins. In late 2001, more than thirty years after it crashed, a team at the Ames Research Center in California announced that the Murchison rock also contained complex strings of sugars called polyols, which had not been found off the Earth before.

Carbohydrates are not required in a healthy human diet. Another way to say this (as proponents of carbohydrate restriction have) is that there is no such thing as an essential carbohydrate. Nutritionists will say that 120 to 130 grams of carbohydrates are required in a healthy diet, but this is because they confuse what the brain and central nervous system will burn for fuel when diets are carbohydrate rich—120 to 130 grams daily—with what we actually have to eat. If there are no carbohydrates in the diet, the brain and central nervous system will run on molecules called “ketones.” These are synthesized in the liver from the fat we eat and from fatty acids, mobilized from the fat tissue because we’re not eating carbohydrates and insulin levels are low, and even from some amino acids. With no carbohydrates in the diet, ketones will provide roughly three-quarters of the energy that our brains use. And this is why severely carbohydrate-restricted diets are known as “ketogenic” diets. The rest of the energy required will come from glycerol, which is also being released from the fat tissue when the triglycerides are broken down into their component parts, and from glucose synthesized in the liver from the amino acids in protein. Because a diet that doesn’t include fattening carbohydrates will still include plenty of fat and protein, there will be no shortage of fuel for the brain.

steep taper, seven day timetable, plenty of loperamide; magnesium supplements and free form amino acids to replenish my burnt-out neurotransmitters; protein powder, electrolyte powder, melatonin (and weed) for sleep as well as various herbal tinctures and potions my fashion intern swore by, licorice root and milk thistle, nettles and hops and black cumin seed oil, valerian root and skullcap extract. I had a shopping bag from the health food store with all the stuff

You should maintain a moderate, not high, intake of protein. When it is digested, dietary protein, such as meat, breaks down into amino acids. Adequate protein is required for good health, but excess amino acids cannot be stored in the body and so the liver converts them into glucose. Therefore, eating too much protein adds sugar to the body. So you should avoid highly processed, concentrated protein sources such as protein shakes, protein bars, and protein powders.

Extensive studies have revealed that the "triage nurses" in our bodies recognize damaged cell parts and then repair them.' The body doesn't just patch these cells; it actually tears them down completely and then rebuilds from scratch. Incredible, isn't it? Damaged proteins become brand-new proteins, made with recycled amino acids. The body repairs altered fats and DNA in a similar matter. It is critical that you understand that the body has an amazing built-in ability to heal itself.

Proteins, in short, are complex entities. Hemoglobin is only 146 amino acids long, a runt by protein standards, yet even it offers 10190 possible amino acid combinations, which is why it took the Cambridge University chemist Max Perutz twenty-three years—a career, more or less—to unravel it. For random events to produce even a single protein would seem a stunning improbability—like a whirlwind spinning through a junkyard and leaving behind a fully assembled jumbo jet, in the colorful simile of the astronomer Fred Hoyle.

Kombu is a species of edible kelp (Laminaria japonica) that thrives in long streamers about a palm's-width wide that can reach up to thirty feet in length. Along with katsuobushi, it is the other main ingredient for making dashi. Kombu contains a high level of the amino acid glutamate, which is the source of the "fifth taste", umami, and a precursor to the flavor enhancer MSG. Japan consumes about 50,000tons of kombu a year--- about half wild, and half farmed--- most of it harvested off the coast of the northern island, Hokkaidō.

For an enzyme to be functional, it must fold into a precise three-dimensional shape. How such a complex folding can take place remains a mystery. A small chain of 150 amino acids making up an enzyme has an extraordinary number of possible folding configurations: if it tested 1,012 different configurations every second, it would take about 1,026 years to find the right one. . . . Yet, a denatured enzyme can refold within fractions of a second and then precisely react in a chemical reaction. . . . [I]t demonstrates a stunning complexity and harmony in the universe.21

Stanley Miller and Harold Urey, was to simulate the conditions on Earth in primordial times, three or four billion years ago, when life appeared for the first time. The experiments were intended to see if they could make something come alive using nothing but nonliving chemicals. Do you know what emerged? Not life, but something fascinating all the same. The chemicals gave rise to significant chemical compounds: a handful of amino acids, essential components in the chemistry of life. Amino acids are molecules that hook together to form the proteins that run almost every aspect of biology.

ASPARTAME AND MSG: EXCITOTOXINS Aspartame is, in fact, an excitotoxin, one of a group of substances, usually acidic amino acids, that in high amounts react with specialized receptors in the brain, causing destruction of certain types of neurons. A growing number of neurosurgeons and neurologists are convinced that excitotoxins play a critical role in the development of several neurological disorders, including migraines, seizures, learning disorders in children, and neurodegenerative disorders such as Alzheimer’s disease, Parkinson’s disease, Huntington’s disease, and amyotrophic lateral sclerosis (ALS).1 Glutamate and aspartate are two powerful amino acids that act as neurotransmitters in the brain in very small concentrations, but they are also commonly available in food additives. Glutamate is in MSG, a flavor enhancer, and in hydrolyzed vegetable protein, found in hundreds of processed foods. Aspartate is one of three components of aspartame (NutraSweet, Equal), a sugar substitute. In higher concentrations as food additives, these chemicals constantly stimulate brain cells and can cause them to undergo a process of cell death known as excitotoxicity—the cells are excited to death.

This “triplet code” hypothesis was also supported by elementary mathematics. If a two-letter code was used—i.e., two bases in a sequence (AC or TC) encoded an amino acid in a protein—you could only achieve 16 combinations, obviously insufficient to specify all twenty amino acids. A triplet-based code had 64 combinations—enough for all twenty amino acids, with extra ones still left over to specify other coding functions, such as “stopping” or “starting” a protein chain. A quadruplet code would have 256 permutations—far more than needed to encode twenty amino acids. Nature was degenerate, but not that degenerate.

The resistant starch found in beans powerfully reduces hunger and, thus, food consumption over many hours, coinciding with the fermentation that takes place in the large intestine hours after eating the beans. So eating beans with lunch will reduce your hunger and appetite for dinner many hours later, overall lowering the amount of calories you desire for the day. For diabetics, beans are critical for lowering the insulin requirement for starch digestion. They also supply amino acids that complement the other vegetables, nuts, and seeds to enhance the biologic value of the protein in the diet, without raising IGF-1.

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.

S-adenosyl-methionine (SAMe) is a natural derivative of an amino acid normally produced by the body, and it plays a role in methylation (see Chapter 5). Levels of SAMe in the body often become depleted by middle age. Multiple clinical trials have shown that SAMe provides substantial benefit for patients with depression. This effect occurs relatively quickly, unlike the requirement to build up levels in the bloodstream that accompanies some prescription drugs for depression. It is, therefore, an effective, natural, and quick-acting treatment for mild depression. Human trials have also shown benefits for strengthening the liver and for relief from osteoarthritis.

Don’t tell me amino acids can be created by accident. Don’t tell me about “billions and billions” of years for life to arise. Don’t tell me about “countless” stars and planets in the universe. It all doesn’t matter. Using simple concepts of number—exponents—one can expose as false claims that life arose by accident. You cannot seriously expect to get a specified protein of 75 linked amino acids in the history of the universe, except as a product of already existing life, even if you assume that everything in the universe is made up of amino acids and even if you assume that amino acids will freely combine into 75-unit chains.n Period. And there actually is no dispute about this fact.

And just as agriculture has displaced species-dense communities with its monocrops, its diet has displaced the nutrient-dense foods that humans need, replacing them with mononutrients of sugar and starch. This displacement led immediately to a drop in human stature as agriculture spread - the evidence couldn’t be clearer. The reasons are just as clear. Meat contains protein, minerals, and fats, fats that we need to metabolize those proteins and minerals. In contrast, grains are basically carbohydrates: what protein they do contain is low quality - lacking essential amino acids - and comes wrapped in indigestible fiber. Grains are essentially sugar with enough opioids to make them addictive.

Try a cognitive enhancer from the list in this chapter to promote healthy brain function and avoid cognitive degeneration as you age. Here is the short list: •​Piracetam: Reduces cognitive decline with age •​Modafinil: Performance enhancing, not anti-aging •​Nicotine: Low doses (not from cigarettes) can be helpful for aging and cognitive performance •​Deprenyl: Works on dopamine receptors for cognitive enhancement •​CoQ10: Helps your mitochondria produce energy •​PQQ: A powerful antioxidant for anti-aging •​L-theanine: An amino acid that helps with memory and mental endurance •​Curcumin: Improves memory and attention while acting as an antioxidant •​He Shou Wu: Longevity-enhancing antioxidant herb that can also help you regrow and regain color in your hair!

For example, all three partners cooperate to make nutrients. To create the amino acid phenylalanine, they need nine enzymes. Tremblaya can build 1,2,5,6,7, and 8; Moranella can make 3,4, and 5; and the mealybug alone makes the 9th. Neither mealybug nor the two bacteria can make phenylalanine on their own; they depend on each other to fill the gaps in their repertoires. This reminds me of the Graeae of Greek mythology: the three sisters who share one ee and one tooth between them. Anything more would be redundant: their arrangement, though odd, still allows them to see and chew. So it is with the mealybug and its symbionts. They ended up with a single metabolic network, distributed between their three complementary genomes. In the arithmetic of symbionts, one plus one plus one can equal one.

During replication, those nucleotides are read and translated into linear strings of amino acids (which make up enzymes and proteins) by a rule-governed process. The set of rules is called the genetic code. The DNA contains the sequence, but the code is implemented by RNA molecules. Certain DNA sequences, called codons, which are made up of three nucleotides, symbolize certain amino acid sequences. There is no ambiguity, but there is also not just one codon for each amino acid. For example, six different codons symbolize arginine, but only one codon symbolizes tryptophan. But the components of the DNA sequence (the symbol) do not resemble the components of the amino acid sequence (its meaning), just as the words that symbolize the components of a recipe do not resemble the components themselves.

The DNA is made up of two opposite spirals, positive and negative, which can easily be considered isomorphic to I Ching's yin () and yang (), or Leibniz's 0 and 1, or Joyce's and . These are bonded by four amino acids—adenine, guanine, cytosine and thymine, which are usually abbreviated A, G, C, T. If one dares to consider these isomorphic with active yang (), passive yang (), active yin () and passive yin (), or Leibniz's 01,11,10 and 00, or Joyce's and , then the parallel becomes staggering. In forming RNA messages—the genetic code—the T (thymine) drops out to be replaced by U (uracil) but we still have four elements—A, G, C, U—and if we permutate them by the now-familiar rule, making all possible combinations of three out of these basic four "letters," we get again 43 or 64 "words," which are the 64 elements of the genetic language.

Oxytocin is an amino acid peptide. A hormone. They call it the love chemical. “So?” Kelsey gave him a dead-eyed stare. “So when you’re further along in your pregnancy, more oxytocin receptors will be created in your uterine muscles. When the baby’s big enough, your oxytocin level will rise, triggering labor, and will help your muscles contract so you can give birth.” “Gross,” said Cory. “No,” Jack said. “Miraculous. Without the oxytocin, your muscles wouldn’t be strong enough to push that baby out. But because of that chemical, you are. You’ll be superhero strong.” He smiled right into Kelsey’s eyes. “Then, when you see your baby, that rush of oxytocin will help you bond. That’s why they call it the love drug. And if you breast-feed, more oxytocin gets released, strengthening that bond. The maternal instinct is the strongest instinct in the world. Chemistry is definitely part of that.

In borrowing from a food culture, pay attention to how a culture eats as well as to what it eats. In the case of the French paradox, for example, it may not be the dietary nutrients that keep the French healthy (lots of saturated fat and white flour?!) as much as their food habits: small portions eaten at leisurely communal meals; no second helpings or snacking. Pay attention, too, to the combinations of foods in traditional cultures: In Latin America, corn is traditionally cooked with lime and eaten with beans; what would otherwise be a nutritionally deficient staple becomes the basis of a healthy, balanced diet. (The beans supply amino acids lacking in corn, and the lime makes niacin available.) Cultures that took corn from Latin America without the beans or the lime wound up with serious nutritional deficiencies such as pellagra. Traditional diets are more than the sum of their food parts.

Recently scientists have found that cephalopods (the family that contains the octopus) can recode their RNA. RNA molecules have the privilege of establishing codes with DNA (in the part of the RNA that recognizes the three-nucleotide DNA codon sequence) and also with proteins (in the separate part of the RNA that recognizes the amino acid). Recoding the RNA means that new proteins can be constructed while the DNA sequence of symbols stays the same. The collective result is the destruction of the one-to-one gene-to-protein correspondence. Recoding allows a single octopus gene to produce many different types of proteins from the same DNA sequence.18 This is a big deal. It is evidence against the three concepts in biology that dismiss semiotic systems in living organisms. The system can change its code. The system has an internal codemaker that can produce biological innovations—new proteins—but not via natural selection. It illustrates the arbitrariness of the connection of a symbol with its meaning in a living system. If symbols within living systems

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In network models of the interactome, these truncating mutations can be thought of as the removal of one node along with all its edges - a node removal. Nonconservative missense mutations of amino acids in the protein core that lead to major folding problems, protein aggregation, and premature protein degradation can also be modeled as node removals. At the other end of the mutational spectrum are small in-frame indels or missense mutations. These can preserve protein folding, but may modify the active site of an enzyme or affect the binding to another protein or macromolecule. In network models, these mutations, which specifically perturb a single molecular interaction, have been labeled as edge-specific or "edgetic". While investigation of the precise interaction defects associated with point mutations is of course not new, the term edgetic promotes a subtle yet meaningful archetype shift from conventional gene-centered models, which emphasize consideration of which specific edges are affected by a mutation, complement and extend classic gene-centric models, which ascertain only whether a gene product is present or not present and neglect less overt alterations of a given gene or gene product.

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.

— PAULING’S ADVOCACY GAVE BIRTH TO a vitamin and supplement industry built on sand. Evidence for this can be found by walking into a GNC center—a wonderland of false hope. Rows and rows of megavitamins and dietary supplements promise healthier hearts, smaller prostates, lower cholesterol, improved memory, instant weight loss, lower stress, thicker hair, and better skin. All in a bottle. No one seems to be paying attention to the fact that vitamins and supplements are an unregulated industry. As a consequence, companies aren’t required to support their claims of safety or effectiveness. Worse, the ingredients listed on the label might not reflect what’s in the bottle. And we seem to be perfectly willing to ignore the fact that every week at least one of these supplements is pulled off the shelves after it was found to cause harm. Like the L-tryptophan disaster, an amino acid sold over the counter and found to cause a disease that affected 5,000 people and killed 28. Or the OxyElite Pro disaster, a weight-loss product that caused 50 people to suffer severe liver disease; one person died and three others needed lifesaving liver transplants. Or the Purity First disaster, a Connecticut company’s vitamin preparations that were found to contain two powerful anabolic steroids, causing masculinizing symptoms in dozens of women in the Northeast.

performance during PMS: Take 250 milligrams of magnesium, 45 milligrams of zinc, 80 milligrams of aspirin (baby aspirin), and 1 gram of omega-3 fatty acids (flaxseed and fish oil) each night for the 7 days before your period starts. Pretraining: Take 5 to 7 grams of branched-chain amino acid supplement (BCAAs) to fight the lack of mojo. These amino acids cross the blood-brain barrier and decrease the estrogen-progesterone effect on central nervous system fatigue. In training: Consume a few more carbohydrates per hour. In this high-hormone phase, aim for about 0.45 gram of carbohydrate per pound of body weight (about 61 grams for a 135-pound woman) per hour. In the low-hormone phase (first 2 weeks of the cycle), you can go a bit lower—about 0.35 gram of carbohydrate per pound of body weight (about 47 grams for a 135-pound woman) per hour. (For reference: 2.2 kilograms = 1 pound.) Post-training: Recovery is critical. Progesterone is extremely catabolic (breaks muscle down) and inhibits recovery. Aim to consume 20 to 25 grams of protein within 30 minutes of finishing your session. Overall you should aim to get 0.9 to 1 gram of protein per pound per day (a 135-pound woman needs about 122 to 135 grams of protein per day; see the Roar Daily Diet Cheat Sheet for Athletes for more information). THE MARTIAL ARTIST WHO BEAT HER BLOAT It may not be nice to fool Mother Nature, but there are definitely times when you need to trick her a little.

Indian farmers grow maize in what is called a milpa. The term means “maize field,” but refers to something considerably more complex. A milpa is a field, usually but not always recently cleared, in which farmers plant a dozen crops at once, including maize, avocados, multiple varieties of squash and bean, melon, tomatoes, chilis, sweet potato, jicama (a tuber), amaranth (a grain-like plant), and mucuna (a tropical legume). In nature, wild beans and squash often grow in the same field as teosinte, the beans using the tall teosinte as a ladder to climb toward the sun; below ground, the beans’ nitrogen-fixing roots provide nutrients needed by teosinte. The milpa is an elaboration of this natural situation, unlike ordinary farms, which involve single-crop expanses of a sort rarely observed in unplowed landscapes. Milpa crops are nutritionally and environmentally complementary. Maize lacks digestible niacin, the amino acids lysine and tryptophan, necessary to make proteins and diets with too much maize can lead to protein deficiency and pellagra, a disease caused by lack of niacin. Beans have both lysine and tryptophan, but not the amino acids cysteine and methionine, which are provided by maize. As a result, beans and maize make a nutritionally complete meal. Squashes, for their part, provide an array of vitamins; avocados, fats. The milpa, in the estimation of H. Garrison Wilkes, a maize researcher at the University of Massachusetts in Boston, “is one of the most successful human inventions ever created.

Hm? These cherry tomatoes... they've been dried. Right, Tadokoro?" "Y-yes, sir! Back home, winter can be really long. In the summer we harvest a lot of vegetables and preserve them so we can have them in winter too. Mostly by sun drying them. When I was little, I'd help with that part. That's when my Ma -um, I mean, my mother- taught me how to dry them in the oven. You cut the cherry tomatoes in half, sprinkle them with rock salt and then slowly dry them at a low temperature, around 245* F. I, um... thought they'd make a nice accent for the terrine..." "Right. Tomatoes are rich in the amino acid glutamate essential in umami. Drying them concentrates the glutamate, greatly increasing the amount of sweetness the tongue senses. In Shinomiya's case... ... his nine-vegetable terrine focused on fresh vegetables, with their bright and lively flavors. But this recette accentuates the savory deliciousness of vegetables preserved over time. Both dishes are vegetable terrines... ... but one centers on the delicacy of the fresh... ... while the other on the savory goodness of the ripe and aged. They are two completely different approaches to the same ingredient- vegetables!" "Mmm! This is the flavor that warms the soul. You can feel my darling Megumi's kindness in every bite." "For certain. If Shinomiya is the "Vegetable Magician"... ... I would say Megumi is... a modest spirit who gifts you with the bounty of nature. a Vegetable Colobuckle!" *A tiny spirit from Ainu folklore said to live under butterbur leaves* "No, that's not what she is! Megumi is a spirit who brings happiness and tastiness... a Vegetable Warashi!" *Childlike spirits from Japanese folklore said to bring good fortune* "Or perhaps she is that spirit which delivers the bounty of vegetables from the snowy north... a Vegetable Yukinoko!" *Small snow sprites* "It's not winter, so you can't call her a snow sprite!" "How come all of you are picking spirits from Japanese folklore anyway?

In describing a protein it is now common to distinguish the primary, secondary and tertiary structures. The primary structure is simply the order, or sequence, of the amino-acid residues along the polypeptide chains. This was first determined by [Frederick] Sanger using chemical techniques for the protein insulin, and has since been elucidated for a number of peptides and, in part, for one or two other small proteins. The secondary structure is the type of folding, coiling or puckering adopted by the polypeptide chain: the a-helix structure and the pleated sheet are examples. Secondary structure has been assigned in broad outline to a number of librous proteins such as silk, keratin and collagen; but we are ignorant of the nature of the secondary structure of any globular protein. True, there is suggestive evidence, though as yet no proof, that a-helices occur in globular proteins, to an extent which is difficult to gauge quantitatively in any particular case. The tertiary structure is the way in which the folded or coiled polypeptide chains are disposed to form the protein molecule as a three-dimensional object, in space. The chemical and physical properties of a protein cannot be fully interpreted until all three levels of structure are understood, for these properties depend on the spatial relationships between the amino-acids, and these in turn depend on the tertiary and secondary structures as much as on the primary. Only X-ray diffraction methods seem capable, even in principle, of unravelling the tertiary and secondary structures. [Co-author with G. Bodo, H. M. Dintzis, R. G. Parrish, H. Wyckoff, and D. C. Phillips]

Did you know that the term 'essential amino acids' is somewhat of a misnomer?! If they were that essential, wouldn't the body finding a way of synthesizing them? They are, however, essential for their presence in food.

For several centuries, the people in Europe, North Africa, North America and Western Asia depend on Elderberries for treatment of coughs and bacterial infections. Elderberries contain powerful antioxidants, vitamins A, B, and C, quercetin, flavonoids, carotenoids, and amino acids. Researchers continuously study the nutritional benefits and medicinal functions of Elderberry for variety of illnesses.

Change the material environment by altering the availability of amino acids or fats or carbohydrates in the diet of young animal, and the gene-environment interactions that occur will change as well, potentially affecting the structural development of the brain or the activity of hormone-releasing organs, with assorted behavioral consequences for the affected individual. Alter the experiential environment by changing the sensory inputs from the physical environment or from social interactions with other animals, and behavioral development will shift as well.

MEATS SHOULD BE UNCURED AND UNPROCESSED AND SHOULD NOT CONTAIN SODIUM NITRITE. Sausage, pepperoni, bacon, salami, and other processed meats often contain the color-fixing chemical sodium nitrite. Upon cooking, sodium nitrite reacts with amino acids in meat, yielding nitrosamines that have been linked to gastrointestinal cancers.

Although we fully understand the genetic code-i.e., how the information in a single gene is used to build a protein-we comprehend virtually nothing of the genomic code-i.e., how multiple genes spread across the human genome coordinate gene expression in space and time to build, maintain, and repair a human organism. The genetic code is simple: DNA is used to build RNA, and RNA is used to build a protein. A triplet of bases in DNA specifies one amino acid in the protein. The genomic code is complex: appended to a gene are sequences of DNA that carry information on when and where to express the gene. We do not know why certain genes are located in particular geographic locations in the genome, and how the tracts of DNA that lie between genes regulate and coordinate gene physiology. There are codes beyond codes, like mountains beyond mountains.

Everyone has an obligation to keep as young as possible. That implies useful work no matter how humble, and some serenity of mind, and normal weight, and daily outdoor exercise, and enough amino acids in fresh fat meat to do a good job of repair on breaking-down arteries.

Our complex, infinitely rich minds are, as is so often the case in the long history of life, the result of cooperative combinations of simple elements. In the case of minds, it is not a matter of cells assembled to form tissues and organs or of genes instructing amino acids to assemble myriad proteins. The basic unit for minds is the image, the image of a thing or of what a thing does, or what the thing causes you to feel; or the image of what you think of the thing; or the images of the words that translate any and all of the above.

SUPPLEMENTS FOR LOW TESTOSTERONE Supplement Dosage Considerations Saw palmetto (standardized to at least 85-percent fatty acids and astaxanthin) 400 mg three times a day. May be used by men to treat low testosterone and improve overall prostate health. Consult your physician before using. Tongkat ali 300 mg twice a day. May be used by men to treat low testosterone. Avoid if you have a prostate condition such as BPH or prostate cancer. Zinc 50 mg once a day. Zinc is important in immunity and acts as an antioxidant. It is also reported to help regulate blood sugar. May also be used by men to treat low testosterone and support prostate health. Take zinc in the form of an amino acid chelate or citrate. Check with your doctor before using.

Consider how the principles of the law of accelerating returns apply to the epochs we discussed in the first chapter. The combination of amino acids into proteins and of nucleic acids into strings of RNA established the basic paradigm of biology. Strings of RNA (and later DNA) that self-replicated (Epoch Two) provided a digital method to record the results of evolutionary experiments. Later on, the evolution of a species that combined rational thought (Epoch Three) with an opposable appendage (the thumb) caused a fundamental paradigm shift from biology to technology (Epoch Four). The upcoming primary paradigm shift will be from biological thinking to a hybrid combining biological and nonbiological thinking (Epoch Five), which will include “biologically inspired” processes resulting from the reverse engineering of biological brains.

You do not have to be a nutritional scientist or dietitian to figure out what to eat, and you don’t need to mix and match foods to achieve protein completeness. Any combination of natural foods will supply you with adequate protein, including all eight essential amino acids as well as nonessential amino acids.

Inspired in part by the uncanny ability of viruses to splice new genetic information into the DNA of bacterial cells, the pioneers of this early gene therapy realized they could use viruses to deliver therapeutic genes to humans. The first reported attempts came in the late 1960s from Stanfield Rogers, an American physician who had been studying a wart-causing virus in rabbits, Shope papillomavirus. Rogers was particularly interested in one aspect of the Shope virus: It caused rabbits to overproduce arginase, an enzyme their bodies used to neutralize arginine, a harmful amino acid. The sick rabbits had much more arginase in their systems, and much less arginine, than healthy rabbits. What’s more, Rogers found that researchers who had worked with the virus also had lower-than-normal levels of arginine in their blood. Apparently these scientists had contracted the infections from the rabbits, and these infections had led to lasting changes in the researchers’ bodies as well. Rogers suspected that the Shope virus was ferrying a gene for heightened arginase production into cells. As he marveled at the virus’s ability to transfer its genetic information so effectively, he began to wonder if an engineered version could deliver other, useful genes. Many years later, Rogers would recall: “It was clear that we had uncovered a therapeutic agent in search of a disease!” Rogers didn’t have to wait long for a disease

In addition to being essential for metabolism, individual B vitamins have also been identified for their role in neurotransmitter production. Vitamin B6 is required for the production of dopamine, serotonin, and an amino acid neurotransmitter called gamma-aminobutyric acid (GABA). GABA promotes relaxation and reduces stress and anxiety. Widely touted as the “anxiety amino acid,” GABA is our body’s version of Valium. And to get that effect, rather than popping a pill you can eat foods high in vitamin B6 including skipjack tuna, chicken, bell peppers, turnip greens, shiitake mushrooms, and spinach.

Lp(a). People with high concentrations of Lp(a), an LDL variant, are at increased risk of heart problem and should focus on heart-healthy practices (exercise, low carbs). APO-E4. Apolipoproteins are a family of proteins that coat LDL, HDL, and chylomicron particles in order to make them water soluble. The APO-E4 subtype is a strong risk factor for Alzheimer’s and heart disease. Again, the best way to fight it, indeed, the only way, is through heart-healthy practices. Celiac Disease. This is caused by a reaction to gluten, which is found primarily in wheat. It can be quite serious if undiagnosed. Some cannot digest wheat. The solution is simple, though: no wheat or other glutens. LDL particle size. A predominance of small LDL particles causes heart disease. The size is determined by diet and exercise, but also genetically. Again heart-healthy practices can counteract this. Homeostatic weight. If you are on a low-carb diet and exercise, your body will regulate to the weight that your hypothalamus thinks is your healthiest. Further weight loss is difficult. The specific level is largely genetic. MTHFR. A deficiency of this could result in high homocysteine. Homocysteine is a toxic breakdown product of the essential amino acid methionine. Stress

Oral liquid EDTA chelation removes plaque from blood vessels by dissolving it away. Dissolved plaque exits the body via the kidneys. Blood pressure is reduced to normal (there is no prescription drug that can achieve this youthful result). L-arginine, L-Citrulline which are amino acids (proteins), and antioxidants to stimulate the body’s natural production of Nitric Oxide. These supplements restore youthful flexibility to blood vessels and reduces blood pressure (again, there is no prescription drug that can achieve this youthful result) IMPORTANT NOTE

These are the nine essential amino acids: leucine**, isoleucine**, valine**, lysine, threonine, tryptophan, methionine, phenylalanine, and histidine.

life’s business in a fundamentally different way—using a molecule other than DNA or RNA as genetic material, for example, or a different set of amino acids to build proteins.

Even if DNA is the only viable genetic molecule, there is no reason why the same amino acids in similar combinations would be used as enzymes by all life. Alien and terrestrial life forms simply wouldn’t mesh, so the aliens couldn’t eat our plants and animals.

The genetic program as a vital factor is not the same as the DNA molecules in the genes, for these are just molecules, not mindlike entities. The fact that qualities of mind are commonly projected onto the genes, especially the qualities of selfish, competitive people within capitalist societies, makes it easy to forget that they are just chemicals. As such, they play a chemical role, and their activity is confined to the chemical level. The genetic code in the DNA molecules determines the sequence of amino-acid building blocks in protein molecules , the so-called primary structure of the proteins. The genes dictate the primary stucture of proteins, not the specific shape of a duck's foot or a lamb's kidney or an orchid. The way the proteins are arranged in cells, the ways cells are arranged in tissues, and tissues in organs, and organs in organisms are not programmed in the genetic code , which can only program protein molecules. Given the right genes and hence the right proteins, and the right systems by which protein synthesis is controlled, the organism is somehow supposed to assemble itself automatically. This is rather like delivering the right materials to a building site at the right times and expecting a house to grow spontaneously.

In all known life, there are primarily twenty different amino acids. Stringing these twenty amino acids together in varied sequences produces varied proteins, just as intelligently stringing together the twenty-six letters of the English alphabet in varied sequences will produce varied sentences and sonnets.

While dining, the bats inject their victims with an anticoagulant enzyme to keep the nutrients flowing smoothly. And what might this glycoprotein be called? Draculin, of course. You may consume it yourself one day. Draculin’s four-hundred-plus amino acids are many times stronger than any other known anticoagulant; as a consequence, a drug derived from it, desmoteplase, has been approved for victims of stroke or heart attack.

In another study on Alzheimer's the risk of getting the disease was 3.3 times greater among people whose blood folic acid levels were in the lowest one-third range and 4.5 times greater when blood homocysteine levels were in the highest one-third. What are folic acid and homocysteine? Folic acid is a compound derived exclusively from plant-based foods such as green and leafy vegetables. Homocysteine is an amino acid that is derived primarily from animal protein. This study found that it was desirable to maintain low blood homocysteine and high blood folic acid. In other words, the combination of a diet high in animal-based foods and low in plant-based foods raises the risk of Alzheimer's disease

Chronic carbohydrate consumption, in general, ultimately depletes serotonin stores and greatly depletes the B vitamins required to convert amino acids into many needed neurotransmitters. Careful

HMMs are at the heart of speech-recognition systems like Siri. In speech recognition, the hidden states are written words, the observations are the sounds spoken to Siri, and the goal is to infer the words from the sounds. The model has two components: the probability of the next word given the current one, as in a Markov chain, and the probability of hearing various sounds given the word being pronounced. (How exactly to do the inference is a fascinating problem that we’ll turn to after the next section.) Siri aside, you use an HMM every time you talk on your cell phone. That’s because your words get sent over the air as a stream of bits, and the bits get corrupted in transit. The HMM then figures out the intended bits (hidden state) from the ones received (observations), which it should be able to do as long as not too many bits got mangled. HMMs are also a favorite tool of computational biologists. A protein is a sequence of amino acids, and DNA is a sequence of bases. If we want to predict, for example, how a protein will fold into a 3-D shape, we can treat the amino acids as the observations and the type of fold at each point as the hidden state. Similarly, we can use an HMM to identify the sites in DNA where gene transcription is initiated and many other properties.

Chen turned back to the box and examined the picture through the glass. White smudges were appearing on the front and back surfaces of the photograph, but he still had a long way to go. Fingerprints were nothing but sweat. After the water evaporated, an organic residue was left. The fumes from the superglue reacted with the amino acids, glucose, and peptides in the organics to form a white goo, but growing the goo took time. John figured he still had another ten or fifteen minutes before the prints would be usable.

Whey protein can be taken anytime, but it’s particularly effective as a post-workout source of protein because it’s rapidly digested, which causes a dramatic spike in amino acids in the blood (especially in leucine). CARBOHYDRATE

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.

Our hair is as much as 14 percent L-cysteine, an amino acid commonly used to make meat flavorings and to elasticize dough in commercial baking. How commonly? Enough to merit debate among scholars of Jewish dietary law, or kashrut. “Human hair, while not particularly appetizing, is Kosher,” states Rabbi Zushe Blech, the author of Kosher Food Production, on Kashrut.com “There is no ‘guck’ factor,” Blech maintained, in an e-mail. Dissolving hair in hydrochloric acid, which creates the L-cysteine, renders it unrecognizable and sterile.

I still opt for a scoop of plant-based protein powder from time to time—after a particularly brutal workout, if I’m feeling overly fatigued from training, or when I know I haven’t sourced quite enough whole food protein from my meals. I prefer to combine a variety of plant-based proteins for this purpose, such as hemp, pea, and sprouted brown rice, to ensure maximum bioavailability and assimilation of all the essential amino acids our bodies can’t produce themselves. In fact, I recently formulated my own plant-based protein recovery supplement, in cooperation with microbiologist Compton Rom of Ascended Health, called Jai Repair. Infused with a proprietary blend of additional reparative nutrients like Cordyceps mushroom extracts, L-glutamine, vitamin B12, and antioxidants such as resveratrol, Jai Repair is scientifically devised to enhance rapid recovery from exercise-induced stress and is a formula I’ve come to rely on as a key component in my training regime.

Meat, fish, dairy, poultry, and eggs almost universally have high levels of sulfur-containing amino acids, which are metabolized by the body into sulfuric acid. The

Our hair is as much as 14 percent L-cysteine, an amino acid commonly used to make meat flavorings and to elasticize dough in commercial baking. How commonly? Enough to merit debate among scholars of Jewish dietary law, or kashrut. “Human hair, while not particularly appetizing, is Kosher,