Cell Nucleus Quotes

However, there is a way to know for certain that Noah’s Flood and the Creation story never happened: by looking at our mitochondrial DNA (mtDNA).  Mitochondria are the “cellular power plants” found in all of our cells and they have their own DNA which is separate from that found in the nucleus of the cell.  In humans, and most other species that mitochondria are found in, the father’s mtDNA normally does not contribute to the child’s mtDNA; the child normally inherits its mtDNA exclusively from its mother.  This means that if no one’s genes have mutated, then we all have the same mtDNA as our brothers and sisters and the same mtDNA as the children of our mother’s sisters, etc. This pattern of inheritance makes it possible to rule out “population bottlenecks” in our species’ history.  A bottleneck is basically a time when the population of a species dwindled to low numbers.  For humans, this means that every person born after a bottleneck can only have the mtDNA or a mutation of the mtDNA of the women who survived the bottleneck. This doesn’t mean that mtDNA can tell us when a bottleneck happened, but it can tell us when one didn’t happen because we know that mtDNA has a rate of approximately one mutation every 3,500 years (Gibbons 1998; Soares et al 2009). So if the human race were actually less than 6,000 years old and/or “everything on earth that breathed died” (Genesis 7:22) less than 6,000 years ago, which would be the case if the story of Adam and the story of Noah’s flood were true respectively, then every person should have the exact same mtDNA except for one or two mutations.  This, however, is not the case as human mtDNA is much more diverse (Endicott et al 2009), so we can know for a fact that the story of Adam and Eve and the story of Noah are fictional.   There

A wallet shows a person’s personality and lifestyle. Just like a cell phone, it is at the center, forming the nucleus of the owner’s secrets, everything he carries on him.

In our every cell, furled at the nucleus, there is a ribbon two yards long and just ten atoms wide. Over a hundred million miles of DNA in very human individual, enough to wrap five million times around our world and make the Midgard serpent blush for shame, make even the Ourobouros worm swallow hard in disbelief. This snake-god, nucleotide, twice twisted, scaled in adenine and cytosine, in thymine and in guanine, is a one-man show, will be the actors, props and setting, be the apple and the garden both. The player bides his time, awaits his entrance to a drum-roll of igniting binaries. This is the only dance in town, this anaconda tango, this slow spiral up through time from witless dirt to paramecium, from blind mechanic organism to awareness. There, below the birthing stars, Life sways and improvises. Every poignant gesture drips with slapstick; pathos; an unbearably affecting bravery. To dare this stage, this huge and overwhelming venue. Squinting through the stellar footlights, hoping there's an audience, that there's someone out there, but dancing anyway. But dancing anyway.

A three-day-old human embryo is a collection of 150 cells called a blastocyst. There are, for the sake of comparison, more than 100,000 cells in the brain of a fly. If our concern is about suffering in this universe, it is rather obvious that we should be more concerned about killing flies than about killing three-day-old human embryos… Many people will argue that the difference between a fly and a three-day-old human embryo is that a three-day-old human embryo is a potential human being. Every cell in your body, given the right manipulations, every cell with a nucleus is now a potential human being. Every time you scratch your nose, you’ve committed a holocaust of potential human beings… Let’s say we grant it that every three-day-old human embryo has a soul worthy of our moral concern. First of all, embryos at this stage can split into identical twins. Is this a case of one soul splitting into two souls? Embryos at this stage can fuse into a chimera. What has happened to the extra human soul in such a case? This is intellectually indefensible, but it’s morally indefensible given that these notions really are prolonging scarcely endurable misery of tens of millions of human beings, and because of the respect we accord religious faith, we can’t have this dialogue in the way that we should. I submit to you that if you think the interests of a three-day-old blastocyst trump the interests of a little girl with spinal cord injuries or a person with full-body burns, your moral intuitions have been obscured by religious metaphysics.

Because cells are surrounded with a lipid membrane, essential oils are attracted to and able to penetrate the cell membrane to deliver nutrients to the cell nucleus.[103],[104],[105],[106],[107] This suggests that essential oils can affect cell function and behavior, thus influencing overall well-being. At the same time, the aroma of the essential oil that is inhaled travels to the limbic system where a cascade of psychophysiological effects is triggered in response.

If one stretches out the DNA contained in the nucleus of a human cell, one obtains a two-yard-long thread that is only ten atoms wide. This thread is a billion times longer than its own width. Relatively speaking, it is as if your little finger stretched from Paris to Los Angeles.

In the human body, each of approximately a trillion cells holds within its nucleus a complete and identical sequence of DNA. That is about 1.5 gigabytes of genetic information, and it would fill two CD-ROMs, yet the DNA sequence itself would fit on the point of a well-sharpened pencil.

school you may have learned the basic components of a cell: the nucleus that contains genetic material, the energy-producing mitochondria, the protective membrane at the outside rim, and the cytoplasm in between.

A cell has a nucleus and some other parts like membranes, plasmas and other stuff. Its energy is made up of protons, neurons and electrons. Genetic scientists, however, have discovered that the majority of a cell is made up of something unknown. Something akin to space filled with electromagnetic fibers of light. The human body is made up of some 37 trillion cells. What do you think you are made of? Who do you think you are?

According to Dr. Bruce Lipton, gene activity can change on a daily basis. If the perception in your mind is reflected in the chemistry of your body, and if your nervous system reads and interprets the environment and then controls the blood’s chemistry, then you can literally change the fate of your cells by altering your thoughts. In fact, Dr. Lipton’s research illustrates that by changing your perception, your mind can alter the activity of your genes and create over thirty thousand variations of products from each gene. He gives more detail by saying that the gene programs are contained within the nucleus of the cell, and you can rewrite those genetic programs through changing your blood chemistry.

Consider the genesis of a single-celled embryo produced by the fertilization of an egg by a sperm. The genetic material of this embryo comes from two sources: paternal genes (from sperm) and maternal genes (from eggs). But the cellular material of the embryo comes exclusively from the egg; the sperm is no more than a glorified delivery vehicle for male DNA—a genome equipped with a hyperactive tail. Aside from proteins, ribosomes, nutrients, and membranes, the egg also supplies the embryo with specialized structures called mitochondria. These mitochondria are the energy-producing factories of the cell; they are so anatomically discrete and so specialized in their function that cell biologists call them “organelles”—i.e., mini-organs resident within cells. Mitochondria, recall, carry a small, independent genome that resides within the mitochondrion itself—not in the cell’s nucleus, where the twenty-three pairs of chromosomes (and the 21,000-odd human genes) can be found. The exclusively female origin of all the mitochondria in an embryo has an important consequence. All humans—male or female—must have inherited their mitochondria from their mothers, who inherited their mitochondria from their mothers, and so forth, in an unbroken line of female ancestry stretching indefinitely into the past. (A woman also carries the mitochondrial genomes of all her future descendants in her cells; ironically, if there is such a thing as a “homunculus,” then it is exclusively female in origin—technically, a “femunculus”?) Now imagine an ancient tribe of two hundred women, each of whom bears one child. If the child happens to be a daughter, the woman dutifully passes her mitochondria to the next generation, and, through her daughter’s daughter, to a third generation. But if she has only a son and no daughter, the woman’s mitochondrial lineage wanders into a genetic blind alley and becomes extinct (since sperm do not pass their mitochondria to the embryo, sons cannot pass their mitochondrial genomes to their children). Over the course of the tribe’s evolution, tens of thousands of such mitochondrial lineages will land on lineal dead ends by chance, and be snuffed out. And here is the crux: if the founding population of a species is small enough, and if enough time has passed, the number of surviving maternal lineages will keep shrinking, and shrinking further, until only a few are left. If half of the two hundred women in our tribe have sons, and only sons, then one hundred mitochondrial lineages will dash against the glass pane of male-only heredity and vanish in the next generation. Another half will dead-end into male children in the second generation, and so forth. By the end of several generations, all the descendants of the tribe, male or female, might track their mitochondrial ancestry to just a few women. For modern humans, that number has reached one: each of us can trace our mitochondrial lineage to a single human female who existed in Africa about two hundred thousand years ago. She is the common mother of our species. We do not know what she looked like, although her closest modern-day relatives are women of the San tribe from Botswana or Namibia. I find the idea of such a founding mother endlessly mesmerizing. In human genetics, she is known by a beautiful name—Mitochondrial Eve.

DNA doesn’t do much work. It mainly stays at home in the nucleus of our cells, not venturing forth. Its primary activity is protecting the information it encodes and occasionally replicating itself.

In 1683 Leeuwenhoek discovered bacteria, but that was about as far as progress could get for the next century and a half because of the limitations of microscope technology. Not until 1831 would anyone first see the nucleus of a cell—it was found

Einstein said that we only use at most 8% of our brain’s capacity. I know this because one of my favorite things to do each night was to get into bed with her and learn from the books she was reading. She would read out loud to me the facts and then look at me and ask me what I thought. “What do you think is going on with the other 92%?” A cell has a nucleus and some other parts like membranes, plasms and other stuff. Its energy is made up of protons, neurons and electrons. Genetic scientists, however, have discovered that the majority of a cell is made up of something unknown. Something akin to space filled with electromagnetic fibers of light. The human body is made up of some 37 trillion cells. What do you think you are made of? Who do you think you are?

The heart of the cell is the nucleus. It contains the cell’s DNA—three feet of it, as we have already noted, scrunched into a space that we may reasonably call infinitesimal. The reason so much DNA can fit into a cell nucleus is that it is exquisitely thin. You would need twenty billion strands of DNA laid side by side to make the width of the finest human hair. Every cell in your body (strictly speaking, every cell with a nucleus) holds two copies of your DNA. That’s why you have enough to stretch to Pluto and beyond.

If I look at a forest from afar, I see a dark green velvet. As I move toward it, the velvet breaks up into trunks, branches and leaves: the bark of the trunks, the moss, the insects, the teeming complexity. In every eye of every ladybug, there is an extremely elaborate structure of cells connected to neurons that guide and enable them to live. Every cell is a city, every protein a castle of atoms; in each atomic nucleus an inferno of quantum dynamics is stirring, quarks and gluons swirl, excitations of quantum fields. This is only a small wood on a small planet that revolves around a little star, among one hundred billion stars in one of the thousand billion galaxies constellated with dazzling cosmic events. In every corner of the universe we find vertiginous wells of layers of reality.

Whatever their size or shape, nearly all your cells are built to fundamentally the same plan: they have an outer casing or membrane, a nucleus wherein resides the necessary genetic information to keep you going, and a busy space between the two called the cytoplasm.

For it is not cell nuclei, not even individual chromosomes, but certain parts of certain chromosomes from certain cells that must be isolated and collected in enormous quantities for analysis; that would be the precondition for placing the chemist in such a position as would allow him to analyse [the hereditary material] more minutely than [can] the morphologists ... For the morphology of the nucleus has reference at the very least to the gearing of the clock, but at best the chemistry of the nucleus refers only to the metal from which the gears are formed.

The case I’ve presented in this book suggests that humans are undergoing what biologists call a major transition. Such transitions occur when less complex forms of life combine in some way to give rise to more complex forms. Examples include the transition from independently replicating molecules to replicating packages called chromosomes or, the transition from different kinds of simple cells to more complex cells in which these once-distinct simple cell types came to perform critical functions and become entirely mutually interdependent, such as the nucleus and mitochondria in our own cells. Our species’ dependence on cumulative culture for survival, on living in cooperative groups, on alloparenting and a division of labor and information, and on our communicative repertoires mean that humans have begun to satisfy all the requirements for a major biological transition. Thus, we are literally the beginnings of a new kind of animal.1 By contrast, the wrong way to understand humans is to think that we are just a really smart, though somewhat less hairy, chimpanzee. This view is surprisingly common. Understanding how this major transition is occurring alters how we think about the origins of our species, about the reasons for our immense ecological success, and about the uniqueness of our place in nature. The insights generated alter our understandings of intelligence, faith, innovation, intergroup competition, cooperation, institutions, rituals, and the psychological differences between populations. Recognizing that we are a cultural species means that, even in the short run (when genes don’t have enough time to change), institutions, technologies, and languages are coevolving with psychological biases, cognitive abilities, emotional responses, and preferences. In the longer run, genes are evolving to adapt to these culturally constructed worlds, and this has been, and is now, the primary driver of human genetic evolution. Figure 17.1.

But to understand what DNA and genes really are, we have to decouple the two words. They’re not identical and never have been. DNA is a thing—a chemical that sticks to your fingers. Genes have a physical nature, too; in fact, they’re made of long stretches of DNA. But in some ways genes are better viewed as conceptual, not material. A gene is really information—more like a story, with DNA as the language the story is written in. DNA and genes combine to form larger structures called chromosomes, DNA-rich volumes that house most of the genes in living things. Chromosomes in turn reside in the cell nucleus, a library with instructions that run our entire bodies.

All vertebrates except mammals have nuclei in their red blood cells.In mammals, these cells go through an extra stage of development in which the nucleus is discarded. The resulting cells are smaller, can flow through smaller capillaries, can be packed with more hemoglobin, and thus can carry oxygen and carbon dioxide more efficiently.

A nutritive centre, anatomically considered, is merely a cell, the nucleus of which is the permanent source of successive broods of young cells, which from time to time fill the cavity of their parent, and carrying with them the cell wall of the parent, pass off in certain directions, and under various forms, according to the texture or organ of which their parent forms a part.

To visualize this dance, the transparent components of the cell had to be coloured using a stain. As it happened, the stains that were best able to colour the chromosomes were acidic. Unfortunately, these stains tended to dissolve the mitochondria; their obsession with the nucleus meant that cytologists were simply dissolving the evidence. Other stains were ambivalent, colouring mitochondria only transiently, for the mitochondria themselves rendered the stain colourless. Their rather ghostly appearance and disappearance was scarcely conducive to firm belief. Finally Carl Benda demonstrated, in 1897, that mitochondria do have a corporeal existence in cells. He defined them as ‘granules, rods, or filaments in the cytoplasm of nearly all cells … which are destroyed by acids or fat solvents.’ His term, mitochondria (pronounced ‘my-toe-con-dree-uh’), was derived from the Greek mitos, meaning thread, and chondrin, meaning small grain. Although his name alone stood the test of time, it was then but one among many. Mitochondria have revelled in more than thirty magnificently obscure names, including chondriosomes, chromidia, chondriokonts, eclectosomes, histomeres, microsomes, plastosomes, polioplasma, and vibrioden.

When jungles of neurons fire in unison to support a new thought, an additional chemical (a protein) is created within the nerve cell and makes its way to the cell’s center, or nucleus, where it lands in the DNA. The protein then switches on several genes. Since the job of the genes is to make proteins that maintain both the structure and function of the body, the nerve cell then quickly makes a new protein to create new branches between nerve cells.

professor taps his laptop, the images change, and we are lost in the world of red blood cells. The cell’s nucleus is small and round and serves as the cell’s command center. It controls the cell’s growth and reproduction. It is surrounded by a membrane. And on and on. Attached to our petition was Benderschmidt’s full report, including pages of impenetrable stuff on cells and blood. I confess that I have not read it entirely, but something tells me Judge Kumar has.

Historically, chromosomes were not at all easy to study. They spend most of their existence balled up in an indistinguishable mass in the cell nucleus. The only way to count them was to get fresh samples from living cells at the moment of cell division, and that was a tall order. Cell biologists, according to one report, “literally waited at the foot of the gallows in order to fix the testis of an executed criminal immediately after death before the chromosomes could clump.” Even then the chromosomes tended to overlap and blur, making anything but a rough count difficult. But in 1921, a cytologist at the University of Texas named Theophilus Painter announced that he had secured good images and declared with reassuring confidence that he had counted twenty-four pairs of chromosomes. That number stuck, universally unquestioned, for thirty-five years until a closer examination in 1956 showed that in fact we have just twenty-three pairs—a fact that had been clearly evident in photographs for years (including in at least one popular textbook illustration) had anyone taken the trouble to count.

The incredible specified complexity of life becomes obvious when one considers the message found in the DNA of a one-celled amoeba (a creature so small, several hundred could be lined up in an inch). Staunch Darwinist Richard Dawkins, professor of zoology at Oxford University, admits that the message found in just the cell nucleus of a tiny amoeba is more than all thirty volumes of the Encyclopedia Britannica combined, and the entire amoeba has as much information in its DNA as 1,000 complete sets of the Encyclopedia Britannica!2 In other words, if you were to spell out all of the A, T, C, and G in the unjustly called primitive amoeba (as Dawkins describes it), the letters would fill 1,000 complete sets of an encyclopedia! Now, we must emphasize that these 1,000 encyclopedias do not consist of random letters but of letters in a very specific orderjust like real encyclopedias. So heres the key question for Darwinists like Dawkins: if simple messages such as Take out the garbageMom, Mary loves Scott, and Drink Coke require an intelligent being, then why doesnt a message 1,000 encyclopedias long require one?

In 2002 scientists demonstrated beautifully just how random the process of X inactivation really is, by cloning a calico cat. They took cells from an adult female cat, and carried out the standard (but still fiendishly tricky) process of cloning. To do this, they removed the nucleus from the adult cat cell and put it into a cat egg whose own chromosomes they’d removed. This egg was implanted into a surrogate cat mother, and a lively and beautiful female kitten was born. And she didn’t look anything like the genetically identical cat of which she was a clone.18

Let the chromosomes be represented by the keyboard of a grand piano-a very grand piano with thousands of keys. Then each key will be a gene. Every cell in the body carries a microscopic but complete keyboard in its nucleus. But each specialised cell is only permitted to sound one chord, according to its specialty-the rest of its genetic keyboard has been inactivated by scotch tape. The fertilised egg, and the first few generations of its daughter cells, had the complete keyboard at their disposal. But succesive generations have, at each 'point of no return', larger and larger areas of it covered by scotch tape. In the end, a muscle cell can only do one thing: contract-strike a single chord. The scotch tape is known in the language of genetics as the 'repressor'. The agent which strikes the key and activates the gene is an 'inducer'. A mutated gene is a key which has gone out of tune. When quite a lot of key have gone quite a lot out of tune, the result, we were asked to believe, was a much improved, wonderful new melody- a reptile transformed into a bird, or a monkey into a man. It seems that at some point the theory must have gone wrong. The point where it went wrong was the atomistic concept of the gene.

We have seen that the region of our brain known as the amygdala orchestrates emotion and that it communicates with the hypothalamus, the region that houses the nerve cells that control instinctive behavior such as parenting, feeding, mating, fear, and fighting (chapter 3, fig. 3.5). Anderson found a nucleus, or cluster of neurons, within the hypothalamus that contains two distinct populations of neurons: one that regulates aggression and one that regulates mating (fig. 7.8). About 20 percent of the neurons located on the border between the two populations can be active during either mating or aggression. This suggests that the brain circuits regulating these two behaviors are intimately linked.

Well, start with a cell again. Inside the cell is a nucleus, and inside each nucleus are the chromosomes—forty-six little bundles of complexity, of which twenty-three come from your mother and twenty-three from your father. With a very few exceptions, every cell in your body—99.999 percent of them, say—carries the same complement of chromosomes. (The exceptions are red blood cells, some immune system cells, and egg and sperm cells, which for various organizational reasons don’t carry the full genetic package.) Chromosomes constitute the complete set of instructions necessary to make and maintain you and are made of long strands of the little wonder chemical called deoxyribonucleic acid or DNA—“the most extraordinary

Shadow is the blue patch where the light doesn’t hit. It is mystery itself, and mystery is the ancients’ ultima Thule, the modern explorer’s Point of Relative Inaccessibility, that boreal point most distant from all known lands. There the twin oceans of beauty and horror meet. The great glaciers are calving. Ice that sifted to earth as snow in the time of Christ shears from the pack with a roar and crumbles to water. It could be that our instruments have not looked deeply enough. The RNA deep in the mantis’s jaw is a beautiful ribbon. Did the crawling Polyphemus moth have in its watery heart one cell, and in that cell one special molecule, and that molecule one hydrogen atom, and round that atom’s nucleus one wild, distant electron that split showed a forest, swaying?

Self-organizing Systems Biologists have long given up the idea that living organisms are just like machines. Medical practitioners today recognize the ineffectiveness of treating the human body as a separate mechanism. They speak about holistic healing, treating the whole person, and including the person’s social and physical environment. Today living organisms are described as self-regulating systems. They organize themselves, nourish themselves, heal themselves, propagate themselves, protect themselves, and interact creatively with other systems. We used to call this instinct—in animals if not in plants. Today we talk about genes that have coded messages or instructions that connect with one another in a DNA spiral in the nucleus of every living cell. If we were to write out the instructions contained in any one tiny DNA spiral we would fill about a thousand books of six hundred pages each.

The information capacity recorded in DNA is of a size which astonishes scientists. There is enough information in a single human DNA molecule to fill a million encyclopedia pages or 1,000 volumes. To put it another way, the nucleus of a cell contains information, equivalent to that in a 1 million-page encyclopedia. It serves to control all the functions of the human body. To make a comparison, the 23-volume Encyclopedia Britannica, one of the largest encyclopedias in the world, contains a total of 25,000 pages. Yet a single molecule in the nucleus of a cell, and which is so much smaller than that cell, contains a store of information 40 times larger than the world's largest encyclopedias. That means that what we have here is a 1,000-volume encyclopedia, the like of which exists nowhere else on Earth. This is a miracle of design and creation within our very own bodies, for which evolutionists and materialists have no answer.

It was the magnesium. The addition of the ion was critical: with the solution supplemented with magnesium, the ribosome remained glued together, and Brenner and Jacob finally purified a miniscule amount of the messenger molecule out of bacterial cells. It was RNA, as expected-but RNA of a special kind. The messenger was generated afreah when a gene was translated. Like DNA, these RNA molecules were built by stringing together four bases-A,G,C, and U (in the RNA copy of a gene, remember, the T found in DNA is substituted for U). Notably, Brenner and Jacob later discovered the messenger RNA was a facsimile of the DNA chain-a copy made from the original. The RNA copy of a gene then moved from the nucleus to the cytosol, where its message was decoded to build a protein. The messenger RNA was neither an inhabitant of heaven nor of hell-but a professional go-between. The generation of an RNA copy of a gene was termed transcription-referring to the rewriting of a word or sentence in a language close to the original. A gene's code (ATGGGCC...) was transcribed into an RNA code (AUGGGCC...).

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.

Suppose you entered a boat race. One hundred rowers, each in a separate rowboat, set out on a ten-mile race along a wide and slow-moving river. The first to cross the finish line will win $10,000. Halfway into the race, you’re in the lead. But then, from out of nowhere, you’re passed by a boat with two rowers, each pulling just one oar. No fair! Two rowers joined together into one boat! And then, stranger still, you watch as that rowboat is overtaken by a train of three such rowboats, all tied together to form a single long boat. The rowers are identical septuplets. Six of them row in perfect synchrony while the seventh is the coxswain, steering the boat and calling out the beat for the rowers. But those cheaters are deprived of victory just before they cross the finish line, for they in turn are passed by an enterprising group of twenty-four sisters who rented a motorboat. It turns out that there are no rules in this race about what kinds of vehicles are allowed. That was a metaphorical history of life on Earth. For the first billion years or so of life, the only organisms were prokaryotic cells (such as bacteria). Each was a solo operation, competing with others and reproducing copies of itself. But then, around 2 billion years ago, two bacteria somehow joined together inside a single membrane, which explains why mitochondria have their own DNA, unrelated to the DNA in the nucleus.35 These are the two-person rowboats in my example. Cells that had internal organelles could reap the benefits of cooperation and the division of labor (see Adam Smith). There was no longer any competition between these organelles, for they could reproduce only when the entire cell reproduced, so it was “one for all, all for one.” Life on Earth underwent what biologists call a “major transition.”36 Natural selection went on as it always had, but now there was a radically new kind of creature to be selected. There was a new kind of vehicle by which selfish genes could replicate themselves. Single-celled eukaryotes were wildly successful and spread throughout the oceans.

In physical terms, we know that every human action can be reduced to a series of impersonal events: Genes are transcribed, neurotransmitters bind to their receptors, muscle fibers contract, and John Doe pulls the trigger on his gun. But for our commonsense notions of human agency and morality to hold, it seems that our actions cannot be merely lawful products of our biology, our conditioning, or anything else that might lead others to predict them. Consequently, some scientists and philosophers hope that chance or quantum uncertainty can make room for free will. For instance, the biologist Martin Heisenberg has observed that certain processes in the brain, such as the opening and closing of ion channels and the release of synaptic vesicles, occur at random, and cannot therefore be determined by environmental stimuli. Thus, much of our behavior can be considered truly “self-generated”—and therein, he imagines, lies a basis for human freedom. But how do events of this kind justify the feeling of free will? “Self-generated” in this sense means only that certain events originate in the brain. If my decision to have a second cup of coffee this morning was due to a random release of neurotransmitters, how could the indeterminacy of the initiating event count as the free exercise of my will? Chance occurrences are by definition ones for which I can claim no responsibility. And if certain of my behaviors are truly the result of chance, they should be surprising even to me. How would neurological ambushes of this kind make me free? Imagine what your life would be like if all your actions, intentions, beliefs, and desires were randomly “self-generated” in this way. You would scarcely seem to have a mind at all. You would live as one blown about by an internal wind. Actions, intentions, beliefs, and desires can exist only in a system that is significantly constrained by patterns of behavior and the laws of stimulus-response. The possibility of reasoning with other human beings—or, indeed, of finding their behaviors and utterances comprehensible at all—depends on the assumption that their thoughts and actions will obediently ride the rails of a shared reality. This is true as well when attempting to understand one’s own behavior. In the limit, Heisenberg’s “self-generated” mental events would preclude the existence of any mind at all. The indeterminacy specific to quantum mechanics offers no foothold: If my brain is a quantum computer, the brain of a fly is likely to be a quantum computer, too. Do flies enjoy free will? Quantum effects are unlikely to be biologically salient in any case. They play a role in evolution because cosmic rays and other high-energy particles cause point mutations in DNA (and the behavior of such particles passing through the nucleus of a cell is governed by the laws of quantum mechanics). Evolution, therefore, seems unpredictable in principle.13 But few neuroscientists view the brain as a quantum computer. And even if it were, quantum indeterminacy does nothing to make the concept of free will scientifically intelligible. In the face of any real independence from prior events, every thought and action would seem to merit the statement “I don’t know what came over me.” If determinism is true, the future is set—and this includes all our future states of mind and our subsequent behavior. And to the extent that the law of cause and effect is subject to indeterminism—quantum or otherwise—we can take no credit for what happens. There is no combination of these truths that seems compatible with the popular notion of free will.

The Greek word for kernel is karys, so the word used to describe creatures without a nucleus is prokaryotic—the name, originally procariotique, was coined in the 1930s by Edouard Chatton, a French marine biologist—while creatures with nuclei are eukaryotic. Bacteria are prokaryotes. Pretty much everything else, from yeast to elephants, are eukaryotes. This realization resulted in the creation of a fifth Kingdom, dividing one-celled eukaryotes, who retained the Protist name, from prokaryotes. Thus, by the time the dust had settled, in the 1970s, the hierarchical tree of life had two domains—Prokarya and Eucarya—and five kingdoms: Plantae, Animalae, Fungi, Protista, and Bacteria.*

Drugs of abuse alter the same brain circuits. The drive to seek out life-sustaining environmental cues like food and water is maintained because these substances activate the central players in the brain motivation circuit, dopamine-using neurons of the ventral tegmental area. These neurons manufacture the neurotransmitter dopamine and release it onto their downstream target cells in brain regions like the nucleus accumbens that are also important components of the motivation circuit. Dopamine neuron firing appears to signal the things we urgently need to survive, and dopamine cells become active in response to food, water, warmth, and even sex.

For people who study these domains, the difference is clear. Both the Bacteria and the Archaea do not have nuclei. Whereas, you and I do … in our cells. That’s why we are said to be Eukaryotes; it’s from Greek words meaning “having nut” (having nucleus). The Archaea and Bacteria are Prokaryotes, meaning “before nut” (before nucleus). This turns out to be of astonishing significance in the natural history of living things. The

That need for surprise is what it’s all about. Surprise is visceral and immediate, and stokes our dopamine and our nucleus accumbens. But it’s fleeting, and rarely does any happiness come out of it. In fact, the frequent checking of cell phones, waiting for something to change, is linked to anxiety and depression.6 Of course, again, correlation is not causation. Do cell phones cause depression? Or are depressed people trying to eke out a little dopamine rush? Or both? I’ll tell you one thing: cell phones certainly don’t bring serenity.

Humans are primates, and primates are mammals. The first mammals appeared on earth between 200 and 250 million years ago—a very short time in evolutionary units. To put that figure in perspective, the first primitive unicellular organisms appeared roughly 4,500 million years ago; the first cell with a proper nucleus appeared about 1,500 million years ago;7 and the first animals with bones inside their body appeared on land only 380 million years ago.

So how does a cell go about ending its own existence? The actual mechanism of ‘cell suicide’ depends upon mitochondria, termed the ‘angels of death’ by Nick Lane in his book, Power, Sex and Suicide: Mitochondria and the Meaning of Life . The first change occurs in the mitochondrial inner membrane, which becomes damaged by aberrant biochemical activity, leading to the formation of pores in the mitochondrial membrane (Figure 12b, d). At this point, the mitochondrion becomes committed to trigger apoptosis, and releases cytochrome c (a protein crucial to its normal function of energy production) which exits through the newly formed pores. This information came to light as a result of some neat experiments in which apoptotic mitochondria were introduced into perfectly healthy cells, resulting in apoptosis. The released cytochrome c binds to several other proteins in the cytoplasm to form a complex called the apoptosome which, in turn, activates a cascade of ‘executioner enzymes’ which not only kill the cell but cause fragmentation of the nucleus and cytoplasm into bite-size pieces ready to be phagocytosed by neighbouring cells.

Although the nucleus might have been recognized by Antonie van Leeuwenhoek in the late 17th century, it was not until 1831 that it was reported as a specific structure in orchid epidermal cells by a Scottish botanist, Robert Brown (better known for recognizing ‘Brownian movement’ of pollen grains in water). In 1879, Walther Flemming observed that the nucleus broke down into small fragments at cell division, followed by re-formation of the fragments called chromosomes to make new nuclei in the daughter cells. It was not until 1902 that Walter Sutton and Theodor Boveri independently linked chromosomes directly to mammalian inheritance. Thomas Morgan’s work with fruit flies (Drosophila) at the start of the 20th century showed specific characters positioned along the length of the chromosomes, followed by the realization by Oswald Avery in 1944 that the genetic material was DNA. Some nine years later, James Watson and Francis Crick showed the structure of DNA to be a double helix, for which they shared the Nobel Prize in 1962 with Maurice Wilkins, whose laboratory had provided the evidence that led to the discovery. Rosalind Franklin, whose X-ray diffraction images of DNA from the Wilkins lab had been the key to DNA structure, died of cancer aged 37 in 1958, and Nobel Prizes are not awarded posthumously. Watson and Crick published the classic double helix model in 1953. The final piece in the jigsaw of DNA structure was produced by Watson with the realization that the pairing of the nucleotide bases, adenine with thymine and guanine with cytosine, not only provided the rungs holding the twisting ladder of DNA together, but also provided a code for accurate replication and a template for protein assembly. Crick continued to study and elucidate the base pairing required for coding proteins, and this led to the fundamental ‘dogma’ that ‘DNA makes RNA and RNA makes protein’. The discovery of DNA structure marked an enormous advance in biology, probably the most significant since Darwin’s publication of On the Origin of Species .

In the stratum granulosum, or granular layer, the cells flatten, release their fats and lose their nucleus, the cell’s gene-containing brain.

much of the nucleus remains a mystery: the doors to the command center of the cell are still partially closed. As one biologist put it, “We can only hope that what the geneticist J. B. S. Haldane posited on the cosmos will prove not to be true for the nucleus: “ ‘Now, my suspicion is that the universe is not only queerer than we suppose, but queerer than we can suppose.

Whenever we describe the genome we talk about it in very two-dimensional terms, almost like a railway track. Peter Fraser’s laboratory at the Babraham Institute outside Cambridge has published some extraordinary work showing it’s probably nothing like this at all. He works on the genes that code for the proteins required to make haemoglobin, the pigment in red blood cells that carries oxygen all around the body. There are a number of different proteins needed to create the final pigment, and they lie on different chromosomes. Doctor Fraser has shown that in cells that produce large amounts of haemoglobin, these chromosome regions become floppy and loop out like tentacles sticking out of the body of an octopus. These floppy regions mingle together in a small area of the cell nucleus, waving about until they can find each other. By doing this, there is an increased chance that all the proteins needed to create the functional haemoglobin pigment will be expressed together at the same time2

Paul declares the “invisible things of him from the creation of the world” can help us understand “his eternal power and Godhead” (Romans 1:20). The truth that God is a “tri-unity” of two invisible persons (Father and Spirit) and one visible person (Jesus) is evident even in creation. The universe is composed of three structures: space, matter, and time. Of these three, only matter is visible. Space requires length, height, and width to constitute space. Each dimension is separate and distinct in itself, yet the three form space—if you remove height, you no longer have space. Time is also a tri-unity of past, present, and future. Two are invisible (past and future), and one visible (present). Each is separate and distinct, as well as essential for time to exist. Man is also a “tri-unity,” having physical, mental, and spiritual components. Again, two are invisible (mental and spiritual) and one visible (physical). Cells compose the fundamental structural unit of all living organisms. All organic life is made up from cells that consist of three primary parts: the outer wall, the cytoplasm, and the nucleus (like the shell, white, and yoke of an egg). If any one is removed, the cell dies. In each of these examples, the removal of any one component results in the demise of the whole. In like manner, the Godhead contains three distinct persons: Father, Son, and Holy Spirit. Each is God (Ephesians 4:6; Titus 2:13; Acts 5:3, 4), yet there is one God. The removal of one person destroys the unity of the whole. Even the gospel story illustrates the interdependency of threes. The sanctuary had three places: the Courtyard, the Holy Place, and the Most Holy Place. There are three stages of salvation: justification, sanctification, and glorification. In Isaiah 6:3, the angels around God’s throne cry “Holy, Holy, Holy” three times—once for the Father, once for the Son, and once for the Holy Spirit.

Amygdala and Prefrontal Circuits Underlying the Conditioning and Extinction of Defense Responses. Threat conditioning involves convergence of the conditioned stimulus (CS) and the unconditioned stimulus (US) in the lateral amygdala (LA). LA sends connections to the intercalated cells (ITC), lateral part of the central nucleus (CeAL), and threat neurons in the basal amygdala (BA). BA threat neurons connect with ITC and the medial part of the central nucleus (CeAm). Within CeAl different cells receive inputs from LA and ITC, but the two cell populations are interconnected. The prelimbic region of the prefrontal cortex (PFCPL) connects and regulates threat neurons in BA. Outputs of CeAl connect to CeAM, which connects with response control areas. Similar circuits are involved in extinction except that the PFCIL connects with extinction rather than threat neurons in BA. Extinction neurons in BA then regulate CeAM. BASED ON LEE ET AL (2013).

There are at least three components to the process that prevent the original CS-US association from being expressed after extinction.28 One is that the CS–no US association exerts inhibitory control over LA processing (thus weakening the ability of the CS to activate the CS-US association). Another is that connections from the infralimbic cortex to inhibitory cells in the basal nucleus and the intercalated area further suppress the ability of the CS to flow from the LA to the CeA. Finally, extinction interferes with the balance between the lateral and medial areas of the CeA and prevents the expression of outputs of the medial CeA to response control circuits.

Reprogramming is what John Gurdon demonstrated in his ground-breaking work when he transferred the nuclei from adult toads into toad eggs. It’s what happened when Keith Campbell and Ian Wilmut cloned Dolly the Sheep by putting the nucleus from a mammary gland cell into an egg. It’s what Yamanaka achieved when he treated somatic cells with four key genes, all of which code for proteins highly expressed naturally during this reprogramming phase. The egg is a wonderful thing, honed through hundreds of millions of years of evolution to be extraordinarily effective at generating vast quantities of epigenetic change, across billions of base-pairs. None of the artificial means of reprogramming cells comes close to the natural process in terms of speed or efficiency. But the egg probably doesn’t quite do everything unaided. At the very least, the pattern of epigenetic modifications in sperm is one that allows the male pronucleus to be reprogrammed relatively easily. The sperm epigenome is primed to be reprogrammed6. Unfortunately, these priming chromatin modifications (and many other features of the sperm nucleus), are missing if an adult nucleus is reprogrammed by transferring it into a fertilised egg. That’s also true when an adult nucleus is reprogrammed by treating it with the four Yamanaka factors to create iPS cells. In both these circumstances, it’s a real challenge to completely reset the epigenome of the adult nucleus. It’s just too big a task. This is probably why so many cloned animals have abnormalities and shortened lifespans. The defects that are seen in these cloned animals are another demonstration that if early epigenetic modifications go wrong, they may stay wrong for life. The abnormal epigenetic modification patterns result in permanently inappropriate gene expression, and long-term ill-health.

The major mechanisms by which cells transmit signals to each other, and how these signals are conveyed from the cell membrane to the nucleus to modulate gene expression, commonly referred to as cell signalling, are also covered in Chapter 2.

cell, for example, has about 2 m of DNA—a length about 250,000 times greater than the cell’s diameter. Yet before the cell can divide to form genetically identical daughter cells, all of this DNA must be copied, or replicated, and then the two copies must be separated so that each daughter cell ends up with a complete genome. The replication and distribution of so much DNA is manageable because the DNA molecules are packaged into structures called chromosomes, so named because they take up certain dyes used in microscopy (from the Greek chroma, color, and soma, body) (Figure 12.3). Each eukaryotic chromosome consists of one very long, linear DNA molecule associated with many proteins (see Figure 6.9). The DNA molecule carries several hundred to a few thousand genes, the units of information that specify an organism’s inherited traits. The associated proteins maintain the structure of the chromosome and help control the activity of the genes. Together, the entire complex of DNA and proteins that is the building material of chromosomes is referred to as chromatin. As you will soon see, the chromatin of a chromosome varies in its degree of condensation during the process of cell division. Every eukaryotic species has a characteristic number of chromosomes in each cell nucleus. For example, the nuclei of human somatic cells (all body cells except the reproductive cells) each contain 46 chromosomes, made up of two sets of 23, one set inherited from each parent. Reproductive cells, or gametes—sperm and eggs—have half as many chromosomes as somatic cells, or one set of 23 chromosomes in humans. The Figure 12.4 A highly condensed, duplicated human chromosome (SEM). Circle one sister chromatid of the chromosome in this micrograph. DRAW IT Sister chromatids Centromere 0.5μm number of chromosomes in somatic cells varies widely among species: 18 in cabbage plants, 48 in chimpanzees, 56 in elephants, 90 in hedgehogs, and 148 in one species of alga. We’ll now consider how these chromosomes behave during cell division. Distribution of Chromosomes During Eukaryotic Cell Division When a cell is not dividing, and even as it replicates its DNA in preparation for cell division, each chromosome is in the form of a long, thin chromatin fiber. After DNA replication, however, the chromosomes condense as a part of cell division: Each chromatin fiber becomes densely coiled and folded, making the chromosomes much shorter and so thick that we can see them with a light microscope. Each duplicated chromosome has two sister chromatids, which are joined copies of the original chromosome (Figure 12.4). The two chromatids, each containing an identical DNA molecule, are initially attached all along their lengths by protein complexes called cohesins; this attachment is known as sister chromatid cohesion. Each sister chromatid has a centromere, a region containing

(mRNA), in a process called transcription. This mRNA then leaves the nucleus to enter the cytoplasm, where it is translated into protein by large multiprotein complexes called ribosomes. The proteins resulting from translation are then folded and glycosylated correctly by various means and directed towards their required location in the cell

Patterns and connections began to emerge, and I soon interpreted a thousand-year-old Native American medicine wheel as a stylized version of a cell. See plate 4 in the color insert to see a medicine wheel pictograph at the Palakti ruins. It has the same construction as a cell: its center circle is like the core nucleus; the lines on the outer surrounding circle could represent cell receptors and markers of identity. The four sets of three spokes point to the four directions, a central concept of

White blood cells are the only fully functional cells in the circulation. Red blood cells have lost their nuclei by the time they enter the bloodstream, and platelets, which also lack a nucleus, are cell fragments that have split off a relatively large parent cell known as a megakaryocyte {mega, extremely large + karyon, kernel + -cyte, cell}.

Even single cells have astonishing regenerative abilities. Acetabularia, the mermaid’s wineglass, is a single-celled green alga about five centimeters long, with three main parts: root-like structures called rhizoids that attach it to a rock, a stem and a cap about a centimeter wide (Figure 5.2). This very large cell has a single nucleus in one of the rhizoids. As the plant grows, its stem lengthens, it forms a series of whorls of hairs that later drop off, and finally forms the cap. If the cap is cut off by snipping the stem in two, after the cut has healed, a new tip grows and the stem forms a series of whorls of hairs and then a new cap, in a similar way to the normal pattern of growth. This can happen over and over again if the cap is cut off repeatedly.2 As discussed in the following chapter, the usual assumption is that genes somehow control or “program” the development of form, as if the nucleus, containing the genes, is a kind of brain controlling the cell. But Acetabularia shows that morphogenesis can take place without genes. If the rhizoid containing the nucleus is cut off, the alga can stay alive for months, and if the cap is cut off, it can regenerate a new one. Even more remarkable, if a piece is cut out of the stem, after the cuts have healed, a new tip grows from the end where the cap used to be and makes a new cap (Figure 5.2).3 Morphogenesis is goal-directed, and moves toward a morphic attractor even in the absence of genes. FIGURE 5.2. Regeneration of the alga Acetabularia mediterranea, an unusually large single-celled organism, up to 5cm tall, containing a green cap at the top of a long stalk, anchored at the base by root-like rhizoids. There is a large nucleus (shown as a black oval) in the basal part of the cell. When the stalk is cut off near the bottom, the basal part of the cell regenerates a new stalk and cap (shown on the right). When a part of the upper stalk is cut out, it grows a new cap and more stalk, even though it contains no nucleus.

In Berridge and Robinson’s view, pleasure is divided into “wanting” (hunt) and “liking” (feast). As we’ll see, the distinction is especially important in addiction because each type has a different influence on learning. Like many discoveries in science, this one was made when the researchers were trying to understand why an experiment didn’t work out as they’d predicted. They’d used a chemical that selectively destroys dopamine cells in the nucleus accumbens of rats to eliminate their “pleasure centers.” Not surprisingly, after these key dopamine cells were eliminated, the rodents became so amotivated that if the researchers hadn’t manually fed them, they would have starved to death. “They wouldn’t want to eat. They wouldn’t want to drink,” Berridge says. “We’d have to artificially nurse them and artificially feed them, the way you would in a hospital intensive care ward.” The rats behaved as though they had extremely severe Parkinson’s, which they essentially did. Destroying their dopamine cells had taken away their motivation, leaving them with no desire or will to do anything at all, even what was necessary for survival.

cells have “organs” that are called organelles, like the nucleus, the information center of your cell—a pretty large structure with its own protective border wall that houses your DNA, your genetic code. There are mitochondria, generators that transform food and oxygen into chemical energy that keeps your cells running. There is a specialized transport network, a packaging center, parts for digestion and recycling, construction centers.

The conclusion is inescapable: Crick in Cambridge and Brenner in Johannesburg were thinking well ahead of the biochemical pack. But then, about fifteen minutes later in that same discussion, Walter Sampson Vincent, an instructor in anatomy from the State University of New York at Syracuse, got up to report some experiments with the RNA of unfertilized egg cells of starfish. “Both Dr. Borsook and Dr. Zamecnik have suggested that there should be two RNA fractions in the cell, with differing characteristics,” Vincent said. He had found the same thing himself, and proceeded to tell how, at length. His biological specimens—starfish eggs—were unfamiliar; his methods were the well-known ones of Torbjörn Caspersson and Jean Brachet (he had spent a year with Brachet as a postdoc); and worse than that, late in such a meeting, when scientist after scientist has risen to talk about his experiments, however tenuously related to the chief topic, the audience gets numb and drifts away. Vincent’s data suggested, he said in conclusion, that the nucleus contained two classes of RNA, “one a soluble, metabolically very active, fraction, representing only a small portion of the total.” His last words were about that fraction: “One exciting implication of the active, or labile, form would be that it is involved in the transfer of nuclear ‘information’ to the synthetic centers of the cytoplasm.” This astonishing suggestion went unnoticed.

In a simple way, the region of unlikeness called life, at the level of humble cells—without and with a nucleus—or of large multicellular organisms such as we humans are, can be defined by these two traits: the ability to regulate its life by maintaining internal structures and operations for as long as possible, and the possibility of reproducing itself and taking a stab at perpetuity. It is as if, in an extraordinary way, each of us, each cell in us, and every other cell were part of one single, gigantic, supertentacular organism, the one and only organism that began 3.8 billion years ago and still keeps going.

Cells can generally replicate themselves only forty to seventy times before stopping. Hayflick correctly intuited this as a form of cellular aging, which happens in the nucleus, where the chromosomes are contained.

Scientists and engineers tend to divide their work into two large categories, sometimes described as basic research and directed research. Some of the most crucial inventions and discoveries of the modern world have come about through basic research—that is, work that was not directed toward any particular use. Albert Einstein’s picture of the universe, Alexander Fleming’s discovery of penicillin, Niels Bohr’s blueprint of the atomic nucleus, the Watson-Crick “double helix” model of DNA—all these have had enormous practical implications, but they all came out of basic research. There are just as many basic tools of modern life—the electric light, the telephone, vitamin pills, the Internet—that resulted from a clearly focused effort to solve a particular problem. In a sense, this distinction between basic and directed research encompasses the difference between science and engineering. Scientists, on the whole, are driven by the thirst for knowledge; their motivation, as the Nobel laureate Richard Feynman put it, is “the joy of finding things out.” Engineers, in contrast, are solution-driven. Their joy is making things work. The monolithic idea was an engineering solution. It worked around the tyranny of numbers by reducing the numbers to one: a complete circuit would consist of just one part—a single (“monolithic”) block of semiconductor material containing all the components and all the interconnections of the most complex circuit designs. The tangible product of that idea, known to engineers as the monolithic integrated circuit and to the world at large as the semiconductor chip, has changed the world as fundamentally as did the telephone, the light bulb, and the horseless carriage. The integrated circuit is the heart of clocks, computers, cameras, and calculators, of pacemakers and Palm Pilots, of deep-space probes and deep-sea sensors, of toasters, typewriters, cell phones, and Internet servers. The National Academy of Sciences declared the integrated circuit the progenitor of the “Second Industrial Revolution.” The first Industrial Revolution enhanced man’s physical prowess and freed people from the drudgery of backbreaking manual labor; the revolution spawned by the chip enhances our intellectual prowess and frees people from the drudgery of mind-numbing computational labor. A British physicist, Sir Ieuan Madlock, Her Majesty’s Chief Science Advisor, called the integrated circuit “the most remarkable technology ever to hit mankind.” A California businessman, Jerry Sanders, founder of Advanced Micro Devices, Inc., offered a more pointed assessment: “Integrated circuits are the crude oil of the eighties.” All

Like most children of her era, she’d been taught to believe that the genome—the sequence of base pairs expressed in the chromosomes in every nucleus of the body—said everything there was to say about the genetic destiny of an organism. A small minority of those DNA sequences had clearly defined functions. The remainder seemed to do nothing, and so were dismissed as “junk DNA.” But that picture had changed during the first part of the twenty-first century, as more sophisticated analysis had revealed that much of that so-called junk actually performed important “roles in the functioning of cells by regulating the expression of genes. Even simple organisms, it turned out, possessed many genes that were suppressed, or silenced altogether, by such mechanisms. The central promise of genomics—that by knowing an organism’s genome, scientists could know the organism—had fallen far short as it had become obvious that the phenotype (the actual creature that met the biologist’s eye, with all of its observable traits and behaviors) was a function not only of its genotype (its DNA sequences) but also of countless nanodecisions being made from moment to moment within the organism’s cells by the regulatory mechanisms that determined which genes to express and which to silence. Those regulatory mechanisms were of several types, and many were unfathomably complex. Had it not been for the sudden intervention of the Agent, the biologists of Old Earth would have devoted at least the “remaining decades of the century to cataloging these mechanisms and understanding their effects—a then-new science called epigenetics. Instead of which, on Cleft, in the hands of Eve Moira and the generations of biologists she reared, it became a tool. (...) Thousands of years later, epigenetics was sufficiently well understood to be programmed into the DNA of some of the newly created species that would be let loose on the surface of New Earth. And one of the planks in the Get It Done platform was to use epigenetics for all it was worth. So rather than trying to sequence and breed a new subspecies of coyote that was optimized for, and that would breed true in, a particular environment, the GID approach was to produce a race of canines that would, over the course of only a few generations, become coyotes or wolves or dogs—or something that didn’t fit into any of those categories—depending on what happened to work best. They would all start with a similar genetic code, but different parts of it would end up being expressed or suppressed depending on circumstances. And no particular effort would be made by humans to choose and plan those outcomes. They would seed New Earth and see what happened. If an ecosystem failed to “take” in a particular area, they “they would just try something else. In the decades since such species had been seeded onto New Earth, this had been going on all the time. Epigenetic transformation had been rampant. Still, when it led to results that humans saw, and happened to find surprising, it was known as “going epi.

Today I learned that our home is basically a cell unit. The walls are nothing but membranes. For you, I'm the nucleus. And Maa, you're the powerhouse of this beautiful cell we reside in. You're my mitochondria.

The pons is active during meditation, as we breathe deeply and regularly. It’s associated with the production of delta and theta waves in the brain, which research shows turns on a host of healthy processes in your cells. These include increased stem-cell production and the repair of skin, bone, muscle, nerves, and cartilage. These brain waves also lengthen our telomeres, the most reliable marker of longevity. A remarkable ability of humans is that we are able to activate or deactivate all of these brain regions by consciousness alone. We can shift our thoughts deliberately with meditative practices or simply by focusing on different stimuli. The brain responds accordingly. We’ll see the extraordinary neural effects of this superpower of “selective attention” in Chapter 6, and the evolutionary implications in Chapter 8. Pons Activation Benefits Increases Decreases Quality REM sleep Insomnia Cell repair Longevity Energy Cell metabolism Melatonin Delta brain waves Theta brain waves Dream frequency and quality Lucid dreaming To the Brain, Imagination Is Reality For thousands of years, sages have assured us that our minds create our reality. In Proverbs 23:7, the poet tells us that, “As a man thinketh in his heart, so is he.” Two thousand years ago the Buddha said, “We are what we think. All that we are arises with our thoughts. With our thoughts, we make the world.” Now neuroscience is showing us how true this is. An ingenious study measured how our brains respond to scenarios that exist only in our imaginations. A research team at the University of Colorado at Boulder took 68 people and gave them a mild electric shock accompanied by a sound. They were then divided into three groups. The first group heard the sound repeatedly, though this time without the shock. The second group imagined the sound in their heads repeatedly. The third group imagined the pleasant natural music of rain and birds. The group imagining the sound showed the same brain activity as the one actually hearing the sound. Two brain regions, the ventromedial prefrontal cortex and the nucleus accumbens, lit up. As we’ve seen, the first regulates emotions like fear in the limbic system, while the second processes reward and aversion. Later, people in the “rain and birds” group were still afraid of the sound even when it was repeated many times without the shock. But those in the group that heard the real sound, as well as those imagining it, unlearned their fear. In neuroscience, this revision of reality is called “extinction learning.

One reason coffee is healthy is because it contains mildly toxic substances that activate an alarm-protein, called Nrf2, in our cells. When Nrf2 detects these mildly toxic plant substances in the coffee, it travels to the DNA in the cell nucleus, where it starts up the production of our own body antioxidant and detoxification proteins. Detoxification proteins are activated because the cells want to eliminate these mildly toxic substances as quickly as possible.

My mother lived in dread of my father. I think that’s pretty much all I can say about her, leaving aside her obsession with gardening and miniature goats. She was a thin woman, with long limp hair. I don’t know if she existed before meeting him. I imagine she did. She must have resembled a primitive life form—single-celled, vaguely translucent. An amoeba. Just ectoplasm, endoplasm, a nucleus, and a digestive vacuole. Years of contact with my father had gradually filled this scrap of nothing with fear.

Twenty-one years after the release of Kubrick’s film, a strangely similar scene played out in a University of California laboratory—with one major difference. In Alex’s place was an adult cat. Researchers led by Dr. Yang Dan, an assistant professor of neurobiology, anesthetized a cat with Sodium Pentothal, chemically paralyzed it with Norcuron, and secured it tightly in a surgical frame. They then glued metal posts to the whites of its eyes, forcing it to look at a screen. Scene after scene played on the screen, but instead of images of graphic violence, the cat had to watch something almost as terrifying—swaying trees and turtleneck-wearing men. This was not a form of Clockwork Orange–style aversion therapy for cats. Instead, it was a remarkable attempt to tap into another creature’s brain and see directly through its eyes. The researchers had inserted fiber electrodes into the vision-processing center of the cat’s brain, a small group of cells called the lateral geniculate nucleus. The electrodes measured the electrical activity of the cells and transmitted this information to a nearby computer. Software then decoded the information and transformed it into a visual image.

This heterogeneity [of vasopressin cells] is not by design but by accident. The patterns of gene expression in any neuron are not rigidly fixed by genetic nature, they arise from the unique experience of each cell in its life from birth to adulthood. The innervation of each cell is not predetermined with precision. Axons that reach the supraoptic nucleus may be guided there by developmental cues, but which particular cells each axon contacts is an opportunistic accident. There are mistakes; developmental cues are imperfect and some axons get lost or misled and make inappropriate connections. The brain has to be robust against such imperfection; the cost of doing everything perfectly is too high. Vasopressin cells are complex, but this does not make them clever, and the differences between cells certainly do mot make each cell uniquely clever. I am not interested in the idea that the brain does clever things because it hosts 100 billion clever machines. The wonder is that it does clever things with machines that are messy, noisy, and imperfect.

in 1974, scientists made a breakthrough. For the first time, they isolated and copied genes — those little segments of DNA molecules, found in the nucleus of every cell, that direct an organism to carry out its myriad functions. In other words, they cloned them. This created the potential for inserting genes into the DNA of a target cell. Here the genes would be incorporated into the cell’s genetic machinery and direct the cell to carry out some desired function. The scope of possibilities seemed almost unlimited. We could now guide plants to synthesize the insecticidal proteins or enzymes critical for the formation of natural anticancer substances.

You by Maisie Aletha Smikle You are loved You are precious You are marvelous You are original You are one of one kind You cannot be cloned You cannot be another Only you can be you No one can be you except you Every nucleus fiber and muscle Were weaved together by the Creator In the shelter of the womb you were placed to grow From cells you miraculously multiplied Into organs tissues and bones according to the Master Plan According to the Original Blue Prints You were given finger prints like no other You are indeed special Not made in a hurry Only two were made in a day Neither of the two were you God took months to mold you Because you are undoubtedly special You might get no visits You might get no gifts You might get no cards You might get no wishes You might get neither cash You might get neither kind Remember your gift of Life More precious than coins silver and gold God gave the gift of Life to you Every single day you get this gift You are indeed loved To have been given the most precious gift of all An incomparable gift like no other A gift that's larger than wealth and treasure

Like a strand of DNA, the mRNA is a chain of letters, and its sequence matches the sequence of the DNA it copied (the only major exception being that T gets replaced by U). The mRNA is exported out of the cell’s nucleus and delivered to a protein-synthesizing factory called a ribosome, which translates the four-letter language of RNA (A, G, C, and U) into the twenty-letter language of proteins (the twenty amino acids). This translation proceeds according to the genetic code, a cipher in which every three-letter RNA combination, called a codon, instructs the ribosome to add one specific amino acid.

from the juice of the library grape, and sent here to age. The library grape had been sequenced by the avout of the Concent of the Lower Vrone in the days before the Second Sack. Every cell carried in its nucleus the genetic sequences, not just of a single species, but of every naturally occurring species of grape that the Vrone avout had ever heard of—and if those people hadn’t heard of a grape, it wasn’t worth knowing about. In addition, it carried excerpts from the genetic sequences of thousands of different berries, fruits, flowers, and herbs: just those snatches of data that, when invoked by the biochemical messaging system of the host cell, produced flavorful molecules. Each nucleus was an archive, vaster than the Great Library of Baz, storing codes for shaping almost every molecule nature had ever produced that left an impression on the human olfactory system.

Human Cloning: The Least Interesting Application of Cloning Technology One of the most powerful methods of applying life’s machinery involves harnessing biology’s own reproductive mechanisms in the form of cloning. Cloning will be a key technology—not for cloning actual humans but for life-extension purposes, in the form of “therapeutic cloning.” This process creates new tissues with “young” telomere-extended and DNA-corrected cells to replace without surgery defective tissues or organs. All responsible ethicists, including myself, consider human cloning at the present time to be unethical. The reasons, however, for me have little to do with the slippery-slope issues of manipulating human life. Rather, the technology today simply does not yet work reliably. The current technique of fusing a cell nucleus from a donor to an egg cell using an electric spark simply causes a high level of genetic errors.57 This is the primary reason that most of the fetuses created by this method do not make it to term. Even those that do make it have genetic defects. Dolly the Sheep developed an obesity problem in adulthood, and the majority of cloned animals produced thus far have had unpredictable health problems.58

we are now finding that more than one genome can be found in the nucleus of a single human cell. More specifically, some people have been found with groups of cells that contain multiple gene mutations occurring nowhere else in their body. This can happen when the genomes of two different eggs fuse together into one egg. A pregnant mother can even gain new genomes in her cells from her child, who leaves fetal cells behind after birth. These cells can migrate to the mother’s organs, even the brain, and be absorbed. This event is known as mosaicism, and it looks to be far more common than ever imagined. In some cases, mosaicism is believed to contribute to diseases like schizophrenia, but for the most part it is considered benign. Even among Darwinian

The egg made the clone. In the experiments, the scientists extracted a cell from the udder of an adult sheep, and they removed the nucleus from the cell, the nucleus being the storehouse of the cell’s genes. They wanted those adult genes, and they could have taken them from any organ. Every cell in an animal’s body has the same set of genes in it. What distinguishes an udder cell from a pancreatic cell from a skin cell is which of those tens of thousands of genes are active and which are silenced.

I absolutely can’t stand science, especially biology, which was what we were studying. I couldn’t keep all those terms straight: cell and nucleus, species and phylum and genus, RNA and DNA and who knows what else. You know what is really stupid? The word species. If you have two different kinds of animals or something, then you have two species. But if you have only one kind, then you still have a species. Why not a specie? Or a specy? You don’t have two cats and one cats. Oh, well.

The gamma ray, yet another form of nuclear radiation, is an electromagnetic wave similar to ultraviolet light or x-rays, only it is far more energetic. A gamma ray of sufficient energy can penetrate your car door, go clean through your body, and out the other side, leaving an ionized trail of molecular corruption in its path. It is the product of a rearrangement or settling of the structure of an atomic nucleus, and it naturally occurs often when a nucleus is traumatized by having just emitted an alpha or a beta particle. Gamma rays can be deadly to living cells, but, unlike the clumsy alpha particle, they can enter and leave without losing all their energy in your flesh. It’s the difference between being hit with a full-metal-jacketed .223 or a 12-gauge dumdum. Both hurt.

About 99% of the DNA in a human cell is in the nucleus. Half of this is inherited from your mother and half from your father. But about 1% of the human genome is in 1,000 to 2,000 tiny subcellular structures called mitochondria.

From this perspective of cancer as a metabolic disease, insulin and IGF promote the cancer process through a series of steps. First, insulin resistance and elevated levels of insulin trigger an increased uptake of blood sugar (glucose) as fuel for precancerous cells. These cells then begin producing energy through a mechanism known as aerobic glycolysis that is similar to what bacteria do in oxygen-poor environments. (This phenomenon is known as the Warburg effect and was discovered in the 1920s by the German biochemist and later Nobel Laureate Otto Warburg, although its importance in the cancer process was not embraced until recently.) Once cancer cells make this conversion, they burn enormous amounts of glucose as fuel, providing them, apparently, with the necessary raw materials to proliferate. By metabolizing glucose at such a rapid rate, as Thompson suggests, these cancer cells generate relatively enormous amounts of compounds known technically as “reactive oxygen species” and less technically as “free radicals,” and these, in turn, have the ability to mutate the DNA in the cell nucleus. The more glucose a cell metabolizes and the faster it does so, the more free radicals are generated to damage DNA, explains Thompson. And the more DNA damage, the more mutations are generated, and the more likely it is that one of those mutations will bestow on the cells the ability to proliferate without being held in check by the cellular processes that work to prevent this pathological process in healthy cells. The result is a feed-forward acceleration of tumor growth. While this is happening, the insulin and IGF in the circulation both work to signal the cell to keep proliferating, and to inhibit the mechanism (technically known as apoptosis, or cell suicide) that would otherwise kick in to shut it down.

Another insect, a scale insect, has an even more bizarre genetic parasite. When its eggs are fertilized, sometimes more than one sperm penetrates the egg. If this happens, one of the sperm fuses with the egg’s nucleus in the normal way; the spare sperm hang around and begin dividing as the egg divides. When the creature matures, the parasitic sperm cells eat out its gonads and replace them with themselves. So the insect produces sperm or eggs that are barely related to itself, an astonishing piece of genetic cuckoldry.

There is compelling evidence to argue that cells can sense and respond to the stiffness of their ECM and that they transmit these cues to the nucleus to alter their shape and modify their chromatin accessibility either directly or indirectly by modulating cellular metabolism. What has yet to be determined is whether these tension-induced changes in chromatin modification and chromosomal localization are accompanied by specific differences in gene expression and whether altering the metabolic state of the cell could modify these phenotypes. Moreover, whether similar effect occur in fibrotic, stiffened tumor tissues and if this influences gene expression to drive a tumor-like behavior in the cells and tissue remain unclear.

No one knows how old E. coli is precisely, but estimates hover between three and four billion years. The organism has no nucleus and reproduces by the primitive but extremely efficient process known as asexual binary fission (in other words, by splitting in two). Imagine a cell filled, essentially, with DNA, that can take in nutrients (usually from other cells that it attacks and absorbs) directly through its cellular wall. Then imagine that it can simultaneously copy several

I look at a forest from afar, I see a dark green velvet. As I move toward it, the velvet breaks up into trunks, branches and leaves: the bark of the trunks, the moss, the insects, the teeming complexity. In every eye of every ladybug, there is an extremely elaborate structure of cells connected to neurons that guide and enable them to live. Every cell is a city, every protein a castle of atoms; in each atomic nucleus an inferno of quantum dynamics is stirring, quarks and gluons swirl, excitations of quantum fields. This is only a small wood on a small planet that revolves around a little star, among one hundred billion stars in one of the thousand billion galaxies constellated with dazzling cosmic events. In every corner of the universe we find vertiginous wells of layers of reality.

Under the microscope, a cell looks a lot like a fried egg: It has a white (the cytoplasm) that’s full of water and proteins to keep it fed, and a yolk (the nucleus) that holds all the genetic information that makes you you. The cytoplasm buzzes like a New York City street. It’s crammed full of molecules and vessels endlessly shuttling enzymes and sugars from one part of the cell to another, pumping water, nutrients, and oxygen in and out of the cell. All the while, little cytoplasmic factories work 24/7, cranking out sugars, fats, proteins, and energy to keep the whole thing running and feed the nucleus—the brains of the operation. Inside every nucleus within each cell in your body, there’s an identical copy of your entire genome. That genome tells cells when to grow and divide and makes sure they do their jobs, whether that’s controlling your heartbeat or helping your brain understand the