Genome chapter summaries Ashley Yao Chapter 1: Life DNA is comprised of chemical codes, written in letters of A, C, G, and T.

Most scientists in the beginning thought that the secret of life lie in physics, rather than biology. Proteins and DNA are needed together, as proteins make more proteins through DNA, and vice versa. RNA, unlike DNA, can catalyze chemical reactions, and is considered the word that established life. Bacteria, during the earliest stages of life, could acquire genes from other bacteria, and this means that we came from a whole community of living organisms. The first modern organisms were not bacteria, but instead a more complex organism with genomes fragmented into several linear chromosomes. Bacteria has evolved to be simpler and dropped the old RNAs. I found it interesting that ten years before the discovery of DNA, Crick, Watson, Wilkins, and Franklin were all doing different things and did not focus on cracking the code. Also I find it interesting that the genes in the cells of our bodies are descendants of the first replicator molecules. It is intriguing to see how DNA is explained as a helpless, passive piece of mathematics as opposed to the source and key of life we usually think of it as. RNA is then detailed as the word, and it is said that it can copy itself without assistance, and that everything in a cell is RNAdependent. Chapter 2: Species Twenty-three pairs of chromosomes are found in the human body, while Chimpanzees and gorillas and orangutans have 24. This is because Chromosome 2 is thought to be formed from a fusion of two medium-sized ape chromosomes. Chimpanzees and humans are 98% alike genetically, which I found interesting because of course my first question was, how come we look so different?. But of course this question was answered as the author replied that we share many genetic qualities, like the fact that we share every bone in our body with chimpanzees and more. Also the population of the Pliocene apes split in half (there are many different theories that arise) perhaps because a river or mountain range divided the species, leaving the ancestors of humans in a different climate than the descendants of chimpanzees. Changes found in the ancestors of humans include: less hairy skin that sweats more in the heat and a different style of walking (that didnt include the knuckle-walking of other apes) which suggested that these ancestors were walking in the sunlight. Also due to the unique developing monogamy of the ancestors of our species, they eventually became carnivorous (the sharing of plant food gathered by women gave men the chance to hunt, which was a risk). Natural selection is the process by which our genes changed their sequences. I found it interesting that we are so similar to chimpanzees and that factors like the climate that we lived in created the differences that seem so enormous to us now. Also it is intriguing to realize that even these minute differences in the genes cannot be altered in any way to produce a human from the nucleus of a chimp cell. Chapter 3: History The main purpose of genes is to store the recipe for making proteins. This recipe is used as a translation to make proteins. Every protein in the body is made from a gene by this translation. I find it interesting that in Mendels life, although unsuccessful in many parts, triumphed and went unnoticed for the most part until modern times. He dedicated much of his life to this organized and systematic experiment. Also stated in this chapter is the fact that heredity was found out to be not a mixture of blood from ancestors, but instead a temporary comingling of genes and some genes reappeared in the next generation. DNA was first isolated in 1869 by Friedrich Miescher. In 1951 Watson and Crick teamed

up together to prove that genes are made of DNA and not protein. I find it interesting that the study of DNA brought together these two unlike characters: one outgoing, personable Brit who had no doctorate, and an American also obsessed with experimenting with DNA. This gene for homogentisate dioxygenase represents the chemical unity of life. Chapter 4: Fate Many genes are described primarily by the disease they cause. Ridley accuses this process as ignorant as it is like saying the purpose of the heart is to cause heart attacks. A mutation in gene number 4, called Huntingtons mutation, causes jerking limbs and sends people into deep depressions. The disease is incurable and the disease can only be received through the genes. This disease was the first mainly dominant human genetic disease to be out in the open. Huntingtons and other neurological diseases contain a multitude of CAG repeats in the gene. Also many other diseases of nerve degeneration contain words that start with C and end in G. The reason this C and G phenomenon is important, is because in the copying of genes, the more repeats of CAG there are, the more likely the copying machine will slip up and repeat an extra CAG. Huntingtons disease interested me this chapter, as it brought up the idea of ignorance and the option of it. Many of these patients who think they might have Huntingtons choose to either not take the genetic test, or to not ask the doctor whether they have the disease or not. These patients can live a shorter life, but a life that is lived in ignorance, but also a happier life. Chapter 5: Environment Pleiotropy and pluralism are introduced in this chapter. Chromosome 5 is also introduced as the point where genetics starts becoming less distinguished and more ambiguous. Some genes that lead to asthma are found in chromosome 5. People with asthma are more likely to be allergic to something, because these are both caused by the same mast cells in the body, alerted and triggered by the same immunioglobulin-E molecules. Many things are supposedly causing the increase in asthma, some blame pollution while others blame the over-hygienic nature of children in the modern times. This overhygienic nature basically causes allergies because the immune system is built for certain types of bacteria, and when not present, the system is prone to allergies. Except this theory and others can explain why in general, asthma is on the rise, while only differences in genes may specifically explain why one person in a family gets asthma and the other doesnt. Cookson, an Oxford geneticist, eventually found their gene and pinned down a mutation within it that people with asthma had more often than others. Chapter 6: Intelligence Genes main purpose is not to cause disease. These genes that cause diseases are not broken but are actually just a different flavor. Robert Plomin announced in 1997 that he and his colleagues had discovered a gene for intelligence. Many IQ tests are taken within a specific time limit and therefore limits the test takers ability. There are three types of intelligence: analytical, creative and practical. In any case, the intelligence gene needs environmental stimulation in order to develop. Also, there is no accepted definition of intelligence. Many people are good at things like music, sports, other languages, but not be academically intelligent. I find the story of two twin girls, Beth and Amy, separated at birth and placed into two polar opposite homes. Although in two different situations, Beth and Amy grew up and had remote differences in their personality. Also another fact I found interesting was that in tests done, being raised in the same family for adopted children had no effect on IQ. Although this is true, environment does have some effect on intelligence. Chapter 7: Instinct

Chromosome 7 equips humans with instinct and this instinct lies at the heart of all human culture. One example is the universal speech pattern that all humans possess. Although we grow up in different areas and therefore have different cultures and languages, Chomsky discovered similarities in all different types of languages. Also, children are believed to affect the way mixes of languages develop over time. In one example, the pidgin language of Hawaii developed after a generation of children transformed the pidgin language as their instinct as they learned to speak the language developed it. Over the years, human beings evolved their already complex behavior by adding instinctive aspects to those of their ancestors. In the end, a conclusion that genetics ultimately does affect behavior appears. Although this seems not good enough for non-scientists, Ridley explains that the idea of genes for behavior is no more strange than the idea of genes for development. Chromosomes X and Y: Conflict The X and Y chromosomes in human beings determine sex. Everyone inherits an X chromosome from his or her mother. However, if one inherits a Y chromosome from the father, then the outcome will be a boy; if one inherits an X chromosome from the father, then the outcome will be a girl. This story is one of the most unexepected in the whole history of genetics. Today, the lack of the sex-determining gene makes us female and the existence of it makes us male. For males, many of their masculine habits stem from a gene called SRY, the gene that changes boys into men. SRY is a gene thats evolved the least over the past 200,000 years. Scientists finally came to the conclusion that species that are able to communicate are more likely to experience sexual antagonism stemming from the genes. While there are may be many causes to homosexuality in males, the best explanation involves three active genes on the Y chromosome. Theyre called the H-Y minor histocompatibility antigens. Put simply, they cause males to be attracted to other males and not females. The idea of genes in conflict eith each other is unknown to most outside of the group of evolutionary biologists. Chromosome 8: Self-Interest Three percent of our genomes consist of true genes. The rest ninety-seven percent consists of junk, or selfish, DNA. Those terms signify that most of those junk genes never provide recipes that create proteins. Each gene is far more complicated than it needs to be. It is broken up into paragraphs (called exons) and in between lie long stretches (called introns) of nonsense or junk. In any case, these long stretches of useless, repetitive paragraphs are only just good at replicating itself. It was discovered that the whole of genome is filled with parasitic and selfish stretches of text that are only good at duplicating themselves. In human bodies, mutating agents like LINE-IS and Alus cause mutations landing in the middle of genes. In any case, because of these kinds of junk genes and junk DNA, DNA testing became more and more common in global society. It even became used as a sort of evidence to vindicate or make charges against someone. Chromosome 9: Disease On the 9th chromosome the gene that determines our ABO blood group. Other than DNA fingerprinting, this was something the court systems could use blood grouping to help in cases, whether it was to disprove or prove someone innocent. There exists 4 blood types: A, which can be donated to A

and AB blood types, B, which can be donated to B and AB blood types, AB, which can be donated to AB blood types, and O, which can be donated to all blood types, earning it the title of universal donor. People with one blood type may be resistant to some diseases, while people with other blood types may be resistant to other diseases. For example, a person who is AB is more likely to resist diseases like cholera than others. Another example is that people with type O blood are more likely to resist getting diseases like malaria. Its resistances like these that keep the blood types from becoming extinct. Up until recently, people like doctors always thought that many diseases were due to deleterious effects of the environment, but it turns out that they are due to side-effects of chronic infections with little known viruses or bacteria. A way that this kind of situation applies to genetics overall is that, since AA people will want to breed with BB people to have cholera resistant AB offspring (in a time of cholera outbreaks), the advantage of being sexually attracted to the genetic opposite is conspicuously obvious. Through this we can see that genetics is constantly changing, in a state of fluctuation. Chromosome 10: Stress Our bodies take in a range of different steroids. Even the hormone that triggers the shedding of an insects skin and vitamin D are examples of steroids. However, out of all of them, cortisol is the only hormone/steroid that is synonymous with stress. The buildup of stress, due to a rapid increase in cortisol in the body (therefore weakening white blood cells), actually makes the immune system weaker and more vulnerable. That is why people who show signs of having stress often are more likely to catch colds and other infections. While cortisol may seem like the cause for stress, it is actually the hypothalamus of the brain that sends out signals to the pituitary gland to secrete a hormone which in turn tells the adrenal gland to secrete cortisol. The hypothalamus just receives and processes information from the external environment and acts accordingly. The truth in the matter is that no one thing is fully in charge. Chromosome 11: Personality If we look at the chemicals of the mind we can see the full extent of the genes effect on personality. Each of us has a unique personality, whether we are anxious, quiet, relaxed, talkative, shy, etc. Dopamine is a chemical that can be found in chromosome 11 and can be described as the brains motivation chemical. The D4DR gene in the chromosome shows frequent patterns that are associated with personality, as well as dopamine. The larger the number of repeats, the more ineffective the dopamine receptor is at acquiring dopamine. A long D4DR gene indicates a low responsiveness to dopamine and vice versa. Parenting, if done certain ways, can also help develop peoples personalities. A chemical thats related to dopamine is called serotonin, whose characteristics may be difficult to define. However, if you have high levels of it in your brain, your personality will be compulsive. If not, then your behavior will be more impulsive. A way to change your serotonin levels on your own is to alter your eating habits. However, it should not be thought that serotonin levels dictate peoples personalities. Actually, if an individual has high self-esteem and social rank relative to others, then he or she will have a high serotonin level as a result. Although personality does have some effect from genetics, it is being used in some very non-genetic therapy.

Chromosome 12: Self-Assembly Although humans have replicated almost every organ in the human body, replicating the development of the human body from merely a blob, or a fertilized egg, remains the only thing to be done. Genes hold the recipe for the rest of this human form. A large cluster of these genes were found in the middle of chromosome 12. At first, when the fertilized egg turns into an embryo, its merely an undifferentiated blob. Gradually, however, it starts to form two asymmetries: the head-tail axis and a front-back axis. Genes that control processes like telling cells what to do are called homeotic genes. While experimenting with fruit flies, mutations occurred in the sense that wings and antennae, for example, were in the wrong places. When the gene structure on the chromosome was analyzed, it was found that they were lined up in the same order as the part of the fly they affected. There was a second surprise coming. They had the same paragraph of text (180 letters), which was called a homeobox. This homeobox was found in many animals, ordered from head parts to the tail parts. Like how many biological things have its artificial counterparts, in an analogous sense, genes are just software that can run on basically any system. In the end, they simply do the same jobs. Chromosome 13: Pre-History DNA is a code written in a simple alphabet, a language. Just as languages like Italian, French, Spanish and Romanian share their origins with Latins, so DNA found in modern day animals share its origins with DNA from prehistoric animals. The differences between French genes and German genes may be similar to the differences between their languages. In the past, when different groups migrated into new areas, new genetics, as well as linguistics, were introduced into those areas. The genetic geography of the world plays a huge role in making up history and pre-history. Chromosome 14: Immortality So far, genome has been proven to be immortal, as species like ours are still alive today through natural selection and similar genetic and biological processes. However, it is unlikely that species like ours will give way to a new kind of species (we are already about 5 million years into the 10 million year life span of a species). The genes in your body have been and are constantly photocopied, which blur their initial purposes and messages. Substances called telomerase are in charge of re-lengthening the shortened ends of chromosomes and the telomeres. In some ways, telomerase seems to behave like elixirs of eternal life for cells. The lack of it, however, is the reason why cells grow old and die and, furthermore, there is good evidence that it also explains why bodies grow old. Natural selection gives our body parts just enough time to just see our children grow independent. Chapter 15: Sex Genes remember which parent they come from. The body either uses and expresses the gene it inherited from the father or the mother. On a related note, it was then discovered that paternal genes are responsible for making the placenta, while maternal genes are responsible for making the greater part of an embryo. A process known as imprinting is only specific to placental mammals and some plants, as well. It would also appear that pairs of imprinted genes (one from the father and one from the

mother) are antagonistic to each other. If the two genes were to be turned off, then an embryo would grow to be a healthy living being. Later, scientists claimed that due to the imprinting theory deemed it impossible to clone mammals. The imprinting theory also suggests that boys get social diseases like dyslexia, autism, etc. more often than girls do. Nature is more involved in the determining of gender than people think. Chromosome 16: Memory Genome itself may take its time processing information, waiting to change things about a species genetics for several generations. However, thanks to the brain, we are able to process that information in a matter of minutes or even seconds. Learning is directly the opposite of instinct. While instinct is genetically determined behavior, learning is behavior that comes from experience. In fact, learning gives way to instinct. Our whole genome, in the past 4 billion years, can be thought of as an accumulative learning experience. Species like sea slugs are capable of developing intelligence through learning, just as human beings and dogs are. A protein called CREB, which, when activated, turns on other genes and altering the shape & function of a synapse, is believe to be the heart of learning and memory mechanisms. The lack of the protein results in not being able to remember something for more than an hour. Research further suggests that the tightening of neurons in the brain has something to do with memory; when you learn something, the physical network of neurons in your brain change. Chromosome 17: Death The loss of brain cells, however, is deemed necessary, or else our brains would be overloaded and would not have the ability to think, at all. Cancer was later thought not to be a single disease but many disorders caused by a copious amount of reasons. Later, scientists figured out that cancer can be caused by chemicals and radiation. These would include coal tar and X-rays, both of which have one thing in common: they have the ability to significantly damage DNA. Another breakthrough resulted when scientists discovered that genes alone could cause cancer. The mutation of the TP53 gene is the primary cause of lethal cancers. Radiation causes P53, a protein synthesized in TP53, to become dysfunctional and damaged. Cancer doubles in terms of frequency every decade or so and is the primary disease of old age. Eventually, cancer will find a way to circumvent tumor-suppressing genes and will induce more fatal diseases. TP53 is often referred to as the Guardian of the Genome from the way it encodes cells to basically destroy itself if ever infected by cancerous disease. The process is called apotsis. Chromosome 18: Cures In the 21st century, its become more of a possibility that we can remove faulty genes and replace them with functioning ones. Its like copying a text and pasting it somewhere else. An enzyme called ligase acts as the glue, stitching together loose sentences of DNA whenever it comes across them. Restriction enzymes, which act as scissors, fussily cut strands of DNA where they find a particular sequence of letters. Over the past few decades, biotechnology developed, both as science and business ventures. Genetic engineering also experienced many breakthroughs. The Human Genome Project was started to figure out the whole human genome in less than 20 years. Although little progress was made

in 14 years, by 2000, gene-sequencing machines sped up the process and soon, the recipe to the human genome was produced. Agriculture is another field that can be affected by genetic engineering. Later, more and more issues regarding ethics about genetic engineering rose around the world, particularly in Europe and North America. Genetic diagnosis followed by a cure is probably the genomes greatest benefit to medicine. Chromosome 19: Prevention In the 21st century, something can always be done about disease. Two diseases we are always at risk of getting are coronary heart disease, which is a swift killer, and Alzheimers, which is a slow and painful killer. The heart disease is treatable and can be prevented. All it takes is genetic diagnosis to see who is at risk and who is not. For Alzheimers, however, it is a bit more difficult. A gene called APOE, originally thought to serve as a blood-lipid gene, was soon figured out to be a cause of Alzheimers. That can explain why people with the disease often have high cholesterol. People with E4 genes are susceptible to the disease. Although Alzheimers is incurable, there are ways to alleviate its symptoms. At least 3 new Alzheimers drugs are/have been developed and tested. However, a drug could affect everyone differently, according to the genes he or she may have. Chromosome 20: Politics The discovery of a gene called PRP, which led to the presentation of two Nobel prizes, stirred up many political controversies in 1996. Before, a disease known as scrapie came about, but this, time no one knew the cause of it. It was later deduced that the disease was due to a microbe. Through studying many rituals of the Fore tribe, located in Papua, New Guinea, scientists caught on to something: the women and children who eat the organs and brains of dead people, who previously had a similar disease known as kuru, are most likely to get kuru as well. This suggests that scrapie (and kuru) may be infectious. Later scientists then suggested that scrapie was caused by something that didnt have genes, RNA, or DNA. Stanley Prusiner, a geneticist, soon discovered the gene PRP, or the protease-resistant protein. His theory was that its a normal gene but produces prion, a sticky protein that can change its shape and form. It can also tell other prions to form into one distinct shape. This doesnt alter any sequences, but changes the way they fold up. All genes consist of 253 letters, and changing even one letter in chromosome 20 can cause a diseases. Prions then went on to become the cause of the madcow disease, which produced mass hysteria. It was not heard of that such a thing, which was capable of causing disease, which cannot replicate itself. In the end, the improper folding of one prion is the ultimate cause of a disease. Chromosome 21: Eugenics Chromosome 21 is often thought to be the smallest one (until chromosome 22 was discovered). Its possible to be born with more than one of the same type of chromosome. Down Syndrome is something that can occur when theres more than one chromosome 21 present in a body. Darwinism, along with its related branch social Darwinism, is considered the embodiment of eugenics. The survival of the fittest came to the minds of many. In these same minds, people also thought to promote eugenics. Soon, people were classified as the best and the worst. It soon went from halting the

breeding of the dysgenic, rather than promoting the breeding of the eugenic. Sterilization starting becoming more and more practiced in countries like America, Sweden, Canada, Norway, Finland, Estonia, Iceland, etc. Germany was notoriously known for sterilizing over 400,000 people. While eugenics shows the dangers of letting genetics out of control, we have mostly the government to blame for going out of control, itself. Chromosome 22: Free-Will Freedom and free-will doesnt stem from genes, unlike many other characteristics that dictate our behaviors. Free will comes from society, culture and nurture. Freedom is everything that is not determined by our genes. Stemming back to the discussion about biological/genetic determinism, everybodys fate is determined by his or her controlled environment and not by genes. For example, its common for teenagers to go against what their teachers, parents, etc. have taught them and go out and smoke and drink. People who do one thing rear children to do the same thing. Stress is something that many people did not know came from free-will. They can alter the expression of genes. Human behavior can be thought of as predictable on the long run, but erratic and impulsive at any given moment. We cant change the course of biological/genetic determinism, but we can distinguish between the good and the bad kind. Freedom is simply the expression of your own determinism.