Summary of "Survival of the Sickest" Chapter 6

   Chapter 6 begun with the creation of vaccination. Edward Jenner, a country doctor in Gloucestershine, England, created the first vaccine in the end of the 18th century. He discovered that milk maids who had cowpox were immune to smallpox. Thus, he tested out his assumption by giving a hamrless verison of cowpox to a group of young boys. Turned out, they all were able to produce antibodies to protect themselves from smallpox.
*Fun Fact: The word "vaccine" comes from the Latin word for cow "vacca", and the Latin name of cowpox "vaccinia".
   By creating the first vaccine, bioscientists found that genes could change. Each human beings starts off with exactly the same number of cells as the simpliest form of bacteris, one single cell --- zygote. inside of zygote has every single genetic instruction. These instructions carry 3 billion pairs of nucleotides (DNA base pairs) that have 30,000 genes. The genes of a person are organized in 23 pairs of chromosomes. One set of chromosomes comes from mother, and the other set comes from father. Yet, less than 3% of DNA contains instructions for building cells. The rest of DNA (about 97%) are noncoding DNA. Scientists changed the name of "Junk DNA" into noncoding DNA because the 97% of DNA are not directly involved in creating protein doesn't neccessarily means they are junks. Later the author mentioned mitochondria, the microscopic workhorses. Function as powering plants, producing energy to run cells. They are once independent, parasitic bacteria that evolved mutually beneficial relationship with some of premammal evolutionary predecessors. They have their own inheritable DNA, mtDNA. Back to the point that genes could change, genetic changes are the product of accidental mutations caused by random and rare errors. Mutatin happened when an error gets through and forms a new combination of DNA sequences( rearranging DNA). Mutations also occur when organisms are exposed to radiation or powerful chemicals. Outbreakers and pandemics are caused by either antigenic drift, which is when mutations occur in DNA of a virus, or antigenic shift, which is when a virus acquires new genes from a related strain.
    Last but not least, the author covered another topic, the "Jumping genes". In recent years, scientists have discovered that DNA can be modified in more ways that only by random mutations. In 1950's, Barbara McClintock dicovered "jumping genes" --- whole sequence of DNA that moved from one place to another over times of environmental stress. She dicovered this by observing the genetic of corn, in which the plants seemed to be undergoes a kind of intentional mutation. There are two types of "junoing genes"(transposons). The first one is DNA transposons, which perform a cut-and-paste process. The second one is DNA retrotransposons, which perform a copy-and-paste process. Moreover, large portions of our noncoding DNA/ Junk DNA are made of jumping genes. On the other hand, retroviruses are made of RNA, and can be written into DNA. HIV is a retrovirus. The retroviruses that are part of our DNA are called HERVs, human endogenous retroviruses that play a number of roles, such as producing a healthy placenta.  
 
   

From Atoms to Traits

 1.  Gregor Mendel swept away the confusion about blending inheritance of Darwin’s theory by implementing his famous breeding experiments with peas, conducted in the 1850s and 1860s. His experiment showed when true-breeding pea plants of contrasting types were crossed, the off – spring usually resembled one of the two parents. With further crosses, both forms of a trait could reappear in undiluted form in future generation; yet, the genetic information for alternative forms had not blended away.

     Mendel’s experiment changed the general perception of heritable variants from ephemeral and blendable to discreet entities passed from parents to offspring, present even though they are not always visible. Furthermore, Mendel’s experiment answered the question how new traits could spread in subsequent generations that Darwin was unable to solve.

2.   James D. Watson and Francis Crick proposed a structure for the DNA (deoxyribonucleic acid) molecule in 1953, with stunning implications for our physical understanding of heredity and variation. DNA is a long; two- stranded helix, with a backbone made of repetitive chains of sugar and phosphate. The complementary pairing between four possible chemical bases: adenine, cytosine, guanine, and thymine holds the two strands of the polymer together. On the other hand, these four possible chemical bases also form the foundation of a simple genetic language (A, C, G, T)

     The four chemical letters in the DNA alphabet can occur in any sequence along one strand of the helix, spelling out different instructions that are passed down from parents to offspring. The double-stranded helix provides a clear mechanism for copying genetic information as well. Cs always pair with Gs, and As pair with Ts across the middle of the DNA molecule

3.  1) Point mutation: substitution of a single letter for another at a particular position in the polymer. For example, in whippet dogs, a single base pair change makes the difference between a slender silhouette and the hulking animal. The mutation inactivates the gene for a signaling molecule that regulates muscle growth. In animals with both copies of the gen mutated, muscle growth is uncontrolled for lack of “stop “ signal. When only one copy of the gene is disabled, the dogs are moderately more muscular and prized as racers.

2) Duplication of new letters. Sequences containing the same base pair repeated eight or more times, known as homopolymers, are highly prone to copying errors. For example, in pigs, the gain of two additional C-G pairs in such a sequence inactivates a gene for a signal receptor in pigment cells producing light-colored coats.  On the other hand, copying mistakes within individual cells may also cause the duplicated sequence to lose bases, restoring the gene’s function and producing dark patches on the body.  

3) Gene copy number. Entire gens can be duplicated by copying errors during cell division, leading to differences between species and to variation among members of the same species. The genome of chimpanzees, which eat green plants, normally contains just a single gene of the starch-digesting enzyme salivary amylase, whereas humans can carry up to 10 copies of the gene.

4) Insertion of new letters. For example, in pea plants, an 800-base-pair sequence inserted into a gene produces peas that are wrinkled rather then smooth. The intruding DNA element disables a gene necessary for starch synthesis, altering the peas’ sugar and water content. Such mobile elements are seen in the genomes of most multicellular organisms, including humans.

5) Regulatory changes. Mutations in the DNA that controls when and where genes are activates can produce profound trait changes by altering the formation of entire body parts during the organism’s development. Changes in the regulatory regions of a single gene that controls patterns of cell division during stem development account for much of the shape difference between the bushy teostinte plant and its descendent, the tall modern cornstalk.  

4.    It’s a subspecialty within evolutionary biology that has come to be known as evo-devo, concentrating on studying the effects of changes in important developmental genes and the role they play in evolution.

5.    An enzyme called lactase, produced in the intestines, allows infants and children to digest the complex milk sugar lactose. Only a minority of people continues to produce lactase as adults. In 2002, this ability was traced in Europeans to mutation in the regulatory DNA that controls the lactase gene. More recently, different mutations affecting the same gene were found to predominate in East African and Saudi Arabian populations who traditionally herd milk-producing animals. The differing DNA changes indicate that the trait of lactase tolerance has arisen independently many times in the past 9,000 years. 

            As we have learnt from the TV documentary, A Journey of Man, people from Africa started to migrate 50,000 years ago. As years passed by, this extraordinary group of people had spread out all over the world. They carried Y-chromosome and passed on genes that allow them to digest the complex milk sugar lactase to the next generations. This is why the ability of digesting was traced in Europe, Saudi Arabia and East Africa.  

  

Trace of A Distant Past --- response to the assigned article

Trace of A Distant Past

   Scientists trace the path of human migrations by using bones, artifacts and DNA, as these are the evidences of evolution. Nevertheless, ancient objects are hard to find and are incomplete, such as fossils and artifacts. Thus, examining DNA is a better way to determine the trace of past. Yet, why DNA can help to determine our past? That is because “almost all our DNA --- 99.9 percent of the three billion nucleotides that make up the human genome is the same from person to person” (Scientific American 56). The last 0.1 percent of nucleotides indicates differences between races. Scientists are able to determine our common ancestor by analyzing the DNA of mitochondria. Mitochondrion is the cell’s energy-producing organelles, which are passed down through maternal line.

    In 1987, Rebecca L. Cann and Allan C. Wilson of the university of California, Berkley reported that “humans from different populations all descended from a single female in Africa who lived about 200,000 years ago” (Scientific American 58). After this groundbreaking paper is published, scientists discover that mitochondrial DNA and the Y-chromosome remain powerful analytical instruments. Furthermore, scientists believe that with the help of mitochondrial DNA and the Y-chromosome, they would be able to prove that Africans are the common ancestors of all the population over the world. In 2010, the National Geographic Society, IBM and the Waitt Family Foundation have joined in the so-called Genographic Project that is primarily devoted to using these tools. This project is to gather DNA from up to 100,000 indigenous people worldwide; moreover, this project is made into a TV documentary, Journey of Man, in 2003. However, not every one agreed with this out-of-Africa theory. Despite lots of research and project indicate that the out-of-Africa theory is valid. (The out-of –Africa theory holds that humans with modern traits left Africa around 50,000 to 60,000 years ago to settle the world.)  Some scientists believe that modern characteristics evolved not only in Africa, but also in archaic hominid populations in Asia and Europe. This competing theory is called the multiregional theory. Furthermore, the multiregional theory also states that interbreeding among all these groups, such as Africans, Asians and Europeans ensure that they remain as a single specie.  

Two competing theories 

Africa contains the most diverse characteristics

Journey of Man --- Part I

Reading question for National Geographic Article

East/Southeast Asia:  Hopping islands and continents and maybe the largest ocean

Li Jin of Fudan University in Shanghai, China. Asks: When did people first reach Taiwan and Japan? What led to the north-south genetic divide among native populations in East Asia? Did ancient seafarers cross the Pacific from Asia to South America, and if so, where did they embark?

·         The written history of Japan begins with brief references in the 1st century AD Twenty-Four Histories, a collection of Chinese historical texts. However, archaeological evidence indicates that people were living on the islands of Japan as early as the upper Palaeolithic period. Following the last Ice age, around 12,000 BC, the rich ecosystem of the Japanese Archipelago fostered human development. The earliest-known pottery belongs to the Jōmon period.

·         The Upper Palaeolithic (or Late Stone Age) is the third and last subdivision of the Paleolithic or Old Stone Age, as it is understood in Europe, Africa and Asia. Very broadly, it dates to between 50,000 and 10,000 years ago, roughly coinciding with the appearance of behavioral modernity and before the advent of agriculture.

·         In the history of Taiwan, Aboriginal peoples ancestors are believed to have been living on the islands for approximately 8,000 years before major Han Chinese immigration began in the 17th century. The Taiwanese Aborigines are Austronesian peoples, with linguistic and genetic ties to other Austronesian ethnic groups, such as peoples of the Philippines, Malaysia, Indonesia and Oceania. Taiwan's Austronesian speakers were traditionally distributed over much of the island's rugged central mountain range and concentrated in villages along the alluvial plains. Today, the bulk of the contemporary Taiwanese Aborigine population reside in the mountains and the cities.

What led to the north-south genetic divide among native populations in East Asia?

·         Climate change

·         Living environment change

·         Historical event

·         Demographical expand

·         Language