The Human Genome Project

(image source: http://www.flickr.com/photos/askpang/9251502638/sizes/c/in/photostream/)

     As surprising as it sounds, we, the mankind, have made it possible to sequence entire genomes, by virtue of the groundbreaking advances in DNA sequencing technologies. The beggining was modest: biologists at first worked on interpreting relatively small genomes like bacteria and viruses. In 1996, biologists successfully discovered that the DNA sequence of the common bacterium Escherichia Coli, contains 4,639,221 base pairs (Wikipedia s.v. Human Genome Project). Then how many base pairs does the human genome contain? Over 6 billion.
     Despite the overwhelming numbers, scientists from all around the world have made rapid progress ever since they embarked on this grand scheme in 1990. The final goal of the human genome project is to completely analyze the human DNA sequence and furthermore shed light on the mysteries of the human body. Along the way, scientists completed the genomes of several other organisms including yeast and the fruit fly. In 2000, which is only ten years after the beginning of the project, the scientists announced that a "working copy of the human genome was essentially complete".
    The process by which the scientists confirmed the human genome is very intriguing. The scientists first determined the "markers", a characteristic sequence of bases that appears within the widely seperated regions of DNA, to locate and return to specific locations in the genome. Scientists then shredded the DNA into small pieces and determineed the sequence of bases in each fragment. The fragments are thoroughly analyzed by the computer and put together in accordance with the overlapping "markers" on the chromosomes--like a jigsaw puzzle put together.







                Works Cited

-Wikipedia, s.v. Human Genome Project
- Miller, Kenneth & Levine, Joseph. Biology, Prentice Hall, Boston ,MA
 

Lethal Genes-I don't wanna die!

     I need to admit that tragedies can often be very interesting. Lethal Genes, tragic as its name suggests, are genes whose phenotypes lead an organism to unconditional death. Death can sometimes not be immediate and take years or even decades. The notion that carriers of lethal genes cannot leave offspring is therefore false; for instance, the notorious Huntington's disease, inherited as an autosomal dominant condition, usually manifests itself when the patient ages over 40, enabling itself to clandestinely pass down to the patient's descents.
     Lethal genes were first discovered by Lucien Cuenot, a French biologist. Cuenot observed unusual genetic patterns while studying inheritnce of a coat color gene in mice. The offsprings of two yellow mice, quite surprisingly, always showed a 2:1 ratio instead of a conventional Mendelian 3:1. The mice happened to never produced a single homozygous yellow mouse. Five years later, W.E. Castle and C.C. Little confirmed the existence of lethal gene by showing that one-quarter of the offspring from crosses between heterozygotes die during embyonic development.

(Image Source: http://www.nature.com/scitable/topicpage/mendelian-ratios-and-lethal-genes-557)


     When an allele causes lethality, this is evidence that the gene must have a critical function in an organism. The discoveries of many lethal alleles have provided information on the functions of genes during development. Additionally, scientists can use conditional and synthetic lethal alleles to study the physiological functions and relationships of genes under specific conditions.

GMO- Blessing or Curse?

    

    

(Image source: http://cpronline.com/whats-really-hidden-inside-your-food-gmos/)

     The somewhat tedious pGlo lab, which I have to written a formal lab report about, actually sparked a somewhat unexpected interest in a rather peripheral subject: GMO. The pGLO plasmid, a product of genetic engineering, consists of several reporter genes including GFP and Ampicillin Resistance Gene that were transplanted into the plasmid after being extracted (isolated) from other organisms. The technology which made such process possible directly pertains to the production of GMO, undoubtedly a huge controversy today.
     The first commercially grown genetically engineered food to be granted a license for human consumption is the Flavr Savr, a tomato that doesn't become soft. Currently 68 varieties of GMO are being cultivated around the globe, many of which demonstrate very impressive characteristics including herbicide/insect resistance. The advocates of GMO are confident that GMO, by virtue of its remarkable toughness and high yield, can help alleviate severe food shortages in third world nations. The opponents, on the other hand, are extremely skeptical about the safety of GMO and warn the devastating impact GMO may cause on the environment.
    Regardless of the intense debate, it seems clear that the opponents of GMO still have lots to prove. Many international science body in the world including EU, WHO, and the Royal Society of London has reviewed multiple independent studies—in some cases numbering in the hundreds—to reach a somewhat unexpected conclusion that GMO crops are "as safe or safer than conventional or organic foods". Recently, a group of Italian scientists catalogued 1783 studies about the safety and environmental impacts of GMO foods. The researchers concluded that none of the 1783 studies showed any credible evidence that GMO foods actually pose harm to humans or animals. “The scientific research conducted so far has not detected any significant hazards directly connected with the use of genetically engineered crops,” the scientists concluded. (Source: http://www.forbes.com/sites/jonentine/2013/10/14/2000-reasons-why-gmos-are-safe-to-eat-and-environmentally-sustainable/) Well, seems I can feel safe and have my potato chips again.

The Selfish Gene- the purpose of our existence

    

     Man never passes on genes. The truth is that the gene uses man to pass itself on. Bitter as it sounds, an organism is no more than a transient medium whereby the gene is carried to future generations. This means that almost every aspect of animal behavior is elaborately coded so as to secure and consequently pass down the gene to the descents. Particularly interesting was the behavior of the Ground Squirrel. Living in groups, Ground Squirrels are renowned for making loud, characteristic alarm calls when they spot a predator. The individual organism that first spots the predator and makes the call is, of course, very likely to be killed by the predator. Underlying such seemingly altruistic behavior is an extremely calculative, even selfish motive. Keep in mind that the true beneficiary of the alarm call is neither the group nor the individual--it is the gene. By sacrificing the individual organism and instead saving many close relatives within the group possessing itself,  the gene has successfully done its purpose of  'self-reproduction.' The will of the individual is of no importance in this grand scheme. Even humans cannot be an exception. Maternal love, often considered noble and even divine, is no more than a small component of the gene's scheme to safely reproduce itself--remember that the child is the direct inheritor of his parents' genes. The conclusion is therefore very clear. Gene rules.
     However, this does not mean that man is not a noble creature. Richard Dawkins is in fact a great humanist despite all the malicious and undeserved rumors and blames targeted towards him by some exceptionally absurd group of people. Dawkins extends his unique argument about 'self-reproduction' to literally everything existing in the universe including ideologies, philosophies, culture, art, and anything created by human beings. These self-reproducing entities are called 'Memes.'  Unlike that between gene and man, the relationship between meme and man is an extremely productive and expansive one. The genes may be extremely transient (the combination of my genes would shrink into 1/8 only after three generations), but the memes, the most majestic and glorious products of human intelligence and creativity, transcend countless number of generations (#Socrates, Plato, Aristotle), greatly contributing to the breathtaking grandeur of mankind. As the Korean proverb "A tiger leaves a skin behind him; a man leaves his name" suggests, the true value of our existence comes from the achievements we make in our lives. The products of such achievements, transcending time and space to which we belong, shall not only illuminate the future but also leave our marks on the universe. The purpose of our existence is therefore clear. Once we are not given the choice to defy the scheme of our genes, the only way we can make ourselves meaningful is contributing to the future with the endless legacies of our achievements.   

10/28 HW

1. Explain the significance of Mendel.

     Through his extensive breeding experiments of peas, Gregor Mendel laid the foundation of modern genetics by shedding light on the concept of 'blending intelligence', the idea that offspring inherit intermidiate characteristics between their parents. He proved that heritable variants are passed from parents to offspring and always exist in the gene even though they are not visible. 


2. Draw the structure of DNA and who discovered this structure.
    

     The double-stranded helix structure of the DNA was discovered by Watson and Crick.   



3. Explain each of the five examples of variations that occur to DNA and give an example of each.

    
 
     A. Substitution of a single letter for another (Point Mutation)
     A point mutation is a type of mutation that causes the replacement of a single base nucleotide with another nucleotide of DNA of RNA. It usually takes place during DNA replication, a process by which one double stranded DNA molecule creates two single strands of DNA. In whippet dogs, for instance, a point mutation causes the drastic size difference between a slender one and a massive, hulking one.
    

     B. Deletion of a block of letters
     Deletion refers to a state in which a certain part of a chromosome, or a sequence of DNA, is missing. Many children with physical abnormalities are victims of microdeletion, a relatively small amount of deletion of a chromosome.


     C. Duplication of new letters
     Gene Duplication refers to any duplication of a part of DNA which contains a gene. Just like any other types of mutation, gene duplication is also a byproduct of errors occured during DNA replication. It is known to be a major cause of various cancers.
    

     D. Insertion of new letters
     Often caused by unequal crossover occurred curing meiosis, an insertion is defined as an addition of one or more nucleotide base pairs into a DNA sequence. A pea plant whose inserted genes cause it to be wrinkled is an example of insertion mutation.
    

    E. Inversion/Translocation of letters already present
    In an inversion mutation, the whole section of DNA becomes reversed; in a translocation mutation, the chromosome segments and the genes included there change positions.


4. What is evo-devo?

Evo-devo is one field of biology which focuses on the development of different organisms and common ancestors by studying the effects and contributions of individual developmental genes to evolution.

5. Make a connection between human migration and the mutation of lactose intolerance.

In the ancient times before 10,000 B.C, humans would naturally lose the ability to digest lactose after reaching about 4 or 5 years old. Drinking the mild of other animals therefore resulted in devastating results including severe stomach cramps and diarrhea. However, as soon as a genetic mutation of lactose intolerance which allowed one to permanently produce lactase occurred near modern day turkey, the number of lactose-tolerant people dramatically increased and successfully inherited their genes to their offspring. The group of lactose-tolerant people then migrated all throughout Eurasia, Great Britain, Scandinavia, Mediterranean, etc. Such phenomenon explains how 80 percent of Europeans became milk-drinkers. 

Founder Mutations

         A founder mutation one type of gene mutation observed with high frequency in a group that is or was geographically or culturally isolated, in which one or more of the ancestors was a carrier of the mutant gene. Unlike hot-spot mutation that pertains to individual units of DNA, founder mutation affects a larger stretch of DNA known as the haplotype, allowing the scientists to trace the origin and estimate the age of mutation—the shorter the haplotype, the greater the age of genetic aberration.

         Although many examples of founder mutation such as sickle cell anemia or cystic fibrosis can be extremely detrimental to humans, they all have survived through countless number of generations and keep on plaguing the people even today. That many founder mutations did not disappear through natural selection explains evolution not as a process of improvement but of adaptation. The genetic mutations that are lethal in the modern American environment could have in fact been beneficial to survival in other places of the ancient times—for instance, back when malaria was an incurable disease that entailed nothing but death in Africa, those who had sickle cell anemia whose deformed anemia prevented them from having malaria had a higher chance of survival even despite detrimental symptoms. As the African population migrated to other regions (in this case through the slave trade) and formed new gene pools by intermingling with other races, the founder mutation that used to be unique to the African continent was widely spread. Unfortunately, in temperate zones like America where malaria was not a practical threat to life, the sickle cell anemia no longer functioned as a beneficial genetic trait but as an extremely harmful one. This phenomenon suggests that evolution is simply a gradual process of 'adaptation' to a particular environment. The byproducts of natural selection which human beings possess and demonstrate today in the environment to which they belong can all go to waste when the environment drastically changes. Adaptation is merely a relative concept, and it is therefore futile to define what's 'superior' or 'inferior' in a long term.             

Evolution doesn't mean improvement

     One thing I used to mistakenly believe was that evolution is a tendency towards perfection. I thought that after millions and billions of generations, humans would become 'superhumans' who are virtually superior than the current human being in almost every respect. However, it turns out that evolution is simply a gradual process of 'adaptation' to a particular environment. This in fact signifies a very uncomfortable fact that the byproducts of natural selection which human beings possess and demonstrate today can all go to waste when the environment drastically change. Adaptation is merely a relative concept, and it is therefore futile to even define what's 'superior' or 'inferior' in a long term.
     Also, I realized that human beings are by no means even close to perfect even after undergoing millions of years of evolution. One interesting imperfection is the human eye.

(Source: theamazingeye.wordpress.com)


     In human eye, the nerve fibers route before the retina, blocking some light and creating a blind spot where the fibers pass through the retina and out of the eye (Wikipedia s.v. blind spot). If evolution is a tendency towards perfection, the species with nerve fibers routed behind the retina should only have survived, passing its heritable traits to its descents.  

Jean-Baptiste Lamarck- the forgotten pioneer

(1744-1829)



Great theories led by great thinkers have great controversies--the fledgling evolution theory was in fact, heavily influenced by the hypotheses made by Jean Baptist Lamarck, a prominent French naturalist who is famous for his fallacious yet stunningly ingenious 'use and disuse theory.' Lamarck was one of the leading thinkers of his era who first recognized that living things have changed over time and furthermore have adapted to their environments. Setting aside the disproved hypotheses, the significance Lamarck has in the history of evolution theory is simply immense. Here are some hypotheses made by Lamarck


1. Tendency towards perfection
Lamarck believed that all organim proceed towards perfection and complexity. As a result, the organism are consistently change and acquire traits that make them fit better to the environment. In Lamark's view, for instance, the complex wings of the birds are byproducts of its ancestor's urge to fly.

2.Use and disuse
The tendency towards perfection eventually caused organisms to alter or develop new ways of using their organs. Lamarck proposed that the selective use or disuse of an organ led to a change in that organ that was then passed on to offspring.

3. Inheritance of acquired traits
Lamarck believed that acquired traits can be inherited. In a nutshell, if you grow huge abs, your children would inherit big muscles as well.

What missing link?

'Walking Whale' Fossil Discovered In Peru: 40-Million-Year-Old Specimen May Be Link Between Aquatic and Land Mammals

By Josh Lieberman on September 20, 2013 12:26 PM EDT

A "walking whale" fossil discovered in Peru may provide new evidence for how whales evolved from land to sea creatures. Above, an artist's rendering of the Rodhocetus, a horrifying ancient creature related to the recently discovered whale. (Photo: Wikimedia Commons)

Paleontologists in Peru have uncovered the fossils of a "walking whale," remains believed to be at least 40 million years old. The whale fossils were found in the Ocucaje desert, one of the richest sources of fossils in the world, and may be evidence of a link between sea mammals and their ancestors living on land.
"We already knew about the paleontological richness of Ocucaje dating back 10-12 million years," said Rodolfo Salas, a paleontologist who was part of the discovery team. "Now we can say that the most important primitive sea mammal deposit in South America is at Ocucaje."
The whale fossils belong to a creature in the suborder Archaeoceti, meaning "ancient whales." These sea mammals share certain characteristics with their land-dwelling ancestors, most notably evidence of legs. The whale had teeth that were more like that of a terrestrial animal, as well as a cavity in the cranium that is more consistent with land mammals than sea mammals.
The first whale ancestors were very different from the whales of today. Some 50 million years ago, the "first whale," a furry, wolf-sized creature, lived on land but ate fish. Whale ancestors lost their hair and acquired web feet; eventually they lost their feet and gained flippers and a more streamlined shape for swimming. By about 45 million years ago, whales had developed into the more familiar, fully aquatic species.     
Fossils from sea mammals as old as the whale found in the Ocucaje desert have never been found in Peru before. Previous ancient sea mammal fossils have been found in Egypt, Pakistan and India. The Ocucaje desert has yielded remains of other marine creatures, and there are probably plenty more to be found.
"There is probably a greater number of fossils in the sand but it takes high-tech equipment to locate and recover them," said paleontologist Cesar Chacaltana.


URL: http://www.isciencetimes.com/articles/6094/20130920/walking-whale-fossil-ocucaje-peru-40-million-years.htm



     There still seem to be countless number of anti evolutionists who exploit the  'Missing Link' rhetoric. Well, what missing link?? The relations among ancient mammals, amphibians, and marine organisms have been elucidated through this recent finding, and once again, the realm of creationism has been shrunken.
     By the way, even I could find about twenty 'missing links' between dinosaurs and birds after less than ten minutes of perfunctory research; to see is to believe.

http://en.wikipedia.org/wiki/Sinosauropteryx_prima
http://en.wikipedia.org/wiki/Caudipteryx_zoui
http://en.wikipedia.org/wiki/Sinornithosaurus_millenii
http://en.wikipedia.org/wiki/Microraptor_zhaoianus
http://en.wikipedia.org/wiki/Dilong_paradoxus
http://en.wikipedia.org/wiki/Jinfengopteryx_elegans
http://en.wikipedia.org/wiki/Juravenator_starki
http://en.wikipedia.org/wiki/Sinocalliopteryx_gigas
http://en.wikipedia.org/wiki/Velociraptor_mongoliensis
http://en.wikipedia.org/wiki/Ornithomimus_edmontonicus
http://en.wikipedia.org/wiki/Jianchangosaurus_yixianensis
http://en.wikipedia.org/wiki/Therizinosaur
http://en.wikipedia.org/wiki/Archaeopteryx_lithographica

 

 

Evolution: just a theory?

South Korea school textbooks drop evolution examples

June 8, 2012 |  8:06 pm

 

SEOUL -- Some major science textbook publishers for South Korea's secondary schools have deleted examples of Darwinism, bowing to petitions by a group that calls evolution "an unconfirmed theory."
Of the seven major science textbook publishers in South Korea, three have agreed to remove or revise references to the evolution of horses, and six publishers  deleted or changed chapters related to avian evolution.
The decision was made after the Society for Textbook Revision, or STR, filed petitions in December and March with South Korea's Ministry of Education, Science and Technology  against the inclusion of the information.
Since its formation in 2009, the STR has continuously  challenged the teaching of the evolution in South Korea.
"We are an academic research society that aims to delete the errors [relating to] evolution, which is an unconfirmed theory," STR President Lee Gwang-won said. "It is important to revise the textbooks and teach the students that evolution is just one of the theories, as it affects how students form their view of the world. "
Lee denied his organization is affiliated with Christian groups or creationist scientists. But  Han Jungyeol, spokesman for the Korea Assn. for Creation Research, told the science journal Nature that the STR is an independent offshoot of his association.
South Korean academics expressed confusion over the publishers' decision, assigning some blame to the government's education ministry because it forwarded the petitions to the publishers without any academic reviews or expert consultation.
"It is hard to believe that such a one-sided petition was easily accepted like this," said Choe Jae-cheon, a scientist at Ewha Woman's University in Seoul. "The education ministry included 'science and technology' in their name, but it is not paying enough attention to the importance of rightful science education."
One of the publishers that revised its texts,  Kyohaksa, was quoted by local media as saying the fact that there was an apparent scientific controversy over the issue prompted its decision.
But Jang Dayk, a scientist at Seoul National University, said the publishers' position was not acceptable. He said the scientific community had ignored the STR up to now "because it was unworthy to confront them. The quality of their argument is sophomoric and based on distorted information."
But the latest move by textbook publishers, Dayk said,  has galvanized the scientific community, pushing it to act.  "We have formed a task force and will put out a statement to halt the textbook revision."

 --Jung-yoon Choi

original link: http://latimesblogs.latimes.com/world_now/2012/06/south-korean-science-textbook-publishers-evolution-deletions.html






More than a year has passed since the controversy occured, but the embarrasment I feel towards my country is simply unbearable even today. Regardless of religious dogmas and individual belief, evolution is a fact. The abundant evidences of evolution are all as extensive as they are evident; to simply iterate some of them I have learned in class, they include but are not limited to fossil records, homologous organs present among different species, genetic structures, cladistics, and embryos. Mainstream science views evolution as an irrefutable fact whose evidences are obtained and confirmed strictly through scientific methodology, and education in schools have an obligation to maintain and secure that theory of a fact in an ironclad lockbox.
The cause of such inconceivable incident in my country is attributable to the rigid education system so characteristic of Korea. Biology education in Korea is extremely test/memoriation oriented, and therefore fails to provide the weary students with firsthand knowledge which can only be obtained through various labs and class activities.  The dry lectures and intense cramming that take place in classrooms give a wrong signal to both the students and the entire society that evolution is a mere theory of the books, barely supported by real, tangible evidence which we can actually see and feel.
It is fortunate to be studying in a country (well, in a state at least) in which no man sabotages proper scientific education. Underlying such great achievement of America is undoubtedly the vivid education epitomized by the unbounded intellectual stimulants I relish in this school.



15/10/13
Sid Moon
 

The evolution of Horse

     Among many different fossilized mammals, the Horse is perhaps the one whose evolutionary process is the most well known and well supported by abundant fossils found in North America, South America and Europe. The oldest common ancestor of Horse is known to be Eohippus, a fox-sized mammal that lived in the woods of North America 58 million years ago. Eohippus was in fact very different from the modern day horse: its forefoot and hindfoot had four and three toes respectively, and its height didn't exceed 1 feet. As Eohippus evolved into Orohippus and Epihippus, its body size significantly increased and its number of toes became three, but it was not until 36 million years ago that the Mesohippus appeared, resembling the modern day horse with its unprecedented hoof. The number of toes decreased into one 13 million years ago along with the advent of Philohippus, and 10 million years later eventually appeared Equus, which is congeneric to the modern day horse.
     The evolution of horse shows a consistent tendency towards a decrease in the number of toes, increase in the body size, and enlargement of the cerebrum.

27/9 Evidence for evolution quiz

1. Even though the whale-resembling Basilosaurus ostensibly looked different from Mesonychid, scientists have discovered from fossil records that beneath Basilosaurus's flippers were fingers that are anatomically similar to those of a Mesonychid. Such existence of a vestigial organ (trace of homologous organ in other species)  serves as a powerful evidence that an evolution had occurred.

2. E

3. The three organisms exemplify a convergent evolution, a process by which unrelated organisms independantly evolve similar trait(s); in this case, wings. We may assume that the three organisms, despite fundamental differences, were pressured into adapting to similar environments where flying was necessary for survival.

4. Organisms which share a more recent common ancestor are more closely related in terms of their DNA structures; to be more precise, in terms of their genetic sequence. By comparing the DNAs of different organisms in the Common Descent Lab, we can get a glimpse about the so-called 'evolutionary tree', a branching diagram that accounts for the degree of change of a certain specie. Many primates we know including monkeys are in the same evolutionary branch as humans. This means that humans are not direct descents of monkeys, but share a common ancestor with them.

5. Structures that have different mature forms but develop from the same embryonic tissues are called homologous structures, and homology refers to the appearance of such homologous structures among different organisms. For example, the limbs of the four modern vertebrates: turtle, aligator, bird and mammal are homologous structures that consist of same basic bones.

Day 3 prep for Osmosis Lab- Notetaking

Day 2 Class Activity

Question: Why do humans sweat while dogs don't?

Answer: Unlike dogs, humans have sweat glands. The sweat secreted by the sweat glands  conistently vaporizes on our skin and therefore allows our body to cool down spontaneously--water absorbs certain amount of heat when vaporized (heat of vaporization). The only way dogs can moderate their body temperature is panting. The cool air lowers the temperature of the exposed tongue and consequently moderates the body temperature. 

Day 2 prep notetaking- Properties of Water

 

Class 1: An informal, hypothetical lab report of the 'Dancing Milk' experiment

   

A.   Hypothesis

The drop of dish soap, which is a surfactant, had caused the food coloring to disperse throughout the surface of the milk.

 

B.    Procedures

1.    Pour enough milk into three separate pans.

2.    Add several drops of food coloring to each pan.

3.    Add a drop of dish soap to the first pan, a drop of alcohol to the second, and a drop of sesame oil to the third.

4.    Observe the changes in each pan.

 

C.     Expectation

Surfactant molecules like dish soap are usually known to be amphiphilic, meaning they contain both hydrophilic groups (heads) and hydrophobic groups (tails). As their names suggest, the hydrophilic group of the molecules actively interacts with water (in this case, milk) and the hydrophobic group with oil (food coloring), weakening the surface tension of the milk (by weakening the intermolecular force, the hydrogen bond, existing between the milk molecules) and eventually blending the food coloring with it, a phenomenon ostensibly viewed by the observer as ‘spread’.  

The hypothesis that the dispersion of the coloring is attributable to the amphiphilic property of the dish soap may be verified by adding alcohol and sesame oil, which are substances that are hydrophilic and hydrophobic respectively, to two separate pans of milk and comparing the changes. Since neither of the two are amphiphilic, it is very likely that they do not function as surfactants and consequently not spread the food coloring as the dish soap did.