HyeongJu Kim

Principles of Bioinformatics

Bioprogramming

Genomics

 Genomics is a way of interpretation for genetic information and the link between genetic information and any other traits of organism, including phenotype, genetic relationship and so on. 

Origin of genomics

  The term "genome" was created in 1920 by Hans Winkler¹, professor of botany at the University of Hamburg, Germany. Because -omics refers to a field of study about it follows, genomics was coined referring to a field of study related to genome.

 

History

 The history of genomics is well described in Wikipedia.

http://en.wikipedia.org/wiki/Genomics#History

 

Methods of engineering genomes

 Methods of genome engineering are in various categories, like sequencing, acquisition, analysis of DNA. To be specific, PCR is used to amplify the amount of DNA sequence, Microarray is used to acquire the amount of RNA in cells or tissues and so on.

 There are a lot of methods for genomics study, and you can find more detailed list in here:

http://www.bio.davidson.edu/genomics/methodslist.html

 

Future of genomics

 Researchers have studied intensively on genomes, but still we have a lot of unsolved problems and questions. For me, the greatest success genomics would achieve will be DNA programming. Particularly, it means that we will be possible to construct a new functional protein, a cell and eventually, an organism from the genetic information, DNA. The created organism is analogy to a robot with organic materials. But to achieve the goal with DNA programming, we need a breakthrough in multiple areas including Artificial Intelligence, Proteomics, Systematic Biology and so on.

 

Transcriptomics

Proteomics

Epigenomics and Phenomics

Canceromics and Geromics

What is cancer?

 Cancer is a generic term for a large group of diseases that can affect any part of the body². It involves abnormal ceaseless cell growth.

What is the origin of cancer?

 Causes of cancer are really various. We can often see and hear news about new reports saying like, something causes some percents increase probability of cancer occurrence. They are smoking cigarettes, stress, unbalanced lifestyle and so on.

 It has been on debate but I think it is worth to share an article about cancer, "Cancer etiology. Variation in cancer risk among tissues can be explained by the number of stem cell divisions." by Tomasetti C and Vogelstein B³.

 According to the article, the factor playing the most important role in cancer risk is just the total number of divisions of the normal self-renewing cells maintaining that tissues's homeostasis. More intuitively, I brought a news subject reading, "Bad Luck of Random Mutations Plays Predominant Role in Cancer."⁴

How do you detect cancer?

 Initial recognition of cancer is mostly by signs or symtoms. In hospital, cancer is confirmed through medical tests, X-ray, CT, MRI and examination of a tissue sample.

How do we cure cancer?

 There are several methods to cure cancer. They include surgery to remove cancer tissue physically, and chemotherapy or radiation therapy to inhibit cancer proliferation and eventually make them die.

What is aging?

 Aging is the process of becoming old or becoming worn out⁵.

Why do we get old?

 We get old because of cell damage and loosing potential to recover the damage. One biological explanation of aging process is cutting off some segments of Telomere as cell divided.

How do we measure biological aging?

 By measuring length of telomere.

Additional Materials

What's real?

 As traditionally accepted, human beings have 5 senses - sight, hearing, taste, smell and touch. All human can imagin are based on perceptional information from these sensors. We, human beings, construct our own real world by using these sensors and believe that the world is real. But if the reality is defined as the state of existence, are our senses enough to prove existence of something? I doubt it.

  Existence in here is the state of one's presence in the objective and independent way from any perception. But there are tens of examples that the reality is actually very small portion of the existence and even distorted part of it.

 The endless discussion we had in classroom was because of this disconnection between what we think real and the existence. We can see, touch or even aggressively hear, taste and smell C. elegans to justify our conception of reality about this tiny buddy. For a C. elegans in the cyber world, as far as we saw in the class, we could tell so much discrepancy between our perceptional information about a real C.elegans and the cyber one like whether we can touch or not. However, what if we cannot tell any difference between them, by the improvement of technology. Not taking any additional knowledge except our perception into account, we must admit that the cyber one is real.

  I mentioned "any additional knowledge" which some of classmates made their refutation based upon. These knowledges could be that the cyber one is made of electrical signals while the "real" one is made of atoms and molecules. But note where the knowledge is coming from. Human being's own perceptual world! Though human beings have tried to expand the range of perception using sensors like microscope, telescope, analytic methods and so on, still the constraint is remaining. For an example, can you be really sure that a water molecule is same as the one in your mind?

 In short, all of our knowledge we use to define reality are based on our perception. In addition, the knowledge is not enough evidence for the existence. Therefore, we cannot define the reality as the state of existence but the results of our perception. Then I can say that the cyber C. elegans is real if we cannot find any difference from the "real" one. However, we know the C. elegans is in the cyber space, which is different from the "real" world, so I insist that it is not real.

Note:

     1.   I rephrase the definition of "Existence" from wikipedia.

 

Science articles proven wrong

 First of all, I want to share an article regarding scientific studies proven wrong.

http://www.theguardian.com/science/occams-corner/2013/sep/17/scientific-studies-wrong

It says that scientific studies can be proven wrong but this is how science works!

 

Reference

 1. Winkler, HL (1920). Verbreitung und Ursache der Parthenogenesis im Pflanzen- und Tierreiche. Jena: Verlag Fischer.

 2. World Health Organization (2014). Cancer Fact sheet N⁰297

 3. Tomasetti C, Vogelstein B (2015). Variation in cancer risk among tissues can be explained by the number of stem cell divisions. Science

 4. http://www.hopkinsmedicine.org/news/media/releases/bad_luck_of_random_mutations_plays_predominant_role_in_cancer_study_shows

 5. Collins Cobuild Advanced Learner's English Dictionary