27 June 2010

Who am I?

Who am I? - Philosophers asked this question for thousands of years! Though Darwin discovered the answer 150 years back, now we know the nuts and bolts of life! Life is nothing but certain intricate set of chemical processes working together and its fundamental process involves creating proteins (the building blocks of our body) from the amino acids (food) using a design template called genes (parts of DNA).

[Gene] + [Amino Acids] ---> [Protein]

A gene is a functional part of DNA which corresponds to our one or more physical or mental characteristics. It is represented as a sequence of 4 letters: A, C, G and T (each corresponds to 4 different sub-molecules of DNA). These genetic instructions could be modified or damaged by many environmental factors, for example DNA damage by UV light or smoking. Ultimately, the genes and the environment (includes food, habits, life-style and other internal/external environmental factors) determine who we are!

[Who am I?] = [My Genes] + [My Environment]

Now a days, people are started doing DNA analysis (like blood test) to understand their design makeup - their health , traits and history! DNA analysis can be simply done from our saliva sample, as every cell in our body carries our genetic materials.The picture below shows our nuclear DNA (Our genome consists of 22 pairs of chromosomes and XY chromosomes; chromosomes are the package for DNA) and mitochondrial DNA.
  • 1-22 pairs of chromosomes, one set is from mother and another set is from father.
  • X-chromosome is from mother and Y-chromosome is from father to son (XY determines male sex; for females, it will be XX).
  • MT is mitochondrial DNA. Mitochondria reside outside the nucleus of the cell, and it is not part of our genome. It is only passed from mother to children.
  • For each chromosome, the number of Bases, Genes, SNPs are specified. A Base can be one of A, C, G or T (An example for 10 Bases sequence: CAGGAATGCA. Likewise, the 1st chromosome has 247 Million Bases sequence). Different parts of this sequence form different Genes. SNP (single-nucleotide polymorphism; pronounced as snip) is a single Base variation in the genes. SNP-s are used to identify gene variations in the population.
  • Ultimately our genotype for each SNP is used to determine our specific characteristics as an individual. For example, a SNP from the 1st chromosome (with gene name, position in the sequence, SNP marker, possible versions in that position, and genotype):
[Gene] [Position] [SNP] [Versions] [Genotype]
SDF4 74242 rs3094991 A or G GG

(Note: Possible combination for A or G are AA, AG, GG, GA)

The following lists include some of the things we could know about design makeup.
  • The diseases that we have lower risk or higher risks, such as Diabetes, Rheumatoid Arthritis, Melanoma, Bipolar Disorder, Obsessive-Compulsive Disorder, Obesity, Heart Attack, Cancer, Parkinson's Disease...
  • Our sensitivity response to different drugs or treatment such as Interferon Beta Therapy, Warfarin Sensitivity...
  • Our level of susceptibility to alcohol dependence and Heroin addiction.
  • Our caffeine metabolize rate and related heart attack risk.
  • Our traits such as taste blind, color blind, eye color, hair color, earwax type, Lactose intolerance, muscle type that determines athletics ability, sensitivity to pain, longevity, odds for baldness...
  • Our blood type, HDL cholesterol levels and its make up.
  • Our verbal, non-verbal intelligence, episodic memory (short term memory), long term memory, ...

Our mitochondrial DNA is passed on from mother to children. From the mitochondrial DNA mutations (changes in the genotype) at different point in human history, our ancestry can be traced back to our African ancestors where humans first evolved (it can even be traced back further to our close relatives chimpanzee, gorilla, monkey, etc.). Likewise, our Y-chromosome is passed on from father to son. From the Y-chromosome mutations at different point in human history, our ancestry can be traced. Based on these mutations, groups known as haplogroups are defined.

Before 500 years ago, intercontinental travel is not easy. So, human migration from Africa to Europe, Asia, America and Australia can be traced along with the haplogroups.

The picture shows maternal line migration. For example, Haplogroup M (sub group of L3) (Populations: Indians, Chinese, Tibetans) is one of two branches on the mitochondrial DNA tree that arose about 60,000 years ago, soon after humans first expanded out of Africa. Because of its deep roots it is widespread in southern and eastern Asia, and its branches extend into North America as well.
This is just a beginning of what is possible in the future. Humans are the first species on earth to understand their own design makeup and can possibly transcend themselves into trans-humans!

"In the future...a new generation of artists will be writing genomes as fluently as Blake and Byron wrote verses" -- Freeman Dyson

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06 June 2010

Science of Science

Just throw a stone; what if it goes up faster and faster, or comes down slower and slower, or makes some sharp zigzag path? you would be surprised; even a small kid would be surprised. The thrown-stone is supposed to go up with decreasing speed and come down with increasing speed; and depending on the throw-angle, it would make certain curvature path. Every kid learns this from the experience, without any need of deeper understanding about speed, acceleration, force, gravity, etc. Yet, if the stone followed any different characteristics, intuitively we know that something is odd. But, if we live in an environment where the thrown-stone never comes back, that is what our brain would have learned. Whatever the environment we live in, our brain learns its characteristics and causal effects. As we grow up, our brain learns and collects lots and lots of such inferences which we call commonsense, intuition, hunch or gut feeling. Though commonsense provides very important value, it does not offer deeper understanding; and often it misleads us into many common-non-sense! That is how we think the earth is flat when it is round; that is how we think the sun goes around us when the earth rotates itself and goes around the sun. That is how we think life is designed when it is evolved over billions of years. That is how we think we can freely make decisions and choices beyond our genetic and environmental makeup.

In any case, beyond simple commonsense, people critically thought and discussed about many things. This school of thought is known as philosophy. It invoked and created many ideas such as prime mover (the first root cause of all the chain of cause and effects) and Zeno’s paradox (how motion is impossible). The concept of God is one such idea. Many philosophers critically analyzed it. Some developed great faith in the concept of God beyond human reasoning, yet tried to explain it at philosophical level. This specialized school thought is known as theology. After a while, philosophy as a knowledge gathering process reached its limitation, and stagnated at certain level with just mere back and forth arguments without yielding any new insights about us and the world we live in.

Our commonsense may suggest, heavier objects reach the ground sooner than lighter ones. Galileo first showed experimentally that all objects reach the ground at the same time. Instead of making philosophical and fantasy stories about the moon, planets, the sun and stars, he observed through his telescope. He showed the importance of experimentation, verification and objectiveness. Ultimately he and many others created a systematic process which involves observation, theory making, verification, etc. This school of thought is known as science. It allowed us to understand life and 3.5 billion years of life evolution. It showed our universe that consists of billions of galaxies, each galaxy consists of billions of stars, and 14 billion years of cosmic evolution.

Science is a systematic knowledge gathering process. Based on our brain's architecture (the way it evolved to be) with its capabilities and limitations, science is the best technique we invented so far to understand the complex world we live in and gain deeper insights.

Achilles: But there is science and there is art!

Tortoise: Science = A systematic understanding process. If you want to understand anything, you can have a scientific study for it. There is science of life (biology), and there is science of cosmos (cosmology). There is science of love and there is science of art. There is science of religion and even there is science of science!

Achilles: But science cannot tell us how to live our life...

Tortoise: Our life is infinitely complex and unpredictable. Even ultra powerful super computers cannot fully solve our life choices and decisions. Scientific facts and understandings or philosophical ideas or spiritual and religious teachings can only offer some guidance. It is up to us, how we use those guidelines and live our life artfully.

Achilles: Yet, there are so many things we do not understand...

Tortoise: Our known universe is 14 billion years old, our earth is 4 billion years old, life evolved 3.5 billion years ago, humans evolved few millions years ago, modern humans evolved 100 thousand years ago, recorded human history is few thousand years, science has been around few hundred years, and you have been around few decades! Now you want an easy answer for everything. It takes time and effort.

Achilles: But science cannot answer everything...

Tortoise: Science is not a magic! Science cannot answer anything! We have to find answers ourselves. Science is just a method, a process, a tool for us to find answers.


We use many methods to understand and gain knowledge about anything. These methods could be categorized as below.
  • Intuition: Our brain comes with many inborn intuitive mechanisms that are shaped over the course of our evolution.
  • Commonsense: Our brain automatically learns from the environment and experience, and collects many inferences about the causal effects with no or limited insights.
  • Philosophy: It is based on established belief system that is fundamentally derived and extended from Intuition and Commonsense; and hence, it is constrained by our subjectivity.
  • Theology: This subset category of Philosophy is biased towards one particular belief system. It is highly liberal belief system, and hence heavily constrained by our subjectivity.
  • Science: It is based on highly conservative belief system that "Extraordinary claims require extraordinary evidence". It requires observation, theory/sense making, verification, validation, etc. It offers some window to go beyond our intuitive and commonsense constrains and reach for objectiveness.