Jong's thesis preface
From JongBhak.com
Preface
by Jong Bhak
- Science for me is a paradigm of existence. It is the most important underlying principle and philosophy of all my activities in society. It is more than a career for a living or a fascination for certain topics. I understand Science as the very essence of humanity, (if there is something that can be called human as distinguished from other mental activities found in other living organisms).
It is a group psyche of modern humans and expressed as a profound cultural entity. Therefore, all my work is based on that general premise. It is a way of living, cultural exploration and philosophical development. I wanted to do it seriously with passion and awareness of what it is. I hope any evaluation of my work should be based first upon the understanding on my intention by the people who have deep interests in science as a cultural and philosophical entity.
- I think any serious research work at the level of PhD should involve strong background knowledge of philosophy on human life.
Science is not a craftsmanship nor a clever discovery of nature. It is not a task that can be done by any mind with a good memory and a good understanding on the techniques involved with good class marks from previous schools. It requires a maturity as an educated human personality with proper insights on the processes and consequences of the work involved for the society and all human beings to a far extent. It is a scholastic activity with unselfish and unbiased causes.
I wanted to have a broad understanding of proteins possibly contributing some insights and techniques useful for other scientists. Overall my goal with respect to understanding is achieved. Most significantly a better understanding of the meaning of life as chunks of information was acquired over the years. The sequence and structure relationship of biomolecules seem to reflect the very essence of any materialistic existence as a probablistic information or decision. Secondly the nature of proteins is better understood. How they occur, how they evolve, what they look like and what kind of behaviour they have. Thirdly, various techniques were acquired (mostly computational ones). For a biochemist like me, such computational techniques endow enormous freedom for investigation in time consuming work which require computers. Lastly, the limitations of present computational biology were clearly understood. I came to know the real problems with which contemporary bioinformaticians are faced. It is a pity that the other goal was not achieved. I could not find any generally useful insights, understandings or techniques for my fellow and future scientists. To conclude, even though it was the worst academic period in my life in terms of the degree of openness in exploring, acquiring and digesting new ideas with my own philosophical development, I kept struggling to remind myself how much will I had to at least my best.
The last 3 years were unusual in my life in that there was a continuos reassessment of my ideas on the present human society and the way science is carried out. One superficial outcome is that I became more sceptic. Philosophically I acquired a more critical attitudes to ideas. I think this is natural as present computational biology is in a state where frantic explorations dominate to give birth to a new innovational step-up. Without sceptic eyes it would be too hard to know where we are with the exploding data and trials we have to deal with. Also, the overall academic conduct observed in Cambridge shaped me in such a way.
- The thesis is intended to provide clear 'pictures' on what I have been doing. I tried to put ideas and procedures in figures to represent them succinctly as I myself understand scientific work quicker and better that way.
- Finally, I want to express that education is more a human problem than a national, a regional or a racial one. Therefore, I'd love to see the day when people understand the value of education in that perspective and any person who has an honest and sincere desire for learning (not because she/he is concerned with their careers or for selfish reasons) would get the best possible support regardless of her/his finance, background or origin.
- I give a sincere gratitude to the people who do science with pure, unselfish and honest passion as they are the people who made me grow and appreciate the world in the way I see.
I thank Sarah A. Teichmann for her help in various things.
I thank Alex Bateman 
for many occasions. Without him my academic life could have been much more lonely.
I thank Tim Hubbard 
who supervised me and helped me so much. I learned many things from him and he was always very kind to me. I thank Deco and Kay for being nice to me.
I thank Sonja Linux who did many difficult calculations for me without a single complaint. I thank Kerstin Braig for her reminding me that I am a non-societal wild animal. I thank Anne Glover who gave me big hope.
I thank Cyrus Chothia 
who is another milestone in my life.
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