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Theories, Fictions and Truth May 7, 2007

Posted by sumesh in Cartoons, Culture, Fun/humour, Philosophy of Science, Science.
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It makes a good cartoon to characterize theories as fictions.

It is from


Yearly Packs of Inspiration October 6, 2006

Posted by sumesh in Chemistry, Culture, Nobel Prize, Philosophy of Science, Research, Science.
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It is that time of the year when researchers from varied fields of intellectual enquiry experience the uncommon feelings of overwhelming elation and atypical ecstasy, thanks to the success some of their colleagues or predecessors achieved in carving nature at its joints and revealing some of the mysteries of the world and life. 

It is that kind of great success that makes every researcher humble and as they say, simple.  It often tells you the story of the remarkable, bold and queer steps taken by young researchers; The journey often starts with undergraduates who question everything and dare every ‘unimaginable options’, and pursue them at the cost of everything else, knowing well that the fascinating journey is the only thing that is guaranteed and not the destination.  It is a research-for-research-sake, knowledge-for-knowledge-sake odyssey.  In that journey of self-actualisation the journeyer who strikes out new paths metamorphose him/herself into a light-bearer who has mastered the path.  Prizes or results, if any, in that pursuit are just some extra benefits of continuing this inspired peregrination.

This year’s Nobel Prizes in sciences show the importance of the ground work done by researchers as a team, many researchers significantly contributing to the unraveling of the enigma of life and the world.  It would have been a great gesture if the Nobel Committee at least mentioned all those who contributed in solving the problem, even while bestowing the prize to one, two or more persons.  For science is rarely an individual enterprise, more often than not it is a group work extra ordinary.

Dr. Roger D. Kornberg won this year’s Nobel Prize in Chemistry for visually showing how genes transmit messages to copy cellular functions.  He has not only described the way by which genetic information in DNA is ‘read’ and copied into messenger RNA, but created detailed crystallographic pictures of it also. 

In his meticulous account of ‘the molecular basis of eukaryotic transcription’ which is cited by the Nobel Committee as the kind of “most important chemical discovery” mentioned by Alfred Nobel in his will, Dr. Kornberg details the mechanisms of transcription that suggests possible regulation of the process.

Once we understand the importance of transcription process in constructing and sustaining life in all organisms, we can’t miss out the significance of the prizewinning discovery and its obvious applications. 

In order to tell this story let me take you back to the basics(you may overlook this part altogether, if you consider it too basic to look into)

[[The building blocks of human/animal body are cells (there are approximately 50-100 trillion cells in a human body).  Cells typically have an outer membrane and contain fluid called cytoplasm.  The most important of the parts(organelles) in the cytoplasm is the nucleus.  Within the nucleus there are structures called chromosomes which contain the genetic material of the organism.  This genetic information is stored in long strings of DNA called genes. DNA molecules, as everyone knows, are like spiral staircase.  Each stair in this ‘double helix’ is composed of the DNA bases A, C, T, G which in particular sequences constitute individual genes. In other words, each cell contains  ‘recipe’ for protein production stored in DNA segments which are called genes. 

Human genome, ie. the complete set of genes, though contains around 30, 000 genes, only  a few of them are expressed, ie, used in each cell.  The role these unexpressed genes play in cellular functions is not known.  The expressed genes determine and help synthesize new proteins which construct and sustain the organism.  To put it simply, genes determine the function of particular cells

(#An aside:  Please note that this is a very simplifiedaccount of ‘gene’.  Present understanding of ‘gene’ is extremely complex that one may say that there is nothing like a well-defined gene in a cell.  Further, recent studies give much importance to the workings of RNA as are given in the Nobel Prize winning discoveries in Chemistry and Medicine this year. I put this interesting point as a topic for another blog. For now see these references.  news@nature Published online: 24 May 2006
Nature 441, 398 – 401 (25 May 2006). ]] 

Gene expression is controlled by transcription process in which DNAs in the nuclei of cells are copied to messenger RNAs whose job is to pass the information to the protein synthesizing machinery in the cytoplasm.

Transcription, if you remember,  is the process of copying and transferring genetic information to different parts of cell.  In this process information stored in the genes inside the central nucleus of cells get chemically transcribed into recipes for the proteins that are building blocks of living organisms.  And different parts of the cell work in tandem, as writers, editors, chefs, supervisors and assistants, in executing this highly complex programme and in trouble-free running of the machinery. (If the machinery is not running smooth which means some health-threatening conditions such as cancer, it is possible now at least to find where the problem lies and it may be possible in the near future to correct it)

This kind of transcription process occurs in eukaryotes, i.e., organisms having well-defined nucleus in cell.  Other organisms, for instance bacteria, use different transcription process.

Though it was known this process copied genes using RNA molecules thanks to the equally remarkable research work done by many others, what Dr. Kornberg has shown now(2000 onwards) is the detailed description of the role and workings of RNA, as he provides with the exact development of RNA- strand,   X-ray images of crystallised RNA molecules (this became a standard biochemistry tool since then), and the role of different molecules and even atoms in the process.  He revealed, through his study that spans nearly thirty years, the early phases of the transcription process which involves around sixty different protein molecules in converting DNA into messenger RNA molecules.

The transcription machinery which looked like a dark room in 1990s now turned into a well-lit, complexly organised room suggesting many a conceptual revolutions. 

#Roger D. Kornberg ,59, is a structural biologist at Stanford University School of Medicine.

#His father Arthur Kornberg, 88, a biochemist at Stanford, received the Nobel Prize in Physiology or Medicine in 1959 for his work on DNA replication. The Kornbergs are the sixth father-son duo to win Nobel Prizes.

#His one important article is here. Science 2001, 292, 1863 and 1876.

#Dr. Kornberg has used the simple yeast as a model

#His main research work centered around an enzyme called RNA polymerase that makes RNA and regulates the process of selecting genes from the pool of thousands of them, to produce the only protein a cell needed at any particular time.

#One DNA learning site is here http://www.dnalc.org/home.html

Courtesy: The Royal Swedish Academy of Sciences

[To be continued….]