Sunday, 16 March 2014

The Music of Life: Biology Beyond Genes. By Denis Noble

The Music of Life: Biology Beyond Genes

Denis Noble

Oxford University Press. First published 2006.

The book makes a case for going beyond the gene-eye view of biology and considering Life in terms of Systems Biology. Thus, Life and living organisms are to be considered as systems, in which hundreds of individual components - proteins, tissues, organelles, hormones, etc., etc.,- all come together in harmony to play the 'music of Life'. This is somewhat vaguer and less rigorous than what I know about systems biology as the study of metabolic cycles, the study of whole cell gene expression and control, and so on, i.e all the 'omics' of modern biology - genomics, proteomics, lipidomics, metabolomics.... 

The book is divided into chapters which each have a title taken from the discipline of music. The score is thus the genome; the rhythm section comprises of various beats and cycles, such as the heartbeat, circadian cycles, etc.; the orchestra is made up of the various organs and systems in the body; and finally, most importantly in my opinion, the conductor is what Noble calls 'downward causation'. 

Downward causation is term he gives to control and regulation of genetic expression by environmental and epigenetic factors. He redraws the conventional reductionist causation cascade (that goes from genes to proteins to cells to tissues to organs, functions and finally to the organism) with some some important top-down control pathways as well. Notably these are the following. The control of gene expression by the organism, the organs and the tissues; the control of gene expression by proteins; and the control of cell processes at the level of the organism. He advocates neither a fully top-down causation process, nor a bottom-up approach, but instead speaks about Sydney Brenner's suggestion of a 'middle-out' approach (without however explaining how such a scheme of description is to be actually carried out). He also revives Lamarckism, at least at the molecular level, involving some kind of epigenetic inheritance of acquired characteristics.

The book is well-written. It is short, just a couple of hundred pages, and accessible to non-specialists as well. But his ideas are neither well-argued, nor fully supported, and remain vague and hanging in the air. There is among the thinkers on evolution a kind of fuzzy divide between those who hold that all contemporary life is determined by DNA, and those who believe that evolution occurs at other levels as well. Richard Dawkins and Daniel Dennett are important spokespersons for the former viewpoint. Noble, along with people like S.J. Gould, is on the latter side. In chapter 1, for example, he explicitly rejects the 'selfish gene' concept of Dawkins. This book however, simply introduces Noble's position, and elaborates on some aspects of it, without either making it definite, or arguing for it with any rigour (or vigour!). It may, unfortunately, be read by some as support for mysticism.

Saturday, 15 March 2014

To Kill a Mockingbird. By Harper Lee

To Kill a Mockingbird

Harper Lee

Arrow Books. First published 1960.

This is a famous American book. At its core is a criminal case of the rape of a white woman, made out against a black man in the semi-rural Alabama town of Maycomb in the 1930s. But the novel is more than just that. It works in different ways, which, together, are strong enough to have kept the book in print all these many years. 

The story is told by Jean Louise 'Scout' Finch, the nine-year old daughter of the widower Atticus Finch, who is the lawyer who defends the accused man. A kind and humane man of great integrity and courage, Atticus has an easy, loving relationship with his children - Scout and her older brother Jeremy 'Jem' Finch. He leaves them to their own devices most of the time, but, without imposing himself on them, teaches them all the right values, such as respect for all people, courtesy, egalitarianism, honesty and courage. 

The first third of the book is mostly descriptions of the doings of Scout, Jem and their orphan friend Dill, who comes down from another town to spend the summer with his aunt, neighbour to the Finches. This part is thoroughly identifiable with some aspects of my own childhood, and that of other fictional characters such as Richmal Crompton's William. There is an element of southern Gothic horror in the goings-on at the lonely house situated at the end of the street, which the children's mythology, building on half-heard and little understood scraps of grown people's gossip about a retarded boy, has designated as the dwelling place of a monster. Scout and Jem begin to be made acquainted with the story of the rape and its aftermath when their father is appointed by the court as the defence lawyer. Their friends at school, and many of their neighbours, bully them and tease them and insult them for having a father who's a 'nigger lover'. When they confront their father with this charge, he only counsels patience and ahimsa. He does not explicitly defend his actions. He however makes it clear that he considers it his duty as a human being and as one who must say the truth to stand up for the wronged black man, despite acknowledging the futility of his egalitarian ideals in southern US, even a century after slavery had been abolished. His children get more and more involved in the case, finally being present in the courtroom when the trial is held, seated among the black relatives and supporters of the accused. They leave when the jury adjourns to consider the case, and learn only later that, upon its return, it pronounced the obviously unjust verdict of 'guilty' along with a death sentence. This part of the story then winds down with the tragic death of the prisoner trying to escape from prison, thus cheating the executioner. The rest of the book deals with the quiet aftermath, in which the Finches remain stigmatized by the white society for standing up for the black man. Jem grows up in this time, passing childhood into adolescence, though Scout remains the same. The final denouement reveals the true character of their 'mentally retarded' neighbour.

Harper Lee enunciates very liberal attitudes and ideals, but these go only so far. The most obvious sticking point to a contemporary, independent Indian (or, more generally, non-white, non-American) mind is the fact that all the doers, strong and not-so-strong, good and bad, are whites. As are all the thinkers. The blacks are all nice, but 'thick as a brick'. They are acted upon, they do not act. They are mostly all Uncle Toms. They never get angry at all the injustice they face, only sad and resigned. They keep turning the other cheek, even when they have no cheeks left to turn. While it is difficult not to like Atticus and to cheer him in what he does, any appreciation of his humane qualities are in the context of the knowledge that he appears great only because the rest of the whites are so nasty. Lee, of course, makes it a point to indicate that other whites are also fair-minded, and Finch is not the only one. But he is the hero of the story, and it is his character that stands out on sharp relief, presented to us by the author as a personification of her own thoughts and attitudes, to be admired and emulated. 

The villains of the novel, the Ewells, are aggressively placed outside the pale of 'decent' human consideration, they are really nasty. Their character is set sharply against that of Atticus. This, of course, makes it easy and straightforward to love the lawyer. This choice of black and white by Lee, with very little grey, is what makes this novel less than great, despite being so popular. One must however consider, in the light of all what we know about Anglo-American society, that the Ewells may have been as much a victim of the hyper-libertarian ideals prevalent, then and now, as the blacks. They are dirt poor, and have completely regressive ideas. They are dirty, do not work, do not bathe, and their children do not go to school. They live amidst filth, and one can almost sense the author raising her skirt just above her ankles and holding a scented handkerchief to her nose as she tiptoes past their dwelling. 

The writing is lovely, especially in the early parts of the book. But the sudden shift in the maturity level of Scout, when she starts to describe the court-room scenes, does not jell well with what has gone before. I suppose one must consider that the novel is not actually an account written by a young girl, but by an older women trying to faithfully reproduce her feelings and attitudes as a child. She does not however completely succeed in preventing her more mature thoughts from intruding.    

Sunday, 2 March 2014

'Nedunsalai Vizhakkugal' (Highway Lamps). By P.K. Ponnuswamy

Nedunsalai Vizahkkugal (Highway Lamps)

P.K. Ponnuswamy

New Century Book House. In Tamil. First published 2013.

I read the original Tamil version. This PKP's second book. The first novel, 'Padukalam' was based on his experiences as a child in Udumalpet/Pollachi, and dealt mainly with rural life in those parts, of the land-owning class (caste, actually, Gounders), to which PKP belongs. It was interesting, and though the names were confusing, and the characters and their intrigues unremarkable, and the writing staccato, there were extended descriptions of slices of rural life, such as the temple festival, and the making of molasses from sugar-cane, which earned a B grade for the book. 

The present book earns only a 'D'. Again based on the author's experiences, this time as a PhD student at the University of Madras (though not named as such), the story follows the happenings at the Department of Crystallography and Biophysics, a history with which I am personally familiar. Briefly, the true story is the following. In 1953 G.N. Ramachandran (GNR), along with G. Kartha, used fibre X-ray analyses to propose a structure for collagen. This structure was disputed by Crick and Rich, who went on to propose their own model. (This is the one largely accepted and referred to today, though it is different from the earlier one only in detail. Subsequent experiments have not been able to establish either structure as unequivocally correct, and in any case, the matter is of only very little interest to the science and industry today.) In response to the criticism, GNR, along with students and colleagues, went on to try and show, by computation, that his was the correct structure. He failed in that objective, but his quest led him to develop methods to analyse molecular structures that continue to be in use today, and continue to be expanded upon. These exploits brought GNR international scientific renown, and greats like Dorothy Hodgkin and Linus Pauling were his personal friends. He was not as well regarded or treated within the country, and, especially, by the administrators of the University of Madras. The political situation in Tamilnadu (then called Madras state) changed dramatically in the late nineteen-sixties, when the DMK came to power, riding on the anti-Hindi, anti-brahmin movement. There was a concurrent change of Vice-Chancellor at the University of Madras - N.D. Sundarvadivelu, a man steeped in the traditions of the Dravidian movement, replaced Sir A.L. Mudaliar, until then an almost eternal VC, as head of the more than 100-year old institution. GNR, and his colleagues, brahmins most of them, came under great pressure to diversify the caste composition of the department. GNR left the University and moved to IISc. The department came under the charge of R. Srinivasan (RS), a well-published crystallographer, who, apparently, was even less liberal in his views on caste than GNR. It was during this period, just before GNR left, that PKP joined the department as a PhD student, under the mentorship of a professor who was a career rival of Srinivasan's. 

PKP appears in the book (as Sellamuthu), and so do many other erstwhile members of the department, as thinly disguised characters. GNR (Anandamurthy) has a starring role, though the character is poorly developed, and sometimes positively embarrassing. The major, if villainous, role goes to RS (S. Ranganathan) who is depicted as a really nasty man, responsible for the downfall of the department and of GNR himself. I know that PKP had a venomous hatred of RS, going so far as to vindictively block the latter's retirement benefits when the eventual turn of events made him the VC of Madras University just after RS had retired. All that hatred is evident in this book, and though Sellamuthu himself has only tangential interactions with Ranganathan, it appears often that PKP has embarked on this literary endeavour to express his loathing for and bitterness against his former Head.

There is another storyline involving a chaste, not fully expressed, and ultimately unresolved love affair between Sellamuthu and a medical student, Sathya, who, like him, hails from Kongu Nadu (Udumalpet/Coimbatore/Pollachi...). There is the narrative of the anti-Hindi agitation, taking part in which are Sellamuthu, Satya and several other characters who, probably, are based on students PKP knew at that time. There is the story of one of Ranganathan's senior students, named Mannady (Ambady?), who is treated badly by his boss, and neglects his health and family. There is the story of Mythili, Ranganathan's lady student, who, distastefully to her, is made the object of his amorous advances (which, today, would lead to Ranganathan spending some time in jail). 

But none of these stories jell together, each one is unsatisfactorily and incompletely dealt with. There are no situations and events, or even conversations, which are authentically, or even interestingly described. With better, much better, planning and writing, the book could have had value as a factual account of the rise and fall of a small, but intensely productive and famous academic community. It could have been a psychological study of the people involved. It could have simply been a pleasant read. However, it is none of these. It is partly a rant, and partly a boastful and self-serving depiction of a portion of the author's life, and nothing more.