Jacques Ninio addresses molecular biology from the evolutionist's viewpoint, reviewing major research areas such as acquisitive evolution; the comparison of protein structures in three dimensions; the stability of the genetic code; and prebiotic replication.

Originally published in 1983.

The Princeton Legacy Library uses the latest print-on-demand technology to again make available previously out-of-print books from the distinguished backlist of Princeton University Press. These editions preserve the original texts of these important books while presenting them in durable paperback and hardcover editions. The goal of the Princeton Legacy Library is to vastly increase access to the rich scholarly heritage found in the thousands of books published by Princeton University Press since its founding in 1905.

Auszug. � Genehmigter Nachdruck. Alle Rechte vorbehalten.

Molecular Approaches to Evolution

By Jacques Ninio, Robert Lang

PRINCETON UNIVERSITY PRESS

1 Clearing the ground, 1, 
2 The chemistry of life, 4, 
3 The discreet charm of the sequences, 17, 
4 Evolution in three dimensions, 28, 
5 Can sequences be compared?, 34, 
6 Replication and genetic tinkering, 40, 
7 Populations, 48, 
8 Prebiotic replication, 58, 
9 The genetic code, 63, 
10 The stereochemical hypothesis, 74, 
11 The origin of the genetic code, 79, 
12 Sequence space, 92, 
13 Acquisitive evolution, 98, 
14 Molecular defences, 103, 
15 Molecular crosses, 109, 
16 The great error loop, 116, 
Bibliography, 123, 
References, 125, 
A. Works and articles of initiation or culture, 125, 
B. Books for higher education and research, 125, 
C. Original papers for specialists, 127,

CHAPTER 1

Clearing the ground

We can understand evolution without really knowing what life itself is! This view, held by the great biologist Haldane, was characteristic of a half century of evolutionism which produced models and calculations in the absence of any intimate knowledge of cellular logic. The evolutionist used to try to calculate the outcome of battles for survival just as a General evaluates the chances of victory on a battlefield: will one side score a resounding victory, will the two forces neutralize each other or will they occupy the field alternately? The theory of evolution by natural selection lends itself to all sorts of ramifications. Its principal theme is that since many more individuals of each species are born than can reach reproductive age, those best fitted for the struggle for existence will have more chances of leaving descendants and the characters they carry, passed from generation to generation, will eventually become fixed within the species. If new and even fitter variants appear, they will gradually eliminate the former ones to their own advantage.

I support the doctrine of natural selection in the same way that I recognize the truth of the syllogism that Socrates is a man, all men are mortal, therefore Socrates is mortal – but I go no further than that. A correct idea can become sterile. Renaissance scholars believed that the study of syllogism would enable them to work out the whole of logic. Instead they merely got bogged down in an exploration of Baralipton, Darapti and 254 other outdated forms of syllogism. Of course, evolutionists had to examine closely the fundamental propositions of Wallace and Darwin and assess the possible influences of all imaginable factors: small or large populations, isolated or panmictic, sexed or not. But today we must recognize that this area of evolutionary biology tends to become confined to the study of infinitely increasing variants.

In renewing our conception of living things, molecular biology sheds new light on an evolutionism which until now has been too formal and helps us to redefine the problems. At first molecular biologists were content to verify at their level the validity of concepts developed by the evolutionists 30 years earlier. Duplication of chromosome segments became duplication of DNA segments; comparative anatomy was replaced by comparative molecular anatomy. Fortunately, things did not rest there. After this consolidation phase a new generation of work began which posed the problem of evolution in a completely new manner. In the former view an animal predator with good eyes would be able to capture its prey more easily than one with defective vision and would therefore be selected for. But what made possible the existence of a visual apparatus in animals? Why was this solution realizable and not another? Or, if other solutions were available, what were they? In summary, our aim now is to tackle a problem which not so long ago seemed insoluble: how to evaluate, having taken into account the state of organization of life at any given moment, the various possibilities which are apt to manifest themselves. This is the primary aspect of the new set of problems posed by studying evolution. A secondary aspect is how to decide, once a novelty has appeared, if it will be established or rapidly eliminated. I shall therefore discuss evolution, as far as one can today, in the new perspective as applied to the molecular logic of living things. The genetic code is at the heart of this logic. Above all, we want to know why the code exists and through what tentative stages cellular organization, now so well formed, could have passed. We will tackle step by step all the interesting concepts in molecular biology which revolve around the genetic code.

At first sight the layout and order of the contents will appear disconcerting, but nothing has been left to chance. Those who like to have everything neatly cut and dried will be disappointed. I am not presenting a standard product, aseptic and reassuring, to be offered in a supermarket, but a discourse which sticks to the facts of current research, which refuses to gloss over contradictory aspects of present ideas and which allows, albeit tentatively, social and ideological connotations to show through. Instead of following each statement with ten lines of support, ten against and three of compromise, I concentrate on only one aspect and further on, when I show how the problems can be posed in other ways, I discuss the neglected aspects in other contexts, which lend them their true importance. A major aim of the layout which I have adopted is to produce a text which can be read with profit and interest by readers at very different levels. Technical terms have been kept to a minimum. To avoid tedious exposition of details of molecular biology I have dispersed reminders throughout the text and have placed them in an evolutionary context as soon as they appear.

Initially, of course, the evolutionary approach will be rudimentary: the kind in which molecules from different organisms are compared to deduce ancestral relationships between species. This aspect of molecular evolution has already received wide coverage (it is discussed in Chapter 3). On the other hand, everything else is practically new. No other textbook on evolution deals with comparisons in three dimensions, with acquisitive evolution and with the stability of the genetic code. No other work since the remarkable books of Woese (1967) and Ycas (1969) has discussed the genetic code in depth. After briefly describing constituents (proteins and nucleic acids) and comparing them we shall move on to mechanisms, to the most important cellular processes: information transfer, replication and genetic translation. Having revealed the logic behind these mechanisms, we shall attempt to understand how they could have emerged. Lastly, we shall reach a third stage. The cell is not simply a collection of molecules or a juxtaposition of mechanisms but a coherent entity in which each part is subject to constraints of compatibility with the rest. We shall attempt to clarify this to form concepts which will enable us to understand an evolution which proceeds from one coherent whole to another which is equally coherent.

Free to annoy the purist, I have often preferred to use simple language, close to the spoken word, which is very effective for putting ideas across. The research worker in the laboratory, when he is not writing administrative reports which will be judged by the quality of the typing uses everyday words and images borrowed from daily life. This can hardly be denied by the evolutionists, who...

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