Molecular Approaches to Evolution

Molecular Approaches to Evolution

Jacques Ninio
Translated by Robert Lang
Copyright Date: 1983
Pages: 144
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  • Book Info
    Molecular Approaches to Evolution
    Book Description:

    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.

    ThePrinceton Legacy Libraryuses the latest print-on-demand technology to again make available previously out-of-print books from the distinguished backlist of Princeton University Press. These paperback editions preserve the original texts of these important books while presenting them in durable paperback 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.

    eISBN: 978-1-4008-5624-4
    Subjects: Ecology & Evolutionary Biology

Table of Contents

  1. Front Matter
    (pp. [i]-[iv])
  2. Table of Contents
    (pp. [v]-[vi)
  3. 1 Clearing the ground
    (pp. 1-3)

    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...

  4. 2 The chemistry of life
    (pp. 4-16)

    At any given moment thousands of chemical reactions are occuring in the living cell. The food absorbed serves both as fuel, which supplies energy, and as material for constructing new structures or for replacing parts used by the cell. Only plants and photosynthetic bacteria can draw their energy directly from sunlight. The transformations, degradations and syntheses are chemical in nature. Each reaction in the cell is carried out and controlled by a molecule which is designed for this purpose – an enzyme. The enzyme interacts with the substances which have to be chemically combined and accelerates the speed of the reaction...

  5. 3 The discreet charm of the sequences
    (pp. 17-27)

    Atlas of Protein Sequence and Structure: this is the name of the molecular evolutionist’s Bible of the 1960s, the great Book of Life in which all known protein sequences are to be found. To save space, each amino acid is represented by a single letter: V for valine, M for methionine, etc. Phrases such as KLPP(M,N,O)PR, etc. cover whole pages, the brackets and commas indicating uncertainties. One shudders to think of the next edition of this work, which could contain 500 pages of this prose, representing thousands of years of human labour invested in the determination of structures. But 10000...

  6. 4 Evolution in three dimensions
    (pp. 28-33)

    Proteins initially seem to be compact masses in which the amino acids are tightly packed together, leaving no space for water molecules to circulate. Removing the amino-acid side chains reduces the protein to its skeleton, the turns and folds of which do not seem to obey any logic. Gradually, however, we are learning to see proteins in space. A long education in observation was necessary before these disordered bundles became intelligible, appearing as simple combinations of basic structural patterns with a defined repertoire of zig-zags and turns. The first major progress towards deciphering protein structures was the discovery by Pauling...

  7. 5 Can sequences be compared?
    (pp. 34-39)

    We have been able to exploit the enormous amount of work on determining protein structure in two ways. First, we compared sequences to deduce their family relationships and ancestry in a neo-Darwinian perspective: genes mutate, duplicate and mutate again. Sequences, initially present in low number, diversified through the ages and thus gave rise to the present immense variety of sequences. This is divergent evolution. Later, we compared the three-dimensional structures of various proteins and worked out some laws: the universality of certain structural patterns, restrictions on ways of combining these in higher order arrangements and the preferential use of certain...

  8. 6 Replication and genetic tinkering
    (pp. 40-47)

    By replicating, DNA remains indefinitely like itself. Its invariability is both real and deceptive. When a pure strain of bacteria is cultivated in the laboratory, where it is well isolated, its DNA is reproduced without great changes over many generations. Of the five million base pairs in a bacterial DNA, less than one is changed on average per cell division. DNA is constantly under attack: by ultraviolet rays which induce cross-links between neighbouring thymine residues or by the action of various cellular molecules which can cause breaks in the sequence. Cytosine is slowly and spontaneously transformed into uracil. Enzymes correct...

  9. 7 Populations
    (pp. 48-57)

    The idea of evolution by natural selection has arisen several times in the history of human thought. First mentioned by Lucretius, it was taken up again during the last century by Chambers and Matthews, then officially developed by Wallace and Darwin. It is Darwin’s name above all which we associate with it. The skill with which he created his public image and attached his name alone to the concept of natural selection is exemplary and inspires many scientists today. The theory put forward in theOrigin of Speciesstill holds good. Its major difficulties were resolved by combining it with...

  10. 8 Prebiotic replication
    (pp. 58-62)

    Does life start with DNA? Many theories of evolution suppose that DNA molecules were able to replicate on their own in the prebiotic soup, without enzymes, gradually influencing and mastering their environment. The code would then have been merely the means for a DNA molecule to replicate even faster by using a coded DNA polymerase. Here we shall examine the first floor of this house of cards. Can DNA really replicate without an enzyme? Twelve years of experiments, mainly in Orgel’s laboratory, allow us to define what prebiotic replication of nucleic acids might have been like.

    The first two successful...

  11. 9 The genetic code
    (pp. 63-73)

    It is thought that Dounce was the first person to formulate the central concept in molecular biology: the existence of a code of correspondence between nucleic acids and proteins. In his 1952 paper, Dounce proposed the following: genetic information contained in a DNA sequence is first transcribed into RNA; each set of three nucleotides (now called codons) corresponds to an amino acid; the sequence of codons in a gene determines the order of amino acids in the protein which is the product of the gene; the correspondence is established in an indirect manner with adaptor proteins which recognize both the...

  12. 10 The stereochemical hypothesis
    (pp. 74-78)

    The stereochemical hypothesis retains a following among those who reflect on the origins of the genetic code. It is postulated, for example, that DNA used to govern protein synthesis without the participation of ribosomes, tRNAs or activating enzymes. DNA would have acted as an amino acid trap on which amino acids were bound side by side so that they could link spontaneously. If each zone of the DNA had a preference for a particular amino acid, the polypeptide sequence formed on the DNA would be a sort of translation of the nucleotide sequence. This idea, proposed by Caldwell and Hinshelwood...

  13. 11 The origin of the genetic code
    (pp. 79-91)

    The genetic code, centre-piece of cellular logic, is linked in one way or another with everything which occurs in the cell. When we examine cellular function we can find many tracks by which one can hope to reach the origin of the code. Having chosen his starting point, each author also has his own way of classifying theories on the origin of the code. I distinguish two approaches, that which considers the code as a dictionary, and, much more interesting, that in which the code is understood as a process. The principal concern of the theoreticians in the 1960s seems...

  14. 12 Sequence space
    (pp. 92-97)

    This is just a little metaphor, but it provides a means for rethinking the whole of molecular evolution and making visible the intimate connections between the great questions. First, let us see how these things used to be considered.

    In the Darwinian view, every protein sequence is the result of a sifting by natural selection through all possibilities. Let us try to calculate the number of attempts which were necessary to produce a protein as simple as cytochrome c, only 105 residues long. There is one chance in twenty of synthesizing by a random process a protein which begins with...

  15. 13 Acquisitive evolution
    (pp. 98-102)

    Throw into the fields a herbicide: a product of the chemist’s imagination, newly synthesized in the laboratory, a substance never seen before in nature. Soon you will see bacteria growing which not only are not poisoned by the herbicide, but consume it as freely as if it were sugar. They have equipped themselves with all the enzymes necessary for digesting the new substrate. What has happened; what resources has the bacterium mobilized in response to the new situation? These are the kind of questions to which studies in acquisitive evolution, started only 12 years ago by Mortlock and Wood, are...

  16. 14 Molecular defences
    (pp. 103-108)

    At all levels of life, molecular mechanisms form barriers against novelty. These mechanisms certainly have other functions: to eliminate molecules foreign to the organism when they infiltrate, and to clean cells of their damaged molecules. The simplest bacteria have a set of maintenance enzymes: proteases and nucleases. This system is a sort of automatic kitchen robot with a unique program. At the top of the scale, in higher vertebrates, is found an extraordinary flexible system: immune defence. Its functioning, which is still not perfectly understood, acutely poses the problem of the relationship between mutation and selection, of generation of novelty...

  17. 15 Molecular crosses
    (pp. 109-115)

    When a horse mates with an ass, the fruit of their love has all the vigour and intelligence of its parents but it is sterile. This cross-breeding produces a viable egg which passes through all stages of embryonic development to result in an animal which is whole from all points of view, with four legs of equal length and a brain in good working order. This tells us much about the logic of genetic programmes of development. Those who find pleasure in measuring genetic distances between species will conclude that the ass and the horse are very close relatives. Here...

  18. 16 The great error loop
    (pp. 116-122)

    In population genetics, the actors are individuals possessing well-defined characters. From one generation to the next, characters remain but their proportions in the population change. Under prebiotic conditions on the other hand, a DNA molecule which replicated would be highly unlikely to leave descendants identical to itself and the characteristic of molecular populations would change at each generation. How can we argue in these fuzzy, changing situations? I do not have a complete answer to this ambitious question but I present here arguments which allow us to outline evolution in the transition period between the prebiotic and Darwinian regimes.


  19. Bibliography
    (pp. 123-124)
  20. References
    (pp. 125-133)