Chemical Concept of Life and It’s Limitation

Thursday, November 12, 2009

|| By: Srila Bhaktisvarupa Damodara Maharaja, (T. D. Singh, Ph.D.) ||

Srila Bhaktisvarupa Damodara
Maharaja, (T. D. Singh, Ph.D.)

Founding Director of
Bhaktivedanta Institute

Introduction

What is life? Everyone is curious about life-whether a scientist, a philosopher, a poet, an artist or a religious man or woman. We all want to know about the reality and purpose behind our existence-“Why are we born?”, “why do we die?”, “why do we suffer with diseases and old age?”, “what is our ultimate destination?” The Austrian physicist Erwin Schrödinger, although not a biologist, wrote a classic monograph-What is life? in 1944.

Schrödinger’s Monograph (1944)

In the last few decades, there has been a rapid advancement in the study of genetics and molecular biology, which has provided us additional insights into the questions of life and evolution. Scientists have unraveled many mysteries behind various life processes, structures and functions of biomolecules. However, the answer to the question – ‘what is life?’ still seems far away. In this regard Karl Popper, one of the greatest philosophers of science of the 20th century, also remarked, “The undreamt-of breakthrough of molecular biology has made the problem of the origin of life a greater riddle than it was before: we have acquired new and deeper problems.”[1]

A sincere attempt to have a clear understanding of life either scientifically, philosophically and religiously is of foundational importance and it will have important impact on our life and our world-view. In this paper, the author first presents an overview of modern scientific theories of life and evolution and their incompleteness to explain life. Subsequently, in a separate article he presents an alternative paradigm of life from the Vedantic perspective.

Modern Scientific Theories of Life and its Origin: A Brief Overview

(a) Life and Chemical Evolution:

When the bodies of living organisms are chemically analyzed, we find that they are primarily made up of four elements (H, 0, N and C). Chemicals such as water, proteins, lipids, carbohydrates and nucleic acids constitute 95% of all the molecules present in the body of a living organism. Thus it is tempting to conclude that life could be a product of complex chemical reactions. Based on this concept, practically all research works about life’s origin are focused on the possible synthesis of small and large molecules that make up the bodies of living organisms. But is DNA or RNA molecule life? Will a combination of synthetic biomolecules lead to life? If life is made of chemicals, what will be the difference between life and death? Do the scientists really study life?

Is DNA Life?

According to modern biology, the smallest unit of life is called a cell. All living organisms have cells. Organisms such as bacteria and protozoa have single cells whereas higher living forms like human beings have billions of cells. Cells contain many simple, inorganic chemicals like water and inorganic ions. However, complex organic molecules such as proteins, RNA (Ribonucleic Acid), DNA (Deoxyribonucleic Acid), lipids, etc., provide for most of the essential biological functions of the cell.

Miller’s Experiment

Scientists, in the field of biology, study life and its origin in terms of these biomolecules. They attempt to generate a living cell by combining these biomolecules. Many biologists and evolutionary chemists – such as Oparin, Fox, Miller, Orgel, Ponnamperuma and many others made extensive experimentation to generate life from molecules. Various models have been proposed for understanding how life may have generated from chemicals on earth such as Oparin’s model of coacervates, Fox’s model of protenold microspheres, Cairns-Smith’s model of clay as our grandfather, Christian de Duve’s thioester model, Miller’s electrical discharge reactions to simulate lightening in a so-called primordial gaseous mixture of H2, H2O, NH3, CH4, etc., of the presumed primordial or early earth. It is interesting that Miller himself, one of the main pioneers of prebiotic chemistry, has recently stated, “We really don’t know what the Earth was like three or four billion years ago. So there are all sorts of theories and speculations. The major uncertainty concerns what the atmosphere was like. This is a major area of dispute.”[2] It is beyond the scope of this paper to describe all these models here. However, the author would like to mention that all these models do not show any sign of generating a living cell till the present time.

(b) “Which came first-DNA or protein molecule?”

In 1953, Watson and Crick proposed the double helix model for the structure of DNA. Their discovery helped to explain how genetic material is copied inside the cell-genetic information flows from DNA, in the nucleus of each cell, to RNA, which carries the information out of the nucleus into the body of the cell and uses the instructions encoded in it to produce proteins (which acts as enzymes and also provide the structural framework of cells). However, the duplication of DNA requires numerous enzymes that catalyze those reactions. And enzymes are proteins themselves-the end product of the information coded in DNA. In other words, proteins are required for DNA synthesis and DNA is required for protein synthesis. How then could the first living cell with DNA-based molecular biology have originated by spontaneous chemical processes on the prebiotic earth? This has been the chicken and egg problem of life’s evolution from chemicals -” which came first-DNA or protein molecule?”

(c) The RNA World

In late 1960’s several biologists including Crick, Carl Woese and Leslie Orgel[3] suggested that the ancestor molecule was neither DNA nor protein but RNA. RNA, they suggested, might have catalyzed reactions necessary for replication as well as providing the genetic information necessary to replicate itself. Self-replicating RNA based systems would have arisen first, and DNA and proteins would have been added later. DNA could evolve from RNA and then, being more stable, take over RNA’s role as the guardian of heredity.

This idea further got support in early 1980’s from the independent discoveries of Thomas Cech and Sidney Altman of a kind of RNA that catalyzes a reaction.[4] These catalytic RNA molecules have subsequently been termed as “ribozymes”. In 1986, Walter Gilbert, in an article in Nature, portrayed the primordial world as ‘RNA World’ where RNA molecules catalyze their own synthesis.[5] Since then, the term ‘RNA World’ has stuck to the general hypothesis-RNA first, DNA and protein later and researchers continue to discover new functions for existing RNA, illustrating repeatedly how versatile these molecules can be.

However, there are many difficulties and problems in the RNA world.[6] Leslie Orgel, one of the scientists who first proposed it in the 1960s, himself concedes that researchers who have attempted to illustrate the possibility of spontaneous generation of the chemical elements of RNA itself have had only modest success. Ribose, the sugar that is part of the backbone of the RNA molecule, is difficult to create from hypothetical early earth conditions except in very small quantities.[7] Stanley Miller and his colleagues have also recently reported, “ribose and other sugars have surprisingly short half-lives for decomposition at neutral pH, making it very unlikely that sugars were available as prebiotic reagents.”[8]

RNA world assumes that in the primordial world, ribonucleotides spontaneously condense into polymers to form RNA molecules and RNA molecules once formed would have the catalytic activity to replicate itself, and a population of such self-replicating molecules would arise. However, it is objected that even if RNA could have formed spontaneously, it would have been continuously degraded by spontaneous hydrolysis and other destructive processes operating on the primitive Earth.[9] Joyce and Orgel points out many detailed problems with these postulates of RNA world.[10] They finally suggest not to accept “the myth of a self-replicating RNA molecule that arose de novo from a soup of random polynucleotides. Not only is such a notion unrealistic in light of our current understanding of prebiotic chemistry, but it should strain the credulity of even an optimist’s view of RNA’s catalytic potential.”[11] Similarly, Francis Crick has expressed great doubt about the RNA world. He says, “At present, the gap from the primal “soup” to the first RNA system capable of natural selection looks forbiddingly wide.”[12] Thus the chemical concept of life does not seem to be very promising.

References


[1] Karl R. Popper, “Reduction and the Essential Incompleteness of All Science,” Studies in the Philosophy of Biology, eds. Francisco Jose Ayala and Theodosius Dobzhansky, 1974, p.271.

[2] “From Primordial Soup to the Prebiotic Beach”, Interview with Stanley Miller by Sean Henahan, October 1996, Access Excellence, National Health Museum; web: www.accessexcellence.org/WN/NM/miller.html

[3] Carl Woese, The Genetic Code: The Molecular Basis for Genetic Expression, New York, Harper and Row, 1967; F.H.C. Crick, “The Origin of the Genetic Code”, J. Mol. Biol., 1968, 38:367379; L.E. Orgel “Evolution of the Genetic Apparatus,” J. Mol. Biol., 1968, 38:381-393.

[4] K. Kruger, P.J. Grabowski, A.J. Zaug, J. Sands, D.E. Gottschling, and T.R. Cech, “Self-Splicing RNA: Autoexcision and Autocyc1ization of the Ribosomal RNA Intervening Sequence of Tetrahymena,” Cell, 1982,31:147-157; C. Guerrier-Takada & S. Altman, “Catalytic Activity of an RNA molecule prepared by transcription in vitro”, 1984, Science, 223:285-9.

[5] Walter Gilbert, “The RNA World,” Nature, 1986, 319: 618.

[6] G. Joyce, “RNA evolution and the origins of life,” Nature 338 (1989): 217-224; T.J. Gibson and A.I. Lamond, “Metabolic complexity in the RNA World and implications for the origin of protein synthesis,” J. Mol. Evol. 30 (1990): 7-15; G.F. Joyce and L.E. Orgel, “Prospects for understanding the origin of the RNA World,” in The RNA World, eds. RF. Gesteland and IF. Atkins, New York, Cold Spring Harbor Laboratory Press, 1993, pp.1-25.

[7] Leslie E. Orgel, “The Origin of Life on the Earth”, Scientific American, 1994, vol.271, No.4, pp.76-83. Also refer R Shapiro, “The improbability of prebiotic nucleic acid synthesis,” Origins of Life 14 (1984); 565-570; R Shapiro, “Prebiotic ribose synthesis: a critical analysis,” Origins of Life 18 (1988): 71-85; R Shapiro, “The prebiotic role of adenine: a critical analysis,” Origins of Life and the Evolution of the Biosphere 25 (1995): 83-98.

[8] Rosa Larralde, Michael P. Robertson, and Stanley L. Miller, “Rates of decomposition of ribose and other sugars: Implications for chemical evolution,” Proc. Natl. Acad. Sci. USA, 1995, 92: 8158-8160. The ribose half-lives are very short, Larralde et al. report: 73 minutes at pH 7.0 and 100° C and 44 years at pH 7.0 and 0° C.

[9] C. Thaxton, W. Bradley, and R Olsen, The Mystery of Life’s Origin, New York, Philosophical Library, 1984.

[10] G.F. Joyce and L. E. Orgel, “Prospects for understanding the origin of the RNA World”, The RNA World, eds. RF. Gesteland and I.E Atkins, New York, Cold Spring Harbor Laboratory Press, 1993, pp.I-25. Also refer Gordon C. Mills & Dean Kenyon, “The RNA World: A Critique”, Origins & Design, 17:1, 1996.

[11] Ibid.

[12] Francis Crick, “Foreword”, The RNA World, eds., RF. Gesteland & I.F. Atkins, 1993, p.xiii.