January 1, 2005

IN 1940 Erwin Schrödinger, a Nobel Laureate, launched a new field of biophysics with a lecture titled “What is life?” Why biology was treated as a subject completely separate from physics and chemistry? Frogs, fruit flies and cells on one side, while atoms and molecules, electricity and magnetism on the other. Schrödinger decided to think of living organisms in terms of their molecular and atomic structure.

They all obey the same laws of physics and chemistry, but the reverse is not true, that is, life cannot be created from these laws. Quarks are viewed as the rock bottom of building blocks. Entropy (according to second law of thermodynamics) is concerned with things falling apart; the natural disintegration of order to disorder. Why don’t genes decay? He answered his question in the following words: “life is matter that is doing something. The technical terms ‘metabolism, eating, drinking, breathing assimilating, replicating, birth, death, growth, evolution and entropy are attributes of life.”

One may add here that for higher forms of life emotion, consciousness, intelligence, spiritual craving etc, serve as additional attributes. Thus a set of principles that characterizes the organization of living organisms and the cells that make them up and that distinguishes living from non-living bodies has been built in this article for broader understanding of the purpose of life and its logic.

It is now well-known that life has evolved from lifeless molecules. It is unique in complexity, in its structure, process in all forms, evolution and its pursuit to propagate and preserve high order of living features and structure is remarkable. The way these phenomena are carried out requires a detailed study of life. Lifeless molecules when transformed into life form also exhibit extraordinary attributes not exhibited by a random collection of molecules.

Living beings are highly organized and structurally complicated and composed of many complex molecules. There is a vast amount of organic matter in the universe found in intracellular clouds, comets and meteorites and even planets, while there are one hundred billion times one hundred billion (1022) stars in the universe. Most of these stars may have their own planets and comets.

On Earth, we find clay, sand, rocks, and seawater. Yet there may not be a single molecule as complex and intricate as any of the DNA molecules or protein that makes up the simplest of life such as bacteria.

Every living cell from bacteria to human cells shares tens of thousands of complex molecules working in precise unison that are essential for propagation and replication.

Every cell of a living organism extracts and uses energy from its environment usually in the form of chemicals, nutrients or sunlight and is capable of converting it in order to enable organisms to build and maintain their intricate structures.

Cells store, transmit and process all kinds of genetic information and converts this information to various types of proteins essential for the continuation of life. They also control and give rise to all kinds of bioprocesses such as morphogenesis, metabolism and reproduction.

By contrast, inanimate matter cannot maintain itself like living ones, as it tends to decay towards a disordered state to be at par with its surroundings.

Some basic molecules of life (such as proteins, sugar and nucleotides) were probably formed from simple molecules, for example, hydrogen cyanide joined together to make adenine and formaldehyde molecules joined together to make sugar molecules (Readers may refer here to the writer’s article in Sci-tech World on Oct.30, 2004).

Another characteristic at_tribute of the life is its capacity for precise replication and self-assembly — a quintessential property of living state.

A single bacterial cell when placed in a sterile nutrient medium can give rise to millions of identical “daughter” cells within a span of 24 hours. Each of the cells contains thousands of different molecules, which are all replicas of the original.

This shows that the process of life is wrought in complex molecular information. It is because of this that they are improbable compared to the random arrangement of the same matter.

However, probability favours decay to randomness. The inanimate matter shows no capacity to grow and reproduce in the forms identical in mass, shape and internal structure generation after generation.

Although the ability to self-replicate has no true analogy in the non-living world, there is however, an instructive analogy in the growth of crystals in a saturated solution. Crystallization produces material identical in lattice structure with the original “seed” crystal.

Crystals are much less complex than the simplest living organisms and their structures are static while living cells are dynamic.

Nonetheless, the ability of crystals to “reproduce” themselves led Erwin Schrödinger to propose that the genetic material of cells must have some of the properties of a crystal and described a few characteristics of DNA on the basis of this logic.

Franklin Rosalind, a coal researcher moved from the crystal structure of coal to that of DNA with a view that coal did not make more coal but DNA certainly produces more genes, thereby establishing the crystallography of DNA.

It was because of this idea that Watson and Crick won the Nobel Prize in 1953. The cycle of replication of DNA and protein is the core of living processes.

Each component of a living organism has a specific function not only in macroscopic structures such as leaves and stems in plants (and also hearts and lungs of human beings), but also in microscopic intracellular structures such as chloroplast and the nucleus respectively. Even individual chemical compounds in cells have specific functions.

The interplay among chemical components of a living organism is dynamic — changes in one component cause coordinating or compensating changes in another with the result that the whole ensemble displays a character beyond that of individual constituents. Interplay consists of chance and selection which shapes and alters the progress of life. For example, chance mutations bring about new structures of these in which the “survival of the fittest” reigns supreme.

The tautology that strong cells survive is one of the logics of life. Chance brings change and life’s logic affects selection. In future, random mutation may be replaced by designed evolution.

If living organisms are composed of inanimate molecules, then how do these molecules exhibit the remarkable combination of characteristics, we call life? How is it that a living organism appears to be more than the sum of its inanimate parts?

Philosophers once claimed that living organisms are endowed with mysticism and divine life vital force. However, this doctrine has been firmly rejected by modern science.

The goal of biochemistry is to determine how a collection of inanimate molecules that constitute living organisms interact with each other, to maintain and perpetuate life. Although biochemistry yields important insights and practical applications in medicine and agriculture, it is also ultimately concerned with the wonders of life.

Most molecular constituents of living systems are composed of carbon atoms covalently joined with other carbon, hydrogen, oxygen or nitrogen atoms.

The special bonding properties of carbon permit the formation of a great variety of molecules such as amino acids (protein constituents), nucleotides (DNA) constituents and monosaccharide (glucose units).

A single protein molecule may consist of as many as 1,000 amino acids and DNA has millions of nucleotides. The assemblage of a protein consisting of 1,000 amino acids requires 3,000 nucleotides.

This job is carried out by tRNA to encode those amino acids. A single bacterium (for example, E.coli) contains more than 6,000 different kinds of organic compounds including 3,000 different proteins and a similar number of nucleotide molecules. In humans, these may be hundreds of thousands of different kinds of proteins, sugar molecules and a variety of fatty substances, etc.

Compare, the arrangement of just 26 letters of the English alphabet into a limitless number of words, sentences, books, encyclopedia, etc, with just four letters of the DNA alphabet and 20 letters of the protein alphabet.

With only four letters, DNA stores transmits and processes all kinds of bioinformation and gives rise to all kinds of bioprocesses, such as morphogenesis, metabolism and reproduction. The essence of life is information-processing. The search for the origin of life is in fact the search for a bio-CPU.

According to the second law of thermodynamics, all lifeless processes increase entropy but all life generating processes reduce it. Schrödinger defined life as negative entropy, something not falling into chaos and prevents approaching the critical state of maximum entropy, which is death.

Genes preserve their structure because a chromosome that carries them is an irregular crystal. The arrangement of the units of genes within the crystal constitutes heredity codes.

Energy is a central life form theme. They depend upon a constant supply of energy to combat the inexorable tendency in nature for decay to the lowest energy state. Living cells have evolved highly efficient mechanisms for capturing sunlight or extracting oxidizable energy fuel along with coupling it.

The population of molecules within a cell or organism is a dynamic function. Molecules are synthesized and then broken down by continuous chemical reactions. Hemoglobin molecules, for example, if synthesized today would degrade within the next 1-2 months and in its place a new hemoglobin molecule is synthesized. This, in fact, is the law of nature.

Glucose if ingested now is converted into carbon dioxide within 10-12 hours, and fat and needs to be replaced with a fresh supply of glucose. The amount of haemoglobin and glucose remains constant because the rate of intake of each balances the rate of breakdown, consumption and conversion into some other products. Under the physiologic conditions in an adult, about 1,00,00,000 (1x108) erythrocytes are destroyed per hour.

Thus, a 70kg human turns over approximately six grams of hemoglobin in a day. When hemoglobin in the body is destroyed, the globin may be reused either as such or in the form of its constituent amino acids. Also, the iron of the heme enters the iron pool for reuse.

The continued existence of biological species requires that its genetic information be maintained in a stable form, and at the same time expressed without error. Among the seminal discoveries of twentieth century biology are the chemical nature and three-dimensional structure of DNA.

The sequence of this linear polymer encodes instructions for forming all other cellular components and provides a template for the production of identical DNA molecules to be distributed to progeny at the time of cell division.

The most remarkable property of living things is their ability to reproduce themselves with perfect fidelity for millions of generations. This continuity and inherited traits implies constancy over millions of years in the structure of the molecules that contain genetic information, the secret of Y chromosomes and the descendent of DNA from across the planet.

All the historical records of civilization, even those etched in copper or carved in stone, have lost their existence but genetic instructions in living beings have remained unchanged ever since their inception.

The writer is a genetic scientist.

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