The philosophy of living thing

Life is a characteristic distinguishing physical entities having biological processes, such as signalling and self-sustaining processes, from those that do not, either because such functions have ceased, or because they never had such functions and are classified as inanimate. Various forms of life exist such as plants, animals, fungi, protists, archaea, and bacteria. The criteria can at times be ambiguous and may or may not define viruses, viroids or potential artificial life as living. Biology is the primary science concerned with the study of life, although many other sciences are involved.

The definition of life is controversial. The current definition is that organisms maintain homeostasis, are composed of cells, undergo metabolism, can grow, adapt to their environment, respond to stimuli, and reproduce. However, many other biological definitions have been proposed, and there are also some borderline cases, such as viruses. Biophysicists have also proposed some definitions, many being based on chemical systems. There are also some living systems theories, such as the Gaia hypothesis, the idea that the Earth is alive; the former first developed by James Grier Miller. Another one is that life is the property of ecological systems, and yet another is the complex systems biology, a branch or subfield of mathematical biology. Some other systemic definitions include the theory involving the darwinian dynamic, and the operator theory. However, throughout history, there have been many other theories and definitions about life such as materialism, the belief that everything is made out of matter and that life is merely a complex form of it; hylomorphism, the belief that all things are a combination of matter and form, and the form of a living thing is its soul; spontaneous generation, the belief that life repeatedly emerge from non-life; and vitalism, a discredited scientific hypothesis that living organisms possess a "life force" or "vital spark". A biogenesis is the natural process of life arising from non-living matter, such as simple organic compounds. Life on Earth arose 3.8-4.1 billion years ago. It is widely accepted that current life on Earth descended from an RNA world, but RNA based life may not have been the first. The mechanism by which life began on Earth is unknown, although many hypotheses have been formulated, most based on the Miller–Urey experiment.

Since appearing, life on Earth has changed its environment on a geologic time scale. To survive in most ecosystems, life can adapt and thrive in a wide range of conditions. Some organisms, called extremophiles, can thrive in physically or geochemically extreme conditions that are detrimental to most other life on Earth. Properties common to all organisms are the need for certain core chemical elements needed for biochemical functioning. Aristotle was the first person to classify organisms. Later, Carl Linnaeus introduced his system of binomial nomenclature for the classification of species. Fungi was later classified as its own kingdom. Eventually new groups of life were revealed, such as cells and microorganisms, and even non-cellular reproducing agents, such as viruses and viroids. Cells are the smallest units of life, often called the "building blocks of life". There are two kind of cells, prokaryotic and eukaryotic. Cells consist of cytoplasm enclosed within a membrane, which contains many biomolecules such as proteins and nucleic acids. Cells reproduce through a process of cell division in which the parent cell divides into two or more daughter cells.

Though only confirmed on Earth, many believe in the existence of extraterrestrial life. Artificial life is a computer simulation of any aspect of life, which is used to examine systems related to life. Death is the permanent termination of all biological functions which sustain an organism, and as such, is the end of its life. Extinction is the process by which a group of taxa, normally a species, dies out. Fossils are the preserved remains or traces of organisms.

At a higher level, living beings are thermodynamic systems with an organized molecular structure that can reproduce it and evolve as survival dictates. Thermodynamically, life has been described as an open system, which makes use of gradients in its surroundings to create imperfect copies of itself. Hence, life is a self-sustained chemical system capable of undergoing Darwinian evolution.

Others take a systemic viewpoint that does not necessarily depend on molecular chemistry. One systemic definition of life is that living things are self-organizing and autopoietic (self-producing). Variations of this definition include Stuart Kauffman's definition as an autonomous agent or a multi-agent system capable of reproducing itself or themselves, and of completing at least one thermodynamic work cycle.

Viruses

Whether or not viruses should be considered as alive is a controversial question. They are most often considered as just replicators rather than forms of life; but sometimes the ability to replicate is considered as the crucial property of life. They have been described as "organisms at the edge of life," since they possess genes, evolve by natural selection, and replicate by creating multiple copies of them through self-assembly. However, viruses do not metabolize and they require a host cell to make new products. Virus self-assembly within host cells has implications for the study of the origin of life, as it may support the hypothesis that life could have started as self-assembling organic molecules.

Biophysics

To reflect the minimum phenomena required, other biological definitions of life have been proposed, with many of these being based upon chemical systems. Biophysicists have commented that living things function on negative entropy. In other words, living processes can be viewed as a delay of the spontaneous diffusion or dispersion of the internal energy of biological molecules towards more potential microstates. In more detail, according to physicists such as John Bernal, Erwin Schrödinger, Eugene Wigner, and John Avery, life is a member of the class of phenomena that are open or continuous systems able to decrease their internal entropy at the expense of substances or free energy taken in from the environment and subsequently rejected in a degraded form.

Living systems theories

Gaia hypothesis

The idea that the Earth is alive is found in philosophy and religion, but the first scientific discussion of it was by the Scottish scientist James Hutton. In 1785, he stated that the Earth was a super organism and that its proper study should be physiology. Hutton is considered the father of geology, but his idea of a living Earth was forgotten in the intense reductionism of the 19th century.^[38] The Gaia hypothesis, proposed in the 1960s by scientist James Lovelock, suggests that life on Earth functions as a single organism that defines and maintains environmental conditions necessary for its survival.

Non fraction ability

The first attempt at a general living systems theory for explaining the nature of life was in 1978, by American biologist James Grier Miller. Such a general theory, arising out of the ecological and biological sciences, attempts to map general principles for how all living systems work. Instead of examining phenomena by attempting to break things down into component parts, a general living systems theory explores phenomena in terms of dynamic patterns of the relationships of organisms with their environment. Robert Rosen (1991) built on this by defining a system component as "a unit of organization; a part with a function, i.e., a definite relation between part and whole." From this and other starting concepts, he developed a "relational theory of systems" that attempts to explain the special properties of life. Specifically, he identified the "non fraction ability of components in an organism" as the fundamental difference between living systems and "biological machines."

Life as a property of ecosystems

A systems view of life treats environmental fluxes and biological fluxes together as a "reciprocity of influence",^[45] and a reciprocal relation with environment is arguably as important for understanding life as it is for understanding ecosystems. As Harold J. Markowitz (1992) explains it, life is a property of an ecological system rather than a single organism or species. He argues that an ecosystem definition of life is preferable to a strictly biochemical or physical one. Robert Ulanowicz (2009) highlights mutualism as the key to understand the systemic, order-generating behaviour of life and ecosystems.

Complex systems biology

Complex systems biology (CSB) is a field of science that studies the emergence of complexity in functional organisms from the viewpoint of dynamic systems theory. The latter is often called also systems biology and aims to understand the most fundamental aspects of life. A closely related approach to CSB and systems biology, called relational biology, is concerned mainly with understanding life processes in terms of the most important relations, and categories of such relations among the essential functional components of organisms; for multicellular organisms, this has been defined as "categorical biology", or a model representation of organisms as a category theory of biological relations, and also an algebraic topology of the functional organization of living organisms in terms of their dynamic, complex networks of metabolic, genetic, epigenetic processes and signalling pathways.

Darwinian dynamic

It has also been argued that the evolution of order in living systems and certain physical systems obey a common fundamental principle termed the Darwinian dynamic. The Darwinian dynamic was formulated by first considering how macroscopic order is generated in a simple non-biological system far from thermodynamic equilibrium, and then extending consideration to short, replicating RNA molecules. The underlying order generating process for both types of system was concluded to be basically similar.

Operator theory

Another systemic definition, called the Operator theory, proposes that 'life is a general term for the presence of the typical closures found in organisms; the typical closures are a membrane and an autocatalytic set in the cell', and also proposes that an organism is 'any system with an organisation that complies with an operator type that is at least as complex as the cell. Life can also be modelled as a network of inferior negative feedbacks of regulatory mechanisms subordinated to a superior positive feedback formed by the potential of expansion and reproduction.

History of study

Materialism

Main article: Materialism

Plant growth in the Hoh Rainforest Herds of zebra and impala gathering on the Maasai Mara plain

An aerial photo of microbial mats around the Grand Prismatic Spring of Yellowstone National Park

Some of the earliest theories of life were materialist, holding that all that exists is matter, and that life is merely a complex form or arrangement of matter. Empedocles (430 BC) argued that everything in the universe is made up of a combination of four eternal "elements" or "roots of all": earth, water, air, and fire. All change is explained by the arrangement and rearrangement of these four elements. The various forms of life are caused by an appropriate mixture of elements.

Democritus (460 BC) thought that the essential characteristic of life is having a soul (psyche). Like other ancient writers, he was attempting to explain what makes something a living thing. His explanation was that fiery atoms make a soul in exactly the same way atoms and void account for any other thing. He elaborates on fire because of the apparent connection between life and heat, and because fire moves.

Plato's world of eternal and unchanging Forms, imperfectly represented in matter by a divine Artisan, contrasts sharply with the various mechanistic Weltanschauungen, of which atomism was, by the fourth century at least, the most prominent ... This debate persisted throughout the ancient world. Atomistic mechanism got a shot in the arm from Epicurus ... while the Stoics adopted a divine teleology ... The choice seems simple: either show how a structured, regular world could arise out of undirected processes, or inject intelligence into the system.

The mechanistic materialism that originated in ancient Greece was revived and revised by the French philosopher René Descartes, who held that animals and humans were assemblages of parts that together functioned as a machine. In the 19th century, the advances in cell theory in biological science encouraged this view. The evolutionary theory of Charles Darwin (1859) is a mechanistic explanation for the origin of species by means of natural selection.

Hylomorphism

Hylomorphism is a theory first expressed by Greek philosopher Aristotle (322 BC). The application of Hylomorphism to biology was important to Aristotle, and biology is extensively covered in his extant writings. In this view, everything in the material universe has both matter and form, and the form of a living thing is its soul (Greek psyche, Latin anima). There are three kinds of souls: the vegetative soul of plants, which causes them to grow and decay and nourish themselves, but does not cause motion and sensation; the animal soul, which causes animals to move and feel; and the rational soul, which is the source of consciousness and reasoning, which (Aristotle believed) is found only in man. Each higher soul has all of the attributes of the lower ones. Aristotle believed that while matter can exist without form, form cannot exist without matter, and that therefore the soul cannot exist without the body.

This account is consistent with teleological explanations of life, which account for phenomena in terms of purpose or goal-directedness. Thus, the whiteness of the polar bear's coat is explained by its purpose of camouflage. The direction of causality (from the future to the past) is in contradiction with the scientific evidence for natural selection, which explains the consequence in terms of a prior cause. Biological features are explained not by looking at future optimal results, but by looking at the past evolutionary history of a species, which led to the natural selection of the features in question.

Spontaneous generation

Main article: Spontaneous generation

Spontaneous generation was the belief on the ordinary formation of living organisms without descent from similar organisms. Typically, the idea was that certain forms such as fleas could arise from inanimate matter such as dust or the supposed seasonal generation of mice and insects from mud or garbage.

The theory of spontaneous generation was proposed by Aristotle, who compiled and expanded the work of prior natural philosophers and the various ancient explanations of the appearance of organisms; it held sway for two millennia. It was decisively dispelled by the experiments of Louis Pasteur in 1859, who expanded upon the investigations of predecessors (such as Francesco Redi. Disproof of the traditional ideas of spontaneous generation is no longer controversial among biologists.

Vitalism

Main article: Vitalism

Vitalism is the belief that the life-principle is non-material. This originated with Georg Ernst Stahl (17th century), and remained popular until the middle of the 19th century. It appealed to philosophers such as Henri Bergson, Friedrich Nietzsche, Wilhelm Dilthey, anatomists like Marie François Xavier Bichat, and chemists like Justus von Liebig. Vitalism included the idea that there was a fundamental difference between organic and inorganic material, and the belief that organic material can only be derived from living things. This was disproved in 1828, when Friedrich Wöhler prepared urea from inorganic materials. This Wöhler synthesis is considered the starting point of modern organic chemistry. It is of historical significance because for the first time an organic compound was produced in inorganic reactions.

During the 1850s, Hermann von Helmholtz, anticipated by Julius Robert von Mayer, demonstrated that no energy is lost in muscle movement, suggesting that there were no "vital forces" necessary to move a muscle. These results led to the abandonment of scientific interest in vitalistic theories, although the belief lingered on in pseudoscientific theories such as homeopathy, which interprets diseases and sickness as caused by disturbances in a hypothetical vital force or life force.

Origin

The age of the Earth is about 4.54 billion years. Evidence suggests that life on Earth has existed for at least 3.5 billion years, with the oldest physical traces of life dating back 3.7 billion years; however, some theories, such as the Late Heavy Bombardment theory, suggest that life on Earth may have started even earlier, as early as 4.1-4.4 billion years ago, but the chemistry leading to life may have begun shortly after the Big Bang, 13.8 billion years ago, during an epoch when the universe was only 10–17 million years old. All known life forms share fundamental molecular mechanisms, reflecting their common descent; based on these observations, hypotheses on the origin of life attempt to find a mechanism explaining the formation of a universal common ancestor, from simple organic molecules via pre-cellular life to protocells and metabolism. Models have been divided into "genes-first" and "metabolism-first" categories, but a recent trend is the emergence of hybrid models that combine both categories.

There is no current scientific consensus as to how life originated. However, most accepted scientific models build on the Miller–Urey experiment, and the work of Sidney Fox, which shows that conditions on the primitive Earth favored chemical reactions that synthesize amino acids and other organic compounds from inorganic precursors, and phospholipids spontaneously forming lipid bilayers, the basic structure of a cell membrane.

Living organisms synthesize proteins, which are polymers of amino acids using instructions encoded by deoxyribonucleic acid (DNA). Protein synthesis entails intermediary ribonucleic acid (RNA) polymers. One possibility for how life began is that genes originated first, followed by proteins;^[98] the alternative being that proteins came first and then genes.

However, since genes and proteins are both required to produce the other, the problem of considering which came first is like that of the chicken or the egg. Most scientists have adopted the hypothesis that because of this, it is unlikely that genes and proteins arose independently.

Therefore, a possibility, first suggested by Francis Crick, is that the first life was based on RNA, which has the DNA-like properties of information storage and the catalytic properties of some proteins. This is called the RNA world hypothesis, and it is supported by the observation that many of the most critical components of cells (those that evolve the slowest) are composed mostly or entirely of RNA. Also, many critical cofactors (ATP, Acetyl-CoA, NADH, etc.) are either nucleotides or substances clearly related to them. The catalytic properties of RNA had not yet been demonstrated when the hypothesis was first proposed, but they were confirmed by Thomas Cech in 1986.

One issue with the RNA world hypothesis is that synthesis of RNA from simple inorganic precursors is more difficult than for other organic molecules. One reason for this is that RNA precursors are very stable and react with each other very slowly under ambient conditions, and it has also been proposed that living organisms consisted of other molecules before RNA. However, the successful synthesis of certain RNA molecules under the conditions that existed prior to life on Earth has been achieved by adding alternative precursors in a specified order with the precursor phosphate present throughout the reaction. This study makes the RNA world hypothesis more plausible.

Geological findings in 2013 showed that reactive phosphorus species (like phosphite) were in abundance in the ocean before 3.5 Ga, and that Schreibersite easily reacts with aqueous glycerol to generate phosphite and glycerol 3-phosphate. It is hypothesized that Schreibersite-containing meteorites from the Late Heavy Bombardment could have provided early reduced phosphorus, which could react with prebiotic organic molecules to form phosphorylated biomolecules, like RNA.

In 2009, experiments demonstrated Darwinian evolution of a two-component system of RNA enzymes (ribozymes) in vitro. The work was performed in the laboratory of Gerald Joyce, who stated, "This is the first example, outside of biology, of evolutionary adaptation in a molecular genetics system."

Prebiotic compounds may have extraterrestrial origin. NASA findings in 2011, based on studies with meteorites found on Earth, suggest DNA and RNA components (adenine, guanine and related organic molecules) may be formed in outer space.

In March 2015, NASA scientists reported that, for the first time, complex DNA and RNA organic compounds of life, including uracil, cytosine and thymine, have been formed in the laboratory under outer space conditions, using starting chemicals, such as pyrimidine, found in meteorites. Pyrimidine, like polycyclic aromatic hydrocarbons (PAHs), the most carbon-rich chemical found in the Universe, may have been formed in red giants or in interstellar dust and gas clouds, according to the scientists.

According to the panspermia hypothesis, microscopic life—distributed by meteoroids, asteroids and other small Solar System bodies—may exist throughout the universe.