MODULE 1 : NATURE OF LIVING THINGS

Life (cf. biota) is a characteristic that distinguishes objects that have signaling and self-sustaining processes from those that do not, either because such functions have ceased (death), or else because they lack such functions and are classified as inanimate. Biology is the science concerned with the study of life.Any contiguous living system is called an organism.

Biology Since there is no unequivocal definition of life, the current understanding is descriptive, where life is a characteristic of organisms that exhibit all or most of the following phenomena: 1. Homeostasis: Regulation of the internal environment to maintain a constant state; for example, electrolyte concentration or sweating to reduce temperature. 2. Organization: Being structurally composed of one or more cells, which are the basic units of life. 3. Metabolism: Transformation of energy by converting chemicals and energy into cellular components (anabolism) and decomposing organic matter (catabolism). Living things require energy to maintain internal organization (homeostasis) and to produce the other phenomena associated with life. 4. Growth: Maintenance of a higher rate of anabolism than catabolism. A growing organism increases in size in all of its parts, rather than simply accumulating matter. 5. Adaptation: The ability to change over a period of time in response to the environment. This ability is fundamental to the process of evolution and is determined by the organism's heredity as well as the composition of metabolized substances, and external factors present. 6. Response to stimuli: A response can take many forms, from the contraction of a unicellular organism to external chemicals, to complex reactions involving all the senses of multicellular organisms. A response is often expressed by motion, for example, the leaves of a plant turning toward the sun (phototropism) and by chemotaxis. 7. Reproduction: The ability to produce new individual organisms, either asexually from a single parent organism, or sexually from two parent organisms. 8. Living organisms are morphous. 9. They always have cellular nature. 10. They have the ability of movement and locomotion 11. They have the power of excretion. 12. It has glands (mammary glands – milk). 13. They have specific receptors e.g. sense organs to receive external and internal stimuli, and specific effectors (muscles and glands to give specific response). 14. They have definite life span.They undergo aging after adulthood and then natural death. So, in the light of above properties of living organisms, life can be defined as “Life is a unique, complex organization of molecules, expressing itself through chemical reactions, which lead to growth, development, responsiveness, adaptation and reproduction.”

Scientific evidence suggests that life began on Earth some 3.7 billion years Though the existence of life is only confirmed on Earth, many scientists believe extraterrestrial life is not only plausible but probable. Other planets and moons in the Solar System have been examined for evidence of having once supported simple life, and projects such as SETI have attempted to detect transmissions from possible alien civilizations. According to the panspermia hypothesis, life on Earth may have originated from meteorites that spread organic molecules or simple life that first evolved elsewhere.

Early theories Materialism Some of the earliest theories of life were materialist, holding that all that exists is matter, and that all life is merely a complex form or arrangement of matter. Empedocles (430 BC) argued that every thing 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. For example, growth in plants is explained by the natural downward movement of earth and the natural upward movement of fire. Democritus (460 BC), the disciple of Leucippus, thought that the essential characteristic of life is having a soul (psyche). In common with other ancient writers, he used the term to mean the principle of living things that causes them to function as a living thing. He thought the soul was composed of fire atoms, because of the apparent connection between life and heat, and because fire moves. He suggested that humans originally lived like animals, gradually developing communities to help one another, originating language, and developing crafts and agriculture. The mechanistic model of life that originated with ancient Greeks such as Epicurus was revived and expanded upon during the scientific revolution of the 17th century by the French philosopher René Descartes. He held that animals and humans were assemblages of parts that together functioned as a machine. However, it would not be until the 19th century that cell theory and advances in biological science provided a sound basis for this model. The evolutionary theory of Charles Darwin (1859) provided an explanation for the form and function of all organisms through the mechanism of natural selection. Hylomorphism Hylomorphism is the theory (originating with Aristotle (322 BC)) that all things are a combination of matter and form. Aristotle was one of the first ancient writers to approach the subject of life in a scientific way. Biology was one of his main interests, and there is extensive biological material in his extant writings. According to him, all things in the material universe have both matter and form. 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 the attributes of the lower one. Aristotle believed that while matter can exist without form, form cannot exist without matter, and therefore the soul cannot exist without the body. Consistent with this account is a teleological explanation of life. A teleological explanation accounts for phenomena in terms of their purpose or goal-directedness. Thus, the whiteness of the polar bear's coat is explained by its purpose of camouflage. The direction of causality is the other way round from materialistic science, which explains the consequence in terms of a prior cause. Modern biologists reject this functional view in terms of a material and causal one: biological features are to be explained not by looking forward to future optimal results, but by looking backwards to the past evolutionary history of a species, which led to the natural selection of the features in question. Vitalism Vitalism is the belief that the life-principle is essentially immaterial. This originated with Stahl (17th century), and held sway until the middle of the 19th century. It appealed to philosophers such as Henri Bergson, Nietzsche, Wilhelm Dilthey, anatomists like Bichat, and chemists like Liebig. Vitalism underpinned the idea of a fundamental separation of 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 so-called 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 from inorganic reactants. During the 1850s, Helmholtz, anticipated by Mayer, demonstrated that no energy is lost in muscle movement, suggesting that there were no vital forces necessary to move a muscle. These empirical results led to the abandonment of scientific interest in vitalistic theories, although the belief lingered on in non-scientific theories such as homeopathy, which interprets diseases and sickness as caused by disturbances in a hypothetical vital force or life force.

Alternatives To reflect the minimum phenomena required, other biological definitions of life have been proposed, many of these are 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. At a higher level, living beings are thermodynamic systems that have an organized molecular structure. Looking at it from a long-term perspective, life is matter that can reproduce itself and evolve as survival dictates. 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. Life can be modeled as a network of inferior negative feedbacks of regulatory mechanisms subordinated to a superior positive feedback formed by the potential of expansion and reproduction. From a simplified perspective, life can be said to consist of things with the capacity for metabolism and motion, or that life is self-reproduction "with variations" or "with an error rate below the sustainability threshold." Viruses

Viruses are most often considered replicators rather than forms 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 themselves 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.

Living systems theories The idea that the Earth is alive is probably as old as humankind, but the first public expression of it as a fact of science was by a Scottish scientist, James Hutton. In 1785 he stated that the Earth was a superorganism and that its proper study should be physiology. Hutton is rightly remembered as the father of geology, but his idea of a living Earth was forgotten in the intense reductionism of the 19th century. The Gaia hypothesis, originally proposed in the 1960s by scientist James Lovelock, explores the idea that the life on Earth functions as a single organism which defines and maintains environmental conditions necessary for its survival. In 1978, American biologist James Grier Miller first formulated a general living systems theory to explain the nature of life. 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 the assumption that the explanatory powers of the mechanistic worldview cannot help understand the realm of living systems. One of several important clarifications he made was to define 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 "nonfractionability of components in an organism" as the fundamental difference between living systems and "biological machines." A systems view of life treats environmental fluxes and biological fluxes together as a "reciprocity of influence",and a reciprocal relation with environment is arguably as important for understanding life as it is for understanding ecosystems. As Harold J. Morowitz (1992) explains it, life is a property of an ecological system rather than a single organism or species. He argues that an ecosystemic 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 behavior of life and ecosystems. Origin Main article: Abiogenesis Evidence suggests that life on Earth has existed for about 3.7 billion years, with the oldest traces of life found in fossils dating back 3.4 billion years. All known life forms share fundamental molecular mechanisms, and based on these observations, theories on the origin of life attempt to find a mechanism explaining the formation of a primordial single cell organism from which all life originates. There are many different hypotheses regarding the path that might have been taken from simple organic molecules via pre-cellular life to protocells and metabolism. Many models fall into the "genes-first" category or the "metabolism-first" category, but a recent trend is the emergence of hybrid models that combine both categories. There is no scientific consensus as to how life originated and all proposed theories are highly speculative. However, most accepted scientific models build in one way or another on the following hypotheses:  The Miller-Urey experiment, and the work of Sidney Fox, suggest that conditions on the primitive Earth may have favored chemical reactions that synthesized amino acids and other organic compounds from inorganic precursors.  Phospholipids spontaneously form lipid bilayers, the basic structure of a cell membrane. Life synthesizes proteins, which are polymers of amino acids using instructions encoded by cellular genes; the polymers of 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; the alternative being that proteins came first and then genes. However, because genes are required to make proteins, and proteins are needed to make genes, the problem of considering which came first is like that of the chicken or the egg. Most scientists have adopted the hypothesis that because DNA and proteins function together so intimately, it's unlikely that they arose independently. Therefore, a possibility, apparently first suggested by Francis Crick, is that the first life was based on the DNA-protein intermediary: RNA. RNA has the DNA-like properties of information storage, replication and the catalytic properties of some proteins. Crick and others actually favored the RNA-first hypothesis even before the catalytic properties of RNA had been demonstrated by Thomas Cech. A significant issue with the RNA-first hypothesis is that experiments designed to synthesize RNA from simple precursors have not been nearly as successful as the Miller-Urey experiments that synthesized other organic molecules from inorganic precursors. One reason for the failure to create RNA in the laboratory is that RNA precursors are very stable and do not react with each other under ambient conditions. However, the successful synthesis of certain RNA molecules under conditions hypothesized to exist 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-first hypothesis more plausible. Recent experiments have demonstrated true Darwinian evolution of unique RNA enzymes (ribozymes) made up of two separate catalytic components that replicate each other in vitro. In describing this work from his laboratory, Gerald Joyce stated: "This is the first example, outside of biology, of evolutionary adaptation in a molecular genetic system." Such experiments make the possibility of a primordial RNA world even more attractive to many scientists. 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 extraterrestrially in outer space.

Conditions

The diversity of life on Earth is a result of the dynamic interplay between genetic opportunity, metabolic capability, environmental challenges, and symbiosis. For most of its existence, Earth's habitable environment has been dominated by microorganisms and subjected to their metabolism and evolution. As a consequence of such microbial activities on a geologic time scale, the physical-chemical environment on Earth has been changing, thereby determining the path of evolution of subsequent life. For example, the release of molecular oxygen by cyanobacteria as a by-product of photosynthesis induced fundamental, global changes in the Earth's environment. The altered environment, in turn, posed novel evolutionary challenges to the organisms present, which ultimately resulted in the formation of our planet's major animal and plant species. Therefore this "co-evolution" between organisms and their environment is apparently an inherent feature of living systems. All life forms require certain core chemical elements needed for biochemical functioning. These include carbon, hydrogen, nitrogen, oxygen, phosphorus, and sulfur—the elemental macronutrients for all organisms—often represented by the acronym CHNOPS. Together these make up nucleic acids, proteins and lipids, the bulk of living matter. Five of these six elements comprise the chemical components of DNA; the exception being sulfur. The latter forms a component of the important amino acid methionine. The most essential of these elements is carbon, which has the desirable attribute of forming multiple, stable covalent bonds. This allows carbon-based (organic) molecules to form an immense variety of chemical arrangements. Alternative hypothetical types of biochemistry have been proposed which eliminate one or more of these elements, swap out an element for one not on the list, or change required chiralities or other chemical properties. Range of tolerance The inert components of an ecosystem are the physical and chemical factors necessary for life— energy (sunlight or chemical energy), water, temperature, atmosphere, gravity, nutrients, and ultraviolet solar radiation protection. In most ecosystems the conditions vary during the day and often shift from one season to the next. To live in most ecosystems, then, organisms must be able to survive a range of conditions, called the "range of tolerance." Outside that are the "zones of physiological stress," where the survival and reproduction are possible but not optimal. Beyond these zones are the "zones of intolerance," where life for that organism is implausible. Organisms that have a wide range of tolerance are more widely distributed than organisms with a narrow range of tolerance.

To survive, selected microorganisms can assume forms that enable them to withstand freezing, complete desiccation, starvation, high-levels of radiation exposure, and other physical or chemical challenges. These microorganisms may survive exposure to such conditions for weeks, months, years, or even centuries. Extremophiles are microbial life forms that thrive outside the ranges where life is commonly found. They excel at exploiting uncommon sources of energy. While all organisms are composed of nearly identical molecules, evolution has enabled such microbes to cope with this wide range of physical and chemical conditions. Characterization of the structure and metabolic diversity of microbial communities in such extreme environments is ongoing. Investigation of the tenacity and versatility of life on Earth, as well as an understanding of the molecular systems that some organisms utilize to survive such extremes, will provide a critical foundation for the search for life beyond Earth. In this regard, on April 26, 2012, scientists reported that lichen survived and showed remarkable results on the adaptation capacity of photosynthetic activity within a simulated Martian environment. Form and function Cell theory propounds the concept that cells are the basic unit of structure in every living thing. This idea was formulated by Henri Dutrochet and others during the early nineteenth century, and subsequently became widely accepted. According to this theory, all cells arise from pre-existing cells by division. The activity of an organism depends on the total activity of independent cells, with energy flow occurring within cells. Cells contain hereditary information that is carried forward as a genetic code during cell division. There are two primary types of cells. Prokaryotes lack a nucleus and other membrane-bound organelles, although they have circular DNA and ribosomes. Bacteria and Archaea are two domains of prokaryotes. The other primary type of cells are the eukaryotes, which have distinct nuclei bound by a nuclear membrane and membrane-bound organelles, including mitochondria, chloroplasts, lysosomes, rough and smooth endoplasmic reticulum, and vacuoles. In addition, they possess organized chromosomes which store genetic material. All species of large complex organisms are eukaryotes, including animals, plants and fungi, although most species of eukaryote are protist microorganisms. The conventional model is that eukaryotes evolved from prokaryotes, with the main organelles of the eukaryotes forming through a process of symbiosis between bacteria and the progenitor eukaryotic cell. The molecular mechanisms of cell biology are based on proteins. Most of these are synthesized by the ribosomes through an enzyme-catalyzed process called protein biosynthesis. A sequence of amino acids is assembled and joined together based upon gene expression of the cell's nucleic acid. In eukaryotic cells, these proteins may then be transported and processed through the Golgi apparatus in preparation for dispatch to their destination. Cells reproduce through a process of cell division in which the parent cell divides into two or more daughter cells. This process of asexual reproduction leaves the resulting cell copies identical to each other and to the original cell. For prokaryotes, cell division occurs through a process of fission in which the DNA is replicated, then the two copies are attached to parts of the cell membrane. In eukaryotes, a more complex process of mitosis is followed. However, the end result is the same, leaving two identical copies of the original cell, each capable of further subdivision following an interphase period. Multicellular organisms may have first evolved through the formation of colonies of like cells. These cells can form group organisms through cell adhesion. The individual members of a colony are capable of surviving on their own, whereas the members of a true multi-cellular organism have developed specialties, making them dependent on the remainder of the organism for survival. Such organisms are formed from a single germ cell, which is capable of forming the various specialized cells that form the adult organism. This specialization allows multicellular organisms to exploit resources more efficiently than single cells. Cells have evolved methods to perceive and correctly respond to their microenvironment, thereby enhancing their adaptability. Cell signaling is a form of communication that is used to coordinate cell activities, and hence governs basic cellular activities in multicellular organisms. This can occur through direct cell contact using juxtacrine signalling, or indirectly through the exchange of agents as in the endocrine system. In more complex organisms, coordination of activities can occur through a dedicated nervous system. Classification Main article: Biological classification The hierarchy of biological classification's eight major taxonomic ranks, which is an example of definition by genus and differentia. Life is divided into domains, which are subdivided into further groups. Intermediate minor rankings are not shown. Traditionally, people have divided organisms into the classes of plants and animals, based mainly on their ability of movement. The first known attempt to classify organisms was conducted by the Greek philosopher Aristotle (384–322 BC). He classified all living organisms known at that time as either a plant or an animal. Aristotle distinguished animals with blood from animals without blood (or at least without red blood), which can be compared with the concepts of vertebrates and invertebrates respectively. He divided the blooded animals into five groups: viviparous quadrupeds (mammals), birds, oviparous quadrupeds (reptiles and amphibians), fishes and whales. The bloodless animals were divided into five groups: cephalopods, crustaceans, insects (which included the spiders, scorpions, centipedes, and what we define as insects in the present day), shelled animals (such as most molluscs and echinoderms) and "zoophytes." Though Aristotle's work in zoology was not without errors, it was the grandest biological synthesis of the time and remained the ultimate authority for many centuries after his death. In the late 1740s, Carolus Linnaeus introduced his method, still used, to formulate the scientific name of every species. Linnaeus took every effort to improve the composition and reduce the length of the many-worded names by abolishing unnecessary rhetoric, introducing new descriptive terms and defining their meaning with an unprecedented precision. By consistently using his system, Linnaeus separated nomenclature from taxonomy. This convention for naming species is referred to as binomial nomenclature. The fungi were originally treated as plants. For a short period Linnaeus had placed them in the taxon Vermes in Animalia. He later placed them back in Plantae. Copeland classified the Fungi in his Protoctista, thus partially avoiding the problem but acknowledged their special status.[91] The problem was eventually solved by Whittaker, when he gave them their own kingdom in his five-kingdom system. As it turned out, the fungi are more closely related to animals than to plants. As new discoveries enabled us to study cells and microorganisms, new groups of life were revealed, and the fields of cell biology and microbiology were created. These new organisms were originally described separately in protozoa as animals and protophyta/thallophyta as plants, but were united by Haeckel in his kingdom protista, later the group of prokaryotes were split off in the kingdom Monera, eventually this kingdom would be divided in two separate groups, the Bacteria and the Archaea, leading to the six-kingdom system and eventually to the current three- domain system. The classification of eukaryotes is still controversial, with protist taxonomy especially problematic. As microbiology, molecular biology and virology developed, non-cellular reproducing agents were discovered, such as viruses and viroids. Sometimes these entities are considered to be alive but others argue that viruses are not living organisms since they lack characteristics such as cell membrane, metabolism and do not grow or respond to their environments. Viruses can however be classed into "species" based on their biology and genetics but many aspects of such a classification remain controversial.[95] Since the 1960s a trend called cladistics has emerged, arranging taxa in an evolutionary or phylogenetic tree. It is unclear, should this be implemented, how the different codes will coexist.

Whittake Woese Cavalier- Linnaeus Haeckel Chatton Copeland Woese et al. r et al. Smith 1735[97] 1866[98] 1925[99][100] 1938[91][101] 1977[103][104] 1969[102] 1990[93] 2004[105] 3 3 2 4 5 6 kingdom 2 empires 6 kingdoms domain kingdoms kingdoms kingdoms kingdoms s s Eubacteria Bacteria Prokaryota Monera Monera Archaebacteri Bacteria Archaea (not a Protista treated) Protozoa Protoctista Protista Protista Chromist a Eukaryota Eukarya Plantae Plantae Plantae Vegetabilia Plantae Plantae Fungi Fungi Fungi Animalia Animalia Animalia Animalia Animalia Animalia

Extraterrestrial Main articles: Extraterrestrial life, astrobiology, and Life in the solar system Panspermia hypothesis showing bacteria being carried to Earth by a comet. Earth is the only planet known to harbor life. Other locations within the Solar System that may host life include subsurface Mars, the atmosphere of Venus, and subsurface oceans on some of the moons of the gas giant planets. The Drake equation, which predicts the number of extraterrestrial civilizations in our galaxy with which we might come in contact, has been used to discuss the probability of life elsewhere, but scientists disagree on many of the values of variables in this equation. The region around a main sequence star that could support Earth-like life on an Earth-like planet is known as the habitable zone. The inner and outer radii of this zone vary with the luminosity of the star, as does the time interval during which the zone will survive. Stars more massive than the Sun have a larger habitable zone, but will remain on the main sequence for a shorter time interval during which life can evolve. Small red dwarf stars have the opposite problem, with a smaller habitable zone that is subject to higher levels of magnetic activity and the effects of tidal locking from close orbits. Hence, stars in the intermediate mass range such as the Sun may have a greater likelihood for Earth-like life to develop. The location of the star within a galaxy may have an impact on the likelihood of life forming. Stars in regions of a galaxy that have a greater abundance of heavier elements that can form planets, in combination with a low rate of potentially habitat-damaging supernova events, are predicted to have a higher probability of hosting planets with complex life. Panspermia, also called exogenesis, is a hypothesis which speculates that life originated elsewhere in the universe and was subsequently transferred to Earth in the form of spores perhaps via meteorites, comets or cosmic dust. In October 2011, scientists found that the spectral features of cosmic dust permeating the universe reveals a content of complex organic matter ("amorphous organic solids with a mixed aromatic-aliphatic structure") that could be created naturally, and rapidly, by stars. The compounds are so complex that their chemical structures resemble the makeup of coal and petroleum; such chemical complexity was thought to arise only from living organisms. These recent observations suggests that the majority of organic compounds introduced on Earth by interstellar dust particles can serve as basic ingredients for life thanks to their peculiar surface-catalytic activities.[67][114] Death

Animal corpses, like this African buffalo, are recycled by the ecosystem, providing energy and nutrients for living creatures. Death is the permanent termination of all vital functions or life processes in an organism or cell. It can occur as a result of an accident, medical conditions, biological interaction, malnutrition, poisoning, senescence, or suicide. After death, the remains of an organism become part of the biogeochemical cycle. Organisms may be consumed by a predator or a scavenger and leftover organic material may then be further decomposed by detritivores, organisms which recycle detritus, returning it to the environment for reuse in the food chain. One of the challenges in defining death is in distinguishing it from life. Death would seem to refer to either the moment at which life ends, or when the state that follows life begins. However, determining when death has occurred requires drawing precise conceptual boundaries between life and death. This is problematic, however, because there is little consensus over how to define life. The nature of death has for millennia been a central concern of the world's religious traditions and of philosophical inquiry. Many religions maintain faith in either a kind of afterlife or reincarnation for the soul, or resurrection of the body at a later date. Extinction is the gradual process by which a group of taxa or species dies out, reducing biodiversity. The moment of extinction is generally considered to be the death of the last individual of that species. Because a species' potential range may be very large, determining this moment is difficult, and is usually done retrospectively after a period of apparent absence. Species become extinct when they are no longer able to survive in changing habitat or against superior competition. Over the history of the Earth, over 99% of all the species that have ever lived have gone extinct; however, mass extinctions may have accelerated evolution by providing opportunities for new groups of organisms to diversify. Fossils are the preserved remains or traces of animals, plants, and other organisms from the remote past. The totality of fossils, both discovered and undiscovered, and their placement in fossil-containing rock formations and sedimentary layers (strata) is known as the fossil record. Such a preserved specimen is called a "fossil" if it is older than the arbitrary date of 10,000 years ago. Hence, fossils range in age from the youngest at the start of the Holocene Epoch to the oldest from the Archaean Eon, up to 3.4 billion years old. Artificial life Artificial life is a field of study which examine systems related to life, its processes, and its evolution through simulations using computer models, robotics, and biochemistry. Artificial life imitates traditional biology by trying to recreate some aspects of biological phenomena. Artificial life studies the logic of living systems in artificial environments in order to come to an understanding of the complex information processing that defines such systems. While life is, by definition, alive, artificial life is generally referred to as data being confined to a digital environment and existence. Synthetic biology is a new area of biological research and technology that combines science and engineering. The common goal is the design and construction of new biological functions and systems not found in nature. Synthetic biology includes the broad redefinition and expansion of biotechnology, with the ultimate goals of being able to design and build engineered biological systems that process information, manipulate chemicals, fabricate materials and structures, produce energy, provide food, and maintain and enhance human health and our environment.[124]

Miller–Urey experiment

The Miller and Urey experiment (or Urey–Miller experiment) was an experiment that simulated hypothetical conditions thought at the time to be present on the early Earth, and tested for the occurrence of chemical origins of life. Specifically, the experiment tested Alexander Oparin's and J. B. S. Haldane's hypothesis that conditions on the primitive Earth favored chemical reactions that synthesized organic compounds from inorganic precursors. Considered to be the classic experiment on the origin of life, it was conducted in 1952 and published in 1953 by Stanley Miller and Harold Urey at the University of Chicago.

After Miller's death in 2007, scientists examining sealed vials preserved from the original experiments were able to show that there were actually well over 20 different amino acids produced in Miller's original experiments. That is considerably more than what Miller originally reported, and more than the 20 that naturally occur in life. Moreover, some evidence suggests that Earth's original atmosphere might have had a different composition from the gas used in the Miller–Urey experiment. There is abundant evidence of major volcanic eruptions 4 billion years ago, which would have released carbon dioxide (CO2), nitrogen (N2), hydrogen sulfide (H2S), and sulfur dioxide (SO2) into the atmosphere. Experiments using these gases in addition to the ones in the original Miller–Urey experiment have produced more diverse molecules.

Experiment The experiment used water (H2O), methane (CH4), ammonia (NH3), and hydrogen (H2). The chemicals were all sealed inside a sterile array of glass tubes and flasks connected in a loop, with one flask half-full of liquid water and another flask containing a pair of electrodes. The liquid water was heated to induce evaporation, sparks were fired between the electrodes to simulate lightning through the atmosphere and water vapor, and then the atmosphere was cooled again so that the water could condense and trickle back into the first flask in a continuous cycle.

Within a day, the mixture had turned pink in colour, and at the end of two weeks of continuous operation, Miller and Urey observed that as much as 10–15% of the carbon within the system was now in the form of organic compounds. Two percent of the carbon had formed amino acids that are used to make proteins in living cells, with glycine as the most abundant. Nucleic acids were not formed within the reaction. But the common 20 amino acids (17 of 20 amino acids used in protein synthesis)were formed, in various concentrations.All the purines and pyrimidines used in nucleic acid synthesis were formed also. Analysis was done using paper chromatography. Perhaps most importantly, Miller's experiment showed that organic compounds such as amino acids, which are essential to cellular life, could be made easily under the conditions that scientists believed to be present on the early earth. This enormous finding inspired a multitude of further experiments.

In an interview, Stanley Miller stated: "Just turning on the spark in a basic pre-biotic experiment will yield 11 out of 20 amino acids."

As observed in all subsequent experiments, both left-handed (L) and right-handed (D) optical isomers were created in a racemic mixture. In biological systems, most of the compounds are non-racemic, or homochiral.

The original experiment remains today under the care of Miller and Urey's former student Jeffrey Bada, a professor at UCSD, at the University of California, San Diego, Scripps Institution of Oceanography. The apparatus used to conduct the experiment is on display at the Denver Museum of Nature and Science.

Chemistry of experiment

One-step reactions among the mixture components can produce hydrogen cyanide (HCN), formaldehyde (CH2O), and other active intermediate compounds (acetylene, cyanoacetylene, etc.):

CO2 → CO + [O] (atomic oxygen) CH4 + 2[O] → CH2O + H2O CO + NH3 → HCN + H2O CH4 + NH3 → HCN + 3H2 (BMA process) The formaldehyde, ammonia, and HCN then react by Strecker synthesis to form amino acids and other biomolecules:

CH2O + HCN + NH3 → NH2-CH2-CN + H2O NH2-CH2-CN + 2H2O → NH3 + NH2-CH2-COOH (glycine)

Furthermore, water and formaldehyde can react via Butlerov's reaction to produce various sugars like ribose.

The experiments showed that simple organic compounds of building blocks of proteins and other macromolecules can be formed from gases with the addition of energy.

Other experiments

This experiment inspired many others. In 1961, Joan Oró found that the nucleotide base adenine could be made from hydrogen cyanide (HCN) and ammonia in a water solution. His experiment produced a large amount of adenine, the molecules of which were formed from 5 molecules of HCN.[15] Adenine is of tremendous biological significance as an organic compound because it is one of the four bases in RNA and DNA. It is also a component of adenosine triphosphate, or ATP, which is a major energy releasing molecule in cells. Experiments conducted later showed that the other RNA and DNA bases could be obtained through simulated prebiotic chemistry with a reducing atmosphere. These discoveries created a stir within the science community. Scientists became very optimistic that the questions about the origin of life would be solved within a few decades. This has not been the case, however. Instead, the investigation into life's origins seems only to have just begun. There has been a recent wave of skepticism concerning Miller's experiment because it is now believed that the early earth's atmosphere did not contain predominantly reductant molecules. Another objection is that this experiment required a tremendous amount of energy. While it is believed lightning storms were extremely common on the primitive Earth, they were not continuous as the Miller/Urey experiment portrayed. Thus it has been argued that while amino acids and other organic compounds may have been formed, they would not have been formed in the amounts which this experiment produced. Many of the compounds made in the Miller/Urey experiment are known to exist in outer space

Also, many amino acids are formed from HCN and ammonia under these conditions. Experiments conducted later showed that the other RNA and DNA nucleobases could be obtained through simulated prebiotic chemistry with a reducing atmosphere.

There also had been similar electric discharge experiments related to the origin of life contemporaneous with Miller–Urey. An article in The New York Times (March 8, 1953:E9), titled "Looking Back Two Billion Years" describes the work of Wollman (William) M. MacNevin at The Ohio State University, before the Miller Science paper was published in May 1953. MacNevin was passing 100,000 volt sparks through methane and water vapor and produced "resinous solids" that were "too complex for analysis." The article describes other early earth experiments being done by MacNevin. It is not clear if he ever published any of these results in the primary scientific literature.

K. A. Wilde submitted a paper to Science on December 15, 1952, before Miller submitted his paper to the same journal on February 14, 1953. Wilde's paper was published on July 10, 1953.[18]

Wilde used voltages up to only 600 V on a binary mixture of carbon dioxide (CO2) and water in a flow system. He observed only small amounts of carbon dioxide reduction to carbon monoxide, and no other significant reduction products or newly formed carbon compounds. Other researchers were studying UV-photolysis of water vapor with carbon monoxide. They have found that various alcohols, aldehydes and organic acids were synthesized in reaction mixture.

More recent experiments by chemists Jeffrey Bada and Jim Cleaves at Scripps Institution of Oceanography (in La Jolla, CA) were similar to those performed by Miller. However, Bada noted that in current models of early Earth conditions, carbon dioxide and nitrogen (N2) create nitrites, which destroy amino acids as fast as they form. However, the early Earth may have had significant amounts of iron and carbonate minerals able to neutralize the effects of the nitrites. When Bada performed the Miller-type experiment with the addition of iron and carbonate minerals, the products were rich in amino acids. This suggests the origin of significant amounts of amino acids may have occurred on Earth even with an atmosphere containing carbon dioxide and nitrogen.

Earth's early atmosphere

Some evidence suggests that Earth's original atmosphere might have contained fewer of the reducing molecules than was thought at the time of the Miller–Urey experiment. There is abundant evidence of major volcanic eruptions 4 billion years ago, which would have released carbon dioxide, nitrogen, hydrogen sulfide (H2S), and sulfur dioxide (SO2) into the atmosphere.Experiments using these gases in addition to the ones in the original Miller–Urey experiment have produced more diverse molecules. The experiment created a mixture that was racemic (containing both L and D enantiomers) and experiments since have shown that "in the lab the two versions are equally likely to appear."[8] However, in nature, L amino acids dominate; later experiments have confirmed disproportionate amounts of L or D oriented enantiomers are possible.

Originally it was thought that the primitive secondary atmosphere contained mostly ammonia and methane. However, it is likely that most of the atmospheric carbon was CO2 with perhaps some CO and the nitrogen mostly N2. In practice gas mixtures containing CO, CO2, N2, etc. give much the same products as those containing CH4 and NH3 so long as there is no O2. The hydrogen atoms come mostly from water vapor. In fact, in order to generate aromatic amino acids under primitive earth conditions it is necessary to use less hydrogen-rich gaseous mixtures. Most of the natural amino acids, hydroxyacids, purines, pyrimidines, and sugars have been made in variants of the Miller experiment. More recent results may question these conclusions. The University of Waterloo and University of Colorado conducted simulations in 2005 that indicated that the early atmosphere of Earth could have contained up to 40 percent hydrogen—implying a possibly much more hospitable environment for the formation of prebiotic organic molecules. The escape of hydrogen from Earth's atmosphere into space may have occurred at only one percent of the rate previously believed based on revised estimates of the upper atmosphere's temperature. One of the authors, Owen Toon notes: "In this new scenario, organics can be produced efficiently in the early atmosphere, leading us back to the organic-rich soup-in-the-ocean concept... I think this study makes the experiments by Miller and others relevant again." Outgassing calculations using a chondritic model for the early earth complement the Waterloo/Colorado results in re-establishing the importance of the Miller–Urey experiment.

Conditions similar to those of the Miller–Urey experiments are present in other regions of the solar system, often substituting ultraviolet light for lightning as the energy source for chemical reactions. The Murchison meteorite that fell near Murchison, Victoria, Australia in 1969 was found to contain over 90 different amino acids, nineteen of which are found in Earth life. Comets and other icy outer-solar-system bodies are thought to contain large amounts of complex carbon compounds (such as tholins) formed by these processes, darkening surfaces of these bodies. The early Earth was bombarded heavily by comets, possibly providing a large supply of complex organic molecules along with the water and other volatiles they contributed. This has been used to infer an origin of life outside of Earth: the panspermia hypothesis.

Recent related studies

In recent years, studies have been made of the amino acid composition of the products of "old" areas in "old" genes, defined as those that are found to be common to organisms from several widely separated species, assumed to share only the last universal ancestor (LUA) of all extant species. These studies found that the products of these areas are enriched in those amino acids that are also most readily produced in the Miller–Urey experiment. This suggests that the original genetic code was based on a smaller number of amino acids – only those available in prebiotic nature – than the current one.

Professor Jeffrey Bada, himself Miller's student, inherited the original equipment from the experiment when Miller died in 2007. Based on sealed vials from the original experiment, scientists have been able to show that although successful, Miller was never able to find out, with the equipment available to him, the full extent of the experiment's success. Later researchers have been able to isolate even more different amino acids, 25 altogether. Professor Bada has estimated that more accurate measurements could easily bring out 30 or 40 more amino acids in very low concentrations, but the researchers have since discontinued the testing. Miller's experiment was therefore a remarkable success at synthesizing complex organic molecules from simpler chemicals, considering that all life uses just 20 different amino acids.

In 2008, a group of scientists examined 11 vials left over from Miller's experiments of the early 1950s. In addition to the classic experiment, reminiscent of Charles Darwin's envisioned "warm little pond", Miller had also performed more experiments, including one with conditions similar to those of volcanic eruptions. This experiment had a nozzle spraying a jet of steam at the spark discharge. By using high-performance liquid chromatography and mass spectrometry, the group found more organic molecules than Miller had. Interestingly, they found that the volcano-like experiment had produced the most organic molecules, 22 amino acids, 5 amines and many hydroxylated molecules, which could have been formed by hydroxyl radicals produced by the electrified steam. The group suggested that volcanic island systems became rich in organic molecules in this way, and that the presence of carbonyl sulfide there could have helped these molecules form peptides.

THEORIES ON EVOLUTION OF LIFE

1.Scientific Evolution: This theory relies strongly on the Big Bang theory of the Creation of the Universe, which was the beginning of the formation of matter. This eventually led to the creation of planets, Pangaea and life on earth as it evolved over millions of years in a natural environment of chemicals and enabling elements. Evolution of life can mean many things. Some use the word to refer to any change at all. Obviously the creation/evolution debate is not about that kind of a definition. Creationists agree that many changes take place, but disagree with the theory of evolution when it is used to mean that a gradual progression from molecules to man produced all living things by natural means, that is, without the involvement of an intelligent Creator. 2.Theory of Special Creation According to this theory, all the different forms of life that occur today on planet earth, have been created by God, the almighty. This idea is found in the ancient scriptures of almost every religion. According to Hindu mythology, Lord Brahma, the God of Creation, created the living world in accordance to his wish. According to the Christian belief, God created this universe, plants, animals and human beings in about six natural days. The Sikh mythology says that all forms of life including human beings came into being with a single word of God. Special creation theory believes that the things have not undergone any significant change since their creation. The theory of Special Creation was purely a religious concept, acceptable only on the basis of faith. It has no scientific basis.

3. Biogenesis: The belief that living things come only from other living things (e.g. a spider lays eggs, which develop into spiders). It may also refer to biochemical processes of production in living organisms. The Law of Biogenesis, attributed to Louis Pasteur, states that life arises from pre-existing life, not from nonliving material. Pasteur's (and others') empirical results were summarized in the phrase Omne vivum ex vivo, Latin for "all life [is] from life", also known as the "law of biogenesis". Pasteur stated: "La génération spontanée est une chimère" ("Spontaneous generation is a dream").

4. Abiogenesis: Theory of Spontaneous Generation This theory assumed that living organisms could arise suddenly and spontaneously from any kind of non-living matter. One of the firm believers in spontaneous generation was Aristotle, the Greek philosopher (384-322 BC). He believed that dead leaves falling from a tree into a pond would transform into fishes and those falling on soil would transform into worms and insects. He also held that some insects develop from morning dew and rotting manure. Egyptians believed that mud of the Nile river could spontaneously give rise to many forms of life. The idea of spontaneous generation was popular almost till seventeenth century. Many scientists like Descartes, Galileo and Helmont supported this idea. In fact, Von Helmont went to the extent stating that he had prepared a 'soup' from which he could spontaneously generate rats! The 'soup' consisted of a dirty cloth soaked in water with a handful of wheat grains. Helmont stated that if human sweat is added as an 'active principle' to this, in just 17 days, it could generate rats! The theory of Spontaneous Generation was disproved in the course of time due to the experiment conducted by Fransisco Redi, (1665), Spallanzani (1765) and later by Louis Pasteur (1864) in his famous Swan neck experiment. This theory was disapproved, as scientists gave definite proof that life comes from pre-existing life. In the natural sciences, abiogenesis - also known as spontaneous generation - is the study of how life on Earth could have arisen from inanimate matter. This is also referred to as the "primordial soup" theory of evolution (life began in water as a result of the combination of chemicals from the atmosphere and some form of energy to make amino acids, the building blocks of proteins, which would then evolve into all the species). It should not be confused with evolution, which is the study of how groups of already living things change over time. Most amino acids, often called "the building blocks of life", can form via natural chemical reactions unrelated to life, as demonstrated in the Miller-Urey experiment and similar experiments, which involved simulating the conditions of the early Earth. In all living things, these amino acids are organized into proteins, and the construction of these proteins is mediated by nucleic acids. This of these organic molecules first arose and how they formed the first life is the focus of abiogenesis. Egyptians believed that mud of the Nile River could spontaneously give rise to many forms of life. The idea of spontaneous generation was popular almost till seventeenth century. Many scientists like Descartes, Galileo and Helmont supported this idea.

5.Theory of Catastrophism It is simply a modification of the theory of Special Creation. It states that there have been several creations of life by God, each preceded by a catastrophe resulting from some kind of geological disturbance. According to this theory, since each catastrophe completely destroyed the existing life, each new creation consisted of life form different from that of previous ones. A French scientist Georges Cuvier (1769-1832) and Orbigney (1802 to 1837) were the main supporters of this theory.

6.Cosmozoic Theory (Theory of Panspermia) According to this theory, life has reached this planet Earth from other heavenly bodies such as meteorites, in the form of highly resistance spores of some organisms. This idea was proposed by Richter in 1865 and supported by Arrhenius (1908) and other contemporary scientists. The theory did not gain any support. This theory lacks evidence, hence it was discarded. Some scientists believe that the simplest life-forms, whole cells (especially microbial cells), have been transported to the Earth from extraterrestrial sources. In this way, a process called panspermia (means seeds everywhere) might have initiated life on Earth. Most mainstream scientists have not supported panspermia, but early challenges have been thwarted in recent years due to discoveries such as terrestrial microbes that survive in extreme environments and incredibly aged yet viable microorganisms found in ancient rocks. In addition, water (essential for life) has been discovered on other planets and moons, and organic chemicals have been found on meteorites and in interstellar debris.

7. Inorganic Incubation: Proposed by Professor William Martin, of Düsseldorf University, and Professor Michael Russell, of the Scottish Environmental Research Centre in Glasgow, this theory states that Instead of the building blocks of life forming first, and then forming a cell-like structure, the researchers say the cell came first and was later filled with living molecules. They say that the first cells were not living cells but inorganic ones made of iron sulfide and were formed not at the Earth's surface but in total darkness at the bottom of the oceans. The theory postulates that life is a chemical consequence of convection currents through the Earth's crust and, in principle, could happen on any wet, rocky planet.

8. Endosymbiotic Theory: This theory, espoused by Lynn Margulis, suggests that multiple forms of bacteria entered into symbiotic relationship to form the eukaryotic cell. The horizontal transfer of genetic material between bacteria promotes such symbiotic relationships, and thus many separate organisms may have contributed to building what has been recognized as the Last Universal Common Ancestor (LUCA) of modern organisms. James Lovelock's Gaia theory, proposes that such bacterial symbiosis establishes the environment as a system produced by and supportive of life. His arguments strongly weaken the case for life having evolved elsewhere in the solar system.

9.Cosmogony: Cosmogony is any theory concerning the coming into existence or origin of the universe, or about how reality came to be. In the specialized context of space science and astronomy, the term refers to theories of creation of the Solar System. For example, Greek mythology and some religions of the Ancient Near East refer to chaos, the formless or void state of primordial matter preceding the creation of the universe or cosmos in creation myths. Cosmogony can be distinguished from cosmology, which studies the universe at large and throughout its existence, yet does not inquire directly into the source of life or its origins.

10.Theory of Chemical Evolution

This theory is also known as Materialistic Theory or Physico-chemical Theory. According this theory, Origin of life on earth is the result of a slow and gradual process of chemical evolution that probably occurred about 3.8 billion years ago. This theory was proposed independently by two scientists - A.I.Oparin, a Russian scientist in 1923 and J.B.S Haldane, an English scientist, in 1928. According to this theory,  Spontaneous generation of life, under the present environmental conditions is not possible.  Earth's surface and atmosphere during the first billion years of existence, were radically different from that of today's conditions.  The primitive earth's atmosphere was a reducing type of atmosphere and not oxidising type.  The first life arose from a collection of chemical substances through a progressive series of chemical reactions.  Solar radiation, heat radiated by earth and lighting must have been the chief energy source for these chemical reactions.

Biological organization

Biological organization, or the hierarchy of life, is the hierarchy of complex biological structures and systems that define life using a reductionistic approach.[1] The traditional hierarchy, as detailed below, extends from atoms (or lower) to biospheres. The higher levels of this scheme are often referred to as ecological organization.

Organization is the arrangement of smaller components of any structure into larger ones and so on in a hierarchy or a pyramid in which components of each level coordinate with one another towards a common goal.

Living organisms show three types of organizations :-

1. Molecular Level of Organization

2. Individual Level of Organization

3. Higher level of organization

1. Molecular Level of Organization

All living organisms have cellular nature as the cell is the basic unit of structure and functions of life. The organisms may be unicellular (also called acellular) or multicellular. Unicellular organisms constitute the majority of living organisms. The cell is a mass of living matter called protoplasm bounded by a cell membrane or cell wall Protoplasm is formed by a number of complex organic macro-bio-molecules like protein, carbohydrates, fats, etc. which are polymeric compounds. These in turn are formed by specific monomers interlinked by a specific bond.

Polymeric Compound Monomers Interlinked by

Protein Amino Acid Peptide Bond

Polysaccharides(e.g starch) Monosaccharaides(e.g glucose) Glycosidic Bond

Nucleic Acid (DNA &RNA) Nucleotides Phosphodiester Bond

Atom -- Molecules--Inorganic Compounds----Simple Organic Compound----Complex Organic Compounds-----Protoplasm-----Cell

Note:-

Sydney W. Fox (1957 A.D.) reported that when a mixture of 18-20 amino acids is heated to the boiling point (160 OC to 210 OC for several hours) and then cooled, many amino acids polymerized and formed polypeptides chains, called, proteinoids. Fox stated that these proteinoids with water formed the colloidal aggregates called coacervates or microsphere (0.5- 0.80 mu in diameter). He also reported the formations of nucleotides and ATP from inorganic molecules and HCN.

2. Individual Level of Organization

One celled protozoans e.g Amoeba, Paramecium,etc are acellular animals and perform all metabolic functions like nutrition, reproduction, respiration etc. .In these animals, the division of labour is at the level of cell organelles (living structures of the cell) each performing specific functions. E.g. Mitochondria for cell respiration and energy production, while ribosomes (called protein factories) are for protein synthesis. Such body organization is called protoplasmic body organization.

In sponges(sponges (Eg. Seypha) the body is formed of many cells cells but these do not show any coordination and work independently. It is called cellular level of organization.

In coelenterates(e.g. Hydra) cells similar in form, structure and origin coordinate for covering and protection, connecting tissues for binding structures, muscular tissues for movement and locomotion and nervous tissues for conduction of nerve impulses. Such organization is called tissue organization.

From flatworms (e.g Tapeworms) to mammals different tissues coordinate to form specific functions and form organs e.g. heart, liver, stomach, which coordinate to form systems which in turn coordinate to form an individual. An individual is a self-sufficient unit of the living world. It is called an organ system organization. It is the highest unit of structure and function of an organization. Cell----Tissue----Organ-----Organ System-----Individual

3. Higher level of organization

All the individuals of a species found in the same geographical area and having similar basic characteristics, inter breeding under natural conditions to produce fertile offspring and sharing a common gene pool collectively called population. All the population of different species formed in the same geographical area is collectively called the biotic community of that area.

The biotic organisms and abiotic physic-chemical factors of an area collectively form ecosystem of that area.The term ecosystem was coined by A.G. Tansley (1935). All the ecosystem of the world interact with one another and collectively form biosphere or ecosphere. Biosphere is the highest and most complex level of organization in nature.

Population---Biotic Community----Ecosystems---Biosphere

Each level in the hierarchy represents an increase in organizational complexity, with each "object" being primarily composed of the previous level's basic unit.[2] The basic principle behind the organization is the concept of emergence—the properties and functions found at a hierarchical level are not present and irrelevant at the lower levels.[3]

Organization furthermore refers to the high degree of order of an organism (in comparison to general objects).[4] Ideally, individual organisms of the same species have the same arrangement of the same structures. For example, the typical human has a torso with two legs at the bottom and two arms on the sides and a head on top. It is extremely rare (and usually impossible, due to physiological and biomechanical factors) to find a human that has all of these structures but in a different arrangement.

The biological organization of life is a fundamental premise for numerous areas of scientific research, particularly in the medical sciences.[3] Without this necessary degree of organization, it would be much more difficult—and likely impossible—to apply the study of the effects of various physical and chemical phenomena to diseases and body function. For example, fields such as cognitive and behavioral neuroscience could not exist if the brain was not composed of specific types of cells, and the basic concepts of pharmacology could not exist if it was not known that a change at the cellular level can affect an entire organism. These applications extend into the ecological levels as well. For example, DDT's direct effect occurs at the subcellular level, but affects higher levels up to and including multiple ecosystems. Theoretically, a change in one atom could change the entire biosphere.

Other Levels Classifications

The simple standard biological organization scheme, from the lowest level to the highest level, is as follows:[1]

A-cellular level* The atom and * The molecule, a grouping of atoms Pre-cellular level * The organelle, a functional grouping of biomolecules; biochemical reactions Sub-cellular level and interactions Cellular level * The cell, the basic unit of all life and the grouping of organelles Super-cellular level * The tissue, a functional grouping of cells (Multicellular level) * The organ, a functional grouping of tissues * The organ system, a functional grouping of organs * The organism, the basic living system, a functional grouping of the lower- level components, including at least one cell * The population, a grouping of organisms of the same species * The biocoenosis or community, an interspecific grouping of interacting populations * The ecosystem, a grouping of organisms from all biological domains in conjunction with the physical (abiotic) environment * The biosphere, the complete set of communities * The ecosphere, the complete set of ecosystems

More complex schemes incorporate many more levels. For example, a molecule can be viewed as a grouping of elements, and an atom can be further divided into subatomic particles (these levels are outside the scope of biological organization). Each level can also be broken down into its own hierarchy, and specific types of these biological objects can have their own hierarchical scheme. For example, genomes can be further subdivided into a hierarchy of genes.[5]

Each level in the hierarchy can be described by its lower levels. For example, the organism may be described at any of its component levels, including the atomic, molecular, cellular, histological (tissue), organ and organ system levels. Furthermore, at every level of the hierarchy, new functions necessary for the control of life appear. These new roles are not functions that the lower level components are capable of and are thus referred to as emergent properties.

Every organism is organized, though not necessarily to the same degree.[6] An organism can not be organized at the histological (tissue) level if it is not composed of tissues in the first place. Levels of biological organization:-

Biosphere: Those regions of the Earth’s waters, crust and atmosphere in which organisms/ecosystems can exist.

Ecosystem: consists of all organisms living in a particular area, as well as the nonliving, physical components of the environment, linked by a one way flow of energy and cycling of materials.

Community: An association of populations tied together directly or indirectly by competition of resources, predation and other interactions.

Population: a group of organisms of the same species occupying a any given area in a given interval of time.

Organism: Individual composed of specialized, interdependent cells arrayed in tissues, organs and often organ systems. Within a population there are organisms, just one of those organisms is called and organism. For example, within a population lions, there is a lion.

Organ system: Two or more organs whose separate functions are integrated in the performance of a specific task

Organ: One or more types of tissues interacting as a structural and functional unit.

Tissue: Group of cells and intercellular substances functioning together in a specialized activity

Cell: the smallest unit of life that is able to carry out all the functions of living things and exist independently

Organelle: Membranous sacs or other compartments that separate different metabolic reactions inside the cell

Molecule: A unit of two or more atoms of the same or different elements bounded together

Atom: the smallest unit of matter that has the chemical properties of a particular element.

These levels are all related to each other. For example, a biosphere contains all of the mentioned levels above. So, each level contains the level before it and they all fit into each other like Russian nesting dolls.

Knowing the difference between the levels is helpful because it makes it easier when comparing different things. When studying a lion with a disease, you can break the organism down into different parts and study the disease at these different levels.

This wasn't really part of our assignment but, when I was searching for information about biological organization, I found a website that talked about how these levels are “much too pat.” Sometimes, it is hard to differentiate what level certain things fit into. For example, in class we discussed what level your biceps muscle would be in. It is hard to decide because many would argue that it's just a tissue, while others think it's an organ because it performs a function. The picture below shows the levels of organization. It is a little different than what we learned in class but, it seems like everyone has a different version on what they think is best. Classification of Living Things & Naming With so many flora and fauna on planet Earth, there must be a method to classify each organism to distinguish it from others so it can be correctly identified. Classification does not only apply to biology. For example, supermarkets and grocery stores organise their products by classifying them. Beverages may occupy one aisle, while cleaning supplies may occupy another. In science, the practice of classifying organisms is called taxonomy (Taxis means arrangement and nomos means law). The modern taxonomic system was developed by the Swedish botanist Carolus (Carl) Linneaeus (1707-1788). He used simple physical characteristics of organisms to identify and differentiate between different species.Taxonomy is the functional science which deals with identification, nomenclature, and classification of different kinds of organisms all over the world. Taxonomy can also be defined as the study of the classification of plant and animals and their evolutionary relationship.

Classification Guideline

a. Morphology(external characters) b. Anatomy (internal structure) c. Cytology (cell structure) d. Physiology(life processes) e. Ontogeny(development) f. Reproduction g. Behavior h. Biochemistry

Linneaeus developed a hierarchy of groups for taxonomy. To distinguish different levels of similarity, each classifying group, called taxon (pl. taxa) is subdivided into other groups. To remember the order, it is helpful to use a mnemonic device. The taxa in hierarchical order:  Domain - Archea, Eubacteria, Eukaryote  Kingdom - Plants, Animals, Fungi, Protists, Eubacteria (Monera), Archaebacteria o It is the highest category of taxonomic study.All animals are included in Animal Kingdom and all plants are included in the plant kingdo  Phylum o Many classes with common characteristics are included in the same phylum. Phylum chordate includes pisces, amphibian, mammalia because all have common characters such as presence of notochord, dorsal, hollow nervous system and pharynx perforated by gill slits.  Class o The class is a basic category. Similar order are placed together in a class. Class Mammalia includes orders like carnivora, chiroptera, rodentia, primates. They have few characters in common .E.g. the presence of mammary glands and hair.  Order o A number of families having common characters are placed in an order. The cat, tiger, etc. belong to the family Felidae. The bears are included in family Ursidae because dogs, cats, bears, are carnivorous their families are included under order Carnivora  Family o A number of genera having several common characters form a family. E.g. Solanum and Datura have same characters in common.That is why they have been placed in the same family, Solanceae. The genus, Velpus, shows few characters common with Canis. Thus both genera are placed in family canidae.  Genus (pl. genera) o It forms the taxonomic category higher than species. It is a group of closely related species. E.g. Dog, Jackal, Wolf are placed in the same genus, Canis because they are closely related to each other but belong to different species. Similarly potato, brinjal, etc are placed are placed in the same genus Solanum but belong to different species tuberosum and melongena respectively.Groups of common characters in a species in a genus are called correlated species.Sometimes a genus may be made up of only one species as in man the genus is homo.  Species The lowest category of living organisms is called species. Species include a group of individuals which resemble each other closely in terms of structure and function The domain is the broadest category, while species is the most specific category available. The taxon Domain was only introduced in 1990 by Carl Woese, as scientists reorganise things based on new discoveries and information. For example, the European Hare would be classified as follows: Eukaryote --> Animal --> Chordata --> Mammalia --> Lagomorpha --> Leporidae --> Lepus --> Lepus europaeus. Binomial nomenclature is used to name an organism, where the first word beginning with a capital is the genus of the organism and the second word beginning with lower-case letter is the species of the organism. The name must be in italics and in Latin, which was the major language of arts and sciences in the 18th century. The scientific name can be also abbreviated, where the genus is shortened to only its first letter followed by a period. In our example, Lepus europaeus would become L. europaeus'. Taxonomy and binomial nomenclature are both specific methods of classifying an organism. They help to eliminate problems, such as mistaken identity and false assumptions, caused by common names. An example of the former is the fact that a North American robin is quite different from the English robin. An example of the latter is the comparison between crayfish and catfish, where one might believe that they both are fish when in fact, they are quite different. Eukaryotes & Prokaryotes Recall that there are two basic types of cells: eukaryotes and prokaryotes. Eukaryotes are more complex in structure, with nuclei and membrane-bound organelles. Some characteristics of eukaryotes are:  Large (100 - 1000 μm)  DNA in nucleus, bounded by membrane  Genome consists of several chromosomes.  Sexual reproduction common, by mitosis and meiosis  Mitochondria and other organelles present  Most forms are multicellular  Aerobic Prokaryotes refer to the smallest and simplest type of cells, without a true nucleus and no membrane-bound organelles. Bacteria fall under this category. Some characteristics:  Small (1-10 μm)  DNA circular, unbounded  Genome consists of single chromosome.  Asexual reproduction common, not by mitosis or meiosis.  No general organelles  Most forms are singular  Anaerobic The Three Domains The three domains are organised based on the difference between eukaryotes and prokaryotes. Today's living prokaryotes are extremely diverse and different from eukaryotes. This fact has been proven by molecular biological studies (e.g. of RNA structure) with modern technology. The three domains are as follows: Archea (Archeabacteria) consists of archeabacteria, bacteria which live in extreme environments. The kingdom Archaea belongs to this domain. Eubacteria consists of more typical bacteria found in everyday life. The kingdom Eubacteria belongs to this domain. Eukaryote encompasses most of the world's visible living things. The kingdoms Protista, Fungi, Plantae, and Animalia fall under this category.

The Five/Six Kingdoms Under the three domains are six kingdoms in taxonomy. The five kingdom system of classification of Whittaker replaced the old two kingdom system.It is based on the following criteria:- 1. Complexity of organism’s body 2. Complexity of structure 3. Mode of obtaining nutrition 4. Phylogenic Relationship – The evolutionary history of any group of organisms.

The five kingdoms are :Monera, Protista, Plantae, Fungi, Animalia

1) Kingdom Monera : They are prokaryotes and show the following characters : 1. They lack nuclear membrane 2. They are devoid of plastids, mitochondria, and advanced flagella. 3. They are typically unicellular organisms( but one group moicelial) 4. The predominant mode of nutrition is absorptive but some groups are photosynthetic or chemosynthetic. 5. Reproduction is primarily asexual by fission of body 6. Protosexual phenomenon also occurs 7. Organisms are not motile or move by beating of simple flagella. 8. Monera cells are microscopic. 9. Most organisms bear a cell wall. 2) Kingdom Protista, the third kingdom, was introduced by the German biologist Ernst Haeckel in 1866 to classify micro-organisms which are neither animals nor plants. Since protists are quite irregular, this kingdom is the least understood and the genetic similarities between organisms in this kingdom are largely unknown. For example, some protists can exhibit properties of both animals and plants.

1. Protista include solitary unicellular or colonial unicellular eukaryotic organisms which do not form tissues. 2. Simple multinucleate organisms or stages of life cycles occur in a number of groups 3. The organisms process nuclear membranes (eukaryotes) and mitochondria 4. In many forms, plastids, flagella, and other organelles are present 5. The nutritive modes of three organisms include photosynthesis, absorption, ingestion and a combination of these. 6. The organisms move by flagella or by other means or are non motile

3) Kingdom Fungi are organisms which obtain food by absorbing materials in their bodies. Mushrooms and moulds belong in this kingdom. Originally, they were part of the plant kingdom but were recategorised when they were discovered not to photosynthesise. They are saprophytic or parasites 1. They are eukaryotic, multicellular organisms with heterotrophic nutrition. 2. They lack chlorophyll. 3. There is a limited or no differentiation of somatic tissues. 4. Usually non motile but show the protoplasmic flow in mycellian. 5. Both sexual and asexual methods of reproduction are present.

Eubacteria are bacteria, made up of small cells, which differ in appearance from the organisms in the above kingdoms. They lack a nucleus and cell organelles. They have cell walls made of peptidoglycan.

4) Kingdom Archae (or Archaebacteria) are bacteria which live in extreme environments, such as salt lakes or hot, acidic springs. These bacteria are in their own category as detailed studies have shown that they have unique properties and features (ex. unusual lipids that are not found in any other organism)which differ them from other bacteria and which allow them to live where they live. Their cell walls lack peptidoglycan.

5) Kingdom Plantae :

a. They are multicellular organisms with wall and frequently vacuoles eukaryotic cells b. They contain photosynthetic pigment in plastids. Principal mode of nutrition is photosynthetic. c. Primarily non motile, living anchored to a substrate. d. Structural differentiation leading towards organs of photosynthesis, anchorage, and support and in higher forms towards specialized photosynthetic vascular and covering tissues. e. Reproduction is primarily sexual. f. Haploid generation is progressively reduced in higher members of kingdom . i. Nepenthes – Insectivorous, Pitcher Plant ii. Utricularia – Water plant

6) Kingdom Animalia :

a. They are multicellular organisms. They bear eukaryotic cells and lack stiff cell wall. b. They are devoid of plastids and photosynthetic pigments. c. Nutrition is primarily ingestive with digestion in an internal cavity, but some forms are absorptive and number of groups lack an internal digestive cavity. d. Level of organization and tissue differentiation in higher forms or exceeding that of other kingdoms with evolution of sensory neuromotor systems or motility of organisms based on contractile fibrils e. They have developed cells which have the ability to contract or transmit impulses.

Origins of Diversity The diversity in our planet is attributed to diversity within a species. As the world changed in climate and in geography as time passed, the characteristics of species diverged so much that new species were formed. This process, by which new species evolve, was first described by British naturalist Charles Darwin as natural selection. For an organism to change, genetic mutations must occur. At times, genetic mutations are accidental, as in the case of prokaryotes when they undergo asexual reproduction. For most eukaryotes, genetic mutations occur through sexual reproduction, where meiosis produces haploid gametes from the original parent cells. The fusion of these haploid gametes into a diploid zygote results in genetic variation in each generation. Over time, with enough arrangement of genes and traits, new species are produced. Sexual reproduction creates an immense potential of genetic variety. One goal of taxonomy is to determine the evolutionary history of organisms. This can be achieved by comparing species living today with species in the past. The comparison in anatomy and structure is based on data from development, physical anatomy, biochemistry, DNA, behaviour, and ecological preferences. The following are examples of how such data is used:  Anatomy: Although a horse and a human may look different, there is evidence that their arm structures are quite similar. Their arms' sizes and proportions may be different, but the anatomical structures are quite similar. Such evidence reveals that animals in different taxa may not be that different. Biological features from a common evolutionary origin are known as homologous.  Development  Biochemistry: Biochemical analysis of animals similar in appearance have yielded surprising results. For example, although guinea pigs were once considered to be rodents, like mice, biochemistry led them to be in their taxon of their own. Phylogeny, Cladistics & Cladogram Modern taxonomy is based on many hypotheses' of the evolutionary history of organisms, known as phylogeny. As with the Scientific Method, scientists develop a hypothesis on the history of an animal and utilise modern science and technology to prove the phylogeny. Cladistics is a classification system which is based on phylogeny. Expanding on phylogeny, cladistics is based on the assumption that each group of related species has one common ancestor and would therefore retain some ancestral characteristics. Moreover, as these related species evolve and diverge from their common ancestor, they would develop unique characteristics. Such characteristics are known as derived characteristics The principles of phylogeny and cladistics can be expressed visually as a cladogram, a branching diagram which acts as a family (phylogenetic) tree for similar species. A cladogram can also be used to test alternative hypotheses for an animal's phylogeny. In order to determine the most likely cladogram, the derived characteristics of similar species are matched and analysed.

CELL Prokaryotes are single-celled organisms that are the earliest and most primitive forms of life on earth. As organized in the Three Domain System, prokaryotes include bacteria and archaeans. Prokaryotes are able to live and thrive in various types of environments including extreme habitats such as hydrothermal vents, hot springs, swamps, wetlands, and the guts of animals.

Prokaryotic Cell Structure

Prokaryotic cells are not as complex as eukaryotic cells. They have no true nucleus as the DNA is not contained within a membrane or separated from the rest of the cell, but is coiled up in a region of the cytoplasm called the nucleoid. Using bacteria as our sample prokaryote, the following structures can be found in bacterial cells:

 Capsule - Found in some bacterial cells, this additional outer covering protects the cell when it is engulfed by other organisms, assists in retaining moisture, and helps the cell adhere to surfaces and nutrients.

 Cell Wall - Outer covering of most cells that protects the bacterial cell and gives it shape.

 Cytoplasm - A gel-like substance composed mainly of water that also contains enzymes, salts, cell components, and various organic molecules.

 Cell Membrane or Plasma Membrane - Surrounds the cell's cytoplasm and regulates the flow of substances in and out of the cell.

 Pili - Hair-like structures on the surface of the cell that attach to other bacterial cells. Shorter pili called fimbriae help bacteria attach to surfaces.

 Flagella - Long, whip-like protrusion that aids in cellular locomotion.

 Ribosomes - Cell structures responsible for protein production.

 Plasmids - Gene carrying, circular DNA structures that are not involved in reproduction.

 Nucleiod Region - Area of the cytoplasm that contains the single bacterial DNA molecule.

ANIMAL cell

The cell membrane is located around the outside of the cell. It is a protein lipid bilayer. The hydrophilic heads of the lipids point outwards while the hydrophobic tails occupy the space between the two lipid layers. Several types of proteins are imbedded in the membrane: channel, transport, recognition, receptor, and electron transfer. Channel proteins provide passageways through the membrane for small substances to diffuse through. Transport proteins are involved in the active transport of substances across the membrane. Recognition proteins recognize other cells. Receptor proteins are receptor sites for hormones and other chemicals. Electron transfer proteins are involved in the transfer of electrons in processes like photosynthesis and cellular respiration. Because the proteins constantly shift throughout the cell membrane, it is referred to as a fluid mosaic model. The functions of the cell membrane include: holding cellular material, regulating the movement of materials across the membrane, providing a surface for many chemical reactions, and identifying the cell to the body's immune system.

Cell junctions connect one cell to another. Gap junctions are found in animals and are very, very small channels that allow various ions and other small substances to pass from one cell to another. Tight junctions are seals around cells to prevent leakage. They are important for containing liquids like stomach acids. Desmosomes are spot welds that hold cells together.

The nucleus controls the cell's activities and contains all the genetic material (46 chromosomes in humans).

The nucleolus is involved in the synthesis of ribosomal RNA. It is a dark body inside the nucleus.

The nuclear membrane keeps DNA inside the nucleus but allows mRNA and proteins through. It is a double membrane with large pores.

Ribosomes assemble proteins from RNA codes. They are found free-floating in the cytoplasm throughout the cell or attached to the endoplasmic reticulum.

The smooth endoplasmic reticulum is a series of long canals running throughout the cell. It detoxifies the cell and converts foodstuffs.

The rough endoplasmic reticulum is a series of long canals running throughout the cell with ribosomes attached. It transports proteins to the golgi bodies for packaging.

Golgi bodies (also apparatus or complex) store and package cellular secretions for export out of the cell (usually through the use of vacuoles). Salivary, oil, and digestive glands have very active golgi bodies.

Lysosomes digest and remove worn out cell organelles. In essence, they are vacuoles filled with digestive enzymes.

Mitochondria produce most of the cell's energy. They are composed of two membranes (an outer and a folded inner membrane) and are common in muscle cells.

Centrioles anchor spindle fibers during cell division. They are composed of microtubules and are only found in animal cells.

The cell's cytoskeleton provides the cell with shape and support. It is involved in cell movement (cytoplasmic streaming, muscle contraction, ameboid movement, and cell division). The cytoskeleton is composed of actin filaments, intermediate filaments, and microtubules.

Vacuoles are "bubbles" of material in the cell. Usually vacuoles hold water. They can, however, hold solutions and solid material as well.

Some cells have microvilli to aid in movement or absorption. Differences between plant and animal cell

Animal Cell Plant Cell Cell wall: Absent Present Shape: Round (irregular shape) Rectangular (fixed shape) One or more small vacuoles One, large central vacuole Vacuole: (much smaller than plant cells). taking up 90% of cell volume. Only present in lower plant Centrioles: Present in all animal cells forms. Plant cells have chloroplasts Animal cells don't have Chloroplast: because they make their own chloroplasts food Cytoplasm: Present Present EndoplasmicReticulum Present Present (Smooth and Rough): Ribosomes: Present Present Mitochondria: Present Present Plastids: Absent Present Golgi Apparatus: Present Present Plasma Membrane: only cell membrane cell wall and a cell membrane Microtubules/ Microfilaments: Present Present Flagella: May be found in some cells May be found in some cells Lysosomes: Lysosomesoccur in cytoplasm. Lysosomes usually not evident. Nucleus: Present Present Cilia: Present It is very rare Eukaryotes vs Prokaryotes

Eukaryotic Cell Prokaryotic Cell Nucleus: Present Absent Number of One--but not true More than one chromosomes: chromosome: Plasmids Cell Type: Multicellular Unicellular True Membrane bound Present Absent Nucleus: Example: Animals and Plants Bacteria and Archaea Circular DNA doesn't need Telomeres: Present (Linear DNA) telomeres Genetic Partial, undirectional Mitosis and fusion of gametes Recombination: transfers DNA Lysosomes and Present Absent peroxisomes: Microtubules: Present Absent or rare Endoplasmic Present Absent reticulum: Mitochondria: Present Absent Cytoskeleton: Present May be absent DNA wrapping on Yes No proteins.: Ribosomes: larger smaller Vesicles: Present Present Golgi apparatus: Present Absent Mitosis: Yes No---but has binary fission Absent; chlorophyll Chloroplasts: Present (in plants) scattered in the cytoplasm Microscopic in size; membrane bound; Submicroscopic in size, Flagella: usually arranged as nine doublets composed of only one fiber surrounding two singlets Permeability of Selective not present Nuclear Membrane: Plasma membrane Yes Usually no with steriod: Usually chemically Cell wall: Only in plant cells (chemically simpler) complexed Vacuoles: Present Present Cell size: 10-100um 1-10um Classification of Living Things Practice Questions 1. If taxonomists had to select an existing kingdom to reclassify, which of the six would most likely be chosen? Why? 2. Complete the following without consulting external sources: a) The species caudatum is in the family Paramecidae. What would be the binomial name of this organism? b) Give the abbreviation of the binomial name. 3. a) Irish moss belongs to the genus Chondrus. The name for this species is crispus. Give the binomial name. b) Give the abbreviation of the binomial name. 4. Humans and chimpanzees are alike. Which of the following data would most accurately prove this correct? a) biochemistry b) DNA c) appearance d) development e) A, B, C 5. Which of the following is out of order? a) Kingdom --> Phyllum --> Class b) Class --> Family --> Order c) Family --> Order --> Genus d) Genus --> Species e) A, C f) A, B, D g) B, C 6. A taxonomist discovers Organism A and Organism B and wishes to classify them. Which of the following choices is the most informative? a) Both organisms are brown. b) Both organisms have a tail. c) Both organisms have ears. d) Both organisms are nocturnal. 7. DNA analysis is usually done using DNA found in a cell's mitochondria, and not in a cell's nucleus. From your knowledge of mitosis, explain why this is so. 1. Arachbacteria 3.a) Chondrus crispus b) C. cripus 4. B 5. G 6. B