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Organism
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In biology, an organism is any living thing (such as animal, plant, fungus, or micro-organism). In at least some form, all organisms are capable of response to stimuli, reproduction, growth and development, and maintenance of homeostasis as a stable whole. An organism may either be unicellular (single-celled) or be composed of, as in humans, many billions of cells grouped into specialized tissues and organs. The term multicellular (many-celled) describes any organism made up of more than one cell.
The term "organism" (Greek ???a??sµ?? - organismos, from Ancient Greek ???a??? - organon "organ, instrument, tool") first appeared in the English language in 1701 and took on its current definition by 1834 (Oxford English Dictionary).
Organisms may be divided into the prokaryotic and eukaryotic groups.
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Encyclopedia
In biology, an organism is any living thing (such as animal, plant, fungus, or micro-organism). In at least some form, all organisms are capable of response to stimuli, reproduction, growth and development, and maintenance of homeostasis as a stable whole. An organism may either be unicellular (single-celled) or be composed of, as in humans, many billions of cells grouped into specialized tissues and organs. The term multicellular (many-celled) describes any organism made up of more than one cell.
The term "organism" (Greek ???a??sµ?? - organismos, from Ancient Greek ???a??? - organon "organ, instrument, tool") first appeared in the English language in 1701 and took on its current definition by 1834 (Oxford English Dictionary).
Organisms may be divided into the prokaryotic and eukaryotic groups. The prokaryotes represent two separate domains, the Bacteria and Archaea. All fungi, animals and plants are eukaryotes.
The word "organism" may broadly be defined as an assembly of molecules that function as a more or less stable whole and has the properties of life. However, many sources propose definitions that exclude viruses and theoretically-possible man-made non-organic life forms. Viruses are dependent on the biochemical machinery of a host cell for reproduction.
Chambers Online Reference provides a broad definition: "any living structure, such as a plant, animal, fungus or bacterium, capable of growth and reproduction".
In multicellular life the word "organism" usually describes the whole hierarchical assemblage of systems (for example circulatory, digestive, or reproductive) themselves collections of organs; these are, in turn, collections of tissues, which are themselves made of cells. In some plants and the nematode Caenorhabditis elegans, individual cells are totipotent.
Viruses
Viruses are not typically considered to be organisms because they are incapable of "independent" reproduction or metabolism. This controversy is problematic, though, since some parasites and endosymbionts are also incapable of independent life. Although viruses have a few enzymes and molecules characteristic of living organisms, they are incapable of reproducing outside a host cell and most of their metabolic processes require a host and its 'genetic machinery' such as organelles in eukaryotic hosts and the assemblage of ready-made enzymes (which the virus cannot make by itself) in prokaryotic hosts. While viruses sustain no independent metabolism, and thus are usually not accounted organisms, they do have their own genes and they do evolve by the same mechanisms by which organisms evolve.
Superorganism
A superorganism is an organism consisting of many individuals working together as a single functional or social unit. Ants, and other eusocial invertebrates such as termites, are examples of superorganisms that form large colonies of individuals with highly specialised roles and division of labor. Individuals may be unable to reproduce or to survive for extended periods of time when separated from the colony. By working cooperatively, superorganisms can achieve feats that comparable solitary organisms cannot. Thermoregulation, for example, does not occur in individuals or small groups of honeybees or other invertebrates, but colonies of bees with more than about 5000 individuals can thermoregulate. James Lovelock, with his "Gaia Theory" has paralleled the work of Vladimir Vernadsky, who suggested the whole of the biosphere in some respects can be considered as a superorganism.
The concept of superorganism is under dispute, as many biologists maintain that in order for a social unit to be considered an organism by itself, the individuals should be in permanent physical connection to each other, and its evolution should be governed by selection to the whole society instead of individuals. While it's generally accepted that the society of eusocial animals is a unit of natural selection to at least some extent, most evolutionists claim that the individuals are still the primary units of selection.
The question remains "What is to be considered the individual?". Advocates of evolution like Richard Dawkins suggest that the individual selected is the "Selfish Gene". Others believe it is the whole genome of an organism. E.O. Wilson has shown that with ant-colonies and other social insects it is the breeding entity of the colony that is selected, and not its individual members. This could apply to the bacterial members of a stromatolite, which, because of genetic sharing, in some way comprise a single gene pool. Gaian theorists like Lynn Margulis would argue this applies equally to the symbiogenesis of the bacterial underpinnings of the whole of the Earth.
It would appear, from computer simulations like Daisyworld that biological selection occurs at multiple levels simultaneously.
It is also argued that humans are actually a superorganism that includes microorganisms such as bacteria. It is estimated that "the human intestinal microbiota is composed of 1013 to 1014 microorganisms whose collective genome ("microbiome") contains at least 100 times as many genes as our own[...] Our microbiome has significantly enriched metabolism of glycans, amino acids, and xenobiotics; methanogenesis; and 2-methyl-D-erythritol 4-phosphate pathway–mediated biosynthesis of vitamins and isoprenoids. Thus, humans are superorganisms whose metabolism represents an amalgamation of microbial and human attributes." . An NIH-coordinated and -funded effort is currently in progress to characterize the human microbiome.
Organizational terminology
All organisms are classified by the science of alpha taxonomy into either taxa or clades.
Taxa are ranked groups of organisms which run from the general (domain) to the specific (species). A broad scheme of ranks in hierarchical order is:
To give an example, Homo sapiens is the Latin binomial equating to modern humans. All members of the species sapiens are, at least in theory, genetically able to interbreed. Several species may belong to a genus, but the members of different species within a genus are unable to interbreed to produce fertile offspring. Homo, however, only has one surviving species (sapiens); Homo erectus, Homo neanderthalensis, &c. having become extinct thousands of years ago. Several genera belong to the same family and so on up the hierarchy. Eventually, the relevant kingdom (Animalia, in the case of humans) is placed into one of the three domains depending upon certain genetic and structural characteristics.
All living organisms known to science are given classification by this system such that the species within a particular family are more closely related and genetically similar than the species within a particular phylum.
Chemistry
Organisms are complex chemical systems, organized in ways that promote reproduction and some measure of sustainability or survival. The molecular phenomena of chemistry are fundamental in understanding organisms, but it is a philosophical error (reductionism) to reduce organismal biology to mere chemistry. It is generally the phenomena of entire organisms that determine their fitness to an environment and therefore the survivability of their DNA based genes.
Organisms clearly owe their origin, metabolism, and many other internal functions to chemical phenomena, especially the chemistry of large organic molecules. Organisms are complex systems of chemical compounds which, through interaction with each other and the environment, play a wide variety of roles.
Organisms are semi-closed chemical systems. Although they are individual units of life (as the definition requires) they are not closed to the environment around them. To operate they constantly take in and release energy. Autotrophs produce usable energy (in the form of organic compounds) using light from the sun or inorganic compounds while heterotrophs take in organic compounds from the environment.
The primary chemical element in these compounds is carbon. The physical properties of this element such as its great affinity for bonding with other small atoms, including other carbon atoms, and its small size makes it capable of forming multiple bonds, make it ideal as the basis of organic life. It is able to form small compounds containing three atoms (such as carbon dioxide) as well as large chains of many thousands of atoms which are able to store data (nucleic acids), hold cells together and transmit information (protein).
Macromolecules
The compounds which make up organisms may be divided into macromolecules and other, smaller molecules. The four groups of macromolecule are nucleic acids, proteins, carbohydrates and lipids. Nucleic acids (specifically deoxyribonucleic acid, or DNA) store genetic data as a sequence of nucleotides. The particular sequence of the four different types of nucleotides (adenine, cytosine, guanine, and thymine) dictate the many characteristics which constitute the organism. The sequence is divided up into codons, each of which is a particular sequence of three nucleotides and corresponds to a particular amino acid. Thus a sequence of DNA codes for a particular protein which, due to the chemical properties of the amino acids of which it is made, folds in a particular manner and so performs a particular function.
The following functions of protein have been recognized:
- Enzymes, which catalyze all of the reactions of metabolism;
- Structural proteins, such as tubulin, or collagen;
- Regulatory proteins, such as transcription factors or cyclins that regulate the cell cycle;
- Signaling molecules or their receptors such as some hormones and their receptors;
- Defensive proteins, which can include everything from antibodies of the immune system, to toxins (e.g., dendrotoxins of snakes), to proteins that include unusual amino acids like canavanine.
Lipids make up the membrane of cells which constitutes a barrier, containing everything within the cell and preventing compounds from freely passing into, and out of, the cell. In some multi-cellular organisms they serve to store energy and mediate communication between cells. Carbohydrates also store and transport energy in some organisms, but are more easily broken down than lipids.
Structure
All organisms consist of monomeric units called cells; some contain a single cell (unicellular) and others contain many units (multicellular). Multicellular organisms are able to specialize cells to perform specific functions, a group of such cells is tissue the four basic types of which are epithelium, nervous tissue, muscle tissue and connective tissue. Several types of tissue work together in the form of an organ to produce a particular function (such as the pumping of the blood by the heart, or as a barrier to the environment as the skin). This pattern continues to a higher level with several organs functioning as an organ system to allow for reproduction, digestion, &c. Many multicelled organisms comprise of several organ systems which coordinate to allow for life.
The cell
The cell theory, first developed in 1839 by Schleiden and Schwann, states that all organisms are composed of one or more cells; all cells come from preexisting cells; all vital functions of an organism occur within cells, and cells contain the hereditary information necessary for regulating cell functions and for transmitting information to the next generation of cells.
There are two types of cells, eukaryotic and prokaryotic. Prokaryotic cells are usually singletons, while eukaryotic cells are usually found in multi-cellular organisms. Prokaryotic cells lack a nuclear membrane so DNA is unbound within the cell, eukaryotic cells have nuclear membranes.
All cells, whether prokaryotic oreukaryotic, have a membrane, which envelops the cell, separates its interior from its environment, regulates what moves in and out, and maintains the electric potential of the cell. Inside the membrane, a salty cytoplasm takes up most of the cell volume. All cells possess DNA, the hereditary material of genes, and RNA, containing the information necessary to build various proteins such as enzymes, the cell's primary machinery. There are also other kinds of biomolecules in cells.
All cells share several abilities:
Life span
One of the basic parameters of organism is its life span. Some organisms live as short as one day, while some plants can live thousands of years. Aging is important when determining life span of most organisms, bacterium, a virus or even a prion.
Evolution
In biology, the theory of universal common descent proposes that all organisms on Earth are descended from a common ancestor or ancestral gene pool. Evidence for common descent may be found in traits shared between all living organisms. In Darwin's day, the evidence of shared traits was based solely on visible observation of morphologic similarities, such as the fact that all birds have wings, even those which do not fly.
Today, there is debate over whether or not all organisms descended from a common ancestor, or a "last universal ancestor" (LUA), also called the "last universal common ancestor" (LUCA). The universality of genetic coding suggests common ancestry. For example, every living cell makes use of nucleic acids as its genetic material, and uses the same twenty amino acids as the building blocks for proteins, although exceptions to the basic twenty amino acids have been found. However, throughout history different species of organisms have often evolved with the same biological traits in unrelated lineages that are not descended from a common ancestor (see convergent evolution).
The "last universal ancestor" (LUA), or "last universal common ancestor" (LUCA), is the name given to the hypothetical single cellular organism or single cell that gave rise to all life on Earth 3.5 to 3.8 billion years ago; however, this hypothesis has since been refuted on many grounds. For example, it was once thought that the genetic code was universal (see: universal genetic code), but many variations have been discovered including various alternative mitochondrial codes. Back in the early 1970s, evolutionary biologists thought that a given piece of DNA specified the same protein subunit in every living thing, and that the genetic code was thus universal. This was interpreted as evidence that every organism had inherited its genetic code from a single common ancestor, aka, an LUCA. In 1979, however, exceptions to the code were found in mitochondria, the tiny energy factories inside cells. Researchers studying human mitochondrial genes discovered that they used an alternative code, and many slight variants have been discovered since, including various alternative mitochondrial codes, as well as small variants such as Mycoplasma translating the codon UGA as tryptophan. Biologists subsequently found exceptions in bacteria and in the nuclei of algae and single-celled animals. For example, certain proteins may use alternative initiation (start) codons not normally used by that species. In certain proteins, non-standard amino acids are substituted for standard stop codons, depending upon associated signal sequences in the messenger RNA: UGA can code for selenocysteine and UAG can code for pyrrolysine. Selenocysteine is now viewed as the 21st amino acid, and pyrrolysine is viewed as the 22nd. A detailed description of variations in the genetic code can be found at the .
It is now clear that the genetic code is not the same in all living things and this provides credence that all living things did not evolve on a firmly-rooted tree of life from a single LUCA. Further support that there is no LUCA has been provided over the years by horizontal/lateral gene transfer in both prokaryote and eukaryote single cell organisms. This is why phylogenetic trees cannot be rooted; why almost all phylogenetic trees have different branching structures, particularly near the base of the tree; and why many organisms have been found with codons and sections of their DNA sequence that are sometimes unrelated to other species.
Information about the early development of life includes input from many different fields, including geology and planetary science. These sciences provide information about the history of the Earth and the changes produced by life. However, a great deal of information about the early Earth has been destroyed by geological processes over the course of time.
History of life
The chemical evolution from self-catalytic chemical reactions to life (see Origin of life) is not a part of biological evolution, but it is unclear at which point such increasingly complex sets of reactions became what we would consider, today, to be living organisms.
Not much is known about the earliest developments in life. However, all existing organisms share certain traits, including cellular structure and genetic code. Most scientists interpret this to mean all existing organisms share a common ancestor, which had already developed the most fundamental cellular processes, but there is no scientific consensus on the relationship of the three domains of life (Archaea, Bacteria, Eukaryota) or the origin of life. Attempts to shed light on the earliest history of life generally focus on the behavior of macromolecules, particularly RNA, and the behavior of complex systems.
The emergence of oxygenic photosynthesis (around 3 billion years ago) and the subsequent emergence of an oxygen-rich, non-reducing atmosphere can be traced through the formation of banded iron deposits, and later red beds of iron oxides. This was a necessary prerequisite for the development of aerobic cellular respiration, believed to have emerged around 2 billion years ago.
In the last billion years, simple multicellular plants and animals began to appear in the oceans. Soon after the emergence of the first animals, the Cambrian explosion (a period of unrivaled and remarkable, but brief, organismal diversity documented in the fossils found at the Burgess Shale) saw the creation of all the major body plans, or phyla, of modern animals. This event is now believed to have been triggered by the development of the Hox genes. About 500 million years ago, plants and fungi colonized the land, and were soon followed by arthropods and other animals, leading to the development of land ecosystems with which we are familiar.
The evolutionary process may be exceedingly slow. Fossil evidence indicates that the diversity and complexity of modern life has developed over much of the history of the earth. Geological evidence indicates that the Earth is approximately 4.6 billion years old. Studies on guppies by David Reznick at the University of California, Riverside, however, have shown that the rate of evolution through natural selection can proceed 10 thousand to 10 million times faster than what is indicated in the fossil record.. Such comparative studies however are invariably biased by disparities in the time scales over which evolutionary change is measured in the laboratory, field experiments, and the fossil record.
Horizontal gene transfer, and the history of life
The ancestry of living organisms has traditionally been reconstructed from morphology, but is increasingly supplemented with phylogenetics - the reconstruction of phylogenies by the comparison of genetic (DNA) sequence.
"Sequence comparisons suggest recent horizontal transfer of many genes among diverse species including across the boundaries of phylogenetic 'domains'. Thus determining the phylogenetic history of a species can not be done conclusively by determining evolutionary trees for single genes."
Biologist Gogarten suggests "the original metaphor of a tree no longer fits the data from recent genome research", therefore "biologists [should] use the metaphor of a mosaic to describe the different histories combined in individual genomes and use [the] metaphor of a net to visualize the rich exchange and cooperative effects of HGT among microbes."
Future of life (cloning and synthetic organisms)
In modern terms, the category of organism cloning refers to the procedure of creating a new multicellular organism, genetically identical to another. However, cloning also has the potential of creating entirely new species of organisms. Organism cloning is the subject of much ethical debate (see Bioethics, Ethics of cloning, and Designer baby articles).
The J. Craig Venter Institute has recently assembled a synthetic yeast genome, Mycoplasma genitalium, by recombination of 25 overlapping DNA fragments in a single step. "The use of yeast recombination greatly simplifies the assembly of large DNA molecules from both synthetic and natural fragments." Other companies, such as Synthetic Genomics, have already been formed to take advantage of the many commercial uses of custom designed genomes.
External links
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- Hesiocaeca methanicola In 1997, Charles Fisher, professor of biology at Penn State, discovered this remarkable creature living on mounds of methane ice under half a mile of ocean on the floor of the Gulf of Mexico.
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- Citat: "Number of kingdoms has not been resolved...Bacteria present a problem with their diversity...Protista present a problem with their diversity...",
- . Species 2000 has the objective of enumerating all known species of plants, animals, fungi and microbes on Earth as the baseline dataset for studies of global biodiversity. It will also provide a simple access point enabling users to link from here to other data systems for all groups of organisms, using direct species-links.
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