Biology

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Escherichia coli Tree fern

Gazelle Goliath beetle

Biology is the study of the many varieties of life (clockwise from top-left) E. coli, tree fern, gazelle, Goliath beetle.

 

Biology (from Greek βιολογία - βίος, bios, "life"; -λογία, -logia, study of) is the science that studies living organisms. Prior to the nineteenth century biology came under the general study of all natural objects called natural history. The term biology was first coined by the French naturalist Jean-Baptiste Lamarck. It is now a standard subject of instruction at schools and universities around the world, and over a million papers are published annually in a wide array of biology and medicine journals.  Biology examines the structure, function, growth, origin, evolution, distribution and classification of all living things. Five unifying principles form the foundation of modern biology: cell theory, evolution, gene theory, energy, and homeostasis.

 

Traditionally, the specialized disciplines of biology are grouped by the type of organism being studied: botany, the study of plants; zoology, the study of animals; and microbiology, the study of microorganisms. These fields are further divided based on the scale at which organisms are studied and the methods used to study them: biochemistry examines the fundamental chemistry of life, molecular biology studies the complex interactions of systems of biological molecules, cellular biology examines the basic building block of all life, the cell; physiology examines the physical and chemical functions of the tissues and organ systems of an organism; and ecology examines how various organisms interrelate with their environment.

 

Foundations of modern biology

 

There are five unifying principles of biology:

  • Cell theory. Cell Theory is the study of everything that involves respiration and tissues. All living organisms have parents and are made of at least one cell, the basic unit of function in all organisms. In addition, the core mechanisms and chemistry of all cells in all organisms are similar, and cells emerge only from preexisting cells that multiply through cell division. Cell theory studies how cells are made, how they reproduce, how they interact with their environment, what they are composed of, and how the materials that make up a cell work and interact with other cell sections.
  • Evolution. Through natural selection and genetic drift, a population's inherited traits change from generation to generation.
  • Gene theory. A living organism's traits are encoded in DNA, the fundamental component of genes. In addition, traits are passed on from one generation to the next by way of these genes. All information transfers from the genotype to the phenotype, the observable physical or biochemical characteristics of the organism. Although the phenotype expressed by the gene may adapt to the environment of the organism, that information is not transferred back to the genes. Only through the process of evolution do genes change in response to the environment.
  • Homeostasis. The physiological processes that allow an organism to maintain its internal environment notwithstanding its external environment.
  • Energy. The attribute of any living organism that is essential for its state. (e.g. required for metabolism)

 

Cell Theory

 

Cell theory states that:

  • The cell is the fundamental unit of life.
  • All living things are composed of one or more cells or the secreted products of those cells, such as shells.
  • Cells arise from other cells through cell division.
  • In multi-cellular organisms, every cell in the organism's body is produced from a single cell in a fertilized egg.
  • The cell is considered to be the basic part of the pathological processes of an organism.

 

Evolution

 

A central organizing concept in biology is that life changes and develops through evolution and that all life-forms known have a common origin. Introduced into the scientific lexicon by Jean-Baptiste de Lamarck in 1809, Charles Darwin established evolution fifty years later as a viable theory by articulating its driving force: natural selection (Alfred Russel Wallace is recognized as the co-discoverer of this concept as he helped research and experiment with the concept of evolution). Darwin theorized that species and breeds developed through the processes of natural selection and artificial selection or selective breeding.  Genetic drift was embraced as an additional mechanism of evolutionary development in the modern synthesis of the theory.

 

The evolutionary history of the species— which describes the characteristics of the various species from which it descended— together with its genealogical relationship to every other species is called its phylogeny. Widely varied approaches to biology generate information about phylogeny. These include the comparisons of DNA sequences conducted within molecular biology or genomics, and comparisons of fossils or other records of ancient organisms in paleontology. Biologists organize and analyze evolutionary relationships through various methods, including phylogenetics, phenetics, and cladistics. For a summary of major events in the evolution of life as currently understood by biologists, see evolutionary timeline.

 

Up into the 19th century, spontaneous generation, the belief that life forms could appear spontaneously under certain conditions, was widely believed. This misconception was challenged by William Harvey's diction that "all life [is] from [an] egg" (from the Latin "Omne vivum ex ovo"), a foundational concept of modern biology. It means that there is an unbroken continuity of life from its initial origin to the present time.

 

A group of organisms share a common descent if they share a common ancestor. All organisms on the Earth both living and extinct have been or are descended from a common ancestor or an ancestral gene pool. This last universal common ancestor of all organisms is believed to have appeared about 3.5 billion years ago.  Biologists generally regard the universality of the genetic code as definitive evidence in favor of the theory of universal common descent for all bacteria, archaea, and eukaryotes.

 

Evolution does not always give rise to progressively more complex organisms. For example, the process of dysgenics has been observed among the human population.

 

Gene theory

 

Biological form and the corresponding human protein.

 

The total protein or catalytic protein

 

Homeostasis

 

Homeostasis is the ability of an open system to regulate its internal environment to maintain a stable condition by means of multiple dynamic equilibrium adjustments controlled by interrelated regulation mechanisms. All living organisms, whether unicellular or multi-cellular, exhibit homeostasis. Homeostasis exists at the cellular level, for example cells maintain a stable internal acidity (pH); and at the level of the organism, for example warm-blooded animals maintain a constant internal body temperature. Homeostasis is a term that is also used in association with ecosystems, for example, the roots of plants help prevent soil from eroding, which helps to maintain the ecosystem. Tissues and organs can also maintain homeostasis.

 

Energy

 

The survival of a living organism depends on the continuous input of energy. Chemical reactions that are responsible for its structure and function are tuned to extract energy from substances that act as its food and transform them to form new cells and sustain them. In this process, molecules of chemical substances that constitute food play two roles; first, they contain energy that can be transformed for biological chemical reactions; and also develop molecular structures made up of biomolecules.

 

Nearly all of the energy needed for life processes originates from the Sun, which plants and other autotrophs convert into chemical energy (organic molecules) via photosynthesis in the presence of water and minerals. A few ecosystems, however, depend entirely on energy extracted from methane, sulfides, or other inorganic molecules by chemosynthetic microorganisms. Some of the captured energy is used to produce biomass to sustain life and provide energy for its growth and development. A part of this energy is lost as heat and waste molecules. The common processes for converting energy in chemical substances into energy useful to sustain life are metabolism and respiration.

 

Research

 

Structural

 

Molecular biology is the study of biology at a molecular level. This field overlaps with other areas of biology, particularly with genetics and biochemistry. Molecular biology chiefly concerns itself with understanding the interactions between the various systems of a cell, including the interrelationship of DNA, RNA, and protein synthesis and learning how these interactions are regulated.

 

Cell biology studies the physiological properties of cells, as well as their behaviors, interactions, and environment. This is done both on a microscopic and molecular level. Cell biology researches both single-celled organisms like bacteria and specialized cells in multi-cellular organisms like humans.

 

animal cell

Schematic of typical animal cell depicting the various organelles and structures

 

 

Understanding cell composition and how they function is fundamental to all of the biological sciences. Appreciating the similarities and differences between cell types is particularly important in the fields of cell and molecular biology. These fundamental similarities and differences provide a unifying theme, allowing the principles learned from studying one cell type to be extrapolated and generalized to other cell types.

 

Genetics is the science of genes, heredity, and the variation of organisms. Genes encode the information necessary for synthesizing proteins, which in turn play a large role in influencing (though, in many instances, not completely determining) the final phenotype of the organism. In modern research, genetics provides important tools in the investigation of the function of a particular gene, or the analysis of genetic interactions. Within organisms, genetic information generally is carried in chromosomes, where it is represented in the chemical structure of particular DNA molecules.

 

Developmental biology studies the process by which organisms grow and develop. Originating in embryology, modern developmental biology studies the genetic control of cell growth, differentiation, and "morphogenesis," which is the process that gives rise to tissues, organs, and anatomy. Model organisms for developmental biology include the round worm Caenorhabditis elegans, the fruit fly Drosophila melanogaster, the zebrafish Brachydanio rerio, the mouse Mus musculus, and the weed Arabidopsis thaliana.

 

Physiological

 

Physiology studies the mechanical, physical, and biochemical processes of living organisms by attempting to understand how all of the structures function as a whole. The theme of "structure to function" is central to biology. Physiological studies have traditionally been divided into plant physiology and animal physiology, but the principles of physiology are universal, no matter what particular organism is being studied. For example, what is learned about the physiology of yeast cells can also apply to human cells. The field of animal physiology extends the tools and methods of human physiology to non-human species. Plant physiology also borrows techniques from both fields.

 

Anatomy is an important branch of physiology and considers how organ systems in animals, such as the nervous, immune, endocrine, respiratory, and circulatory systems, function and interact. The study of these systems is shared with medically oriented disciplines such as neurology and immunology.

 

Evolution

 

In population genetics the evolution of a population of organisms is sometimes depicted as if travelling on a fitness landscape. The arrows indicate the preferred flow of a population on the landscape, and the points A, B, and C are local optima. The red ball indicates a population that moves from a very low fitness value to the top of a peak.

 

Evolution is concerned with the origin and descent of species, as well as their change over time, and includes scientists from many taxonomically-oriented disciplines. For example, it generally involves scientists who have special training in particular organisms such as mammalogy, ornithology, botany, or herpetology, but use those organisms as systems to answer general questions about evolution. Evolutionary biology is mainly based on paleontology, which uses the fossil record to answer questions about the mode and tempo of evolution, as well as the developments in areas such as population genetics and evolutionary theory. In the 1980s, developmental biology re-entered evolutionary biology from its initial exclusion from the modern synthesis through the study of evolutionary developmental biology. Related fields which are often considered part of evolutionary biology are phylogenetics, systematics, and taxonomy.

 

population genetics

In population genetics the evolution of a population of organisms is sometimes depicted as if traveling on a fitness landscape.  The arrows indicate the preferred flow of a population of the landscape, and the points A, B, and C are local optima.  The red ball indicates a population that moves from a very low fitness value to the top of a peak.

 

Up into the 19th century, it was believed that life forms were being continuously created under certain conditions. This misconception was challenged by William Harvey's diction that "all life [is] from [an] egg" (from the Latin "Omne vivum ex ovo"), a foundational concept of modern biology. It simply means that there is an unbroken continuity of life from its initial origin to the present time.

 

A group of organisms shares a common descent if they share a common ancestor. All organisms on the Earth have been and are descended from a common ancestor or an ancestral gene pool. This last universal common ancestor of all organisms is believed to have appeared about 3.5 billion years ago. Biologists generally regard the universality of the genetic code as definitive evidence in favor of the theory of universal common descent (UCD) for all bacteria, archaea, and eukaryotes.

 

The two major traditional taxonomically-oriented disciplines are botany and zoology. Botany is the scientific study of plants. Botany covers a wide range of scientific disciplines that study the growth, reproduction, metabolism, development, diseases, and evolution of plant life. Zoology involves the study of animals, including the study of their physiology within the fields of anatomy and embryology. The common genetic and developmental mechanisms of animals and plants are studied in molecular biology, molecular genetics, and developmental biology. The ecology of animals is covered under behavioral ecology and other fields.

 

Taxonomy

 

 Phylogenetic Tree of Life

A phylogenetic tree of all living things, based on rRNA gene data, showing the separation of the three domains bacteria, archaea, and eukaryotes as described initially by Carl Woese. Trees constructed with other genes are generally similar, although they may place some early-branching groups very differently, presumably owing to rapid rRNA evolution. The exact relationships of the three domains are still being debated.

 

 

 

Classification is the province of the disciplines of systematics and taxonomy. Taxonomy places organisms in groups called taxa, while systematics seeks to define their relationships with each other. This classification technique has evolved to reflect advances in cladistics and genetics, shifting the focus from physical similarities and shared characteristics to phylogenetics.

 

Traditionally, living things have been divided into five kingdoms:

1.    Monera

2.    Protista

3.    Fungi

4.    Plantae

5.     Animalia

 

However, many scientists now consider this five-kingdom system to be outdated. Modern alternative classification systems generally begin with the three-domain system:

1.    Archaea (originally Archaebacteria)

2.    Bacteria (originally Eubacteria)

3.    Eukarya (including protists, fungi, plants, and animals.)

 

These domains reflect whether the cells have nuclei or not, as well as differences in the cell exteriors.

 

Further, each kingdom is broken down continuously until each species is separately classified. The order is:

1.    Domain

2.    Kingdom

3.    Phylum

4.    Class

5.    Order

6.    Family

7.    Genus

8.    Species

 

There is also a series of intracellular parasites that are progressively "less alive" in terms of metabolic activity:

1.    Viruses

2.    Viroids

3.    Prions

 

The scientific name of an organism is obtained from its genus and species. For example, humans would be listed as Homo sapiens. Homo would be the genus and sapiens is the species. Whenever writing the scientific name of an organism, it is proper to capitalize the first letter in the genus and put all of the species in lowercase. Additionally, the entire term would be italicized or underlined.

 

The dominant classification system is called Linnaean taxonomy, which includes ranks and binomial nomenclature. How organisms are named is governed by international agreements such as the International Code of Botanical Nomenclature (ICBN), the International Code of Zoological Nomenclature (ICZN), and the International Code of Nomenclature of Bacteria (ICNB). A fourth Draft BioCode was published in 1997 in an attempt to standardize naming in these three areas, but it has yet to be formally adopted. The Virus International Code of Virus Classification and Nomenclature (ICVCN) remains outside the BioCode.

 

Ecology

 

Ecology studies the distribution and abundance of living organisms, and the interactions between organisms and their environment. The environment of an organism includes both its habitat, which can be described as the sum of local abiotic factors such as climate and ecology, as well as the other organisms that share its habitat. Ecological systems are studied at several different levels, from individuals and populations to ecosystems and the biosphere. The term population biology is often used interchangeably with population ecology, although the term with biology is more frequently used when studying diseases, viruses, and microbes, and the term with ecology is used when studying plants and animals. As can be surmised, ecology is a science that draws on several disciplines.

 

Ethology studies animal behavior (particularly of social animals such as primates and canids), and is sometimes considered a branch of zoology. Ethologists have been particularly concerned with the evolution of behavior and the understanding of behavior in terms of the theory of natural selection. In one sense, the first modern ethologist was Charles Darwin, whose book "The Expression of the Emotions in Man and Animals" influenced many ethologists.

 

Biogeography studies the spatial distribution of organisms on the Earth, focusing on topics like plate tectonics, climate change, dispersal and migration, and cladistics.

 

Every living thing interacts with other organisms and its environment. One reason that biological systems can be difficult to study is that so many different interactions with other organisms and the environment are possible, even on the smallest of scales. A microscopic bacterium responding to a local sugar gradient is responding to its environment as much as a lion is responding to its environment when it searches for food in the African savannah. For any given species, behaviors can be co-operative, aggressive, parasitic or symbiotic. Matters become more complex when two or more different species interact in an ecosystem. Studies of this type are the province of ecology.

 

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