Botany

Botany, plant science(s), phytology, or plant biology is a branch of biology that involves the scientific study of plant life. Botany covers a wide range of scientific disciplines concerned with the study of plants, algae and fungi, including structure, growth, reproduction, metabolism, development, diseases, chemical properties, and evolutionary relationships among taxonomic groups. Botany began with early human efforts to identify edible, medicinal and poisonous plants, making it one of the oldest sciences. Today botanists study over 550,000 species of living organisms.

Scope and importance of botany

Hibiscus
As with other life forms in biology, plant life can be studied from different perspectives, from the molecular, genetic and biochemical level through organelles, cells, tissues, organs, individuals, plant populations, and communities of plants. At each of these levels a botanist might be concerned with the classification (taxonomy), structure (anatomy and morphology), or function (physiology) of plant life.
Historically all living things were grouped as animals or plants, and botany covered all organisms not considered animals. Some organisms once included in the field of botany are no longer considered to belong to the plant kingdom – these include fungi (studied in mycology), lichens (lichenology), bacteria (bacteriology), viruses (virology) and single-celled algae, which are now grouped as part of the Protista. However, attention is still given to these groups by botanists, and fungi, lichens, bacteria and photosynthetic protists are usually covered in introductory botany courses.
The study of plants is vital because they are a fundamental part of life on Earth, which generates the oxygen, food, fibres, fuel and medicine that allow humans and other life forms to exist. Through photosynthesis, plants absorb carbon dioxide, a greenhouse gas that in large amounts can affect global climate. Additionally, they prevent soil erosion and are influential in the water cycle. A good understanding of plants is crucial to the future of human societies as it allows us to:

    Produce food to feed an expanding population
    Understand fundamental life processes
    Produce medicine and materials to treat diseases and other ailments
    Understand environmental changes more clearly

Paleobotanists study ancient plants in the fossil record. It is believed that early in the Earth's history, the evolution of photosynthetic plants altered the global atmosphere of the earth, changing the ancient atmosphere by oxidation.

Human nutrition

Nearly all the food we eat comes (directly and indirectly) from 

plants like this American long grain rice
Virtually all foods eaten come from plants, either directly from staple foods and other fruit and vegetables, or indirectly through livestock or other animals, which rely on plants for their nutrition. Plants are the fundamental base of nearly all food chains because they use the energy from the sun and nutrients from the soil and atmosphere, converting them into a form that can be consumed and utilized by animals; this is what ecologists call the first trophic level. Botanists also study how plants produce food we can eat and how to increase yields and therefore their work is important in mankind's ability to feed the world and provide food security for future generations, for example, through plant breeding. Botanists also study weeds, plants which are considered to be a nuisance in a particular location. Weeds are a considerable problem in agriculture, and botany provides some of the basic science used to understand how to minimize 'weed' impact in agriculture and native ecosystems. Ethnobotany is the study of the relationships between plants and people.
Fundamental life processes
Plants are convenient organisms in which fundamental life processes (like cell division and protein synthesis) can be studied, without the ethical dilemmas of studying animals or humans. The genetic laws of inheritanceGregor Mendel, who was studying the way pea shape is inherited. What Mendel learned from studying plants has had far reaching benefits outside of botany. Additionally, Barbara McClintock discovered 'jumping genes' by studying maize. These are a few examples that demonstrate how botanical research has an ongoing relevance to the understanding of fundamental biological processes. were discovered in this way by
Medicine and materials
Many medicinal and recreational drugs, like tetrahydrocannabinol, caffeine, and nicotine come directly from the plant kingdom. Others are simple derivatives of botanical natural products; for example, aspirin is based on the pain killer salicylic acid which originally came from the bark of willow trees. As well, the narcoticanalgesics such as morphine are derived from the opium poppy. There may be many novel cures for diseasesstimulants like coffee, chocolate, tobacco, and tea also come from plants. Most alcoholic beverages come from fermenting plants such as barley (beer), rice (sake) and grapes (wine). provided by plants, waiting to be discovered. Popular
Plants also provide us with many natural materials, such as hemp, cotton, wood, paper, linen, vegetable oils, some types of rope, and rubber. The production of silk would not be possible without the cultivation of the mulberry plant. Sugarcane, rapeseed, soy and other plants with a highly fermentable sugar or oil content have recently been put to use as sources of biofuels, which are important alternatives to fossil fuels (see biodiesel).
Environmental changes
Plants can also help us understand changes in on our environment in many ways.

    Understanding habitat destruction and species extinction is dependent on an accurate and complete catalog of plant systematics and taxonomy.
    Plant responses to ultraviolet radiation can help us monitor problems like ozone depletion.
    Analyzing pollen deposited by plants thousands or millions of years ago can help scientists to reconstruct past climates and predict future ones, an essential part of climate change research.
    Recording and analyzing the timing of plant life cycles are important parts of phenology used in climate-change research.
    Lichens, which are sensitive to atmospheric conditions, have been extensively used as pollution indicators.

In many different ways, plants can act a little like the 'miners' canary', an early warning system alerting us to important changes in our environment. In addition to these practical and scientific reasons, plants are extremely valuable as recreation for millions of people who enjoy gardening, horticultural and culinary uses of plants every day.

Etymology

From Greek βοτάνη = "pasture, grass, fodder", perhaps via the idea of a livestock keeper needing to know which plants are safe for livestock to eat.

History

 

The traditional tools of a botanist
Early botany

Ancient India

Early examples of plant taxonomy occur in the Rigveda, that divides plants into Vṛska (tree), Osadhi (herbs useful to humans) and Virudha (creepers), which are then further subdivided. The Atharvaveda divides plants into eight classes, Visakha (spreading branches), Manjari (leaves with long clusters), Sthambini (bushy plants), Prastanavati (which expands); Ekasṛnga (those with monopodial growth), Pratanavati (creeping plants), Amsumati (with many stalks), and Kandini (plants with knotty joints). The Taittiriya Samhitavṛksa, vana and druma (trees), visakha (shrubs with spreading branches), sasa (herbs), amsumali (a spreading or deliquescent plant), vratati (climber), stambini (bushy plant), pratanavati (creeper), and alasala (those spreading on the ground). classifies the plant kingdom into
Manusmriti – Law book of Hindus – proposed a classification of plants in eight major categories. Charaka Samhitā and Sushruta Samhita and the Vaisesikas also present an elaborate taxonomy.
Parashara, the author of Vṛksayurveda (the science of life of trees), classifies plants into Dvimatrka (Dicotyledons) and Ekamatrka (Monocotyledons). These are further classified into Samiganiya (Fabaceae), Puplikagalniya (Rutaceae), Svastikaganiya (Cruciferae), Tripuspaganiya (Cucurbitaceae), MallikaganiyaApocynaceae), and Kurcapuspaganiya (Asteraceae). (
Important medieval Indian works of plant physiology include the Prthviniraparyam of Udayana, Nyayavindutika of Dharmottara, Saddarsana-samuccaya of Gunaratna, and Upaskara of Sankaramisra.

Ancient Iranic people

The knowledge of medical plants and botany was considered as secret and holy by the ancient Iranic people. There is evidence of such practices in the documents that have survived from the ancient Zoroastrian writings. The practice and use of botany for medical purposes as well as various Iranic cousins and traditions is still common to this day amongst the Iranic people of the Central Asia, Near East and Europe.

Ancient China

In ancient China, the recorded listing of different plants and herb concoctions for pharmaceutical purposes spans back to at least the Warring States (481 BC-221 BC). Many Chinese writers over the centuries contributed to the written knowledge of herbal pharmaceutics. There was the Han Dynasty (202 BC-220 AD) written work of the Huangdi Neijing and the famous pharmacologist Zhang Zhongjing of the 2nd century. There was also the 11th century scientists and statesmen Su Song and Shen Kuo, who compiled treatises on herbal medicine and included the use of mineralogy.

Greco-Roman world

Among the earliest of botanical works in Europe, written around 300 B.C., are two large treatises by Theophrastus: On the History of Plants (Historia Plantarum) and On the Causes of Plants. Together these books constitute the most important contribution to botanical science during antiquity and on into the Middle Ages. Aristotle also wrote about plants. One theory about plants that Greco-Romans came up with about plants was that they ate soil for nutrients.
The Roman medical writer Pedanius Dioscorides (ca.40-90) provides important evidence on Greek and Roman knowledge of medicinal plants. Dioscorides is famous for writing a five volume book in his native Greek Περί ύλης ιατρικής (De Materia Medica - in the Latin translation) that is one of the most influential herbal books in history. In fact, it remained in use until about CE 1600. Approximately 1300-1400 different plant species were known under Roman reign. 

Medieval botany

The earliest known work from the Muslim world dedicated to the study of agriculture was Ibn Wahshiyya's Nabatean Agriculture, which also dealt with the related field of botany and was also an early cookbook.
The Kurdish biologist Abū Ḥanīfa Dīnawarī (828-896) is considered the founder of Arabic botany for his Book of Plants, in which he described at least 637 plants and discussed plant development from germination to death, describing the phases of plant growth and the production of flowers and fruit.
Theophrastus’s Historia Plantarum served as a reference point in botany for many centuries, and was further developed around 1200 A.D. by Giovanni Bodeo da Stapelio, who added a commentarius and drawings: see Historia Plantarum —Selected pages of a 17th century edition of the 1200 A.D. version (in Italian).
Ibn Bassal is known for his famous work named The Classification of Soils. Al-Asma'i was the earliest known Arab biologist, botanist and zoologist. al-Masihi was the first to recognize the science of Botany.[citation needed]
In the early 13th century, the Andalusian-Arabian biologist Abu al-Abbas al-Nabati developed an early scientific method for botany, introducing empirical and experimental techniques in the testing, description and identification of numerous materia medica, and separating unverified reports from those supported by actual tests and observations.His student Ibn al-Baitar (d. 1248) wrote a pharmaceutical encyclopedia describing 1,400 plants, foods, and drugs, 300 of which were his own original discoveries. A Latin translation of his work was useful to European biologists and pharmacists in the 18th and 19th centuries.

Early modern botany

Crantz's Classis cruciformium..., 1769
German physician Leonhart Fuchs (1501–1566) was one of the three founding fathers of botany, along with Otto Brunfels (1489- 1534) and Hieronymus Bock (1498–1554) (also called Hieronymus Tragus)
Valerius Cordus (1515–1554) authored one of the greatest pharmacopoeias and one of the most celebrated herbals in history, Dispensatorium (1546). As early as the 16th century, the Italian Ulisse Aldrovandi was scientifically researching plants. In 1665, using an early microscope, Robert Hooke discovered cells in cork, and a short time later in living plant tissue. The Germans Jacob Theodor Klein and Leonhart Fuchs, the Swiss Conrad von Gesner, and the British author Nicholas Culpeper published herbals that gave information on the medicinal uses of plants.
During the 18th century systems of classification became deliberately artificial and served only for the purpose of identification. These classifications are comparable to diagnostic keys, where taxa are artificially grouped in pairs by few, easily recognisable characters. The sequence of the taxa in keys is often totally unrelated to their natural or phyletic groupings. In the 18th century an increasing number of new plants had arrived in Europe, from newly discovered countries and the European colonies worldwide, and a larger amount of plants became available for study.
In 1754 Carl von Linné (Carl Linnaeus) divided the plant Kingdom into 25 classes. One, the Cryptogamia, included all the plants with concealed reproductive parts (algae, fungi, mosses and liverworts and ferns).more natural affinities between plants, than the sexual system of Linnaeus indicated. Adanson (1763), de JussieuCandolle (1819) all proposed various alternative natural systems that were widely followed. The ideas of natural selection as a mechanism for evolution required adaptations to the Candollean system, which started the studies on evolutionary relationships and phylogenetic classifications of plants. (1789),

Modern botany

A considerable amount of new knowledge today is being generated from studying model plants like Arabidopsis thaliana. This weedy species in the mustard family was one of the first plants to have its genomerice (Oryza sativa) genome, its relatively small genome, and a large international research community have made rice an important cereal/grass/monocot model.[13] Another grass species, Brachypodium distachyon is also emerging as an experimental model for understanding the genetic, cellular and molecular biology of temperate grasses. Other commercially important staple foods like wheat, maize, barley, rye, pearl millet and soybean are also having their genomes sequenced. Some of these are challenging to sequence because they have more than two haploid (n) sets of chromosomes, a condition known as polyploidy, common in the plant kingdom. Chlamydomonas reinhardtii (a single-celled, green alga) is another plant model organism that has been extensively studied and provided important insights into cell biology. sequenced. The sequencing of the
In 1998 the Angiosperm Phylogeny Group published a phylogeny of flowering plants based on an analysis of DNA sequences from most families of flowering plants. As a result of this work, major questions such as which families represent the earliest branches in the genealogy of angiosperms are now understood. Investigating how plant species are related to each other allows botanists to better understand the process of evolution in plants.

Subdisciplines of botany

Agronomy — Application of plant science to crop production     Bryology — Mosses, liverworts, and hornworts     Economic botany — Study of plants of economic use or value     Ethnobotany — Relationship between humans and plants     Forestry — Forest management and related studies     Horticulture — Cultivated plants     Lichenology — The study of lichens     Paleobotany — Fossil plants     Palynology — Pollen and spores         Phycology — Algae     Phytochemistry — Plant secondary chemistry and chemical processes     Phytopathology — Plant diseases     Plant anatomy — Cell and tissue structure     Plant ecology — Role of plants in the environment     Plant genetics — Genetic inheritance in plants     Plant morphology — Structure and life cycles     Plant physiology — Life functions of plants     Plant systematics — Classification and naming of plants

Notable botanists

    Ibn al-Baitar (d. 1248), Andalusian-Arab scientist, botanist, pharmacist, physician, and author of one of the largest botanical encyclopedias.
    L.J.F. Brimble (1904–1965), English botanist and editor of Nature magazine
    Abu al-Abbas al-Nabati (c. 1200), Andalusian-Arab botanist and agricultural scientist, and a pioneer in experimental botany.
    Aimé Bonpland (1773–1858), French explorer and botanist, who accompanied Alexander von Humboldt during five years of travel in Latin America.
    Luther Burbank (1849–1926), American botanist, horticulturist, and a pioneer in agricultural science.
    Augustin Pyramus de Candolle (1778–1841), He originated the idea of "Nature's war", which influenced Charles Darwin.
    Abū Ḥanīfa Dīnawarī (828-896), Persian botanist, historian, geographer, astronomer, mathematician, and founder of Arabic botany.
    David Douglas (1799–1834), Scottish botanical explorer of North America and China, who imported many ornamental plants into Europe.
    Joseph Dalton Hooker (1817–1911), English botanist and explorer. Second winner of Darwin Medal.
    Pedanius Dioscorides (ca. 40-90 AD), physician, pharmacologist, toxicologist and botanist, author of Περὶ ὕλης ἰατρικής (Latin: De Materia Medica, English: "Regarding Medical Matters")
    Thomas Henry Huxley (1825–1895), English biologist, known as "Darwin's Bulldog" for his advocacy of Charles Darwin's theory of evolution. Third winner of Darwin Medal.
    Carl Linnaeus (1707–1778), Swedish botanist, physician and zoologist who laid the foundations for the modern scheme of Binomial nomenclature. He is known as the father of modern taxonomy, and is also considered one of the fathers of modern ecology.
    Gregor Johann Mendel (1822–1884), Augustinian priest and scientist, and is often called the father of genetics for his study of the inheritance of traits in pea plants.
    Charles Sprague Sargent (1841–1927), American botanist, the first director of the Arnold ArboretumHarvard University. at
    Carlos Muñoz Pizarro (1913–1976), Chilean botanist, known for his studies of the Chilean flora, and its conservation.
    Richard Spruce (1817–1893), English botanist and explorer who carried out a detailed study of the Amazon flora.
    Agustín Stahl (1842–1917), conducted investigations and experiments in the fields of ethnology, and zoology in the Caribbean region.
    George Ledyard Stebbins, Jr. (1906–2000), widely regarded as one of the leading evolutionary biologists of the 20th century, developed a comprehensive synthesis of plant evolution incorporating genetics.
    Theophrastus (c. 371 – c. 287 BC), father of botany, established botanical science through his lecture notes, Enquiry into Plants.
    Leonardo da Vinci (1452–1519), Italian polymath; a scientist, mathematician, engineer, inventor, anatomist, painter, sculptor, architect, botanist, musician and writer.

Cell biology

Cell biology (formerly cytology, from the Greek kytos, "container") is an academic discipline that studies cells – their physiological properties, their structure, the organelles they contain, interactions with their environment, their life cycle, division and death. This is done both on a microscopic and molecular level. Cell biology research encompasses both the great diversity of single-celled organisms like bacteria and protozoa, as well as the many specialized cells in multicellular organisms such as humans.

Knowing the components of cells and how cells work is fundamental to all biological sciences. Appreciating the similarities and differences between cell types is particularly important to the fields of cell and molecular biology as well as to biomedical fields such as cancer research and developmental biology. These fundamental similarities and differences provide a unifying theme, sometimes allowing the principles learned from studying one cell type to be extrapolated and generalized to other cell types. Hence, research in cell biology is closely related to genetics, biochemistry, molecular biology, immunology, and developmental biology.

Processes

Movement of proteins

Endothelial cells under the microscope. Nuclei are stained blue with DAPI, microtubles are marked green by an antibody and actin filaments are labelled red with phalloidin.

Each type of protein is usually sent to a particular part of the cell. An important part of cell biology is the investigation of molecular mechanisms by which proteins are moved to different places inside cells or secreted from cells.

Most proteins are synthesized by ribosomes in the cytoplasm. This process is known as protein biosynthesis. Biosynthesis (also called biogenesis) is an enzyme-catalyzed process in cells of living organisms by which substrates are converted to more complex products (also simply known as protein translation). Some proteins, such as those to be incorporated in membranes (known as membrane proteins), are transported into the "rough" endoplasmic reticulum (ER) during synthesis. This process can be followed by transportation and processing in the Golgi apparatus. From the Golgi, membrane proteins can move to the plasma membrane, to other sub-cellular compartments, or they can be secreted from the cell. The ER and Golgi can be thought of as the "membrane protein synthesis compartment" and the "membrane protein processing compartment", respectively. There is a semi-constant flux of proteins through these compartments. ER and Golgi-resident proteins associate with other proteins but remain in their respective compartments. Other proteins "flow" through the ER and Golgi to the plasma membrane. Motor proteins transport membrane protein-containing vesicles along cytoskeletal tracks to distant parts of cells such as axon terminals.

Some proteins that are made in the cytoplasm contain structural features that target them for transport into mitochondria or the nucleus. Some mitochondrial proteins are made inside mitochondria and are coded for by mitochondrial DNA. In plants, chloroplasts also make some cell proteins.

Extracellular and cell surface proteins destined to be degraded can move back into intracellular compartments upon being incorporated into endocytosed vesicles some of which fuse with lysosomes where the proteins are broken down to their individual amino acids. The degradation of some membrane proteins begins while still at the cell surface when they are cleaved by secretases. Proteins that function in the cytoplasm are often degraded by proteasomes.

Other cellular processes

• Active transport and Passive transport - Movement of molecules into and out of cells.
• Autophagy - The process whereby cells "eat" their own internal components or microbial invaders.
• Adhesion - Holding together cells and tissues.
• Reproduction - Made possible by the combination of sperm made in the testiculi(contained in some male cells nucleus') and the egg made in the ovary(contained in the nucleus of a female cell). When the sperm breaks through the hard outer shell of the egg a new cell embryo is formed, which, in humans, grows to full size in 9 months.
• Cell movement: Chemotaxis, Contraction, cilia and flagella.
• Cell signaling - Regulation of cell behavior by signals from outside.
• DNA repair and Cell death
• Metabolism: Glycolysis, respiration, Photosynthesis
• Transcription and mRNA splicing - gene expression.

Internal cellular structures

Electron micrograph.

• Chloroplast - key organelle for photosynthesis (only found in plant cells)
• Cilia - motile microtubule-containing structures of eukaryotes
• Cytoplasm - contents of the main fluid-filled space inside cells
• Cytoskeleton - protein filaments inside cells
• Endoplasmic reticulum - major site of membrane protein synthesis
• Flagella - motile structures of bacteria, archaea and eukaryotes
• Golgi apparatus - site of protein glycosylation in the endomembrane system
• Lipid bilayer - fundamental organizational structure of cell membranes
• Membrane lipid and protein barrier
• Mitochondrion - major energy-producing organelle by releasing it in the form of ATP
• Nucleus - holds most of the DNA of eukaryotic cells and controls all cellular activities
• Organelle - term used for major subcellular structures
• Ribosome - RNA and protein complex required for protein synthesis in cells
• Vesicle - small membrane-bounded spheres inside cells

Techniques used to study cells

Cells may be observed under the microscope. This includes the Optical Microscope, Transmission Electron Microscope, Scanning Electron Microscope, Fluorescence Microscope, and by Confocal Microscopy.

Several different techniques exist to study cells.

• Cell culture is the basic technique of growing cells in a laboratory independent of an organism.
• Immunostaining, also known as immunohistochemistry, is a specialized histological method used to localize proteins in cells or tissue slices. Unlike regular histology, which uses stains to identify cells, cellular components or protein classes, immunostaining requires the reaction of an antibody directed against the protein of interest within the tissue or cell. Through the use of proper controls and published protocols (need to add reference links here), specificity of the antibody-antigen reaction can be achieved. Once this complex is formed, it is identified via either a "tag" attached directly to the antibody, or added in an additional technical step. Commonly used "tags" include fluorophores or enzymes. In the case of the former, detection of the location of the "immuno-stained" protein occurs via fluorescence microscopy. With an enzymatic tag, such as horse radish peroxidase, a chemical reaction is carried out that results in a dark color in the location of the protein of interest. This darkened pattern is then detected using light microscopy.
• Computational genomics is used to find patterns in genomic information
• DNA microarrays identify changes in transcript levels between different experimental conditions.
• Gene knockdown mutates a selected gene.
• In situ hybridization shows which cells are expressing a particular RNA transcript.
• PCR can be used to determine how many copies of a gene are present in a cell.
• Transfection introduces a new gene into a cell, usually an expression construct

Purification of cells and their parts Purification may be performed using the following methods:

• Cell fractionation
  • Release of cellular organelles by disruption of cells.
  • Separation of different organelles by centrifugation.
• Flow cytometry
• Immunoprecipitation
• Proteins extracted from cell membranes by detergents and salts or other kinds of chemicals.

Biophysics

Biophysics is an interdisciplinary science that uses the methods of physical science to study biological systems. Studies included under the branches of biophysics span all levels of biological organization, from the molecular scale to whole organisms and ecosystems. Biophysical research shares significant overlap with biochemistry, nanotechnology, bioengineering, agrophysics and systems biology.

Molecular biophysics typically addresses biological questions that are similar to those in biochemistry and molecular biology, but the questions are approached quantitatively. Scientists in this field conduct research concerned with understanding the interactions between the various systems of a cell, including the interactions between DNA, RNA and protein biosynthesis, as well as how these interactions are regulated. A great variety of techniques are used to answer these questions.

Fluorescent imaging techniques, as well as electron microscopy, x-ray crystallography, NMR spectroscopy and atomic force microscopy (AFM) are often used to visualize structures of biological significance. Conformational change in structure can be measured using techniques such as dual polarisation interferometry and circular dichroism. Direct manipulation of molecules using optical tweezers or AFM can also be used to monitor biological events where forces and distances are at the nanoscale. Molecular biophysicists often consider complex biological events as systems of interacting units which can be understood through statistical mechanics, thermodynamics and chemical kinetics. By drawing knowledge and experimental techniques from a wide variety of disciplines, biophysicists are often able to directly observe, model or even manipulate the structures and interactions of individual molecules or complexes of molecules.

In addition to traditional (i.e. molecular and cellular) biophysical topics like structural biology or enzyme kinetics, modern biophysics encompasses an extraordinarily broad range of research. It is becoming increasingly common for biophysicists to apply the models and experimental techniques derived from physics, as well as mathematics and statistics, to larger systems such as tissues, organs, populations and ecosystems.

Focus as a subfield

Biophysics often does not have university-level departments of its own, but has presence as groups across departments within the fields of molecular biology, biochemistry, chemistry, computer science, mathematics, medicine, pharmacology, physiology, physics, and neuroscience. What follows is a list of examples of how each department applies its efforts toward the study of biophysics. This list is hardly all inclusive. Nor does each subject of study belong exclusively to any particular department. Each academic institution makes its own rules and there is much overlap between departments.

• Biology and molecular biology - Almost all forms of biophysics efforts are included in some biology department somewhere. To include some: gene regulation, single protein dynamics, bioenergetics, patch clamping, biomechanics.
• Structural biology - Ångstrom-resolution structures of proteins, nucleic acids, lipids, carbohydrates, and complexes thereof.
• Biochemistry and chemistry - biomolecular structure, siRNA, nucleic acid structure, structure-activity relationships.
• Computer science - Neural networks, biomolecular and drug databases.
• Computational chemistry - molecular dynamics simulation, molecular docking, quantum chemistry
• Bioinformatics - sequence alignment, structural alignment, protein structure prediction
• Mathematics - graph/network theory, population modeling, dynamical systems, phylogenetics.
• Medicine and neuroscience - tackling neural networks experimentally (brain slicing) as well as theoretically (computer models), membrane permitivity, gene therapy, understanding tumors.
• Pharmacology and physiology - channel biology, biomolecular interactions, cellular membranes, polyketides.
• Physics - biomolecular free energy, stochastic processes, covering dynamics.
• Quantum biophysics involves quantum information processing of coherent states, entanglement between coherent protons and transcriptase components, and replication of decohered isomers to yield time-dependent base substitutions. These studies imply applications in quantum computing.
• Agronomy Agriculture

Many biophysical techniques are unique to this field. Research efforts in biophysics are often initiated by scientists who were traditional physicists, chemists, and biologists by training.

Bioinformatics

Bioinformatics is the application of statistics and computer science to the field of molecular biology.

The term bioinformatics was coined by Paulien Hogeweg in 1979 for the study of informatic processes in biotic systems. Its primary use since at least the late 1980s has been in genomics and genetics, particularly in those areas of genomics involving large-scale DNA sequencing.

Bioinformatics now entails the creation and advancement of databases, algorithms, computational and statistical techniques and theory to solve formal and practical problems arising from the management and analysis of biological data.

Over the past few decades rapid developments in genomic and other molecular research technologies and developments in information technologies have combined to produce a tremendous amount of information related to molecular biology. It is the name given to these mathematical and computing approaches used to glean understanding of biological processes.

Common activities in bioinformatics include mapping and analyzing DNA and protein sequences, aligning different DNA and protein sequences to compare them and creating and viewing 3-D models of protein structures.

The primary goal of bioinformatics is to increase the understanding of biological processes. What sets it apart from other approaches, however, is its focus on developing and applying computationally intensive techniques (e.g., pattern recognition, data mining, machine learning algorithms, and visualization) to achieve this goal. Major research efforts in the field include sequence alignment, gene finding, genome assembly, drug design, drug discovery, protein structure alignment, protein structure prediction, prediction of gene expression and protein-protein interactions, genome-wide association studies and the modeling of evolution.

Introduction

Bioinformatics was applied in the creation and maintenance of a database to store biological information at the beginning of the "genomic revolution", such as nucleotide and amino acid sequences. Development of this type of database involved not only design issues but the development of complex interfaces whereby researchers could both access existing data as well as submit new or revised data.

In order to study how normal cellular activities are altered in different disease states, the biological data must be combined to form a comprehensive picture of these activities. Therefore, the field of bioinformatics has evolved such that the most pressing task now involves the analysis and interpretation of various types of data, including nucleotide and amino acid sequences, protein domains, and protein structures. The actual process of analyzing and interpreting data is referred to as computational biology. Important sub-disciplines within bioinformatics and computational biology include:

• the development and implementation of tools that enable efficient access to, and use and management of, various types of information.
• the development of new algorithms (mathematical formulas) and statistics with which to assess relationships among members of large data sets, such as methods to locate a gene within a sequence, predict protein structure and/or function, and cluster protein sequences into families of related sequences.

Major research areas

Sequence analysis

Since the Phage Φ-X174 was sequenced in 1977, the DNA sequences of thousands of organisms have been decoded and stored in databases. This sequence information is analyzed to determine genes that encode polypeptides (proteins), RNA genes, regulatory sequences, structural motifs, and repetitive sequences. A comparison of genes within a species or between different species can show similarities between protein functions, or relations between species (the use of molecular systematics to construct phylogenetic trees). With the growing amount of data, it long ago became impractical to analyze DNA sequences manually. Today, computer programs such as BLAST are used daily to search the genomes of thousands of organisms, containing billions of nucleotides. These programs can compensate for mutations (exchanged, deleted or inserted bases) in the DNA sequence, in order to identify sequences that are related, but not identical. A variant of this sequence alignment is used in the sequencing process itself. The so-called shotgun sequencing technique (which was used, for example, by The Institute for Genomic Research to sequence the first bacterial genome, Haemophilus influenzae) does not produce entire chromosomes, but instead generates the sequences of many thousands of small DNA fragments (ranging from 35 to 900 nucleotides long, depending on the sequencing technology). The ends of these fragments overlap and, when aligned properly by a genome assembly program, can be used to reconstruct the complete genome. Shotgun sequencing yields sequence data quickly, but the task of assembling the fragments can be quite complicated for larger genomes. For a genome as large as the human genome, it may take many days of CPU time on large-memory, multiprocessor computers to assemble the fragments, and the resulting assembly will usually contain numerous gaps that have to be filled in later. Shotgun sequencing is the method of choice for virtually all genomes sequenced today, and genome assembly algorithms are a critical area of bioinformatics research.

Another aspect of bioinformatics in sequence analysis is annotation, which involves computational gene finding to search for protein-coding genes, RNA genes, and other functional sequences within a genome. Not all of the nucleotides within a genome are part of genes. Within the genome of higher organisms, large parts of the DNA do not serve any obvious purpose. This so-called junk DNA may, however, contain unrecognized functional elements. Bioinformatics helps to bridge the gap between genome and proteome projects--for example, in the use of DNA sequences for protein identification.
See also: sequence analysis, sequence profiling tool, and sequence motif
Genome annotation

In the context of genomics, annotation is the process of marking the genes and other biological features in a DNA sequence. The first genome annotation software system was designed in 1995 by Dr. Owen White, who was part of the team at The Institute for Genomic Research that sequenced and analyzed the first genome of a free-living organism to be decoded, the bacterium Haemophilus influenzae. Dr. White built a software system to find the genes (places in the DNA sequence that encode a protein), the transfer RNA, and other features, and to make initial assignments of function to those genes. Most current genome annotation systems work similarly, but the programs available for analysis of genomic DNA are constantly changing and improving.
Computational evolutionary biology

Evolutionary biology is the study of the origin and descent of species, as well as their change over time. Informatics has assisted evolutionary biologists in several key ways; it has enabled researchers to:

    * trace the evolution of a large number of organisms by measuring changes in their DNA, rather than through physical taxonomy or physiological observations alone,
    * more recently, compare entire genomes, which permits the study of more complex evolutionary events, such as gene duplication, horizontal gene transfer, and the prediction of factors important in bacterial speciation,
    * build complex computational models of populations to predict the outcome of the system over time
    * track and share information on an increasingly large number of species and organisms

Future work endeavours to reconstruct the now more complex tree of life.

The area of research within computer science that uses genetic algorithms is sometimes confused with computational evolutionary biology, but the two areas are not necessarily related.
Analysis of gene expression

The expression of many genes can be determined by measuring mRNA levels with multiple techniques including microarrays, expressed cDNA sequence tag (EST) sequencing, serial analysis of gene expression (SAGE) tag sequencing, massively parallel signature sequencing (MPSS), or various applications of multiplexed in-situ hybridization. All of these techniques are extremely noise-prone and/or subject to bias in the biological measurement, and a major research area in computational biology involves developing statistical tools to separate signal from noise in high-throughput gene expression studies. Such studies are often used to determine the genes implicated in a disorder: one might compare microarray data from cancerous epithelial cells to data from non-cancerous cells to determine the transcripts that are up-regulated and down-regulated in a particular population of cancer cells.
Analysis of regulation

Regulation is the complex orchestration of events starting with an extracellular signal such as a hormone and leading to an increase or decrease in the activity of one or more proteins. Bioinformatics techniques have been applied to explore various steps in this process. For example, promoter analysis involves the identification and study of sequence motifs in the DNA surrounding the coding region of a gene. These motifs influence the extent to which that region is transcribed into mRNA. Expression data can be used to infer gene regulation: one might compare microarray data from a wide variety of states of an organism to form hypotheses about the genes involved in each state. In a single-cell organism, one might compare stages of the cell cycle, along with various stress conditions (heat shock, starvation, etc.). One can then apply clustering algorithms to that expression data to determine which genes are co-expressed. For example, the upstream regions (promoters) of co-expressed genes can be searched for over-represented regulatory elements.
Analysis of protein expression
Protein microarrays and high throughput (HT) mass spectrometry (MS) can provide a snapshot of the proteins present in a biological sample. Bioinformatics is very much involved in making sense of protein microarray and HT MS data; the former approach faces similar problems as with microarrays targeted at mRNA, the latter involves the problem of matching large amounts of mass data against predicted masses from protein sequence databases, and the complicated statistical analysis of samples where multiple, but incomplete peptides from each protein are detected.
Analysis of mutations in cancer

In cancer, the genomes of affected cells are rearranged in complex or even unpredictable ways. Massive sequencing efforts are used to identify previously unknown point mutations in a variety of genes in cancer. Bioinformaticians continue to produce specialized automated systems to manage the sheer volume of sequence data produced, and they create new algorithms and software to compare the sequencing results to the growing collection of human genome sequences and germline polymorphisms. New physical detection technologies are employed, such as oligonucleotide microarrays to identify chromosomal gains and losses (called comparative genomic hybridization), and single-nucleotide polymorphism arrays to detect known point mutations. These detection methods simultaneously measure several hundred thousand sites throughout the genome, and when used in high-throughput to measure thousands of samples, generate terabytes of data per experiment. Again the massive amounts and new types of data generate new opportunities for bioinformaticians. The data is often found to contain considerable variability, or noise, and thus Hidden Markov model and change-point analysis methods are being developed to infer real copy number changes.

Another type of data that requires novel informatics development is the analysis of lesions found to be recurrent among many tumors .
Prediction of protein structure

Protein structure prediction is another important application of bioinformatics. The amino acid sequence of a protein, the so-called primary structure, can be easily determined from the sequence on the gene that codes for it. In the vast majority of cases, this primary structure uniquely determines a structure in its native environment. (Of course, there are exceptions, such as the bovine spongiform encephalopathy - aka Mad Cow Disease - prion.) Knowledge of this structure is vital in understanding the function of the protein. For lack of better terms, structural information is usually classified as one of secondary, tertiary and quaternary structure. A viable general solution to such predictions remains an open problem. As of now, most efforts have been directed towards heuristics that work most of the time.

One of the key ideas in bioinformatics is the notion of homology. In the genomic branch of bioinformatics, homology is used to predict the function of a gene: if the sequence of gene A, whose function is known, is homologous to the sequence of gene B, whose function is unknown, one could infer that B may share A's function. In the structural branch of bioinformatics, homology is used to determine which parts of a protein are important in structure formation and interaction with other proteins. In a technique called homology modeling, this information is used to predict the structure of a protein once the structure of a homologous protein is known. This currently remains the only way to predict protein structures reliably.

One example of this is the similar protein homology between hemoglobin in humans and the hemoglobin in legumes (leghemoglobin). Both serve the same purpose of transporting oxygen in the organism. Though both of these proteins have completely different amino acid sequences, their protein structures are virtually identical, which reflects their near identical purposes.

Other techniques for predicting protein structure include protein threading and de novo (from scratch) physics-based modeling.


Comparative genomics

The core of comparative genome analysis is the establishment of the correspondence between genes (orthology analysis) or other genomic features in different organisms. It is these intergenomic maps that make it possible to trace the evolutionary processes responsible for the divergence of two genomes. A multitude of evolutionary events acting at various organizational levels shape genome evolution. At the lowest level, point mutations affect individual nucleotides. At a higher level, large chromosomal segments undergo duplication, lateral transfer, inversion, transposition, deletion and insertion. Ultimately, whole genomes are involved in processes of hybridization, polyploidization and endosymbiosis, often leading to rapid speciation. The complexity of genome evolution poses many exciting challenges to developers of mathematical models and algorithms, who have recourse to a spectra of algorithmic, statistical and mathematical techniques, ranging from exact, heuristics, fixed parameter and approximation algorithms for problems based on parsimony models to Markov Chain Monte Carlo algorithms for Bayesian analysis of problems based on probabilistic models.

Many of these studies are based on the homology detection and protein families computation.
Modeling biological systems

Systems biology involves the use of computer simulations of cellular subsystems (such as the networks of metabolites and enzymes which comprise metabolism, signal transduction pathways and gene regulatory networks) to both analyze and visualize the complex connections of these cellular processes. Artificial life or virtual evolution attempts to understand evolutionary processes via the computer simulation of simple (artificial) life forms.
High-throughput image analysis

Computational technologies are used to accelerate or fully automate the processing, quantification and analysis of large amounts of high-information-content biomedical imagery. Modern image analysis systems augment an observer's ability to make measurements from a large or complex set of images, by improving accuracy, objectivity, or speed. A fully developed analysis system may completely replace the observer. Although these systems are not unique to biomedical imagery, biomedical imaging is becoming more important for both diagnostics and research. Some examples are:

    * high-throughput and high-fidelity quantification and sub-cellular localization (high-content screening, cytohistopathology, Bioimage informatics)
    * morphometrics
    * clinical image analysis and visualization
    * determining the real-time air-flow patterns in breathing lungs of living animals
    * quantifying occlusion size in real-time imagery from the development of and recovery during arterial injury
    * making behavioral observations from extended video recordings of laboratory animals
    * infrared measurements for metabolic activity determination
    * inferring clone overlaps in DNA mapping, e.g. the Sulston score

Protein-protein docking

In the last two decades, tens of thousands of protein three-dimensional structures have been determined by X-ray crystallography and Protein nuclear magnetic resonance spectroscopy (protein NMR). One central question for the biological scientist is whether it is practical to predict possible protein-protein interactions only based on these 3D shapes, without doing protein-protein interaction experiments. A variety of methods have been developed to tackle the Protein-protein docking problem, though it seems that there is still much work to be done in this field.
Software and tools

Software tools for bioinformatics range from simple command-line tools, to more complex graphical programs and standalone web-services available from various bioinformatics companies or public institutions.
Web services in bioinformatics

SOAP and REST-based interfaces have been developed for a wide variety of bioinformatics applications allowing an application running on one computer in one part of the world to use algorithms, data and computing resources on servers in other parts of the world. The main advantages derive from the fact that end users do not have to deal with software and database maintenance overheads.

Basic bioinformatics services are classified by the EBI into three categories: SSS (Sequence Search Services), MSA (Multiple Sequence Alignment) and BSA (Biological Sequence Analysis). The availability of these service-oriented bioinformatics resources demonstrate the applicability of web based bioinformatics solutions, and range from a collection of standalone tools with a common data format under a single, standalone or web-based interface, to integrative, distributed and extensible bioinformatics workflow management systems.

Astrobiology

Astrobiology is the study of the origin, evolution, distribution, and future of life in the universe. Earth is the only known inhabited planet in the universe to date. However, advancements in the fields of astrobiology, observational astronomy and discovery of large varieties of extremophiles with extraordinary capability to thrive in harshest environments on Earth, have led to speculation that life may possibly be thriving on many of the extraterrestrial bodies in the universe. This interdisciplinary field encompasses the search for habitable environments in our Solar System and habitable planets outside our Solar System, the search for evidence of prebiotic chemistry, laboratory and field research into the origins and early evolution of life on Earth, and studies of the potential for life to adapt to challenges on Earth and in outer space.

Astrobiology makes use of physics, chemistry, astronomy, biology, molecular biology, ecology, planetary science, geography and geology to investigate the possibility of life on other worlds and help recognize biospheres that might be different from the Earth's. Astrobiology concerns itself with an interpretation of existing scientific data; given more detailed and reliable data from other parts of the Universe, the roots of astrobiology itself—physics, chemistry, and biology—may have their theoretical bases challenged. Although speculation is entertained to give context, astrobiology concerns itself primarily with hypotheses that fit firmly into existing scientific theories.

Overview

It is not known whether life elsewhere in the Universe would utilize cell structures like those found on Earth. (Chloroplasts within plant cells shown here.)

The Martian meteorite ALH84001 shows microscopic formations that may have been created by life.

Astrobiology is etymologically derived from the Greek ἄστρον, astron, "constellation, star"; βίος, bios, "life"; and -λογία, -logia, study. While it is an emerging and developing field, the question of whether life exists elsewhere in the universe is a verifiable hypothesis and thus a valid line of scientific inquiry. Though once considered outside the mainstream of scientific inquiry, astrobiology has become a formalized field of study. Planetary scientist David Grinspoon calls astrobiology a field of natural philosophy, grounding speculation on the unknown, in known scientific theory. NASA's interest in exobiology first began with the development of the U.S. Space Program. In 1959, NASA funded its first exobiology project, and in 1960, NASA founded an Exobiology Program; Exobiology research is now one of four elements of NASA's current Astrobiology Program.In 1971, NASA funded the Search for Extra-Terrestrial Intelligence (SETI) to search radio frequencies of the electromagnetic spectrum for signals being transmitted by extraterrestrial life outside the Solar System. NASA’s Viking missions to Mars, launched in 1976, included three biology experiments designed to look for possible signs of life. The Mars Pathfinder lander in 1997 carried a scientific payload intended for exopaleontology in the hopes of finding microbial fossils entombed in the rocks.

In the 21st century, astrobiology is a focus of a growing number of NASA and European Space Agency Solar System exploration missions. The first European workshop on astrobiology took place in May 2001 in Italy, and the outcome was the Aurora programme.Currently, NASA hosts the NASA Astrobiology Institute and a growing number of universities in the United States (e.g., University of Arizona, Penn State University, Montana State University and University of Washington), Britain (e.g., The University of Glamorgan), Canada, Ireland, and Australia (e.g., The University of New South Wales) now offer graduate degree programs in astrobiology.

A particular focus of current astrobiology research is the search for life on Mars due to its proximity to Earth and geological history. There is a growing body of evidence to suggest that Mars has previously had a considerable amount of water on its surface, water being considered an essential precursor to the development of carbon-based life.

Missions specifically designed to search for life include the Viking program and Beagle 2 probes, both directed to Mars. The Viking results were inconclusive, and Beagle 2 failed to transmit from the surface and is assumed to have crashed. A future mission with a strong astrobiology role would have been the Jupiter Icy Moons Orbiter, designed to study the frozen moons of Jupiter—some of which may have liquid water—had it not been cancelled. Recently, the Phoenix lander probed the environment for past and present planetary habitability of microbial life on Mars, and to research the history of water there.

In 2011, NASA plans to launch the Mars Science Laboratory rover which will continue the search for past or present life on Mars using a variety of scientific instruments. The European Space Agency has been developing the ExoMars astrobiology rover, which is to be launched on 2018.

The International Astronomical Union regularly organizes major international conferences through its Commission 51: Bioastronomy. Commission 51 - Bioastronomy: Search for Extraterrestrial Life was established by the IAU in 1982 and is now hosted by the Institute of Astronomy at the University of Hawai'i.

Methodology

Narrowing the task

When looking for life on other planets, some simplifying assumptions are useful to reduce the size of the task of the astrobiologist. One is to assume that the vast majority of life forms in our galaxy are based on carbon chemistries, as are all life forms on Earth. While it is possible that non-carbon-based life exists, carbon is well known for the unusually wide variety of molecules that can be formed around it.

This planetary habitability chart shows where life might exist on extrasolar planets based on our own Solar System and life on Earth.

The presence of liquid water is a useful assumption, as it is a common molecule and provides an excellent environment for the formation of complicated carbon-based molecules that could eventually lead to the emergence of life. Some researchers posit environments of ammonia, or more likely water-ammonia mixtures. These environments are considered suitable for carbon or noncarbon-based life, while opening more temperature ranges (and thus worlds) for life.

A third assumption is to focus on sun-like stars. This comes from the idea of planetary habitability. Very big stars have relatively short lifetimes, meaning that life would not likely have time to evolve on planets orbiting them. Very small stars provide so little heat and warmth that only planets in very close orbits around them would not be frozen solid, and in such close orbits these planets would be tidally "locked" to the star.Without a thick atmosphere, one side of the planet would be perpetually baked and the other perpetually frozen. In 2005, the question was brought back to the attention of the scientific community, as the long lifetimes of red dwarfs could allow some biology on planets with thick atmospheres. This is significant, as red dwarfs are extremely common. (See Habitability of red dwarf systems).

It is estimated that 10% of the stars in our galaxy are sun-like; There are about a thousand such stars within 100 light-years of our Sun. These stars would be useful primary targets for interstellar listening. Since Earth is the only planet known to harbor life, there is no evident way to know if any of the simplifying assumptions are correct.

Elements of astrobiology

Astronomy

Artist's impression of the extrasolar planet OGLE-2005-BLG-390Lb orbiting its star 20,000 light-years from Earth; this planet was discovered with gravitational microlensing.

The NASA Kepler mission, successfully launched in March 2009, searches for extrasolar planets

Most astronomy-related astrobiological research falls into the category of extrasolar planet (exoplanet) detection, the hypothesis being that if life arose on Earth, then it could also arise on other planets with similar characteristics. To that end, a number of instruments designed to detect Earth-like exoplanets are under development, most notably NASA's Terrestrial Planet Finder (TPF) and ESA's Darwin programs. Additionally, NASA has launched the Kepler mission in March 2009, and the French Space Agency has launched the COROT space mission in 2006. There are also several less ambitious ground-based efforts underway. (See exoplanet).

The goal of these missions is not only to detect Earth-sized planets, but also to directly detect light from the planet so that it may be studied spectroscopically. By examining planetary spectra, it would be possible to determine the basic composition of an extrasolar planet's atmosphere and/or surface; given this knowledge, it may be possible to assess the likelihood of life being found on that planet. A NASA research group, the Virtual Planet Laboratory, is using computer modeling to generate a wide variety of virtual planets to see what they would look like if viewed by TPF or Darwin. It is hoped that once these missions come online, their spectra can be cross-checked with these virtual planetary spectra for features that might indicate the presence of life. The photometry temporal variability of extrasolar planets may also provide clues to their surface and atmospheric properties.

An estimate for the number of planets with intelligent extraterrestrial life can be gleaned from the Drake equation, essentially an equation expressing the probability of intelligent life as the product of factors such as the fraction of planets that might be habitable and the fraction of planets on which life might arise: N = R^{*} ~ \times ~ f_{p} ~ \times ~ n_{e} ~ \times ~ f_{l} ~ \times ~ f_{i} ~ \times ~ f_{c} ~ \times ~ L

where, N = The number of communicative civilizations, R* = The rate of formation of suitable stars (stars such as our Sun), fp = The fraction of those stars with planets. (Current evidence indicates that planetary systems may be common for stars like the Sun), ne = The number of Earth-like worlds per planetary system, fl = The fraction of those Earth-like planets where life actually develops, fi = The fraction of life sites where intelligence develops, fc = The fraction of communicative planets (those on which electromagnetic communications technology develops), L = The "lifetime" of communicating civilizations.

However, whilst the rationale behind the equation is sound, it is unlikely that the equation will be constrained to reasonable error limits any time soon. The first term, Number of Stars, is generally constrained within a few orders of magnitude. The second and third terms, Stars with Planets and Planets with Habitable Conditions, are being evaluated for the sun's neighborhood. Another associated topic is the Fermi paradox, which suggests that if intelligent life is common in the Universe, then there should be obvious signs of it. This is the purpose of projects like SETI, which tries to detect signs of radio transmissions from intelligent extraterrestrial civilizations.

Another active research area in astrobiology is Planetary system formation. It has been suggested that the peculiarities of our Solar System (for example, the presence of Jupiter as a protective shield) may have greatly increased the probability of intelligent life arising on our planet. No firm conclusions have been reached so far.

Biology

Hydrothermal vents are able to support extremophile bacteria on Earth and may also support life in other parts of the cosmos.

Extremophiles (organisms able to survive in extreme environments) are a core research element for astrobiologists. Such organisms include biota able to survive kilometers below the ocean's surface near hydrothermal vents and microbes that thrive in highly acidic environments.

Until the 1970s, life was believed to be entirely dependent on energy from the Sun. Plants on Earth's surface capture energy from sunlight to photosynthesize sugars from carbon dioxide and water, releasing oxygen in the process, and are then eaten by oxygen-respiring animals, passing their energy up the food chain. Even life in the ocean depths, where sunlight cannot reach, was believed to obtain its nourishment either from consuming organic detritus rained down from the surface waters or from eating animals that did. A world's ability to support life was thought to depend on its access to sunlight. However, in 1977, during an exploratory dive to the Galapagos Rift in the deep-sea exploration submersible Alvin, scientists discovered colonies of giant tube worms, clams, crustaceans, mussels, and other assorted creatures clustered around undersea volcanic features known as black smokers. These creatures thrive despite having no access to sunlight, and it was soon discovered that they comprise an entirely independent food chain. Instead of plants, the basis for this food chain is a form of bacterium that derives its energy from oxidization of reactive chemicals, such as hydrogen or hydrogen sulfide, that bubble up from the Earth's interior. This chemosynthesis revolutionized the study of biology by revealing that life need not be sun-dependent; it only requires water and an energy gradient in order to exist. It is now known that extremophiles thrive in ice, boiling water, acid, the water core of nuclear reactors, salt crystals, toxic waste and in a range of other extreme habitats that were previously thought to be inhospitable for life. It opened up a new avenue in astrobiology by massively expanding the number of possible extraterrestrial habitats. Characterization of these organisms—their environments and their evolutionary pathways—is considered a crucial component to understanding how life might evolve elsewhere in the Universe. Some organisms able to withstand exposure to the vacuum and radiation of space include the lichen fungi Rhizocarpon geographicum and Xanthoria elegans,the bacterium Bacillus safensis, Deinococcus radiodurans,Bacillus subtilis, yeast Saccharomyces cerevisiae,eds from Arabidopsis thaliana as well as the invertebrate animal Tardigrade. ('mouse-ear cress'),

The origin of life, distinct from the evolution of life, is another ongoing field of research. Oparin and Haldaneorganic compounds from inorganic elements and thus to the formation of many of the chemicals common to all forms of life we see today. The study of this process, known as prebiotic chemistry, has made some progress, but it is still unclear whether or not life could have formed in such a manner on Earth. The alternative theory of panspermia is that the first elements of life may have formed on another planet with even more favorable conditions (or even in interstellar space, asteroids, etc.) and then have been carried over to Earth by a variety of means. See Origin of life. Jupiter's moon, Europa, is now considered to be the most likely location for extant extraterrestrial life in the Solar System. postulated that the conditions on the early Earth were conducive to the formation of

Astrogeology

Astrogeology is a planetary science discipline concerned with the geology of the celestial bodies such as the planets and their moons, asteroids, comets, and meteorites. The information gathered by this discipline allows the measure of a planet's or a natural satellite's potential to develop and sustain life, or planetary habitability.

An additional discipline of astrogeology is geochemistry, which involves study of the chemical composition of the Earth and other planets, chemical processes and reactions that govern the composition of rocks and soils, the cycles of matter and energy and their interaction with the hydrosphere and the atmosphere of the planet. Specializations include cosmochemistry, biochemistry and organic geochemistry.

The fossil record provides the oldest known evidence for life on Earth.By examining this evidence, paleontologists are able to understand better the types of organisms that arose on the early Earth. Some regions on Earth, such as the Pilbara in Western Australia and the McMurdo Dry Valleys of Antarctica, are also considered to be geological analogs to regions of Mars, and as such, might be able to provide clues on how to search for past life on Mars.

Life in the Solar System

Europa, due to the ocean that exists under its icy surface, might host some form of microbial life.

People have long speculated about the possibility of life in settings other than Earth, however, speculation on the nature of life elsewhere often has paid little heed to constraints imposed by the nature of biochemistry.The likelihood that life throughout the universe is probably carbon-based is encouraged by the fact that carbon is one of the most abundant of the higher elements. Only two of the natural atoms, carbon and silicon, are known to serve as the backbones of molecules sufficiently large to carry biological information. As the structural basis for life, one of carbon's important features is that unlike silicon it can readily engage in the formation of chemical bonds with many other atoms, thereby allowing for the chemical versatility required to conduct the reactions of biological metabolism and propagation. The various organic functional groups, composed of hydrogen, oxygen, nitrogen, phosphorus, sulfur, and a host of metals, such as iron, magnesium, and zinc, provide the enormous diversity of chemical reactions necessarily catalyzed by a living organism. Silicon, in contrast, interacts with only a few other atoms, and the large silicon molecules are monotonous compared with the combinatorial universe of organic macromolecules. Indeed, it seems likely that the basic building blocks of life anywhere will be similar to our own, in the generality if not in the detail. Although terrestrial life and life that might arise independently of Earth are expected to use many similar, if not identical, building blocks, they also are expected to have some biochemical qualities that are unique.

Thought on where in the Solar System life might occur was limited historically by the belief that life relies ultimately on light and warmth from the Sun and, therefore, is restricted to the surfaces of planets. The three most likely candidates for life in the Solar System are the planet Mars, the Jovian moon Europa, and Saturn's moon Titan. This speculation is primarily based on the fact that (in the cases of Mars and Europa) the planetary bodies may have liquid water, a molecule essential for life as we know it, for its use as a solvent in cells. Water on Mars is found in its polar ice caps, and newly carved gullies recently observed on Mars and possibly in subsurface environments such as hydrothermal springs as well. At the Martian low temperatures and low pressure, liquid water is likely to be highly saline. As for Europa, liquid water likely exists beneath the moon's icy outer crust.tidal heating. suggest that liquid water may exist, at least transiently, on the planet's surface, This water may be warmed to a liquid state by volcanic vents on the ocean floor (an especially intriguing theory considering the various types of extremophiles that live near Earth's volcanic vents), but the primary source of heat is probably

Another planetary body that could potentially sustain extraterrestrial life is Saturn's largest moon, Titan.Titan has been described as having conditions similar to those of early Earth. On its surface, scientists have discovered the first liquid lakes outside of Earth, but they seem to be composed of ethane and/or methane, not water. After Cassini data was studied, it was reported on March 2008 that Titan may also have an underground ocean composed of liquid water and ammonia.Additionally, Saturn's moon Enceladus may have an ocean below its icy surface.

Research

The systematic search for possible life outside of Earth is a valid multidisciplinary scientific endeavor.The University of Glamorgan, UK, started just such a degree in 2006, and the American government funds the NASA Astrobiology Institute. However, characterization of non-Earth life is unsettled; hypotheses and predictions as to its existence and origin vary widely, but at the present, the development of theories to inform and support the exploratory search for life may be considered astrobiology's most concrete practical application.

Biologist Jack Cohen and mathematician Ian Stewart, amongst others, consider xenobiology separate from astrobiology. Cohen and Stewart stipulate that astrobiology is the search for Earth-like life outside of our solar system and say that xenobiologists are concerned with the possibilities open to us once we consider that life need not be carbon-based or oxygen-breathing, so long as it has the defining characteristics of life.

Research outcomes

Asteroid(s) may have transported life to Earth.

As of 2010, no proof of extraterrestrial life has been identified. Examination of the ALH 84001 meteorite, which was recovered in Antarctica in 1984 and believed to have originated from Mars, is thought by David McKay, Chief Scientist for Astrobiology at NASA's Johnson Space Center, as well as other scientists, to contain microfossils of extraterrestrial origin; this interpretation is controversial

Methane

In 2004, the spectral signature of methane was detected in the Martian atmosphere by both Earth-based telescopes as well as by the Mars Express probe. Because of solar radiation and cosmic radiation, methane is predicted to disappear from the Martian atmosphere within several years, so the gas must be actively replenished in order to maintain the present concentration The Mars Science Laboratory rover will perform precision measurements of oxygen and carbon isotope ratios in carbon dioxide (CO₂) and methane (CH₄) in the atmosphere of Mars in order to distinguish between a geochemical and a biological origin.

Planetary systems

It is possible that some planets, like the gas giant Jupiter in our solar system, may have moons with solid surfaces or liquid oceans that are more hospitable. Most of the planets so far discovered outside our solar system are hot gas giants thought to be inhospitable to life, so it is not yet known whether our solar system, with a warm, rocky, metal-rich inner planet such as Earth, is of an aberrant composition. Improved detection methods and increased observing time will undoubtedly discover more planetary systems, and possibly some more like ours. For example, NASA's Kepler Mission seeks to discover Earth-sized planets around other stars by measuring minute changes in the star's light curve as the planet passes between the star and the spacecraft. Progress in infrared astronomy and submillimeter astronomy has revealed the constituents of other star systems. Infrared searches have detected belts of dust and asteroids around distant stars, underpinning the formation of planets.

Planetary habitability

Efforts to answer questions such as the abundance of potentially habitable planets in habitable zones and chemical precursors have had much success. Numerous extrasolar planets have been detected using the wobble method and transit method, showing that planets around other stars are more numerous than previously postulated. The first Earth-like extrasolar planet to be discovered within its star's habitable zone is Gliese 581 c, which was found using radial velocity^.

Research into the environmental limits of life and the workings of extreme ecosystems is also ongoing, enabling researchers to predict what planetary environments might be most likely to harbor life. Missions such as the Phoenix lander, Mars Science Laboratory, ExoMars to Mars, the Cassini probe to Saturn's moon Titan, and the "Ice Clipper" mission to Jupiter's moon Europa hope to further explore the possibilities of life on other planets in our solar system.

Rare Earth hypothesis

This hypothesis states that based on astrobiological findings, multi-cellular life forms found on earth may actually be more of a rarity than scientists initially assumed. It provides a possible answer to the Fermi paradox which suggests, "If extraterrestrial aliens are common, why aren't they obvious?" It is apparently in opposition to the principle of mediocrity, assumed by famed astronomers Frank Drake, Carl Sagan, and others. The Principle of Mediocrity suggests that life on Earth is not exceptional, but rather that life is more than likely to be found on innumerable other worlds.

The anthropic principle states that fundamental laws of the universe work specifically in a way that life would be possible. The anthropic principle supports the Rare Earth Hypothesis by arguing the overall elements that are needed to support life on earth are so fine-tuned that it is nigh impossible for another just like it to exist by random chance (note that these terms are used by scientists in a different way from the vernacular conception of them). However, Stephen Jay Gould compared the claim that the universe is fine-tuned for the benefit of our kind of life to saying that sausages were made long and narrow so that they could fit into modern hot dog buns, or saying that ships had been invented to house barnacles.