From Wikipedia, the free encyclopedia
Jump to: navigation, search

{q.v. User:Kazkaskazkasako/Books/Physical sciences}



Resolution (electron density): measure of the resolvability in the electron density map of a molecule. X-ray vs (cryo-)EM definition. X-ray crystallography: >4.0 Å - Individual coordinates meaningless.
Fourier shell correlation (FSC [Harauz & van Heel (1986)]; AKA: spatial frequency correlation function [Saxton & Baumeister (1982)]): measures the normalised cross-correlation coefficient between two 3D volumes over corresponding shells in Fourier space (i.e., as a function of spatial frequency); extension of the two-dimensional Fourier ring correlation (FRC) [van Heel (1982)].

Topology and structure[edit]

Linking number: e.g. DNA linking number in plasmids
Kissing number: e.g. materials science, chem, phys - dense packing of atoms: only two possibilities in 3D: FCC (face-centered cubic) and HCP (hexagonal close-packed) [or a hybrid of both]
Euler characteristic: topology, highly symmetrical (yet simple) viral coats

math, groups:

Coxeter group: abstract group that admits a formal description in terms of mirror symmetries.

math, graphs:

Coxeter–Dynkin diagram (Coxeter diagram, Coxeter graph): graph with numerically labeled edges (called branches) representing the spatial relations between a collection of mirrors (or reflecting hyperplanes). Dynkin diagrams: closely related objects, which differ from Coxeter diagrams in two respects: firstly, branches labeled "4" or greater are directed, while Coxeter diagrams are undirected; secondly, Dynkin diagrams must satisfy an additional (crystallographic) restriction, namely that the only allowed branch labels are 2, 3, 4, and 6.

Symmetry in (bio)molecules[edit]

Mathematical 2D and 3D group/symmetry notations[edit]
Symmetry group:
List of planar symmetry groups: what's the diff. with spherical symmetry groups? Plane vs sphere? Classes of discrete planar symmetry groups: 2 rosette groups (2D point groups) + 7 frieze groups (2D line groups) + 17 wallpaper groups (2D space groups)
List of spherical symmetry groups, spherical symmetry groups and point groups have the same notation. Are they qualitatively different? Or it's just the different way of putting graph theory (like binary vs. decimal, but still numbers)
Point group: group of geometric symmetries (isometries) that keep at least one point fixed; 1D, 2D, 3D, ..., 8D:
Point groups in two dimensions; point groups in 2D under crystallographic restriction theorem ⇒ wallpaper group (plane symmetry group or plane crystallographic group) [17]; frieze group
Point groups in three dimensions: 7 infinite families of axial (or prismatic groups), and 7 additional polyhedral (or Platonic groups) (Polyhedral group). Applying the crystallographic restriction theorem to these groups yields: 32 crystallographic point groups ((geometric) crystal classes)
Crystallographic point group (crystal class): tables: in Schoenflies [5*7=35, but 4 are forbidden and other 4 are the same as some others, so 35-4-4=27; add T, Td, Th, O and Oh [5]: 27+5=32], and in Hermann–Mauguin notations [32, table with empty (forbidden) spaces], and correspondence between different notations (crystal family & system, Hermann-Mauguin full & short symbols, Shubnikov, Schoenflies, orbifold, Coxeter, order) [32]
Notations for symmetry groups and point groups:
Coxeter notation (bracket notation): system of classifying symmetry groups, describing the angles between with fundamental reflections of a Coxeter group; uses a bracketed notation, with modifiers to indicate certain subgroups
Schoenflies notation (Schönflies notation): one of two conventions commonly used to describe Point groups; notation is used in spectroscopy (for molecular symmetry). Point group in the Schoenflies convention is completely adequate to describe the symmetry of a molecule; this is sufficient for spectroscopy. The Hermann–Maunguin notation is able to describe the space group of a crystal lattice, while the Schoenflies notation isn't. Thus the Hermann–Mauguin notation is used in crystallography.
Hermann–Mauguin notation (International notation (International Tables For Crystallography)): the other convention to commonly used to describe Point groups; used in crystallography (crystal symmetries in X-ray, neutron, electron, ...). Mirror plane (rotoinversion axis 2) is m, while the other rotoinversion axes are represented by the corresponding number with a macron, n1, 3, 4, 5, 6, 7, 8...
Orbifold notation (orbifold signature): system, invented by William Thurston (William Paul Thurston, of orbifold fame) and popularized by the mathematician John Conway, for representing types of symmetry groups in two-dimensional spaces of constant curvature. The advantage of the notation is that it describes these groups in a way which indicates many of the groups' properties: in particular, it describes the orbifold obtained by taking the quotient of Euclidean space by the group under consideration.
Fibrifold & fibrifold notation (in 3D): extension of orbifold notation for 3D space groups.
Schläfli symbol: notation of the form {p,q,r,...} that defines regular polytopes and tessellations (List of regular polytopes).
Wythoff symbol: first used by Coxeter, Longeut-Higgens and Miller in their enumeration of the uniform polyhedra.

Symmetries in 2D: tiling; crystallographic projections, molecule projections

Question: how is the symmetry number calculated?

Phys(chem(bio)): single molecules/particles, crystals & co[edit]
Crystal system: "In crystallography, the terms crystal system, crystal family, and lattice system each refer to one of several classes of space groups, lattices, point groups, or crystals. Crystal systems, crystal families, and lattice systems are similar but slightly different, and there is widespread confusion between them: in particular the trigonal crystal system is often confused with the rhombohedral lattice system, and the term "crystal system" is sometimes used to mean "lattice system" or "crystal family". Space groups and crystals are divided into 7 crystal systems according to their point groups, and into 7 lattice systems according to their Bravais lattices. Five of the crystal systems are essentially the same as five of the lattice systems, but the hexagonal and trigonal crystal systems differ from the hexagonal and rhombohedral lattice systems. The six crystal families are formed by combining the hexagonal and trigonal crystal systems into one hexagonal family, in order to eliminate this confusion." >>>See the table where "crystal system" from the left and "lattice system" from the right go into "point groups" on the left and into "bravais lattices" on the right and they meet as "space groups": see how "space groups" are split into 3 groups by this meeting from the left (trigonal/hexagonal crystal systems) and the right (rhombohedral/hexagonal lattice systems).
Crystal system: Crystal classes=32 (table of 32 point groups); Lattice systems=7 (subdivided into 14 Bravais lattices). Crystallographic symmetries forbid quite some of the molecular symmetries and only 230 remain (in 3D) (i.e., although molecules have many possible symmetries, they can crystallize only in very few symmetries; everything else is not crystals).
Space group (in crystallography: crystallographic or Fedorov groups; in dimensions other than 3: Bieberbach groups):
Notation for space groups: number (in IUCr tables), International symbol or Hermann–Mauguin notation, Hall notation, Schoenflies notation, Shubnikov symbol, 2D:Orbifold notation and 3D:Fibrifold notation, Coxeter notation
Classification systems for space groups: see the table explaining how space groups are classified into classes (reminds of biological classification into species (correspond to crystallographic space groups), genuses, classes, families...) in 3D: (Crystallographic) space group types [230] ⇒ Affine space group types [219] ⇒ Arithmetic crystal classes [73] ⇒ ((geometric) Crystal classes [32] ⇒ Crystal systems [7] OR Bravais flocks [14] ⇒ Lattice systems [7]) ⇒ Crystal families [6]. Other classifications: Conway, Delgado Friedrichs, and Huson et al. (2001)::
Space groups in other dimensions: table of dimension, # lattice types (OEIS: A004030), # crystallographic point groups (OEIS: A004028), # crystallographic space group types (OEIS: A006227), # affine space group types (OEIS: A004029)
Table of space groups in 3 dimensions: table of: groupings international notation numbers, crystal systems [7], point groups (in international and Schoenflies notations) [32], crystallographic space groups (international short symbol) [230]. Also explanation how to obtain lattice systems from crystal systems (some of space group of the trigonal crystal systems have names beginning with "R" and are rhombohedral lattice systems; the other trigonal crystal systems belong to the hexagonal lattice system); Bravais lattices.
Molecular_symmetry, all symmetry elements applying to the molecules (only a subset of all 3D symmetries), infinite possibilities, limited only by (covalent) bond (number? and) strength, or there is no limitation of number of atoms bonded, as it could branch out more and more from the symmetry core to change the symmetry? Chiral: .

Materials science, nanotechnology (bionanotech)[edit]

Category:Materials science
Category:Condensed matter physics
Category:Microtechnology: 10−4 to 10−7 m
Category:Supramolecular chemistry
Category:Molecular machines
Category:Polymer chemistry
Category:Superconductivity {q.v. User:Kazkaskazkasako/Books/EECS#Superconductivity}
Category:Nanotechnology templates
Materials science: Materials in industry (Ceramics and glasses, Composite materials, Polymers, Metal alloys
Template:Nanotechnology (Template:Nanotech footer is the same) R
List of nanotechnology organizations: MRS (Materials Research Society)
Mechanosynthesis: chemical synthesis in which reaction outcomes are determined by the use of mechanical constraints to direct reactive molecules to specific molecular sites. In biology, the ribosome provides an example of a programmable mechanosynthetic device; diamond mechanosynthesis
Template:Molecular nanotechnology & Molecular nanotechnology (MNT): build structures to complex, atomic specifications by means of mechanosynthesis (reaction outcomes are determined by the use of mechanical constraints to direct reactive molecules to specific molecular sites). Combines physics, chemistry, life molecular machinery, and systems engineering of macroscale factories. Hard vs soft nanotech: hard would use vacuum and ~0 K to engineer stuff while the soft nanotech talks about wetness, stickness, brownian motion, high viscosity - biomimetic nanontech.
Molecular assembler: defined by K. Eric Drexler, is a "proposed device able to guide chemical reactions by positioning reactive molecules with atomic precision" (e.g. ribosome is a real molecular assembler in the liquids of the cell where the instruction is mRNA and the output in protein, while aa-tRNAs are used up). Nanofactories, self-replication. One molecular assembler, like a single ribosome, are slow, but when you have many of them, then you can produce in quantity (that's why cell produces ~2× ribosomes compared to the just-after-the-division point and only then divides into 2 daughter cells).
Drexler–Smalley debate on molecular nanotechnology: from wet/soft MNT (to bootstrap) to hard MNT? Quantum mechanics? Smalley argued that nearly all of modern chemistry involves reactions that take place in a solvent (usually water), because the small molecules of a solvent contribute many things, such as lowering binding energies for transition states. Since nearly all known chemistry requires a solvent, Smalley felt that Drexler's proposal to use a high vacuum environment was not feasible; "fat fingers problem" and the "sticky fingers problem".
Molecular engineering: companies:
ZyvexZyvex Technologies (Zyvex Marine): works with carbon nanotubes embedded into resins to make several times lighter than alloys but as strong as alloys materials.
History of nanotechnology: early 2000s also saw the beginnings of commercial applications of nanotechnology, although these were limited to bulk applications of nanomaterials rather than the transformative applications envisioned by the field. There's Plenty of Room at the Bottom; K. Eric Drexler; Invention of scanning probe microscopy. Fullerenes were discovered in 1985. The National Nanotechnology Initiative is USA federal nanotechnology research and development program. Initial commercial applications: titanium dioxide and zinc oxide nanoparticles in sunscreen, cosmetics and some food products; silver nanoparticles in food packaging, clothing, disinfectants and household appliances such as Silver Nano; carbon nanotubes for stain-resistant textiles; and cerium oxide as a fuel catalyst.
Impact of nanotechnology: extends from its medical, ethical, mental, legal and environmental applications, to fields such as engineering, biology, chemistry, computing, materials science, and communications. Major benefits of nanotechnology include improved manufacturing methods, water purification systems, energy systems, physical enhancement, nanomedicine, better food production methods, nutrition and large-scale infrastructure auto-fabrication. Regulatory bodies such as the United States Environmental Protection Agency and the Health and Consumer Protection Directorate of the European Commission have started dealing with the potential risks of nanoparticles. Nanotoxicology: extremely small size of nanomaterials also means that they are much more readily taken up by the human body than larger sized particles.
Nanobiotechnology (bionanotechnology, nanobiology): intersection of nanotechnology and biology.
Template:Nanotechnology implications
Dynamic random access memory
DNA origami: 2D/3D structures from DNA, the more complex the structure - the longer it takes to fold.

Research & design, companies[edit]

Infineon Technologies
National Physical Laboratory (United Kingdom)

Optics, Quantum Wave optics (diffraction) vs. particle scattering[edit]

Fraunhofer distance
Dynamical theory of diffraction: lots of red links and lots of citation from X-ray field
Eikonal equation: provides a link between physical (wave) optics and geometric (ray) optics
Optical aberration


Microscope: instrument used to see objects that are too small for the naked eye. Light, electron microscopes; scanning probe microscopes.

Photon, electron, atoms/ions: gallium, helium; mixed:

Scanning helium microscope
Transmission electron microscopy: Three-dimensional imaging: "tilt series", tomography
High-resolution transmission electron microscopy (HRTEM)
Transmission Electron Aberration-Corrected Microscope (TEAM): a project between FEI and CEOS with the support of United States Department of Energy (DOE) and 4 US laboratories.
Transmission Electron Aberration-corrected Microscope
Scanning transmission electron microscopy
Energy filtered transmission electron microscopy (EFTEM)
Cryo-electron microscopy (cryo-EM; electron cryomicroscopy)
Single particle analysis
Electron crystallography
Low Voltage Electron Microscopy
Scanning electron microscope
Electron diffraction
Electron beam induced deposition
X-ray microscope: see also Synchrotron X-ray tomographic microscopy (CT)
Staining: auxiliary technique used in microscopy to enhance contrast in the microscopic image. Stains and dyes are frequently used in biology and medicine to highlight structures in biological tissues for viewing, often with the aid of different microscopes. In vivo vs In vitro staining. Common biological stains: Acridine orange, Bismarck brown, Carmine, Coomassie blue, Cresyl violet, Crystal violet, DAPI, Eosin, Ethidium bromide, Acid fuchsine, Haematoxylin, Hoechst stains, Iodine, Malachite green, Methyl green, Methylene blue, Neutral red, Nile blue, Nile red, Rhodamine, Safranin.
Negative stain: contrasting a thin specimen with an optically opaque fluid; background is stained, leaving the actual specimen untouched, and thus visible. TEM: opaqueness to electrons is related to the atomic number; stains: ammonium molybdate, uranyl acetate, uranyl formate, phosphotungstic acid, osmium tetroxide, osmium ferricyanide and auroglucothionate.

{q.v. User:Kazkaskazkasako/Books/EECS#Medical hardware}

Camera (the "eye:retina"): Active pixel sensor vs. Charge-coupled device

Transfer functions and other blurs; their modeling[edit]

X-ray crystallography[edit]

X-ray crystallography
Crystal structure: Unit cell (Within the unit cell is the asymmetric unit, smallest unit the crystal can be divided into using the crystallographic symmetry operations of the space group. The asymmetric unit is also what is generally solved when solving a structure of a molecule or protein by X-ray crystallography.)
[1]: smallest unit of volume that contains all of the structural and symmetry information and that by translation can reproduce a pattern in all of space.
[2], [3]: smallest unit of volume that contains all of the structural information and that by application of the symmetry operations can reproduce the unit cell.
Biological unit (also, @Proteopedia: biological assembly, @PDB wiki: functional unit): smallest number of protein molecules which form a biologically active (e.g. catalytically active) unit (or biologically relevant as found in the cells). Functional form of the protein.
Structure solution methods:
Maximum entropy method
Crystallographic restriction theorem: rotational symmetries of a (3D) crystal are limited to 2-fold, 3-fold, 4-fold, and 6-fold (crystallography forbids 5 fold, 7 fold, and higher rotational symmetries).
But a phase in between the glass and crystal does exist:
Aperiodic tiling
Modified Bragg diffraction in quasicrystals

NMR spectroscopy[edit]

Nuclear magnetic resonance spectroscopy (NMR spectroscopy)
Nuclear magnetic resonance spectroscopy of proteins (Protein NMR)
Nuclear magnetic resonance spectroscopy of nucleic acids
Heteronuclear single quantum coherence spectroscopy (HSQC)
Template:NMR by isotope: 1H, 13C, 15N, 17O, 31P

Electron paramagnetic resonance[edit]

Electron paramagnetic resonance (EPR; electron spin resonance (ESR))


Tomography: Types of tomography
Electron tomography
Cryo-electron tomography (de:Kryoelektronentomographie)
Ultramicrotomy & Microtome:
Diamond knife: conventional hardest material used in microtomes
Nanoknife: a new development; carbon nanotube (like a wire) is used to cut materials
Photoacoustic tomography (PAT, or photoacoustic computed tomography (PACT)): reconstruction of an internal photoacoustic source distribution from measurements acquired by scanning ultrasound detectors over a surface that encloses the source under study. The PA source is the thermal expansion that results from a small temperature rise, which is caused by the absorption of externally applied radiation of pulsed electromagnetic (EM) waves.
Photoacoustic imaging in biomedicine, Photoacoustic spectroscopy
X-ray computed tomography (X-ray CT): computed tomography; computed axial tomography (CAT scan); computer-aided/assisted tomography.
Magnetic resonance imaging (MRI): Neuroimaging; Cardiovascular; Musculoskeletal; Liver and gastrointestinal MRI; fMRI; Oncology.
Functional magnetic resonance imaging (fMRI): functional neuroimaging procedure using MRI technology that measures brain activity by detecting associated changes in blood flow.
Positron emission tomography (PET): nuclear medicine, functional imaging technique that produces a three-dimensional image of functional processes in the body. The system detects pairs of gamma rays emitted indirectly by a positron-emitting radionuclide (tracer), which is introduced into the body on a biologically active molecule.
Radioactive tracer (radioactive label): used in PET: 11C, 13N, 18F, 123I
many others

Signal processing[edit]

Typical signal processing examples: (adaptive) filtering, smoothing, spectrum analysis, digitization (from analog data), modulation, feature extraction, pattern recognition

Wavelet transform: used in JP(E)G; can be used in wavelet thresholding to remove random noise
Multiresolution analysis

Image processing[edit]

Category:Image processing
Category:Computer vision {q.v. User:Kazkaskazkasako/Books/EECS#Computer vision}
Category:Data clustering algorithms

{q.v. User:Kazkaskazkasako/Books/Physical_sciences#Astronomical imaging}

Cluster analysis
Clustering high-dimensional data R?
Correlation clustering R?
k-means clustering
Principal component analysis R
Hierarchical clustering: agglomerative, divisive.
Fuzzy clustering r
Expectation-maximization algorithm r; maximum likelihood
Radon transform R; back projection lines, (common line theorem?)
Tomographic reconstruction
Algebraic reconstruction technique
Projection-slice theorem, aka Fourier slice theorem (aka projection theorem):
  • Fm and FN: m- and N-dimensional Fourier transform operators
  • Pm: m-dimensional projection operator (which projects an N-D function onto a m-D line)
  • Sm: m-dimensional slice of the N-dimensional Fourier transform of a function (consisting of an m-dimensional linear submanifold through the origin in the Fourier space which is parallel to the projection submanifold, produced by Pm)
Sinogram: the mathematical term for Radon transform
X-ray transform: closely related to the Radon transform, and coincides with it in two dimensions. In higher dimensions, the X-ray transform of a function is defined by integrating over lines rather than over hyperplanes as in the Radon transform.
Structural similarity
Template:Noise (Noise (in physics and telecommunications)): Peak signal-to-noise ratio, Signal-to-noise ratio, Image noise
Mathematical morphology: theory and technique for the analysis and processing of geometrical structures, based on set theory, lattice theory, topology, and random functions. Morphological dilation and erosion.


Homology modeling (comparative modeling): constructing an atomic-resolution model of the "target" protein from its amino acid sequence and an experimental three-dimensional structure of a related homologous protein (the "template").

Chemistry, chemical physics[edit]




Category:Branches of biology
Category:Cell biology
Category:Molecular biology
Category:Structural biology
Biosafety level: all survival horror fans' beloved facilities in truth
Brain-computer interfacing
Biological organisation (hierarchy of life, ecological organization): hierarchy of complex biological structures and systems that define life using a reductionistic approach; each level in the hierarchy represents an increase in organizational complexity, with each "object" being primarily composed of the previous level's basic unit; basic principle behind the organization is the concept of emergence—the properties and functions found at a hierarchical level are not present and irrelevant at the lower levels. A-cellular level and Pre-cellular level {atom/molecule} → biomacromolecular complexes {structural and machines} → Sub-cellular level {organelle} → Cellular level {cell} → Super-cellular level (Multicellular level) {tissue} → {organ → organ system → organism → population → biocoenosis/community → ecosystem → biosphere → [ecosphere (magnetosphere + atmosphere + biosphere + hydrosphere + pedosphere + geosphere)]}

Molecular Biology (Biochemistry) + Cellular Biology:

Wikipedia:WikiProject Molecular and Cell Biology: aims to better organize information in articles related to molecular and cell biology on Wikipedia. {q.v. Gene Wiki; Portal:Gene Wiki}
Wikipedia:WikiProject Molecular and Cell Biology/Style guide (gene and protein articles): scope of a gene/protein article is the human gene/protein (included all splice variants derived from that gene) as well as orthologs (as listed in HomoloGene) that exist in other species. If there are paralogs in humans (and by extension other species), then a gene family article in addition to the gene specific articles (see for example dopamine receptor) would be appropriate. Article name: if short, recommended UniProt protein name should be used as the article name; if verbose, either a widely used protein acronym or the official HUGO gene symbol, followed by "(gene)" if necessary to disambiguate. Abbreviations of genes are according to HUGO Gene Nomenclature Committee and written in italic font style, human gene names are written in capitals {q.v. #Genetics: Gene nomenclature}
Portal:Molecular and cellular biology


Evolutionary developmental biology (evolution of development, informally: evo-devo): compares the developmental processes of different organisms to determine the ancestral relationship between them, and to discover how developmental processes evolved

Quantum mechanics and biology[edit]

Quantum biology, R ***
Quantum Aspects of Life, R

Biochemistry and Molecular Biology[edit]

Category:Molecular biology
Category:Biomolecules by type
Category:Biomolecules by physiological function
Hypothetical types of biochemistry

Transcription Translation

Trans-acting (trans-regulatory, trans-regulation; la: "across from"): "acting from a different molecule" (i.e., intermolecular). In the context of transcription regulation, a trans-acting element is usually a DNA sequence that contains a gene. This gene codes for a protein (or microRNA or other diffusible molecule) that will be used in the regulation of another target gene.
Cis-regulatory element (cis-element; la: "on the same side as"): region of DNA or RNA that regulates the expression of genes located on that same molecule of DNA (often a chromosome). A cis-element may be located upstream of the coding sequence of the gene it controls (in the promoter region or even further upstream), in an intron, or downstream of the gene's coding sequence, either in the translated or untranscribed region.

Biochemical substances, pharmacy, pharmacology[edit]

Saponin=Sapogenin (key organic feature: steroid or other triterpene frameworks) +. :
  1. Quinoa saponins are classified as a mild eye and respiratory irritant and a low gastrointestinal irritant
  2. medicinal uses: e.g. digoxin (from Digitalis sp., cardiac glycoside: treat heart diseases), eleutheroside A (from Eleutherococcus senticosus, aka Siberian Ginseng), ginsenoside (Panax sp., aka ginseng; Rb1 group: Rb1, Rb2, Rc, Rd; Rg1 group: Rg1, Re, Rf, Rg2)
Physiologically based pharmacokinetic modelling (PBPK): mathematical modeling technique for predicting the absorption, distribution, metabolism and excretion (ADME) of synthetic or natural chemical substances in humans and other animal species. PBPK modeling is used in pharmaceutical research and drug development, and in health risk assessment for cosmetics or general chemicals.

Proteins, enzymes[edit]

Category:Protein families
Category:Protein structure
Category:Protein domains

{q.v. #Structural biology; #Biomacromolecular complexes}

Template:Posttranslational modification: the enzymes and proteins involved: chaperons (heat shock or chaperonins); protein targeting - signal peptide; ubiquitin: E1, E2, E3, deubiquitinating enzymes; SUMO.
Template:Protein primary structure (Protein primary structure and posttranslational modifications): PTM modified amino acids: S/T, Y, C, D, E, N, Q, K, R, P, H, W. Disulfide bond (C-C), ...
Proteinogenic amino acid: 22 standard amino acids, but only 21 are found in eukaryotes. 21st and 22nd: selenocysteine and pyrrolysine are incorporated into proteins by distinctive biosynthetic mechanisms; other 20 are directly encoded by the universal genetic code.
PYLIS downstream sequence (PYLIS: pyrrolysine insertion sequence): stem-loop mRNA structure; causes the UAG (amber) stop codon to be translated to the amino acid pyrrolysine instead of ending the protein translation. In archaea the PYLIS downstream sequence is positioned straight after the UAG codon which is translated as pyrrolysine.
SECIS element (SECIS: selenocysteine insertion sequence): stem-loop mRNA structure of around 60 nts; translate UGA codons as selenocysteines. In bacteria the SECIS element appears soon after the UGA codon it affects. In archaea and eukaryotes, it occurs in the 3' UTR of an mRNA, and can cause multiple UGA codons within the mRNA to code for selenocysteine. In Methanococcus (archeon) it is located in the 5' UTR.
Posttranslational modification (PTM): chemical modification of a protein after its translation.
Protein phosphorylation: PTM of proteins in which S, T or Y is phosphorylated by a protein kinase by the addition of a covalently bound phosphate group. Regulation of proteins by phosphorylation is one of the most common modes of regulation of protein function, and is often termed "phosphoregulation". In almost all cases of phosphoregulation, the protein switches between a phosphorylated and an unphosphorylated form, and one of these two is an active form, while the other one is inactive, respectively. In mammals proteins are phosphorylated predominantly on S (86%), T (12%) and Y (2%).
Phosphatase: enzyme that removes a phosphate group from its substrate by hydrolysing phosphoric acid monoesters into a phosphate ion and a molecule with a free hydroxyl group. This action is directly opposite to that of phosphorylases and kinases, which attach phosphate groups to their substrates by using energetic molecules like ATP. Protein phosphatases (PPs) can be grouped into three main classes based on sequence, structure and catalytic function: phosphoprotein phosphatase (PPP) family (contains also protein phosphatase Mg2+- or Mn2+-dependent (PPM) family); protein Tyr phosphatase (PTP) super-family; aspartate-based protein phosphatase group.
Metallothionein: family of cysteine-rich, 0.5 to 14 kDa proteins; localized to the membrane of the Golgi apparatus; bind both physiological (such as zinc, copper, selenium) and xenobiotic (such as cadmium, mercury, silver, arsenic) heavy metals through the thiol group of its cysteine residues, which represents nearly the 30% of its amino acidic residues
Engineered monoclonal antibodies.
Fragment antigen-binding (Fab): region on an antibody that binds to antigens. Composed of one constant and one variable domain of each of the heavy and the light chain.
Single-chain variable fragment (scFv): fusion protein of the variable regions of the heavy (VH) and light chains (VL) of immunoglobulins, connected with a short linker peptide of ten to about 25 amino acids.
Short linear motifs (SLiMs): short stretches of protein sequence that mediate protein protein interaction. SLiMs are generally situated in intrinsically disordered regions (over 80% of known SLiMs), however, upon interaction with a structured partner secondary structure is often induced.
Protein families[edit]
Category:Protein families
Category:Protein structure
Category:Protein domains
DExD/H box proteins: refer to the DEAD box, DEAH, and the Ski families of proteins; quite distinct from one another and there is not one protein that belongs to more than one of these families; each family has a specific role in RNA metabolism
DEAD/DEAH box helicase: family of proteins whose purpose is to unwind nucleic acids. "DEAD box and DEAH box proteins NTPase activities become stimulated by RNA, but DEAD box proteins use ATP and DEAH does not" {from "DExD/H box proteins"}.
DEAD box: involved in an assortment of metabolic processes that typically involve RNAs, but in some cases also other nucleic acids; highly conserved in nine motifs and can be found in both prokaryotes and eukaryotes. "Involved in various aspects of RNA metabolism, including nuclear transcription, pre mRNA splicing, ribosome biogenesis, nucleocytoplasmic transport, translation, RNA decay and organellar gene expression" {from "DEAD/DEAH box helicase"}.

Addictive substances, addiction[edit]

Category:Psychedelic drugs
Rat Park: study into drug addiction conducted in the late 1970s (and published in 1980) by Canadian psychologist Bruce K. Alexander and his colleagues at Simon Fraser University in British Columbia, Canada. Alexander's hypothesis was that drugs do not cause addiction, and that the apparent addiction to opiate drugs commonly observed in laboratory rats exposed to it is attributable to their living conditions, and not to any addictive property of the drug itself. He told the Canadian Senate in 2001 that prior experiments in which laboratory rats were kept isolated in cramped metal cages, tethered to a self-injection apparatus, show only that "severely distressed animals, like severely distressed people, will relieve their distress pharmacologically if they can."
Drug policy of Portugal: put in place in 2000, and was legally effective from July 2001. The new law maintained the status of illegality for using or possessing any drug for personal use without authorization. However, the offense was changed from a criminal one, with prison a possible punishment, to an administrative one if the amount possessed was no more than ten days' supply of that substance. After-care and social re-integration of drug users in Portugal is organised through three major programmes targeting different regions in Portugal (Programa Vida Emprego, Programa Quadro Reinserir and the PIDDAC incentives for re-integration). All three programmes finance different initiatives and projects supporting drug users through training opportunities, employment support, and/or housing.
Drugs: addiction & lethal dose.


Drugs: addiction & lethal dose.


Drugs: mean physical harm and mean dependence.
Alcohol belts in Europe: vodka, beer, wine (from "coldest" to the "warmest" climate EtOH containing drinks).
Empathogen-entactogen: used to describe a class of psychoactive drugs that produce distinctive emotional and social effects similar to those of MDMA (ecstasy). Putative members of this class include 2C-B, 2C-I(at 2-14mg), MDMA, MDA, MDEA, MBDB, 6-APB and mephedrone among others. The chemical structure of many entactogens contains a substituted amphetamine core, and most belong to the phenethylamine class of psychoactive drugs, although several (AET and AMT) are tryptamines. When referring to MDMA and its counterparts, the term 'MDxx' is often used with the exception of MDPV.
Substituted amphetamine
MDMA (3,4-Methylenedioxymethamphetamine; ecstasy): psychoactive drug used primarily as a recreational drug. Desired effects of MDMA include increased empathy, pleasure, and heightened sensations. When taken by mouth, effects begin after 30–45 minutes and last 3–6 hours. Adverse effects of MDMA use include addiction, memory problems, paranoia, difficulty sleeping, teeth grinding, blurred vision, sweating, and a rapid heartbeat. Use may also lead to depression and fatigue. Deaths have been reported due to increased body temperature and dehydration.
Methamphetamine: strong CNS stimulant that is mainly used as a recreational drug and less commonly as a treatment for attention deficit hyperactivity disorder and obesity. Methamphetamine was discovered in 1893 and exists as two enantiomers: dextromethamphetamine and levomethamphetamine. Methamphetamine properly refers to a specific chemical, the racemic free base, which is an equal mixture of levomethamphetamine and dextromethamphetamine in their pure amine forms. Dextromethamphetamine is a much stronger central stimulant than levomethamphetamine. Both enantiomers are neurotoxic and addictive.
Nora Volkow: addiction science
Behavioral addiction
Compulsive buying disorder (CBD): found in 5.8% of the United States population, approximately 80% of those affected are female
Overeating & Binge eating
Problem gambling
Self-harm (SH) (deliberate self-harm (DSH), self-poisoning, self-mutilation): self-harm is found in 40–60% of suicides; generalising self-harmers to be suicidal is, in the majority of cases, inaccurate.
Sexual addiction
Workaholic: Workaholism is not the same as working hard. Despite logging in an extraordinary amount of hours and sacrificing their health and loved ones for their jobs, workaholics are frequently ineffective employees.
Computer & Internet:
Computer addiction
Internet addiction disorder (IAD)
Information addiction
Video game addiction
Delirium tremens (latin: "shaking frenzy"; "the horrors" or "the shakes"): acute episode of delirium that is usually caused by withdrawal from alcohol (or other sedative-hypnotics, such as benzodiazepines, or barbiturates), first described in 1813; can result in death. Withdrawal from other drugs which are not sedative-hypnotics such as caffeine, cocaine, etc. does not have major medical complications, and is not life-threatening.
The Natural History of Alcoholism Revisited (1955): book by psychiatrist George E. Vaillant that describes two multi-decade studies of the lives of 600 American males, non-alcoholics at the outset, focusing on their lifelong drinking behaviours. By following the men from youth to old age it was possible to chart their drinking patterns and what factors may have contributed to alcoholism. Another study followed 100 severe alcoholics from a clinic eight years after their detoxification. Some of the main conclusions of Vaillant’s book are:
  • That alcoholism is as much a social as a medical condition. "Alcoholism can simultaneously reflect both a conditioned habit and a disease."
  • Factors predicting alcoholism were related to ethnic culture, alcoholism in relatives, and a personality that is antisocial and extroverted. An unhappy childhood predicted mental illness but not alcoholism—unless the family problems were due to alcoholism.
  • That alcoholism was generally the cause of co-occurring depression, anxiety, and sociopathic (delinquent) behaviour, not the result.
  • That even though alcoholism is not solely a medical condition, it is therapeutically effective to explain it as a disease to patients. The disease concept encourages patients to take responsibility for their drinking, without debilitating guilt.
  • That for most alcoholics, attempts at controlled drinking in the long term end in either abstinence or a return to alcoholism.
  • That there is as yet no cure for alcoholism, and that medical treatment can only provide short-term crisis intervention.
  • Achieving long-term sobriety usually involves (1) a less harmful, substitute dependency; (2) new relationships; (3) sources of inspiration and hope; and (4) experiencing negative consequences of drinking.

Biochemistry methods[edit]

Category:Biochemistry methods
Category:Polymerase chain reaction
Cross-link: cross-links in synthetic polymer chemistry; crosslinks in the biological sciences: protein-protein interaction, photo-reactive aa analogs (mass spectrometry); uses for crosslinked polymers: polyacrylamide gels for gel electrophoresis, rubber.
Real-time polymerase chain reaction: The Minimum Information for Publication of Quantitative Real-Time PCR Experiments (MIQE) guidelines propose that the abbreviation qPCR be used for quantitative real-time PCR and that RT-qPCR be used for reverse transcription–qPCR. The acronym "RT-PCR" commonly denotes reverse transcription polymerase chain reaction and not real-time PCR, but not all authors adhere to this convention.
TaqMan: probes are hydrolysis probes that are designed to increase the specificity of quantitative PCR. TaqMan probe principle relies on the 5´–3´ exonuclease activity of Taq polymerase to cleave a dual-labeled probe during hybridization to the complementary target sequence and fluorophore-based detection.
Taq polymerase: thermostable DNA polymerase named after the thermophilic bacterium Thermus aquaticus from which it was originally isolated by Chien et al. in 1976.
Φ29 DNA polymerase: enzyme from the bacteriophage Φ29. It is being increasingly used in molecular biology for multiple displacement DNA amplification procedures, and has a number of features that make it particularly suitable for this application.
Multiple displacement amplification: non-PCR based DNA amplification technique. This method can rapidly amplify minute amounts of DNA samples to a reasonable quantity for genomic analysis. The reaction starts by annealing random hexamer primers to the template: DNA synthesis is carried out by a high fidelity enzyme, preferentially Φ29 DNA polymerase, at a constant temperature. Compared with conventional PCR amplification techniques, MDA generates larger sized products with a lower error frequency. This method has been actively used in whole genome amplification and is a promising method for application to single cell genome sequencing and sequencing-based genetic studies.
Proteinase K: broad-spectrum serine protease. The enzyme was discovered in 1974 in extracts of the fungus Engyodontium album. Proteinase K is able to digest hair (keratin), hence, the name "Proteinase K". The predominant site of cleavage is the peptide bond adjacent to the carboxyl group of aliphatic and aromatic amino acids with blocked alpha amino groups. It is commonly used for its broad specificity. M_r = 28,900 daltons (28.9 kDa). Activated by calcium, the enzyme digests proteins preferentially after hydrophobic amino acids (aliphatic, aromatic and other hydrophobic amino acids). Although calcium ions do not affect the enzyme activity, they do contribute to its stability. Proteins will be completely digested if the incubation time is long and the protease concentration high enough.
Dialysis (biochemistry): process of separating molecules in solution by the difference in their rates of diffusion through a semipermeable membrane, such as dialysis tubing. Dialysis membranes are produced and characterized according to MWCO limits. While membranes with MWCOs ranging from 1-1,000,000 kDa are commercially available, membranes with MWCOs near 10 kDa are most commonly used.
Molecular weight cut-off (MWCO): lowest molecular weight solute (in daltons) in which 90% of the solute is retained by the membrane, or the molecular weight of the molecule (e.g. globular protein) that is 90% retained by the membrane.
Spin column-based nucleic acid purification: solid phase extraction method to quickly purify nucleic acids. This method relies on the fact that nucleic acid will bind to the solid phase of silica under certain conditions.

Biophysics, physical chemistry[edit]

{q.v. User:Kazkaskazkasako/Books/Physical_sciences#Biophysics, physical chemistry}

Structural biology[edit]

Category:Structural biology

{q.v. #Structure-function}

Template:Biomolecular structure & Biomolecular structure
Template:Protein structural analysis
Nucleic acid structure determination: Physical methods (X-ray, NMR, EM...); RNA sequencing; Chemical methods (Hydroxyl radical probing, DMS, CMCT, Kethoxal, Selective 2′-hydroxyl acylation analyzed by primer extension (SHAPE)); In-line probing; Nucleotide analog interference mapping
Nucleic acid design

Biomacromolecular complexes[edit]

Biomacromolecular complexes are studied in bio, chem, phys, maths, CS/IT(dynamics(molecular,modeling,...)); sometimes (NOT always) called "-somes", from Greek soma->body.

Biomolecular complex (macromolecular complex, biomacromolecular complex): any biological complex made of more than one molecule of protein, RNA, DNA, lipids, carbohydrates; interactions between these biomolecules are non-covalent; studied structurally by X-ray crystallography, NMR spectroscopy of proteins, cryo-electron microscopy and successive single particle analysis, and electron tomography.

RNA containing complexes[edit]

{q.v. #Cell nucleus}

Template:Post transcriptional modification
Ribonucleoprotein (RNP): nucleoprotein that contains RNA, i.e. protein + RNA.
Ribonucleoprotein particle: complex formed between RNA and RBPs. 'RNP foci' is used to denote an intracellular compartment involved in processing of RNA transcripts. RNP granules: stress granules, processing bodies, and exosomes in somatic cells; cell type and/or species specific.


Small nucleolar RNA (snoRNAs): primarily guide chemical modifications of other RNAs, mainly: rRNAs, tRNAs, snRNAs. Two main classes of snoRNA: the C/D box snoRNAs which are associated with methylation, and the H/ACA box snoRNAs which are associated with pseudouridylation. Commonly referred to as guide RNAs but should not be confused with the guide RNAs that direct RNA editing in trypanosomes.
Template:Small nucleolar RNA: J; MB; Me; psi; R, SNORA; SNORD; snR; TBR; U (e.g. U3; U2-19; U8); Z; other.
Small Cajal body-specific RNA (scaRNAs): specifically localise to the Cajal body, a nuclear organelle involved in the biogenesis snRNPs; guide the modification (methylation and pseudouridylation) of RNA polymerase II transcribed spliceosomal RNAs U1, U2, U4, U5 and U12.
RNA processing[edit]
Capping enzyme: addition of the cap occurs co-transcriptionally, after the growing RNA molecule contains about 30 nucleotides. The enzyme can only catalyze its reaction when bound to the phosphorylated carboxyl-terminal domain of RNA polymerase II; therefore it is specific to RNAs synthesized by this polymerase rather than those synthesized by RNA polymerase I or RNA polymerase III.
RNA polymerase (esp. RNA polymerase II)
transcription factors
splicing {q.v. #Spliceosome, splicing}
RNA polymerase (RNAP, RANpol; DNA-dependent RNA polymerase)
RNA polymerase I (Pol I): in higher eukaryotes, the enzyme that only transcribes 18S, 5.8S, 28S rRNA (but not 5S rRNA, which is synthesized by RNA Polymerase III), a type of RNA that accounts for over 50% of the total RNA synthesized in a cell. rDNA transcription is confined to the nucleolus where several hundreds of copies of rRNA genes are present, arranged as tandem head-to-tail repeats. Pol I transcribes one large transcript, encoding an rDNA gene over and over again; fastest-acting polymerase.
RNA polymerase II (RNAP II, Pol II): transcription of DNA to synthesize precursors of mRNA and most snRNA and microRNA; 550 kDa complex of 12 subunits, RNAP II is the most studied type of RNA polymerase. Carboxy-terminal domain (CTD) of Pol II typically consists of up to 52 repeats of the sequence YSPTSPS.
RNA polymerase II holoenzyme: form of eukaryotic Pol II that is recruited to the promoters of protein-coding genes in living cells; consists of Pol II, a subset of general transcription factors, and regulatory proteins known as SRB proteins. CTD phosphorylation.
Mediator (coactivator) (Vitamin D Receptor Interacting Protein (DRIP) coactivator complex and the Thyroid Hormone Receptor-associated Proteins (TRAP)): multiprotein complex that functions as a transcriptional coactivator in all eukaryotes; required for the successful transcription of nearly all class II gene promoters in yeast. Human mediator complex: 26+ subunits, 1.2 MDa.
RNA polymerase III (Pol III): transcribes DNA to synthesize 5S rRNA, tRNA and other small RNAs
RNA polymerase IV: specific to plants genomes and is required for the synthesis of over 90% of 24-nt heterochromatic siRNA
RNA polymerase V: synthesizes RNAs involved in siRNA-directed heterochromatin formation in plants.
Post-transcriptional modification (co-transcriptional modification)
Non-coding RNA (ncRNA; sometimes: non-protein-coding RNA (npcRNA), non-messenger RNA (nmRNA), functional RNA (fRNA)): functional RNA molecule that is not translated into a protein; DNA sequence from which a non-coding RNA is transcribed is often called an RNA gene. tRNA, rRNA, snoRNA, microRNA, siRNA, snRNA, exRNA, piRNA, long ncRNA...
Long non-coding RNA (lncRNA {pronounced: lincRNA}): non-protein coding transcripts longer than 200 nucleotides:: somewhat arbitrary limit distinguishes lncRNAs from small regulatory RNAs: miRNAs, siRNAs, piRNAs, snoRNAs, and other short RNAs. Many well-described long ncRNAs, such as Air and Xist, are poorly conserved, suggesting that ncRNAs may be subject to different selection pressures; selection may conserve only short regions of long ncRNAs that are constrained by structure or sequence-specific interactions; selection act only over small regions of the long ncRNA transcript. Those conserved regions of the human genome that are subject to recent evolutionary change relative to the chimpanzee genome occurs mainly in non-coding regions, many of which are transcribed
Piwi-interacting RNAs (piRNAs)
Bacterial small RNA
Small hairpin RNA (short hairpin RNA (shRNA)): makes a tight hairpin turn that can be used to silence target gene expression via RNAi
Polyadenylation (addition of poly(A) tail): to RNA. In eukaryotes, polyadenylation is part of the process that produces mature mRNA for translation. Nuclear polyadenylation: Function, Mechanism.Cytoplasmic polyadenylation: germ line, early embryogenesis, post-synaptic sites of neurons. Tagging for degradation in eukaryotes. Evolution: polyadenylation is seen in almost all organisms, it is not universal.
RNA-binding protein (RBP): bind to the ds or ss RNA; contain RRMs.
Spliceosome, splicing[edit]
RNA splicing (splicing)
alternative splicing (differential splicing): regulated process during gene expression that results in a single gene coding for multiple proteins.
LSm several duplications: SmD1/LSm10 paralog pair and the SmD2/LSm11 paralog pair exist only in animals, fungi, and the amoebozoa; the SmB/SmN (neural tissue Sm) paralog pair is seen only in the placental mammals. SmB has alternatively spliced variant SmB'; very similar protein, SmN replaces SmB'/B in certain (mostly neural) tissues. LSm's are found in U1, U2, U4, U5, U6 as a ring around Sm motif in U1, U2, U4, U5, U6 RNAs.
Sm ring: SmG, SmD3, SmB/SmB'/SmN, SmD1, SmD2, SmF. + U1, U2, U4, U5, U11, U12, U4atac snRNAs.
Lsm2-8 ring: (Theorized order: LSm5, LSm7, LSm4, LSm8, LSm2, LSm3, LSm6.) ~20 times less abundant than the Sm rings. + U6, U6atac, snRNAs; + U8 snoRNA (for rRNA, tRNA processing in nucleolus).
Sm10/Sm11 ring: LSM10 replace SmD1 and LSm11 replaces SmD2. + U7 snRNA.
Lsm1-7 ring: same as Lsm2-8 except LSm1 replaces LSm8. Localizes in the cytoplasm where it assists in degrading messenger RNA in ribonucleoprotein complexes.
SMN complex: SMN + Gemins 2-8. Gemin 6 and Gemin7 have been discovered to have the LSm structure, and to form a heterodimer. PRMT5 complex stabilizes SmB+SmD3 dimer, SmD1+SmD2 dimer, and SmD1+SmD2+SmF+SmE+SmG pentamer by attaching pICln to these. The pentamer and SmB+SmD3 dimer are loaded onto the SMN complex, which in turn loads the Sm ring onto snRNAs. SnRNP#Assembly of core snRNPs in the SMN complex: involved in the assembly of snRNPs.
GEMINs 2-8: GEMIN8 (Gem-associated protein 8) + GEMIN7 + GEMIN6 + GEMIN5 + GEMIN4 + DDX20 (Probable ATP-dependent RNA helicase DDX20; aka GEMIN3) + Survival of motor neuron protein-interacting protein 1 (SIP1 gene; aka GEMIN2)
Survival of motor neuron (SMN1 gene): due to SMN1 deletion, (incomplete SMN complex?) results in widespread splicing defects, especially in spinal motor neurons, and is one cause of spinal muscular atrophy (SMA)
PRMT5 complex = Protein arginine methyltransferase 5 + CLNS1A (pICln) + WD repeat-containing protein 77 (Mep50)
LSm12-16 and other multi-domain LSm proteins: ataxin-2 is large protein and has N-terminal LSm domain.
Archaeal Sm rings: Sm1 (SmAP1) and Sm2 (SmAP2) form homoheptamer or homohexamer rings; reported to associate with RNase P RNA. Crenarchaeotes have Sm3.
Bacterial LSm rings: Hfq - homohexamer rings; YlxS (sometimes also called YhbC) - two-domain protein with a N-terminal LSm domain. MscS
SnRNPs (pronounced "snurps"; small nuclear ribonucleoproteins): U1, U2, U5, U5, U6 (in addition, in metazoans: U11 snRNA, U12 snRNA, U4atac snRNA, U6atac snRNA). Also: U7 snRNP, which processes 3′ loop of histone pre-mRNA. Biogenesis.
Small nuclear RNA (snRNA; U-RNA): found within the nucleus of eukaryotic cells; length of an average snRNA is approximately 150 nt
U7 snRNP = U7 small nuclear RNA + Sm10/Sm11 ring + ZPF100 + (HBP (aka SLBP) + Histone 3' UTR stem-loop). For histone 3' UTR stem-loop processing.
Histone 3' UTR stem-loop: involved in nucleocytoplasmic transport of the histone mRNAs, and in the regulation of stability and of translation efficiency in the cytoplasm; mRNAs of metazoan histone genes lack polyadenylation and a poly-A tail, instead 3' end processing occurs at a site between this highly conserved stem-loop and a purine rich region around 20 nucleotides downstream (the histone downstream element, or HDE).
SLBP (histone RNA hairpin-binding protein (HBP) or stem-loop binding protein):
Minor spliceosome: splices atypical class of spliceosomal introns (U12-type) from eukaryotic messenger RNAs in plant, insects, vertebrates and some fungi. U12-type introns represent less than 1% of all introns in human cells. However they are found in genes performing essential cellular functions.
Spliceosome and spliceosomal "subunits" and complexes (U1, U2 (SF3a + SF3b), U4/6&U5 (tri-snRNP) → U1+U2+U4/6&U5 (B) → U2/6&U5 (Bact, B*, C))
Introns + Exons = pre-mRNA; pre-mRNA-(Spliceosome)→mRNA
U1 snRNP = U1 spliceosomal RNA + SnRNP70 (aka, U1 small nuclear ribonucleoprotein 70 kDa) + Sm ring + U1-A
U2 snRNP = U2 spliceosomal RNA + PRPF8 {2335 AA} (YPrp8)
U4 snRNP = U4 spliceosomal RNA + (+ PRPF3)
U5 snRNP = U5 spliceosomal RNA + WDR57 (Y????)
U6 snRNP = U6 spliceosomal RNA + Lsm2-8 ring + (+ PRPF3)
U4/U6-U5 tri-snRNP = U4 + U6 + U5 + PRPF31
Splicing factor: protein involved in the removal of introns from pre-mRNA.
U2AF2 (U2 small nuclear RNA auxiliary factor 1): required for binding of U2 snRNP to pre-mRNA; PAP1 (RP9) interacts with U2AF
EFTUD2 (interacts with WDR57 and PRPF8)
SR protein: conserved family of proteins involved in RNA splicing; protein domain with long repeats of S and R aa; length of SR proteins: 50-300 aa; RS domain and at least one RRM domain; more commonly found in the nucleus than the cytoplasm, but several SR proteins are known to shuttle between the nucleus and the cytoplasm. Metazoans appear to have SR proteins and unicellular organisms lack SR proteins. Important in constitutive and alternative pre-mRNA splicing, mRNA export, genome stabilization, NMD, and translation. 9 human genes: SFRS1, SFRS2, SFRS3, SFRS4, SFRS5, SFRS6, SFRS7, SFRS9, SFRS11. mRNA export; Genomic stabilization; NMD; Translation. Diseases: Cancer; HIV-1; Spinal muscular atrophy.
RNA recognition motif (RRM, RNP-1): putative RNA-binding domain of about 90 aa that are known to bind single-stranded RNAs; found in many eukaryotic proteins
Kinases: Serine/threonine-protein kinases: SRPK1, SRPK2; CLK1
Heterogeneous ribonucleoprotein particle (hnRNP): present in the cell nucleus during gene transcription and subsequent post-transcriptional modification of pre-mRNA. Proteins involved in the hnRNP complexes are collectively known as heterogeneous ribonucleoproteins
Polypyrimidine tract-binding protein (PTB): plays a regulatory role in alternative splicing.
Protein K (gene expression); K-homology or KH domains
pre-mRNA structures:
Polypyrimidine tract: region of mRNA that promotes the assembly of the spliceosome. PTB and U2AF associate with polypyrimidine tract.
Exonic splicing enhancer (ESE): DNA sequence motif consisting of 6 bases within an exon that directs, or enhances, accurate splicing of hnRNA or pre-mRNA into mRNA.
Exonic splicing silencer (ESS): small region of an exon that inhibits or silences splicing of pre-mRNA.
Precursor mRNA (pre-mRNA is the major part of heterogeneous nuclear RNA (hnRNA)): immature single strand of mRNA. Processed pre-mRNA is called "mature mRNA" or simply "mRNA".
Splicing-associated genetic diseases:
Retinitis pigmentosa (RP): a group of genetic eye conditions that lead to incurable blindness. RPs linked to splicing: RP13=PRPF8, RP11=PRPF31, RP18=PRPF3, RP9=PAP1.
Exon junction complex (EJC): has major influences on translation, surveillance and localization of the spliced mRNA
Nonsense-mediated decay (NMD): surveillance pathway that exists in all eukaryotes. Its main function is to reduce errors in gene expression by eliminating mRNA transcripts that contain premature stop codons.
mRNA surveillance: mechanisms are pathways utilized by organisms to ensure fidelity and quality of mRNA; function at various steps of the mRNA biogenesis pathway to detect and degrade transcripts that have not properly been processed.
Trans-splicing & de:Transspleißen: special form of pre-mRNA processing in eukaryotes where exons from two different primary RNA transcripts are joined end to end and ligated.
Processome: the "-some" which processes at least 16S rRNA of ribosome and assembles the small subunit of ribosome; made of U3 snoRNP, tUTP, bUTP, BMS1/RCL1.
Ribosomal RNA (rRNA): RNA component of the ribosome, and is essential for protein synthesis in all living organisms. It constitutes the predominant material within the ribosome, which is approximately 60% rRNA and 40% protein by weight. Ribosomes contain two major rRNAs and 50 or more proteins. rRNA is one of only a few gene products present in all cells; therefore, genes that encode the rRNA (rDNA) are sequenced to identify an organism's taxonomic group, calculate related groups, and estimate rates of species divergence.
  • Bacterial 16S ribosomal RNA, 23S ribosomal RNA, and 5S rRNA genes are typically organized as a co-transcribed operon.
  • Eukaryotes generally have many copies of the rRNA genes organized in tandem repeats; in humans approximately 300–400 repeats are present in five clusters (on chromosomes 13, 14, 15, 21 and 22).
Ribosomal DNA (rDNA): DNA sequence that codes for ribosomal RNA. rDNA of eukaryotes consists of a tandem repeat of a unit segment, an operon, composed of NTS, ETS, 18S, ITS1, 5.8S, ITS2, and 28S tracts. rDNA has another gene, coding for 5S rRNA, located in the genome in most eukaryotes. In the nucleus, the rDNA region of the chromosome is visualized as a nucleolus which forms expanded chromosomal loops with rDNA
5S ribosomal RNA (5S rRNA): ~120 nt ribosomal RNA molecule with a mass of 40 kDa. It is a structural and functional component of the large subunit of the ribosome in all domains of life (bacteria, archaea, and eukaryotes), with the exception of mitochondrial ribosomes of fungi and animals. Current evidence indicates that mitochondrial DNA of only a few groups, notably animals, fungi, alveolates and euglenozoans lacks the gene. The central protuberance, otherwise occupied by 5S rRNA and its associated proteins (see Figure 2), was remodeled in various ways. In the fungal mitochondrial ribosomes, 5S rRNA is replaced by LSU rRNA expansion sequences. In kinetoplastids (euglenozoans), the central protuberance is made entirely of evolutionarily novel mitochondrial ribosomal proteins. Lastly, animal mitochondrial ribosomes have coopted a specific mitochondrial tRNA to substitute the missing 5S rRNA.
23S ribosomal RNA (in E. coli 2904 nt): component of the large subunit (50S) of the bacterial ribosome.
16S ribosomal RNA: component of the 30S small subunit of prokaryotic ribosomes. The genes coding for it are referred to as 16S rDNA and are used in reconstructing phylogenies, due to the slow rates of evolution of this region of the gene. Multiple sequences of 16S rRNA can exist within a single bacterium. Universal primers: 16S rRNA gene is used for phylogenetic studies as it is highly conserved between different species of bacteria and archaea. Some (hyper)thermophilic archaea (i.e. order Thermoproteales) contain 16S rRNA gene introns that are located in highly conserved regions and can impact the annealing of "universal" primers. Mitochondrial and chloroplastic rRNA are also amplified. PCR applications: 16S rRNA gene sequences contain hypervariable regions that can provide species-specific signature sequences useful for identification of bacteria. As a result, 16S rRNA gene sequencing has become prevalent in medical microbiology as a rapid and cheap alternative to phenotypic methods of bacterial identification.
5.8S ribosomal RNA (5.8S rRNA): non-coding RNA component of the large subunit of the eukaryotic ribosome and so plays an important role in protein translation.
28S ribosomal RNA: large subunit of eukaryotic cytoplasmic ribosomes.
18S ribosomal RNA: component of the small eukaryotic ribosomal subunit (40S). The genes coding for 18S rRNA are referred to as 18S rDNA. Sequence data from these genes is widely used in molecular analysis to reconstruct the evolutionary history of organisms, especially in vertebrates, as its slow evolutionary rate makes it suitable to reconstruct ancient divergences. 18S rRNA is eukaryotic nuclear homologue of 16S ribosomal RNA in Prokaryotes and mitochondria.
MT-RNR1 (Mitochondrially encoded 12S RNA)
MT-RNR2 (Mitochondrially encoded 16S RNA)
RNase P: cleave off an extra, or precursor, sequence of RNA on tRNA molecules. Bacterial RNase P has two components: an RNA chain, called M1 RNA, and a polypeptide chain, or protein, called C5 protein (class A and B). Archaeal RNase P ribonucleoproteins consist of 4-5 protein subunits that are associated with RNA.
Nuclear RNase P: eukaryotic RNase P.
Spliceosomal introns: in nuclear protein-coding genes that are removed by spliceosomes
Introns in nuclear and archaeal transfer RNA genes that are removed by proteins (tRNA splicing enzymes)
Group I catalytic intron: large self-splicing ribozymes; catalyze their own excision from mRNA, tRNA and rRNA precursors in Eukaryota, Bacteria, Viruses.
Group II intron: large class of self-catalytic ribozymes as well as mobile genetic element found within the genes of all three domains of life. Self-splicing can occur under high-salt conditions in vitro; however, assistance from proteins is required for in vivo splicing.
Group III intron: found in mRNA genes of chloroplasts in euglenoid protists; have a conventional group II-type dVI with a bulged adenosine, a streamlined dI, no dII-dV, and a relaxed splice site consensus. Much shorter than other self-splicing intron classes, ranging from 95 to 110 nucleotides amongst those known to Christopher and Hallick, and identified in chloroplasts; conserved sequences proximal to the splicing sites have similarities to those of group II introns, but have fewer conserved positions; very A+T rich.

Protein complexes[edit]

Category:Protein complexes
Multiprotein complex (protein complex): group of two or more associated polypeptide chains; distinct from a multienzyme polypeptide, in which multiple catalytic domains are found in a single polypeptide chain. Unfortunately, many of the techniques used to break open cells and isolate proteins are inherently disruptive to such large complexes, so their protein complexes within the cell may be even more widespread than can be detected. Obligate vs non-obligate protein complex; Transient vs permanent/stable protein complex; Fuzzy complex.
Protein–protein interaction (PPI): two or more proteins bind together, often to carry out their biological function
Proteasome: the center for protein and peptide degradation:
20S: core of proteasome; lids: 19S (10-protein base and 9-protein lid); 11S
11S+20S=PA28/REG (11S is induced by interferon gamma; responsible for the generation of peptides for MHC)
Anaphase-promoting complex (cyclosome; APC/C): E3 ubiquitin ligase that marks target cell cycle proteins for degradation by the 26S proteasome.
Nuclear pore complex (NPC)
Rhodopsin = Opsin + retinal
Cap binding complex (CBC): DE version has structures [12/02/09]
Origin recognition complex (ORC): multi-subunit DNA binding complex (6 subunits: ORC1-ORC6); binds in all eukaryotes to origins of replication in ATP-dependent manner. Serves as foundation for assembly of pre-replication complex (pre-RC; complex of Cdc6, Tah11 (aka Cdt1), Mcm2-Mcm7).
Cdc6 (Cell Division Cycle 6, in S. cerevisiae): essential regulator of DNA replication and plays important roles in the activation and maintenance of the checkpoint mechanisms in the cell cycle that coordinate S phase and mitosis. In humans: CDC6 (cell division control protein 6 homolog).
Segrosome: ensure accurate segregation (partitioning) of plasmids or chromosomes during bacterial cell division; "minimalist spindles".
SMC protein (Structural Maintenance of Chromosomes): large family of ATPases that participate in many aspects of higher-order chromosome organization and dynamics. Any relation between SMCs and segrosome?
Oxidative phosphorylation#Organization of complexes: "respirasomes"
Globins: related family of proteins, which are thought to share a common ancestor.
Myoglobin: iron- and oxygen-binding protein found in the muscle tissue of vertebrates in general and in almost all mammals.
Hemoglobin (Hb): iron-containing oxygen-transport metalloprotein in the red blood cells of all vertebrates as well as the tissues of some invertebrates.
Hemocyanins: respiratory proteins in the form of metalloproteins containing two copper atoms that reversibly bind a single oxygen molecule.

Microtubule organizing center (MTOC): structure found in eukaryotic cells from which microtubules emerge; two main functions: the organization of eukaryotic flagella and cilia and the organization of the mitotic and meiotic spindle apparatus, which separate the chromosomes during cell division. Centriole: usually 9*3 MTs; absent in higher plants and fungi. D. melanogaster embryos: 9*2; C. elegans sperm cells and early eambryos: 9*1; crabs maybe 9*2.

Centrosome: organelle that serves as the main MTOC of the animal cell as well as a regulator of cell-cycle progression; composed of two orthogonally arranged centrioles surrounded by an amorphous mass of protein termed PCM.
Pericentriolar material (PCM): amorphous mass of protein which makes up the part of the animal centrosome that surrounds the two centrioles.
Basal body (basal granule, kinetosome): organelle formed from a centriole, and a short cylindrical array of microtubules. Found at the base of a eukaryotic undulipodium and serves as a nucleation site for the growth of the axoneme microtubules; 9*3 helicoidal configuration forms a hollow cylinder.
Undulipodium (9+2 organelle): eukaryotic flagella and cilia; extension of the cell membrane containing both cytoplasm and a regular arrangement of microtubules known as an axoneme.
Axoneme: inner core of the undulipodium. Motile cilia/flagela: 9*2+2 axoneme; non-motile/primary cilia: no dynein arms are found, 9*2+0 (sometimes 9*2+1), (sensory functions?).

Tubulin: most common members of the tubulin family are α-tubulin and β-tubulin (αβ dimers make up microtubules). FtsZ is a prokaryotic homolog of eukaryotic tubulins. γ-tubulin important in the nucleation and polar orientation of microtubules, found in centrosomes. Tubulin/FtsZ family, GTPase domain - evolutionary conserved protein domain.

Microtubule nucleation (γ-tubulin ring complex (γ-TuRC)): cap of the (−) end while microtubule growth continues towards the (+) direction; found typically in MTOC.
Microtubules (MTs): component of the cytoskeleton; outer diameter of microtubule is ~25 nm. Kinesins are motor proteins binding MTs; katanin severs MTs & co.
Inositol trisphosphate receptor (InsP3R; IP3R; type = 1,2,3): membrane glycoprotein complex acting as a Ca2+ channel activated by IP3; very diverse among organisms, and is necessary for the control of cellular and physiological processes including cell division, cell proliferation, apoptosis, fertilization, development, behavior, learning and memory; strong evidence suggesting that IP3R plays an important role in the conversion of external stimuli to intracellular Ca2+ signals characterized by complex patterns relative to both space and time; (e.g. Ca2+ waves and oscillations). Rat cerebellum IP3R is type 1 (IP3R1).
Ryanodine receptors (RyRs): form a class of intracellular calcium channels in various forms of excitable animal tissue like muscles and neurons; major cellular mediator of calcium-induced calcium release (CICR) in animal cells. In the muscle cells RyRs are in the membrane of sarcoplasmic reticulum. Similar to IP3R. Small amount of Ca2+ in the cytosol near RyR will cause it to release even more Ca2+ (CICR).
Calcium-induced calcium release (CICR)
Calcium (Ca2+) sparks
Template:ATPase & ATPase (EC; adenylpyrophosphatase, ATP monophosphatase, triphosphatase..., ATP hydrolase...): cation(s) pump vs ATP. Cations: H+; Na+/K+; H+/K+; Ca++; Mg++; Cu++.
ATP synthase (EC; TCDB 3.A.2 (F-type, V-type and A-type ATPase (sometimes just F-ATPase) superfamily))
F-ATPase: bacterial plasma membranes, in mitochondrial inner membranes, and in chloroplast thylakoid membranes. F0 + F1
V-ATPase: vacuoles and other intracellular organelles of eukaryotes and in bacteria. V0 + V1
A-ATPase: found in archaea.
E-ATPase: cell-surface enzymes that hydrolyse a range of NTPs, including extracellular ATP.


Category:Classical genetics
Category:Genetic engineering
The image above contains clickable links
The structure of a prokaryotic operon of protein-coding genes. Regulatory sequence controls when expression occurs for the multiple protein coding regions (red). Promoter, operator and enhancer regions (yellow) regulate the transcription of the gene into an mRNA. The mRNA untranslated regions (blue) regulate translation into the final protein products.[1]
The image above contains clickable links
The structure of a eukaryotic protein-coding gene. Regulatory sequence controls when and where expression occurs for the protein coding region (red). Promoter and enhancer regions (yellow) regulate the transcription of the gene into a pre-mRNA which is modified to remove introns (light grey) and add a 5' cap and poly-A tail (dark grey). The mRNA 5' and 3' untranslated regions (blue) regulate translation into the final protein product.[1]
Gene Wiki: project that facilitates transferring information on human genes to Wikipedia article stubs with the goal of promoting collaboration and expansion of the articles.
Portal:Gene Wiki: dedicated to the goal of applying community intelligence to the annotation of gene and protein function. {} mirror of the Gene Wiki project on Wikipedia, running on top of the Semantic Mediawiki framework.
Portal:Gene Wiki/Other Wikis
genome sizes for the various groupings of organisms.
Genome size: 1 pg = 978 Mb; 1991 Drake proposed a rule: that the mutation rate within a genome and its size were inversely correlated.
C-value: amount, in picograms, of DNA contained within a haploid nucleus (e.g. a gamete) or one half the amount in a diploid somatic cell of a eukaryotic organism; in polyploids the C-value may represent two or more genomes contained within the same nucleus.
C-value enigma (C-value paradox): observation that genome size does not correlate with organismal complexity.
List of sequenced eukaryotic genomes: all the eukaryotes known to have publicly available complete nuclear and organelle genome sequences that have been assembled, annotated and published; draft genomes are not included, nor are organelle-only sequences.
Whole genome sequencing (full genome sequencing, complete genome sequencing, entire genome sequencing): entails sequencing all of an organism's chromosomal DNA as well as DNA contained in the mitochondria and, for plants, in the chloroplast. Almost all truly complete genomes are of microbes; the term "full genome" is thus sometimes used loosely to mean "greater than 95%". The remainder of this article focuses on nearly complete human genomes. Cells used for sequencing: single cell genome sequencing
Phylogenetic tree shows the relationship between the best-documented instances of paleopolyploidy in eukaryotes.
Polyploid: containing more than two paired (homologous) sets of chromosomes; most eukaryotic species are diploid, meaning they have two sets of chromosomes — one set inherited from each parent, however polyploidy is found in some organisms and is especially common in plants.
Paleopolyploidy: result of genome duplications which occurred at least several mya; most paleopolyploids, through evolutionary time, have lost their polyploid status through a process called diploidization, and are currently considered diploids.
Gene–environment interaction (genotype–environment interaction, G×E)
Genomic imprinting: certain genes are expressed in a parent-of-origin-specific manner; inheritance process independent of the classical Mendelian inheritance. Forms of genomic imprinting have been demonstrated in insects, mammals and flowering plants. Epigenetic process that involves DNA methylation and histone methylation in order to achieve monoallelic gene expression without altering the genetic sequence; epigenetic marks are established in the germline and are maintained throughout all somatic cells of an organism. At least 80 imprinted genes in humans and mice, many of which are involved in embryonic and placental growth and development [~2005-2006]. Mouse: ~80% of imprinted genes are found in clusters such as these, called imprinted domains, suggesting a level of co-ordinated control [2001]. In the developing sperm (during spermatogenesis), a paternal imprint is established, whereas in developing oocytes (oogenesis), a maternal imprint is established. Majority of imprinted genes in mammals have been found to have roles in the control of embryonic growth and development, including development of the placenta. Beckwith–Wiedemann syndrome (BWS); Silver–Russell syndrome (SRS; Silver–Russell dwarfism; Russell–Silver syndrome (RSS)); Angelman syndrome (AS); Prader–Willi syndrome (P.W.S)
Experiments on Plant Hybridization (1865; de: Versuche über Pflanzen-Hybriden): by Mendel; result after years spent studying genetic traits in pea plants; Mendel discovered that one inheritable trait would invariably be dominant to its recessive alternative.
Gene nomenclature: scientific naming of genes, the units of heredity in living organisms; international committee published recommendations for genetic symbols and nomenclature in 1957. For many genes and their corresponding proteins, an assortment of alternate names is in use across the scientific literature and public biological databases, posing a challenge to effective organization and exchange of biological information.
  • Bacterial genetic nomenclature: standards were proposed in 1966 by Demerec et al. Each bacterial gene is denoted by a mnemonic of three lower case letters which indicate the pathway or process in which the gene-product is involved, followed by a capital letter signifying the actual gene; in some cases, the gene letter may be followed by an allele number; all letters and numbers are underlined or italicised.
  • Vertebrate gene and protein symbol conventions: HGNC is responsible for providing human gene naming guidelines and approving new, unique human gene names and symbols (short form abbreviations); research communities of vertebrate model organisms have adopted guidelines whereby genes in these species are given, whenever possible, the same names as their human orthologs. Human: italicised, with all letters in uppercase (e.g. SHH); proteins not italicised, first letter uppercase and the rest lowercase (e.g. Shh/SHH). Mouse and rat: similar to human (Shh and SHH). Chicken (Gallus sp.): the same as humans (SHH and SHH). Frog (Xenopus sp.): shh and Shh. Zebrafish: shh and Shh.
Genetic recombination: process by which two DNA molecules exchange genetic information, resulting in the production of a new combination of alleles
Homologous recombination: ype of genetic recombination in which nucleotide sequences are exchanged between two similar or identical molecules of DNA. It is most widely used by cells to accurately repair harmful breaks that occur on both strands of DNA, known as double-strand breaks.
Holliday junction: mobile junction between four strands of DNA; highly conserved structures, from prokaryotes to mammals.
Branch migration: ability of a DNA strand partially paired with its complement in a duplex to extend its pairing by displacing the resident strand with which it is homologous.
Homologous chromosome: set of one maternal chromosome and one paternal chromosome that pair up with each other inside a cell during meiosis; copies have the same genes in the same locations, or loci. Genetic recombination occurs during meiosis in cells containing these parental chromosomes, producing genotypes in the offspring that are new and different combinations of the parental alleles.
E. coli:
RecBCD: initiates recombinational repair from potentially lethal double strand breaks in DNA; both a helicase that unwinds, or separates the strands of DNA, and a nuclease that makes single-stranded nicks in DNA.
RecA (38 kDa): essential for the repair and maintenance of DNA; RecA structural and functional homolog has been found in every species in which one has been seriously sought and serves as an archetype for this class of homologous DNA repair proteins.
Chi site: short stretch of DNA in the genome of a bacterium near which homologous recombination is more likely than expected to occur; Chi sequence serves as a signal to the RecBCD helicase-exonuclease that triggers a major change in the activities of this enzyme.
RuvABC: complex of three proteins that mediate branch migration and resolve the Holliday junction created during homologous recombination in bacteria; critical to bacterial DNA repair.
Origin of replication: particular sequence in a genome at which replication is initiated.
ori (genetics): DNA sequence that signals for the origin of replication, sometimes referred to simply as origin. In E. coli, ori is some 250 nucleotides in length for the chromosomal origin (oriC). The plasmid ori sequences are similar to oriC, and are called oriV (origin of vegetative replication).

Statistical genetics[edit]

Category:Statistical genetics
Genetic linkage: tendency of alleles that are close together on a chromosome to be inherited together during the meiosis phase of sexual reproduction. Genes whose loci are nearer to each other are less likely to be separated onto different chromatids during chromosomal crossover, and are therefore said to be genetically linked. This distance is expressed in terms of a genetic map unit (m.u.), or a centimorgan and is defined as the distance between genes for which one product of meiosis in 100 is recombinant. A recombinant frequency (RF) of 1% is equivalent to 1 m.u.
Imputation (genetics): statistical inference of unobserved genotypes. It is achieved by using known haplotypes in a population, for instance from the HapMap or the 1000 Genomes Project in humans, thereby allowing to test initially-untyped genetic variants for association with a trait of interest.
Gametic phase: represents the original allelic combinations that an individual received from its parents.
Identity by descent: IBS (identical by state) segment is identical by descent (IBD) in two or more individuals if they have inherited it from a common ancestor without recombination, that is, the segment has the same ancestral origin in these individuals. DNA segments that are IBD are IBS per definition, but segments that are not IBD can still be IBS due to the same mutations in different individuals or recombinations that do not alter the segment.
Genetic architecture: underlying genetic basis of a phenotypic trait and its variational properties. Phenotypic variation for quantitative traits is, at the most basic level, the result of the segregation of alleles at QTLs; broad term that can be described for any given individual based on information regarding gene and allele number, the distribution of allelic and mutational effects, and patterns of pleiotropy, dominance, and epistasis.
Quantitative trait locus (QTL) is a section of DNA (the locus) that correlates with variation in a phenotype (the quantitative trait); linked to, or contains, the genes that control that phenotype. QTLs are mapped by identifying which molecular markers (such as SNPs or AFLPs) correlate with an observed trait. This is often an early step in identifying and sequencing the actual genes that cause the trait variation. QTLs are often found on different chromosomes. Knowing the number of QTLs that explains variation in the phenotypic trait tells us about the genetic architecture of a trait.
Expression quantitative trait loci (eQTL): genomic loci that contribute to variation in expression levels of mRNAs.
Genome-wide association study (GWAS): examination of many common genetic variants in different individuals to see if any variant is associated with a trait; this approach is known as phenotype-first, in which the participants are classified first by their clinical manifestation(s), as opposed to genotype-first. If one type of the variant (one allele) is more frequent in people with the disease, the variant is said to be associated with the disease. In contrast to methods that specifically test one or a few genetic regions, the GWA studies investigate the entire genome. After odds ratios and P-values have been calculated for all SNPs, a common approach is to create a Manhattan plot. In the context of GWA studies, this plot shows the negative logarithm of the P-value as a function of genomic location. Thus the SNPs with the most significant association stands out on the plot, usually as stacks of points because of haploblock structure. Rapidly decreasing price of complete genome sequencing have also provided a realistic alternative to genotyping array-based GWA studies; it can be discussed if the use of this new technique is still referred to as a GWA study, but high-throughput sequencing does have potential to side-step some of the shortcomings of non-sequencing GWA.


CpG site: regions of DNA where a cytosine nucleotide occurs next to a guanine nucleotide in the linear sequence of bases along its length. "CpG" is shorthand for "—C—phosphate—G—", that is, cytosine and guanine separated by only one phosphate; phosphate links any two nucleosides together in DNA. The "CpG" notation is used to distinguish this linear sequence from the CG base-pairing of cytosine and guanine. CpG islands (or CG islands) are regions with a high frequency of CpG sites, though objective definitions for CpG islands are limited. The usual formal definition of a CpG island is a region with at least 200 bp, and a GC percentage that is greater than 50 %, and with an observed-to-expected CpG ratio that is greater than 60 %.
Dutch famine of 1944: children of pregnant women exposed to famine were more susceptible to diabetes, obesity, cardiovascular disease, microalbuminuria...; children of the women who were pregnant during the famine were smaller, as expected. However, surprisingly, when these children grew up and had children those children were also smaller than average. These data suggested that the famine experienced by the mothers caused some kind of epigenetic changes that were passed down to the next generation.
Överkalix study: study conducted on the physiological effects of various environmental factors on transgenerational epigenetic inheritance. The study was conducted utilizing historical records, including harvests and food prices, in Överkalix, a small isolated municipality in northeast Sweden. The study was of 303 probands, 164 men and 139 women, born in 1890, 1905, or 1920, and their 1,818 children and grandchildren. 44 were still alive in 1995 when mortality follow-up stopped. Mortality risk ratios (RR) on children and grandchildren were determined based on available food supply, as indicated by historical data. The paternal grandfather's food supply was only linked to the mortality RR of grandsons and not granddaughters. The paternal grandmother's food supply was only associated with the granddaughters' mortality risk ratio.

Transcription factors[edit]

Category:Transcription factors
Category:Forkhead transcription factors
FOX proteins (Forkhead box): family of transcription factors that play important roles in regulating the expression of genes involved in cell growth, proliferation, differentiation, and longevity. Many FOX proteins are important to embryonic development. Founding member and namesake of the FOX family is the fork head transcription factor in Drosophila, discovered by Detlef Weigel and Herbert Jäckle.
Fork head domain: 80-100 aa; binds DNA; "winged helix".
FOXP2 and human evolution: ability of humans to communicate in complex ways through speech and language is unique to this species, where our closest relatives the chimpanzee show a more primitive level of communication

Population genetics[edit]

Category:Population genetics
Genetic history of Europe

Human genetics[edit]

Category:Human genome projects
Category:Genetic epidemiology
Human chromosomes (Template:Chromosomes)
Pseudoautosomal region, PAR1 and PAR2: homologous sequences of nucleotides on the X and Y chromosomes
Human genome: complete set of nucleic acid sequence for humans (Homo sapiens), encoded as DNA within the 23 chromosome pairs in cell nuclei and in a small DNA molecule found within individual mitochondria. Human genomes include both protein-coding DNA genes and noncoding DNA. Haploid human genomes, which are contained in germ cells (the egg and sperm gamete cells created in the meiosis phase of sexual reproduction before fertilization creates a zygote) consist of three billion DNA base pairs, while diploid genomes (found in somatic cells) have twice the DNA content. While there are significant differences among the genomes of human individuals (on the order of 0.1%), these are considerably smaller than the differences between humans and their closest living relatives, the chimpanzees (approximately 4%) and bonobos. There are an estimated 20,000-25,000 human protein-coding genes (about 1.5% of whole genome), the rest is associated with non-coding RNA, regulatory DNA sequences, LINEs, SINEs, introns, and noncoding DNA (no function yet found). Size of protein-coding genes: median size of an exon is 122 bp (mean = 145 bp), the median number of exons is 7 (mean = 8.8), and the median coding sequence encodes 367 amino acids (mean = 447 amino acids).
Human evolutionary genetics: Speciation of humans and the African apes. Genetic differences between humans and other great apes: Gene loss (80 genes were lost in the human lineage after separation from the last common ancestor with the chimpanzee. 36 of those were for olfactory receptors. Genes involved in chemoreception and immune response are overrepresented.); Hair keratin gene KRTHAP1 (loss of that particular gene may have caused the thinning of human body hair); Myosin gene MYH16 (mutation that led to the inactivation (a two base pair deletion) occurred 2.4 million years ago → marked by a strong increase in cranial capacity). Genetic differences between modern humans and Neanderthals. Sequence divergence between humans and apes.
Human accelerated regions (HARs): set of 49 segments of the human genome that are conserved throughout vertebrate evolution but are strikingly different in humans; named according to their degree of difference between humans and chimpanzees (HAR1 showing the largest degree of human-chimpanzee differences). Several of the HARs encompass genes known to produce proteins important in neurodevelopment. HAR1 sequence is found (and conserved) in chickens and chimpanzees but is not present in fish or frogs that have been studied. HAR2 includes HACNS1 a gene enhancer "that may have contributed to the evolution of the uniquely opposable human thumb, and possibly also modifications in the ankle or foot that allow humans to walk on two legs"; of the 110,000 gene enhancer sequences identified in the human genome, HACNS1 has undergone the most change during the evolution of humans following the split with the ancestors of chimpanzees.
Ultra-conserved element (UCE): region of DNA that is identical in at least two different species
UCbase: 100% identity among human, mouse and rat = 481 UCEs have been identified in the human genome longer than 200 nt

Map of the human mitochondrial DNA genome (16569 bp, NCBI sequence accession NC_012920).
Template:Human genetics:
Human genetic engineering
Human genetic clustering: ~85% of genetic variation is found within groups, ~6–10% between groups within the same continent and ~6–10% is found between continental groups (e.g. Human Genome Project states: "two random individuals from any one group are almost as different [genetically] as any two random individuals from the entire world.", 85% vs 15%). The more markers are used the better one can cluster the individuals into "subgroups", but these "subgroups" depend a bit on the classification/clustering methods used. Heavy statistics and models.
Human Genetic Diversity: Lewontin's Fallacy
Human genetic variation: genetic differences both within and among populations. There may be multiple variants of any given gene in the human population (genes), leading to polymorphism. Many genes are not polymorphic, meaning that only a single allele is present in the population: the gene is then said to be fixed. On average, in terms of DNA sequence all humans are 99.5% similar to any other humans. SNPs, Structural variation, Copy number variation, ...
Human geneology:
Human Y-chromosome DNA haplogroup: male line (father to son), so the longer ago in history, the smaller the portion of contribution (besides Y chromosome, which has its own doubts), i.e. 1/2 for father, 1/4 for paternal grandfather, for 10 generations back,
Template:Y-chromosome haplogroups by populations:
Y-DNA haplogroups in European populations
Category:Genetic genealogy projects
Human Genome Diversity Project (HGDP): was started by Stanford University's Morrison Institute and a collaboration of scientists around the world; many years of work by Luigi Cavalli-Sforza. Some NGOs, human rights organizations, indigenious communities objected to the project; concern about misuse of the gathered data (also: insurance and genetic sequencing).
Genographic Project: Indigenous Peoples Council on Biocolonialism (IPCB) protested against the project because of the connections with HGDP
List of haplogroups of historical and famous figures
Human microbiome
Human Microbiome Project: USA NIH initiative with the goal of identifying and characterizing the microorganisms which are found in association with both healthy and diseased humans (the Human microbiome).
Template:Human group differences
Genetic studies on Jews
Sequencing and interpretation genomes, human genomes[edit]
Category:Repetitive DNA sequences
Human Genome Organisation (HUGO): Human Genome Project (HGP); HGNC is the hugest subgroup of HUGO (bio nomenclature).
Knome: sells human whole genome and exome (exons) analysis and sequencing services to researchers and consumers.
1000 Genomes Project (launched 2008.01): international research effort to establish by far the most detailed catalogue of human genetic variation. Scientists plan to sequence the genomes of at least 1000 anonymous participants from a number of different ethnic groups till 2012[???], using newly developed technologies which are faster and less expensive. In late 2010: production phase with a target - upwards of 2000 individuals. UK (Wellcome Trust Sanger Institute), PRC (Beijing Genomics Institute, Shenzhen), USA (NHGRI).
Personal Genome Project: long term, large cohort study which aims to sequence and publicize the complete genomes and medical records of 100,000 volunteers, in order to enable research into personalized medicine.
Hendrikje van Andel-Schipper#Genome: senility research; old-age disease research (cardiovascular; various dementias)
Beijing Genomics Institute (BGI): one of the world’s premier genome sequencing centers
ENCODE (Encyclopedia of DNA Elements): public research project launched by the US National Human Genome Research Institute (NHGRI) in September 2003. Intended as a follow-up to the Human Genome Project, the ENCODE project aims to identify all functional elements in the human genome.
Retrotransposon: (transposons via RNA intermediates): genetic elements that can amplify themselves in a genome and are ubiquitous components of the DNA of many eukaryotic organisms. They are one of the two subclasses of transposon, where the other is DNA transposon, which does not involve an RNA intermediate. They are particularly abundant in plants, where they are often a principal component of nuclear DNA. In maize, 49–78% of the genome is made up of retrotransposons. In wheat, about 90% of the genome consists of repeated sequences and 68% of transposable elements. In mammals, almost half the genome (45% to 48%) is transposons or remnants of transposons. Around 42% of the human genome is made up of retrotransposons, while DNA transposons account for about 2–3%.
LTR retrotransposons:
Long terminal repeat (LTR): dentical sequences of DNA that repeat hundreds or thousands of times found at either end of retrotransposons or proviral DNA formed by reverse transcription of retroviral RNA.
Non-LTR retrotransposons:
Long interspersed nuclear element (LINE): group of non-LTR retrotransposons which are widespread in the genome of many eukaryotes. They make up around 20% of the human genome. LINEs make up a family of transposons, where each LINE is about 7000 bp long.
SINEs: Short Interspersed Nuclear Elements are short DNA sequences (<500 bases) that represent reverse-transcribed RNA molecules originally transcribed by RNA polymerase III into transfer RNA, 5S ribosomal RNA, and other small nuclear RNAs. The mechanism of retrotransposition of these elements is more complicated than LINEs, and less dependent solely on the actual elements that they encode. SINEs do not encode a functional reverse transcriptase protein and rely on other mobile elements for transposition. In some cases they may have their own endonuclease that will allow them to cleave their way into the genome, but the majority of SINEs integrate at chromosomal breaks by using random DNA breaks to prime reverse transcriptase. With about 1,500,000 copies, SINEs make up about 11% of the human genome.
Alu element: short stretch of DNA originally characterized by the action of the Alu (Arthrobacter luteus) restriction endonuclease. Alu elements of different kinds occur in large numbers in primate genomes. In fact, Alu elements are the most abundant transposable elements in the human genome. They are derived from the small cytoplasmic 7SL RNA, a component of the signal recognition particle. The event, when a copy of the 7SL RNA became a precursor of the Alu elements, took place in the genome of an ancestor of Supraprimates. There are over one million Alu elements interspersed throughout the human genome, and it is estimated that about 10.7% of the human genome consists of Alu sequences.
Variable number tandem repeat (VNTR): location in a genome where a short nucleotide sequence is organized as a tandem repeat. These can be found on many chromosomes, and often show variations in length between individuals.
Minisatellite: tract of repetitive DNA in which certain DNA motifs (ranging in length from 10–60 base pairs) are typically repeated 5-50 times.
Microsatellite: tract of repetitive DNA in which certain DNA motifs (ranging in length from 2–5 base pairs) are repeated, typically 5–50 times.

Sequencing DNA, RNA[edit]

DNA sequencing:
gel (microfluidic: :Sanger method and its comparison to other methods in 2009 Feb.)
pyrosequencing (454)
Polony sequencing: multiplex sequencing technique
Ion semiconductor sequencing (aka: ion torrent sequencing, pH-mediated sequencing, silicon sequencing, or semiconductor sequencing): detection of hydrogen ions that are released during the polymerization of DNA. Released Feb., 2010.
future: sequencing by hybridization, mass spectrometry, electron microscopy, AFM, ...

{q.v. #Bioinformatics}

Wikipedia:WikiProject RNA
Wikipedia:Wikiproject RNA/external links: number of good databases for RNA that might be consulted for further information: Rfam, The noncoding RNA database, RNAdb: mammalian noncoding RNA database, fRNAdb: functional RNA database, miRBase: microRNA database, methylation guide snoRNA database, snoRNAbase: human H/ACA and C/D box snoRNA database, tRNA database, tmRDB: database of tmRNA sequences, ...



Gender, sex, reproductive biology[edit]

Sex-determination system (sex chromosomes (gonosomes)): biological system that determines the development of sexual characteristics in an organism. Determination genetically is generally through chromosome combinations of XY, ZW, XO, ZO, or haplodiploid.
Heterogametic sex (digametic sex): sex of a species in which the sex chromosomes are not the same, e.g. human and Drosophila males have an X and a Y sex chromosome, while birds' and some reptiles' females have one Z and one W chromomose. The opposite is referred to as the homogametic sex (females for humans and Drosophila, while males for birds and some reptiles).
Reproductive isolation (mechanisms of reproductive isolation; hybridization barriers): collection of mechanisms, behaviors and physiological processes that prevent the members of two different species that cross or mate from producing offspring, or which ensure that any offspring that may be produced is not fertile; maintain the integrity of a species over time, reducing or directly impeding gene flow between individuals of different species, allowing the conservation of each species’ characteristics.


Category:Biological engineering
Category:Biochemical engineering {q.v. User:Kazkaskazkasako/Books/Physical_sciences#Chemical engineering}
Category:Biomedical engineering
Category:Synthetic biology
Category:Tissue engineering
Category:Stem cell research
Biological engineering (bioengineering)
BioBrick standard biological parts: DNA sequences of defined structure and function; they share a common interface and are designed to be composed and incorporated into living cells such as E. coli to construct new biological systems.
International Genetically Engineered Machine (iGEM) competition: worldwide Synthetic Biology competition aimed at undergraduate university students.
Biological systems engineering (biosystems engineering)
Biomedical engineering: application of engineering principles and design concepts to medicine and biology for healthcare purposes; to close the gap between engineering and medicine, combining the design and problem solving skills of engineering with medical and biological sciences to advance health care treatment, including diagnosis, monitoring, and therapy. Regulatory issues: medical device engineering area is among the most heavily regulated fields of engineering, and practicing biomedical engineers must routinely consult and cooperate with regulatory law attorneys and other experts.
Organ-on-a-chip: multi-channel 3-D microfluidic cell culture chip that simulates the activities, mechanics and physiological response of entire organs and organ systems, a type of artificial organ. Organs that have been simulated by microfluidic devices include the heart, the lung, kidney, artery, bone, cartilage, skin and more. Replacing animal testing with organs-on-chips.
Lung on a chip: complex, 3D model of a living, breathing human lung on a microchip. The device is made using human lung and blood vessel cells and it can predict absorption of airborne nanoparticles and mimic the inflammatory response triggered by microbial pathogens.
Synthetic biology[edit]
Category:Synthetic biology
BioBrick: parts are DNA sequences which conform to a restriction-enzyme assembly standard.
Biomedical engineering[edit]


Topics in population genetics (Template:Popgen):
Founder effect

Rare diseases[edit]

Category:Rare diseases
Category:Genetic disorders
Progeroid syndromes: group of rare genetic disorders that mimic physiological aging, making affected individuals appear to be older than they are.
Progeria (Hutchinson–Gilford progeria syndrome): extremely rare genetic disorder wherein symptoms resembling aspects of aging are manifested at a very early age. Farnesyl group remains attached to prelamin A, which is named progerin. Progerin is anchored to the nuclear rim, results in abnormally shaped nucleus.

Genetic diseases[edit]

Rare disease (orphan disease): a window to human mutations (mainly) and some extremely rare pathogens (seldom); lots of discoveries into human biology and genetics.
Finnish disease heritage
European Organization for Rare Diseases (EURORDIS, non-governmental patient-driven alliance of patient organizations and individuals active in the field of rare diseases)
National Organization for Rare Disorders (NORD, American non-profit organization aiming to provide support individuals with rare diseases)
Orphan drug: politics and economics of rare disease treatment
Gene therapy[edit]
Jesse Gelsinger (1981.06.18-1999.09.17): first person publicly identified as having died in a clinical trial for gene therapy. 1999.09.13 he was injected with adenoviral vector carrying corrected gene to test the safety of the procedure; died 4d. later apparently having suffered a massive immune response.
Alipogene tiparvovec (Glybera): gene therapy treatment that compensates for lipoprotein lipase deficiency (LPLD), which can cause severe pancreatitis. In 2012.07, the European Medicines Agency recommended it for approval, the first recommendation for a gene therapy treatment in either Europe or US.


The Race Question: UNESCO statement issued on 18 July 1950 following World War II. No "race", only "ethnic groups". In the current scientific light: "ethnic groups" as everything non-hereditary (culture, language, religion...) while human genetic groups (in the older times called "races") as everything hereditary (genes and from genotypes coming phenotypes).

Cell biology[edit]

Category:Cell biology
Category:Cell anatomy
Subcellular localization: eukaryotes vs prokaryotes
Protein subcellular localization prediction
Pseudo amino acid composition
Low-frequency collective motion in proteins and DNA: solitons
Hayflick limit: number of times a normal human cell population will divide until cell division stops. Empirical evidence shows that the telomeres associated with each cell's DNA will get slightly shorter with each new cell division until they shorten to a critical length.

Cell culture[edit]

Category:Cell culture
Category:Growth media
Category:Microbiological media
Trypticase soy agar (TSA; Tryptone Soya Agar): growth media for the culturing of bacteria. They are general-purpose, non-selective media providing enough nutrients to allow for a wide variety of microorganisms to grow. They are used for a wide range of applications, including culture storage, enumeration (counting), isolation of pure cultures, or simply general culture. TSA contains enzymatic digests of casein and soybean meal, which provides amino acids and other nitrogenous substances, making it a nutritious medium for a variety of organisms. Glucose is the energy source. Sodium chloride maintains the osmotic equilibrium, while dipotassium phosphate acts as buffer to maintain pH. Agar extracted from any number of organisms is used as a gelling agent.
Tryptone: assortment of peptides formed by the digestion of casein by the protease trypsin.
Casein: name for a family of related phosphoproteins (αS1, αS2, β, κ). These proteins are commonly found in mammalian milk, making up 80% of the proteins in cow's milk and between 20% and 45% of the proteins in human milk. Casein has a wide variety of uses, from being a major component of cheese, to use as a food additive, to a binder for safety matches. As a food source, casein supplies amino acids, carbohydrates, and the two inorganic elements calcium and phosphorus.
Cell bank: facility that stores cells of specific genome for the purpose of future use in a product or medicinal needs. They often contain expansive amounts of base cell material that can be utilized for various projects. The advantages of cell banks is that the facilities will include a "detailed characterization of the cell line" and will have a "decrease in the likelihood and an increase in the detection" of cross-contamination of a cell line.
Vero cell: 'Vero' lineage was isolated from kidney epithelial cells extracted from an African green monkey (Chlorocebus sp.; formerly called Cercopithecus aethiops, this group of monkeys has been split into several different species). The lineage was developed in 1962.03.27, by Yasumura and Kawakita at the Chiba University in Chiba, Japan.
Chinese hamster ovary cell (CHO)

Cell nucleus[edit]

{q.v. #RNA processing; #Spliceosome, splicing}

Cell nucleus: membrane-enclosed organelle found in eukaryotic cells; contains most of the cell's genetic material, organized as multiple long linear DNA molecules in complex with a large variety of proteins, such as histones, to form chromosomes. Nuclear envelope; Nuclear pores; Nuclear lamina; Chromosomes; subnuclear bodies: Nucleolus; Cajal bodies and gems; RAFA and PTF domains; PML bodies; Paraspeckles; Splicing speckles (At the fluorescence-microscope level they appear as irregular, punctate structures, which vary in size and shape, and when examined by electron microscopy they are seen as clusters of interchromatin granules). Nuclear transport; Assembly and disassembly. Anucleated and multinucleated cells.
Cajal body (CB): spherical sub-organelles of 0.3-1.0 µm in diameter found in the nucleus of proliferative cells like embryonic cells and tumor cells, or metabolically active cells like neurons (hence the finding by Santiago Ramón y Cajal in 1903: nucleolar accessory bodies); largely consisting of proteins and RNA. Rediscovered by electron microscopists and named coiled bodies, according to their appearance as coiled threads on EM images, and later renamed after their discoverer. Marker protein: p80/coilin. Implicated in RNA-related metabolic processes such as snRNP biogenesis, maturation and recycling, histone mRNA processing and telomere maintenance
Nuclear dots ("Nuclear bodies", "nuclear domains", "PML bodies")
Paraspeckle: irregularly shaped, 0.2-1 μm in size, found in the nucleus' interchromatin space; "para" is short for parallel and the "speckle" refers to the splicing speckles to which they are always in close proximity; function not known [2013], but they may localize proteins in the nucleus; in the absence of RNA polymerase II transcription the paraspeckle disappears

Cell cycle, cell division[edit]

Category:Cell cycle
Image of the mitotic spindle in a human cell: microtubules - green, chromosomes - blue, kinetochores - red.
Cell cycle checkpoint: control mechanisms in eukaryotic cells which ensure proper division of the cell. Three known checkpoints: the G1 checkpoint, also known as the restriction or start checkpoint; the G2/M checkpoint; and the metaphase checkpoint, also known as the spindle checkpoint.
Spindle checkpoint: prevents separation of the duplicated chromosomes until each chromosome is properly attached to the spindle apparatus. Spindle assembly checkpoint (SAC).
Aurora kinases: serine/threonine kinases that are essential for cell proliferation. The enzyme helps the dividing cell dispense its genetic materials to its daughter cells. More specifically, Aurora kinases play a crucial role in cellular division by controlling chromatid segregation. Defects in this segregation can cause genetic instability, a condition which is highly associated with tumorigenesis. Elevated expression profiles in many human cancers.
Aurora A kinase (serine/threonine-protein kinase 6; AURKA): activity peaks during the G2 phase to M phase transition in the cell cycle. Aurora A is critical for proper formation of mitotic spindle; required for the recruitment of several different proteins important to the spindle formation.
Aurora B kinase: attachment of the mitotic spindle to the centromere. Aurora B localizes to the chromosomes in prophase, the centromere in prometaphase and metaphase, and the central mitotic spindle in anaphase. Inhibition of Aurora B function by RNA interference or microinjection of blocking antibodies impairs the alignment of chromosomes at the equator of the mitotic spindle.
Aurora C (AURKC)
Aurora inhibitor

Developmental bio[edit]

X-inactivation: random in placental mammals, inactivation in marsupials applies exclusively to the paternally derived X chromosome
Anencephaly: cephalic disorder that results from a neural tube defect that occurs when the rostral (head) end of the neural tube fails to close, usually between the 23rd and 26th day of conception, resulting in the absence of a major portion of the brain, skull, and scalp. With very few exceptions, most babies with this disorder do not survive.
Baby K (1992-1995): was an anencephalic baby who became the center of a major U.S. court case and a debate among bioethicists; kept alive much longer than most anencephalic babies.


Wrongful birth: legal cause of action in some common law countries in which the parents of a congenitally diseased child claim that their doctor failed to properly warn of their risk of conceiving or giving birth to a child with serious genetic or congenital abnormalities. Wrongful conception (vasectomy, tubal ligation, or other sterilization procedure); Wrongful adoption.
Wrongful life: name given to a legal action in which someone is sued by a severely disabled child (through the child's legal guardian) for failing to prevent the child's birth.


Category:Neural engineering

{q.v. #Cognitive science, cognitive neuroscience, computational neuroscience, brain, mind, mental health, psychology, psychiatry}

Neuroscience Information Framework (NIF): repository of global neuroscience web resources, including experimental, clinical, and translational neuroscience databases, knowledge bases, atlases, and genetic/genomic resources and provides many authoritative links throughout the neuroscience portal of wikipedia.
NeuroLex: dynamic lexicon of neuroscience concepts; structured as a semantic wiki, using Semantic MediaWiki

Soliton vs Hodgin-Huxley model:

Hodgkin–Huxley model: mathematical model (a type of scientific model) that describes how action potentials in neurons are initiated and propagated. It is a set of nonlinear ordinary differential equations that approximates the electrical characteristics of excitable cells such as neurons and cardiac myocytes.
Soliton model: proposes that the signals travel along the cell's membrane in the form of certain kinds of sound (or density) pulses known as solitons.
Mirror test: animals that have passed the mirror test: mainly mammals: all great apes, 3*Gibbons, Bottlenose dolphins, orcas, elephants, and:
European Magpie (Pica pica): the most intelligent bird, one of the most intelligent animals. The pairs are monogamous, and remain together for the duration of their lives. Should one of the two die, the widow or widower will find a new partner from the stock of yearlings. Possible subspieces or neighboring species: Korean Magpie (Asian, Chinese Magpie), Yellow-billed Magpie (California), Black-billed Magpie (N. America)
List of animals by number of neurons: Whole nervous system; Cerebral cortex.
Encephalization quotient (EQ, encephalization level): measure of relative brain size defined as the ratio between actual brain mass and predicted brain mass for an animal of a given size, which is hypothesized to be a rough estimate of the intelligence of the animal. More refined than raw brain-to-body mass ratio by taking allometric effects. Ew(brain) = 0.12w(body)2/3. EQ(human)=7.44, EQ(tucuxi dolphin)=4.56, EQ(bottlenose dolphin)=4.14, EQ(chimp)=2.49, EQ(dog)=1.17, EQ(cat)=1.00, EQ(mouse)=0.5
Dolphin intelligence
Behavioral contagion: propensity for certain behavior exhibited by one person to be copied by others either in the vicinity of the original user, or who have been exposed to media coverage describing the behavior of the original actor.
Neural top down control of physiology: direct regulation by the brain of physiological functions (in addition to smooth muscle and glandular ones). Regulation occurs through the sympathetic and parasympathetic system (the autonomic nervous system), and their direct innervation of body organs and tissues that starts in the brainstem. There is also a noninnervation hormonal control through the hypothalamus and pituitary (HPA). These lower brain areas are under control of cerebral cortex ones. Pavlovian conditioning shows that brain control over basic cell level physiological function can be learnt.
Mind uploading (whole brain emulation, mind transfer): hypothetical process of transferring or copying a conscious mind from a brain to a non-biological substrate by scanning and mapping a biological brain in detail and copying its state into a computer system or another computational device. The computer would have to run a simulation model so faithful to the original that it would behave in essentially the same way as the original brain, or for all practical purposes, indistinguishably.
Blue Brain Project (BBP): attempt to create a synthetic brain by reverse-engineering the mammalian brain down to the molecular level. Simulation of rat neocortical column (2 mm tall, 0.5 mm in diameter, 108 synapses) was completed in 2006.12.
Human Brain Project (HBP): research project which aims to simulate (with supercomputers) and better understand the human brain. EU gave >1 bln € to this project.
Tonic–clonic seizure (formerly: grand mal seizures): type of generalized seizure that affects the entire brain; most commonly associated with epilepsy and seizures in general, though it is a misconception that they are the only type.
Electroconvulsive therapy (ECT; formerly: electroshock therapy): standard psychiatric treatment in which seizures are electrically induced in patients to provide relief from psychiatric illnesses. ECT is usually used as a last line of intervention for major depressive disorder, schizophrenia, mania and catatonia. Administered under anesthetic with a muscle relaxant. Although a large amount of research has been carried out, the exact mechanism of action of ECT remains elusive, and successful ECT is usually followed by medication treatment.
Brain stimulation reward: phenomenon in which direct stimulation of regions of the brain through either electrical or chemical means is rewarding and can serve as an operant reinforcer; stimulation activates the reward system and establishes response habits similar to those established by natural rewards such as food and water; stimulation of the lateral hypothalamus and other regions of the brain associated with natural reward was both rewarding as well as drive inducing. Relationship to natural rewards and drives: Strength of drive: Rats will perform lever-pressing at rates of several thousand responses per hour for days in order to obtain direct electrical stimulation of the lateral hypothalamus; Addiction: Rats and monkeys have been shown to work in a compulsive manner to achieve intravenous injections of stimulants, and when access to the drugs is not limited, they will self-administer the drugs to the point of severe weight loss and death.
Operant conditioning (instrumental conditioning): type of learning in which an individual's behavior is modified by its antecedents and consequences
Deep brain stimulation (DBS): surgical treatment involving the implantation of a medical device called a brain pacemaker, which sends electrical impulses to specific parts of the brain. Possible therapeutic benefits for chronic pain, Parkinson's, tremor, dystonia; sexual arousal; tested on patients with post-tramatic coma; could change behavior drastically. Despite the long history of DBS, its underlying principles and mechanisms are still not clear.
Wirehead (science fiction): when fiction meets DBS.
Brain stimulation reward: phenomenon in which direct stimulation of regions of the brain through either electrical or chemical means is rewarding and can serve as an operant reinforcer. The stimulation activates the reward system and establishes response habits similar to those established by natural rewards such as food and water.
P300 (neuroscience): event related potential (ERP) component elicited in the process of decision making. It is considered to be an endogenous potential, as its occurrence links not to the physical attributes of a stimulus, but to a person's reaction to it. When recorded by electroencephalography (EEG), it surfaces as a positive deflection in voltage with a latency (delay between stimulus and response) of roughly 250 to 500 ms.

Cognitive science, cognitive neuroscience, computational neuroscience, brain, mind, mental health, psychology, psychiatry[edit]

Category:Cognitive science
Category:Cognitive neuroscience
Category:Neuropsychological assessment
Category:Memory processes
Category:Biomedical cybernetics
Category:Computational neuroscience
Category:Cognitive science
Category:Mental health
Category:History of mental health
Category:Clinical psychology



Cognitive science: interdisciplinary scientific study of the mind and its processes; includes research on intelligence and behavior, especially focusing on how information is represented, processed, and transformed (in faculties such as perception, language, memory, reasoning, and emotion) within nervous systems (human or other animal) and machines (e.g. computers). Multiple research disciplines, including psychology, artificial intelligence, philosophy, neuroscience, linguistics, and anthropology.
Computational neuroscience (theoretical neuroscience): study of brain function in terms of the information processing properties of the structures that make up the nervous system. It is an interdisciplinary science that links the diverse fields of neuroscience, cognitive science, and psychology with EECS, mathematics, and physics. Computational neuroscience is distinct from psychological connectionism and from learning theories of disciplines such as machine learning, neural networks, and computational learning theory in that it emphasizes descriptions of functional and biologically realistic neurons (and neural systems) and their physiology and dynamics. Major topics: Single-neuron modeling; Development, axonal patterning, and guidance; Sensory processing; Memory and synaptic plasticity; Behaviors of networks (connections are, unlike most ANNs, sparse and usually specific); Cognition, discrimination, and learning; Consciousness; Computational clinical neuroscience.
Center for Applied Rationality: organisation based in the San Francisco Bay Area, Berkeley, CA whose focus is to "[take] the results of cognitive science research, and turn them into techniques that people can practice and use in their own lives." It was created in mid-2012, by Julia Galef a statistician, writer, and prominent figure in the skeptic movement, Anna Salamon, an ex-researcher from NASA and the Machine Intelligence Research Institute, and two Mathematics PhD holders, Michael Smith and Andrew Critch. CFAR develops and tests strategies of cognitive tools and triggers that are known from research in the field of cognitive science on how people form and change their beliefs.
Bayesian approaches to brain function: investigate the capacity of the nervous system to operate in situations of uncertainty in a fashion that is close to the optimal prescribed by Bayesian statistics. This term is used in behavioural sciences and neuroscience and studies associated with this term often strive to explain the brain's cognitive abilities based on statistical principles.
Sparse distributed memory (SDM): mathematical model of human long-term memory introduced by Pentti Kanerva in 1988 while he was at NASA Ames Research Center. It is a generalized random-access memory (RAM) for long (e.g., 1,000 bit) binary words. These words serve as both addresses to and data for the memory. The main attribute of the memory is sensitivity to similarity, meaning that a word can be read back not only by giving the original write address but also by giving one close to it, as measured by the number of mismatched bits (i.e., the Hamming distance between memory addresses).
Hierarchical temporal memory: unsupervised to semi-supervised online machine learning model developed by Jeff Hawkins and Dileep George of Numenta, Inc. that models some of the structural and algorithmic properties of the neocortex. HTM is a biomimetic model based on the memory-prediction theory of brain function described by Jeff Hawkins in his book On Intelligence. HTM is a method for discovering and inferring the high-level causes of observed input patterns and sequences, thus building an increasingly complex model of the world.
Autobiographical memory: memory system consisting of episodes recollected from an individual's life, based on a combination of episodic (personal experiences and specific objects, people and events experienced at particular time and place) and semantic (general knowledge and facts about the world) memory. Event-specific knowledge (ESK) is vividly detailed information about individual events, often in the form of visual images and sensory-perceptual features. Originating events (events that mark the beginning of a path towards long-term goals), turning points (events that re-direct plans from original goals), anchoring events (events that affirm an individuals beliefs and goals) and analogous events (past events that direct behaviour in the present) are all event specific memories that will resist memory decay. The sensory-perceptual details held in ESK, though short-lived, are a key component in distinguishing memory for experienced events from imagined events. Unlike lifetime periods and general events, ESK are not organized in their grouping or recall; instead, they tend to simply 'pop' into the mind. Remember vs. Know: source of a remembered memory is attributed to personal experience; source of a known memory is attributed to an external source, not personal memory.
Source-monitoring error: type of memory error where a specific recollected experience is incorrectly determined to be the source of a memory. These errors are most prevalent in elderly individuals and young children.
Remember versus know judgements: different processes are involved in remembering something versus knowing whether it is familiar.


Monoamine neurotransmitter: contain one amino group that is connected to an aromatic ring by a two-carbon chain (-CH2-CH2-); derived from aromatic amino acids like phenylalanine, tyrosine, tryptophan, and the thyroid hormones by aromatic amino acid decarboxylase enzymes; function of monoamine is not clear but it is thought to trigger crucial components such as emotion, arousal, and cognition; drugs used to increase the effect of monoamine may be used to treat patients with psychiatric disorders, including depression, anxiety, and schizophrenia.

Vision and brain[edit]

Category:Visual perception
Category:Optical illusions
Blindsight: defined as the ability of people who are cortically blind due to lesions in their striate cortex, also known as primary visual cortex or V1, to respond to visual stimuli that they do not consciously see. There is signal processing all the way from the retinal ganglions to the visual cortex. Damage to visual cortex only leaves the other signal processing intact and the cortically blind can "see". Exact mechanism unknown.
Opponent process: color theory that states that the human visual system interprets information about color by processing signals from cones and rods in an antagonistic manner.
Optical illusions[edit]
Spinning Dancer

Intelligence, IQ[edit]

Heritability of IQ: IQ is a polygenic trait, however, certain single gene genetic disorders can severely affect intelligence, with phenylketonuria as an example. Estimates of heritability vary from below 0.5 to as high as 0.9.
Environment and intelligence: environmental influences: family, peer group, education, training and interventions, environmental enrichment; bio influences: nutrition, exposure to toxic chemicals and other substances (lead, Fetal alcohol spectrum disorder), birth complications (perinatal factors); development of genius; training: musical (Mozart effect: listening to classical music boosts IQ scores in specific area), chess (boosts math and comprehension performance).
G factor (psychometrics) ("general factor"): construct developed in psychometric investigations of cognitive abilities. g is highly heritable; g's biological correlates: brain size.
Genetic Studies of Genius (Terman Study of the Gifted): Terman: "At any rate, we have seen that intellect and achievement are far from perfectly correlated". Longitudinal study begun in 1921.
Flynn effect: substantial and long-sustained increase in intelligence test scores measured in many parts of the world.
Fertility and intelligence: Other correlates of IQ include income and educational attainment, which are also inversely correlated with fertility rate, and are to some degree heritable.


Category:Sleep physiology
Sleep (non-human): nematode C. elegans is the most primitive organism in which sleep-like states have been observed. Sleep in fish is not extensively studied; EEG pattern in reptilian sleep differs from what is seen in mammals and other animals; significant similarities between sleep in birds and sleep in mammals, which is one of the reasons for the idea that sleep in higher animals with its division into REM and NREM sleep has evolved together with warm-bloodedness (opinions partly differ about sleep in migratory birds); mammals: daily need for sleep is highest in carnivores, lower in omnivores and lowest in herbivores. Unihemispheric sleep: birds, some aquatic mammals, maybe certain species of lizards. Eared seals and whales show unihemispheric sleep; earless seals sleep bihemispherically like most mammals.
Torpor: umbrella-term used to categorize a state of regulated metabolic suppression in animals, typically to levels below what are normally essentially the minimum, so-called, basal metabolic rate (BMR); this does not exclude the possibility that torpor can be triggered from an elevated metabolic position and may terminate before reaching below BMR (e.g. diving).


Hemispherectomy: very rare surgical procedure where one cerebral hemisphere (half of the brain) is removed or disabled.
Ahad Israfil: gunshot victim from Dayton, Ohio, remarkable for his recovery from an injury that destroyed most of one of his cerebral hemispheres.
Split-brain: lay term to describe the result when the corpus callosum connecting the two hemispheres of the brain is severed to some degree; surgical operation to produce this condition is called corpus callosotomy, and is usually a last resort to treat refractory epilepsy. After surgery, neuropsychological assessments are often performed to determine where functions of the brain are lateralized. For example, language is said to be lateralized in the left hemisphere while facial recognition is said to be lateralized in the right hemisphere. "Scientists have often wondered whether split-brain patients, who have had the two hemispheres of their brain surgically disconnected, are 'of two minds'" (Zilmer, 2001). Initially, partial callosotomies are performed; if this operation does not succeed, a complete callosotomy is performed to mitigate the risk of accidental physical injury by reducing the severity and violence of epileptic seizures.

Mind, psychology, mental health, psychiatry[edit]

Wilhelm Reich (1897.03.24–1957.11.03) was an Austrian psychoanalyst. Author of several influential books – most notably Character Analysis (1933), The Mass Psychology of Fascism (1933) and The Sexual Revolution (1936) – Reich became known as one of the most radical practitioners of psychiatry.
  • His father was by all accounts a cold and jealous man. Both parents were Jewish, but decided against raising the boys as Jews. Reich and his brother, Robert, were brought up to speak only German, were punished for using Yiddish expressions and forbidden from playing with the local Yiddish-speaking children.
  • As an adult, Reich wrote extensively in his diary of his sexual precocity. He maintained that his first sexual experience was at the age of four when he tried to have sex with the family maid (with whom he shared a bed), that he would regularly watch the animals have sex, that he used a whip handle sexually on the horses while masturbating, and that he had almost daily sexual intercourse from the age of 11 with another of the servants. He wrote of regular visits to brothels, the first of which occurred when he was 15 years old, and said he was visiting them daily from the age of about 17. He also developed sexual fantasies about his mother, writing when he was 22 that he masturbated while thinking about her. It is impossible to judge the truth of these diary entries, but Reich's second daughter, psychiatrist Lore Reich Rubin, told Christopher Turner that she believed Reich had been a victim of child sexual abuse, and that this explained his lifelong interest in sex and childhood sexuality.
  • Orgastic potency, Rest cure in Switzerland (TB), Orgonomy
Category:Branches of psychology
Category:Applied psychology
Category:Clinical psychology


Template:Jungian psychology (Analytical psychology):
Psychometrics and Employment testing, Myers-Briggs Type Indicator, Keirsey Temperament Sorter
Personality test: Sexological testing, Online dating service & Comparison of online dating websites: even more subjective than psychology? Can few questions find the "personality type"?
Basic science (psychology): concern of psychology as a basic science is in understanding the laws and processes that underlie behavior, cognition, and emotion. Abnormal psychology; Biological psychology (Neuropsychology, Physiological psychology, Cognitive neuroscience); Cognitive psychology; Developmental psychology; Experimental psychology; Evolutionary psychology; Mathematical psychology; Neuropsychology; Personality psychology; Psychophysics; Social psychology.
Differential psychology: studies the ways in which individuals differ in their behavior.
Personality psychology: studies personality and its variation between individuals.
Applied psychology: Clinical psychology; Educational psychology; Forensic psychology and legal psychology; Health psychology; Human factors and ergonomics; Industrial and organizational psychology; Neuropsychology; Occupational health psychology; School psychology; Sport psychology (related to exercise psychology); Environmental psychology.
Asch conformity experiments: "When the confederates are not unanimous in their judgment, even if only one confederate voices a different opinion, participants are much more likely to resist the urge to conform than when the confederates all agree. This finding illuminates the power that even a small dissenting minority can have. Interestingly, this finding holds whether or not the dissenting confederate gives the correct answer. As long as the dissenting confederate gives an answer that is different from the majority, participants are more likely to give the correct answer."
Mass psychogenic illness (MPI; mass sociogenic illness): "the rapid spread of illness signs and symptoms affecting members of a cohesive group, originating from a nervous system disturbance involving excitation, loss or alteration of function, whereby physical complaints that are exhibited unconsciously have no corresponding organic aetiology"
Dancing mania (dancing plague, choreomania, St John's Dance, historically: St. Vitus' Dance; 14th-17th c.): social phenomenon that occurred primarily in mainland Europe.
Dancing Plague of 1518: case of dancing mania that occurred in Strasbourg, Alsace (then part of the Holy Roman Empire). Numerous people took to dancing for days without rest, and, over the period of about one month, some of the people died from heart attack, stroke, or exhaustion.
Tanganyika laughter epidemic (1962): outbreak of mass hysteria rumored to have occurred in or near the village of Kashasha on the western coast of Lake Victoria in the modern nation of Tanzania (formerly Tanganyika) near the border of Kenya.
Diagnostic and Statistical Manual of Mental Disorders (DSM): current version, published on 2013.05.18, is the DSM-5 (fifth edition).
Personality disorder
Wikipedia:Copyright problems/2010 March 9#DSM Complaint .28Ticket:2010030910040817.29: publisher of DSM complained about the copyrighted material usage on Wikipedia.
Trait theory: approach to the study of human personality; measurement of traits, which can be defined as habitual patterns of behavior, thought, and emotion; traits are relatively stable over time, differ across individuals (e.g. some people are outgoing whereas others are shy), and influence behavior. Virtually all trait models, and even ancient Greek philosophy, include extraversion vs. introversion as a central dimension of human personality; another prominent trait that is found in nearly all models is Neuroticism, or emotional instability.
Mental breakdown (nervous breakdown): colloquial term for an acute, time-limited psychiatric disorder that manifests primarily as severe stress-induced depression, anxiety or dissociation in a previously functional individual, to the extent that they are no longer able to function on a day-to-day basis until the disorder is resolved.
Impostor syndrome (impostor phenomenon, fraud syndrome): psychological phenomenon in which people are unable to internalize their accomplishments.
Attribution (psychology): process by which individuals explain the causes of behavior and events
Category:Positive psychology
Category:Social psychology
Positive psychology: branch of psychology that uses scientific understanding and effective intervention to aid in the achievement of a satisfactory life, rather than treating mental illness. Concerned with four topics: (1) positive experiences, (2) enduring psychological traits, (3) positive relationships and (4) positive institutions. Midlife crisis: researchers specify people in both their 20s and 70s are happier than during midlife, although the extent of happiness changes at different rates, e.g., feelings of stress and anger tend to decline after age 20, worrying drops after age 50, and enjoyment very slowly declines in adulthood but finally starts to rise after age 50. "Proven fact married people are happier than unmarried people". Happiness tended to spread through close relationships like friends, siblings, spouses, and next-door neighbors; researchers reported happiness spread more consistently than unhappiness through the network; "eight hugs a day, you'll be happier, and the world will be a better place".
Culture and positive psychology
Meaningful life: broad term encompassing a varied number of definitions having to do with the pursuit of life satisfaction. While the specific theories vary, there are two common aspects: a global way to understand one's life and the belief that life itself is meaningful. Those possessing a sense of meaning are generally found to have lower levels of negative emotions and lower risk of mental illness. Through the structured society we are able to create a symbolic immortality which can take various forms, e.g., monuments, theatrical productions, children, etc. Culture's order reduces death anxiety as it allows the individual to live up to the societal standards and in living up to such ideals; one is given self-esteem which counterbalances the mortal anxiety.
Carol Dweck: according to Dweck, individuals can be placed on a continuum according to their implicit views of where ability comes from. Some believe their success is based on innate ability; these are said to have a "fixed" theory of intelligence (fixed mindset). Others, who believe their success is based on hard work, learning, training and doggedness are said to have a "growth" or an "incremental" theory of intelligence (growth mindset). Dweck argues that the growth mindset will allow a person to live a less stressful and more successful life. For example, children given praise such as "good job, you're very smart" are much more likely to develop a fixed mindset, whereas if given compliments like "good job, you worked very hard" they are likely to develop a growth mindset.


Anxiety Arousal Flow (psychology) Control (psychology) Relaxation (psychology) Boredom Apathy Worry
Mental state in terms of challenge level and skill level, according to Csikszentmihalyi's flow model.[2][page needed] (Click on a fragment of the image to go to the appropriate article)
Category:Psychological states
Altered state of consciousness
Flow (psychology): mental state of operation in which a person performing an activity is fully immersed in a feeling of energized focus, full involvement, and enjoyment in the process of the activity. In essence, flow is characterized by complete absorption in what one does. Flow has many of the same characteristics as (the positive aspects of) hyperfocus. However, hyperfocus is not always described in a positive light. Some examples include spending "too much" time playing video games or getting side-tracked and pleasurably absorbed by one aspect of an assignment or task to the detriment of the overall assignment. Education; Music; Sports; Religion and spirituality; Gaming: game designers strive to integrate flow principles into their projects
Category:Organizational behavior
Self-determination theory: macro theory of human motivation and personality that concerns people's inherent growth tendencies and innate psychological needs. It is concerned with the motivation behind choices people make without external influence and interference.
Occupational burnout (job burnout): characterized by exhaustion, lack of enthusiasm and motivation, feelings of ineffectiveness, and also may have the dimension of frustration or cynicism, and as a result reduced efficacy within the workplace. Burnout is becoming a more common result as the modern workplace changes.
Boreout: management theory that posits that lack of work, boredom, and consequent lack of satisfaction are a common malaise affecting individuals working in modern organizations, especially in office-based white collar jobs.
Plutchik's Wheel of Emotions


Contrasting and categorization of emotions: describes how emotions are thought to relate to each other. Various recent proposals of such groupings are described in the following sections.
Pleasure: broad class of mental states that humans and other animals experience as positive, enjoyable, or worth seeking. It includes more specific mental states such as happiness, entertainment, enjoyment, ecstasy, and euphoria.
Boredom: boredom can be a symptom of clinical depression. Boredom related to drug abuse, pathological gambling (hypothesis that pathological gamblers seek stimulation to avoid states of boredom and depression).
I am lonely will anyone speak to me
Gallows humor (de:Galgenhumor): humor in the face of or about very unpleasant, serious, or painful circumstances. Any humor that treats serious matters, such as death, war, disease, crime, etc., in a light, silly or satirical fashion is considered gallows humor. Gallows humor is typically made by or about the victim of such a situation, but not the perpetrator of it.

Category:Psychiatry-related fields
Category:Clinical psychology
Psychiatry: medical specialty devoted to the study, diagnosis, treatment, and prevention of mental disorders, among which are affective, behavioural, cognitive and perceptual abnormalities.
Rosenhan experiment: was a famous experiment done in order to determine the validity of psychiatric diagnosis, conducted by psychologist David Rosenhan and published by the journal Science in 1973 under the title "On being sane in insane places"; study is considered an important and influential criticism of psychiatric diagnosis. The study concluded "it is clear that we cannot distinguish the sane from the insane in psychiatric hospitals" and also illustrated the dangers of dehumanization and labeling in psychiatric institutions. Rosenhan and the other pseudopatients reported an overwhelming sense of dehumanization, severe invasion of privacy, and boredom while hospitalized.
Anti-psychiatry: view that psychiatric treatments are ultimately more damaging than helpful to patients. According to anti-psychiatry, psychiatry involves an unequal power relationship between doctor and patient, and a highly subjective diagnostic process, leaving too much room for opinions and interpretations. Dangerous treatments from before in medicine/psychiatry: electroconvulsive therapy, lobotomy, over-prescription of Valium and other sedatives; immediate concern lies in the significant increase in prescribing psychiatric drugs for children. Contemporary issues: freedom vs coercion, mind vs brain, nature vs nurture, and the right to be different. Some ex-patient groups have become anti-psychiatric, often referring to themselves as "survivors" rather than patients. Challenges to psychiatry: Civilization as a cause of distress; Normality and illness judgments (Asperger syndrome or autism: "neurodiversity" and "neurotypical"); Psychiatric labeling; Tool of social control (According to Franco Basaglia, Giorgio Antonucci and Bruce E. Levine, whose approach pointed out the role of psychiatric institutions in the control and medicalization of deviant behaviors and social problems, psychiatry is used as the provider of scientific support for social control to the existing establishment, and the ensuing standards of deviance and normality brought about repressive views of discrete social groups); Psychiatry and the pharmaceutical industry; Political abuse of psychiatry (USSR); "Therapeutic State" (Thomas Szasz: "modern man has no more right to be a madman than medieval man had a right to be a heretic because if once people agree that they have identified the one true God, or Good, it brings about that they have to guard members and nonmembers of the group from the temptation to worship false gods or goods", separation of church and state → separation of psychiatry and state); "Total Institution" (Goffman placed psychiatric hospitals in the same category as concentration camps, prisons, military organizations, orphanages, and monasteries; institutionalisation process socialises people into the role of a good patient, someone ‘dull, harmless and inconspicuous’). Psychiatry as pseudoscience and failed enterprise. 1990s+: Anti-psychiatry crusades have thus been charged with failing to put suffering individuals first, and therefore being similarly guilty of what they blame psychiatrists for; rise of anti-psychiatry in Italy was described by one observer as simply "a transfer of psychiatric control from those with medical knowledge to those who possessed socio-political power".
Psychiatric survivors movement (consumer/survivor/ex-patient movement)
Political abuse of psychiatry: abuse of psychiatry including one for political purposes is deliberate action of getting citizens certified, who, because of their mental condition, need neither psychiatric restraint nor psychiatric treatment. Psychiatrists have been involved in human rights abuses in states across the world when the definitions of mental disease were expanded to include political disobedience.
Political abuse of psychiatry in the Soviet Union
Psikhushka: Russian ironic diminutive for psychiatric hospital
Asylums (book) (1961 by Erving Goffman): was a key text in the development of deinstitutionalization.
Deinstitutionalisation (deinstitutionalization): process of replacing long-stay psychiatric hospitals with less isolated community mental health services for those diagnosed with a mental disorder or developmental disability.
Care in the Community: British policy of deinstitutionalization, treating and caring for physically and mentally disabled people in their homes rather than in an institution.
Psychiatric reform in Italy: after the passing of Basaglia Law in 1978 and terminated with the very end of the Italian state mental hospital system in 1998. Among European countries, Italy was the first to publicly declare its repugnance for a mental health care system which led to social exclusion and segregation.
Diagnostic and Statistical Manual of Mental Disorders (DSM): provides a common language and standard criteria for the classification of mental disorders.
DSM-5 (2013.05.18)

Model organisms[edit]

Template:Model Organisms:

Schizosaccharomyces pombe (fission yeast) & Saccharomyces cerevisiae (budding yeast):
Schizosaccharomyces pombe#Comparison with budding yeast (Saccharomyces cerevisiae)
  • diverged 300-600 mya
  • cerevisiae: 250 introns; pombe: ~5000
  • cerevisiae: 16 chromosomes; pombe: 3
  • cerevisiae: often diploid; pombe: often haploid
  • cerevisiae: in G1 phase (cell cycle) for an extended period (G1-S transition tightly controlled); pombe: in G2 (G2-M transition tightly controlled)
  • both share genes with higher eukaryotes that they do not share with each other: pombe: RNAi machinery genes; cerevisiae has greatly simplified heterochromatin compared to pombe; cerevisiae has well-developed peroxisomes, while pombe does not
  • cerevisiae: small point centromere of 125 bp, and sequence-defined replication origins of about the same size; pombe: large, repetitive centromeres (40–100 kb) more similar to mammalian centromeres, and degenerate replication origins of at least 1kb
Saccharomyces Genome Database
Thermus thermophilus: Gram negative eubacterium used in a range of biotechnological applications, including as a model organism for genetic manipulation, structural genomics, and systems biology. The bacterium is extremely thermophilic, with an optimal growth temperature of about 65 °C. rTth DNA polymerase is a recombinant thermostable DNA polymerase derived from Thermus thermophilus, with optimal activity at 70-80 °C, used in some PCR applications; this enzyme possesses efficient reverse transcriptase activity in the presence of manganese.

Human medicine and human biology[edit]

Category:Health sciences
All drugs prevent something, but also bring something; everything is drug: even food and water (too much water (drowning) can kill you!):
Triple-negative breast cancer#Oral contraceptive a risk factor: any breast cancer that does not express the genes for estrogen receptor (ER), progesterone receptor (PR) or Her2/neu
Template:Medicinal herbs & fungi (Medicinal herbs and fungi)
Template:Traditional Medicine
Alternative medicine
Traditional Chinese medicine
Chinese classic herbal formula
Kampo: Japanese study and adaptation of Traditional Chinese medicine
Kampo herb list
Kampo list
Patent medicine: medical compounds of questionable effectiveness sold under a variety of names and labels. E.g. "snake oil".
Information-theoretic death: destruction of the information within a human brain (or any cognitive structure capable of constituting a person) to such an extent that recovery of the original person is theoretically impossible by any physical means; distinct from clinical death and legal death.
Placebo: simulated or otherwise medically ineffectual treatment for a disease or other medical condition intended to deceive the recipient. Sometimes patients given a placebo treatment will have a perceived or actual improvement in a medical condition, a phenomenon commonly called the placebo effect. Expectancy and classical conditioning; placebo and brain → brain and body
Program in Placebo Studies (Beth Israel Deaconess Medical Center and the Harvard Medical School; 2011-): placebo response and the impact of medical ritual, the patient-physician relationship and the power of imagination, hope, trust, persuasion, compassion and empathic witnessing in the healing process.
Institute for Health Metrics and Evaluation (IHME): global health statistics and evaluation; core grant funding from the Bill & Melinda Gates Foundation and the state of Washington.
List of causes of death by rate
International Statistical Classification of Diseases and Related Health Problems (ICD): UN-sponsored WHO's "standard diagnostic tool for epidemiology, health management and clinical purposes"; designed as a health care classification system, providing a system of diagnostic codes for classifying diseases, including nuanced classifications of a wide variety of signs, symptoms, abnormal findings, complaints, social circumstances, and external causes of injury or disease.

Human reproduction and reproductive organs[edit]

Category:Human reproduction
Category:Obstetrical procedures
Template:Reproductive physiology (Human physiology and endocrinology of sexual reproduction)
Template:Menstrual cycle
Ovarian follicle atresia
Maternal age effect
Grandmother hypothesis
Blood–testis barrier (Sertoli cell barrier): physical barrier between the blood vessels and the seminiferous tubules of the animal testes; formed between Sertoli cells of the seminiferous tubule and as such isolates the further developed stages of germ cells from the blood.
Chorionic villus sampling (CVS): determine chromosomal or genetic disorders in the fetus; usually with FISH or PCR.
Amniocentesis (amniotic fluid test, AFT): chromosomal abnormalities and fetal infections, and also used for Sex Determination in which a small amount of amniotic fluid, which contains fetal tissues, is sampled from the amnion or amniotic sac surrounding a developing fetus, and the fetal DNA is examined for genetic abnormalities.
Cell-free fetal DNA: fetal DNA circulating freely in the maternal blood stream. It can be sampled by venipuncture on the mother. Studies have shown that cffDNA can first be observed as early as 7 weeks gestation, and the amount of cffDNA increases as the pregnancy progresses; no longer detectable in the maternal blood approximately 2 hours after birth; fragments approximately 200bp in size.
Microchimerism: presence of a small number of cells that originate from another individual and are therefore genetically distinct from the cells of the host individual. In humans (and perhaps in all Placentals) the most common form is fetomaternal microchimerism (also known as fetal cell microchimerism or fetal chimerism) whereby cells from a fetus pass through the placenta and establish cell lineages within the mother. Fetal cells have been documented to persist and multiply in the mother for several decades.
Egg cell: female reproductive cell (gamete) in oogamous organisms. The egg cell is typically not capable of active movement, and it is much larger (visible to the naked eye) than the motile sperm cells.
Cumulus oophorus: cluster of cells (called cumulus cells) that surround the oocyte both in the ovarian follicle and after ovulation.
Corona radiata (embryology): innermost layer of the cumulus oophorus and is directly adjacent to the zona pellucida, the outer protective layer of the ovum; main purpose in many animals is to supply vital proteins to the egg cell.
Zona pellucida: glycoprotein layer surrounding the plasma membrane of mammalian oocytes. It is a vital constitutive part of the oocyte. The zona pellucida first appears in unilaminar primary oocytes. It is secreted by both the oocyte and the follicular cells.
Human embryogenesis
Prenatal development
Zygote: eukaryotic cell formed by a fertilization event between two gametes. The zygote's genome is a combination of the DNA in each gamete, and contains all of the genetic information necessary to form a new individual. In multicellular organisms, the zygote is the earliest developmental stage. In single-celled organisms, the zygote can divide asexually by mitosis to produce identical offspring.
Cleavage (embryo): division of cells in the early embryo. The zygotes of many species undergo rapid cell cycles with no significant growth, producing a cluster of cells the same size as the original zygote. The different cells derived from cleavage are called blastomeres and form a compact mass called the morula. Cleavage ends with the formation of the blastula.
Morula: early stage embryo consisting of cells (called blastomeres) in a solid ball contained within the zona pellucida.[
Blastocyst: structure formed in the early development of mammals. It possesses an inner cell mass (ICM) which subsequently forms the embryo. The outer layer of the blastocyst consists of cells collectively called the trophoblast. This layer surrounds the inner cell mass and a fluid-filled cavity known as the blastocoele. The trophoblast gives rise to the placenta.

Mind, psychology, mental health, psychiatry[edit]

{q.v. #Cognitive science, cognitive neuroscience, computational neuroscience, brain, mind, mental health, psychology, psychiatry}

Parenthood, birth, children[edit]

Multiple birth: culmination of one multiple pregnancy, wherein the mother delivers two or more offspring. A term most applicable to placental species, multiple births occur in most kinds of mammals, with varying frequencies.
List of multiple births: some of them are identical. With the use of reproductive technology such as fertility drugs and in vitro fertilization (IVF) twin and triplet births have become increasingly common.
Dionne quintuplets (born 1934.05.28): first quintuplets known to survive their infancy; born two months premature; identical sisters. Émilie and Marie shared an embryonic sac, Annette and Yvonne shared an embryonic sac, and it is believed that Cécile shared an embryonic sac with the miscarried sixth fetus. Each girl became emotionally the closest to whomever they shared a sac with; Cécile tended to be alone the most. All but Émilie were/are right-handed; all but Marie have/had a counter-clockwise whorl in their hair.
Lina Medina (1933.09.27-): youngest confirmed mother in medical history, giving birth at the age of five years, seven months and 17 days.
List of people with the most children: mother with the most children: 69 children to Mrs. and Mr. Feodor Vassilyev. Father with the most children can be in the 1000s, because of the medical sperm donation.
Category:Conjoined twins
Conjoined twins: Two contradicting theories exist to explain the origins of conjoined twins. The older theory is fission, in which the fertilized egg splits partially. The second and more generally accepted theory is fusion, in which a fertilized egg completely separates, but stem cells (which search for similar cells) find like-stem cells on the other twin and fuse the twins together. Conjoined twins share a single common chorion, placenta, and amniotic sac.
Parasitic twin
Vanishing twin (fetal resorption; twin embolisation syndrome or vanishing twin syndrome (VTS)): fetus in a multi-gestation pregnancy which dies in utero and is then partially or completely reabsorbed by the twin. "These very high resorption rates, which cannot be explained on the basis of the expected abortion rate, again suggest intense fetal competition for space, nutrition, or other factors during early gestation, with frequent loss or resorption of the other twin(s)."
Craniopagus parasiticus: rare type of craniopagus occurring in about 4 to 6 of 10,000,000 births; parasitic twin head with an undeveloped body is attached to the head of a developed twin.
Fetus in fetu: developmental abnormality in which a mass of tissue resembling a fetus forms inside the body.
Twin reversed arterial perfusion: rare complication of monochorionic twin pregnancies, involving an acardiac twin whose structural defects are incompatible with life, and an otherwise normal "pump" twin. Acardiac twin is a parasitic twin that fails to develop a head, arms and a heart.
Craniopagus twins: conjoined twins who are fused at the cranium; represents the rarest of congenital abnormalities only accounting for 2-6% of all conjoined twins; union in craniopagus twins may occur on any portion of the calvarium, but does not include either the face or the foramen magnum; thorax and abdomen are separate and each twin has its own ubilicus and umbilical cord. Genres of Craniopagus Twins: Partial; Total. If the parents choose to continue the pregnancy, mother and babies will be closely monitored throughout the pregnancy; in almost all cases a surgical procedure (C-section) delivery is planned often two to three weeks before the due date.
Chang and Eng Bunker (1811.05.11-1874.01.17): were conjoined twin brothers whose condition and birthplace became the basis for the term "Siamese twins". Chang and his wife had 10 children; Eng and his wife had 11. In time, the wives squabbled and eventually two separate households were set up just west of Mount Airy, North Carolina in the community of White Plains – the twins would alternate spending three days at each home.
Lori and George Schappell (1961.09.18-): siblings are craniopagus conjoined twins joined at the head. Lori and George spent the first 24 years of their lives living in an institution in Reading, Pennsylvania, in which the majority of patients were suffering from severe intellectual disabilities. Although neither is intellectually disabled, George's physical condition required special care. A court decision was made that their parents would be unable to care for them properly and they were removed and institutionalized. In 2007, George, who was at that time known as Reba Schappell, stated that although assigned female at birth, he identified as male and changed his name to George.
Abigail and Brittany Hensel (1990.03.07-): dicephalic parapagus twins, meaning that they are conjoined twins, each of whom has a separate head, but whose bodies are joined; several vital organs are doubled up; each twin has a separate heart (2 hearts in a shared circulatory system), stomach, spine, and spinal cord. By coordinating their efforts, they are able to walk, run, swim, and ride a bicycle normally—all tasks that they learned at a normal speed. 1 liver, Y-shaped small intestine, which experiences a slightly spastic double peristalsis at the juncture, 1 large intestine (one colon), 3 kidneys: 2 left, 1 right, 1 bladder, 1 set of reproductive organs.
Lakshmi Tatma
Krista and Tatiana Hogan (2006.10.25-): joined at the top, backs, and sides of their heads. There is suspicion that they can see through each other's eyes due to brain conjoining. Their thalamuses are joined.

Human (mammal?) hormones[edit]

Category:Hormones by functional axis
Category:Hormones of the hypothalamus-pituitary axis
Category:Hormones of the hypothalamus-pituitary-adrenal axis
Category:Hormones of the hypothalamus-pituitary-gonad axis
Category:Hormones of the hypothalamus-pituitary-thyroid axis
Category:Hormones of the somatotropic axis: Growth-hormone-releasing hormone, Somatostatin, Tesamorelin
Category:Human homeostasis
Endocrine system
Hypothalamic–pituitary–adrenal axis (HPA or HTPA axis; limbic-hypothalamic-pituitary-adrenal axis (LHPA axis), hypothalamic-pituitary-adrenal-gonadotropic axis): Stress and disease: mood disorders.
Hypothalamic–pituitary–gonadal axis (HPG axis): Function: Reproduction, Life cycle, Sexual dimorphism and behavior
Hypothalamic–pituitary–thyroid axis (HPT axis)
Thyroid hormone: triiodothyronine (T3) and thyroxine (T4); tyrosine-based hormones produced by the thyroid gland that are primarily responsible for regulation of metabolism; iodine is necessary for the production of T3 and T4; T4:T3=20:1 released into the blood; T4 → T3 (by deiodinases (5'-iodinase) inside the cells), T3 is 3-4× more potent than T4. These are further processed by decarboxylation and deiodination to produce iodothyronamine (T1a) and thyronamine (T0a); all three isoforms of the deiodinases are selenium-containing enzymes, thus dietary selenium is essential for T3 production.
Renin–angiotensin system (RAS; renin-angiotensin-aldosterone system (RAAS)): hormone system that regulates blood pressure and water (fluid) balance.

Medicinal ethics and law[edit]

Futile medical care: continued provision of medical care or treatment to a patient when there is no reasonable hope of a cure or benefit. One could say that it is impossible to reach a firm definition of futile medical care, because this would depend upon universal agreement about the point at which there is no further benefit to intervention, and different involved parties may always disagree about the amount and type of benefit under discussion. For instance, a cancer patient may be willing to undergo yet more chemotherapy with a very expensive medication for the benefit of a few weeks of life, while medical staff, the insurance company, and close relatives may all feel otherwise, for different reasons.
Baby Doe Law (Baby Doe Amendment; 1984): set forth specific criteria and guidelines for the treatment of seriously ill and/or disabled newborns, regardless of the wishes of the parents.
Template:Medical ethics cases:
David Vetter ("David, the bubble boy"; 1971.09.21-1984.02.22): severe combined immunodeficiency; a few months after unmatched bone marrow transplant from his sister Katherine, he died from Burkitt's lymphoma due to the dormant Epstein-Barr virus in the donor bone marrow.


Invasiveness of surgical procedures
The future surgeries are the least invasive, e.g.:
High-intensity focused ultrasound (HIFU, or sometimes FUS): highly precise medical procedure using high-intensity focused ultrasound to heat and destroy pathogenic tissue rapidly through ablation. Clinical HIFU is image-guided: Magnetic Resonance-guided Focused Ultrasound (MRgHIFU or MRgFUS); Ultrasound-guided Focused Ultrasound (USgFUS). Limited by the precision of imaging (MRI or US), by the precision of HIFU lenses and how HIFU travels and gets distorted in the tissues, and by the computational models how HIFU travels from the source to the destination (e.g. breathing/moving patient).

Medical research[edit]

Category:Medical research
Category:Animal testing
Great ape research ban: severe restrictions on the use of non-human great apes in research, is currently in place in NL, NZ, UK, SE, DE, AT.
Evidence-based practices[edit]
Category:Evidence-based practices
Category:Evidence-based medicine
Category:Systematic review
Evidence-based medicine: defined as "the conscientious, explicit and judicious use of current best evidence in making decisions about the care of individual patients."
Cochrane Collaboration: independent, non-profit, NGO consisting of a group of more than 31,000 volunteers in more than 120 countries. Formed to organize medical research information in a systematic way to facilitate the choices that health professionals, patients, policy makers and others face in health interventions according to the principles of evidence-based medicine. Conducts systematic reviews of randomized controlled trials of health-care interventions.
Cochrane Library: collection of databases in medicine and other healthcare specialties provided by the Cochrane Collaboration and other organizations. At its core is the collection of Cochrane Reviews, a database of systematic reviews and meta-analyses which summarize and interpret the results of medical research.
Systematic review: literature review focused on a research question that tries to identify, appraise, select and synthesize all high quality research evidence relevant to that question. Systematic reviews of high-quality randomized controlled trials are crucial to evidence-based medicine.


List of epidemics
Plague of Justinian (541-542)




Category:Eating behaviors
Category:High-fat diets
Category:Low-carbohydrate diets
Postprandial somnolence (food coma, carb coma): normal state of drowsiness or lassitude following a meal. Postprandial somnolence has two components: a general state of low energy related to activation of the parasympathetic nervous system in response to mass in the gastrointestinal tract, and a specific state of sleepiness caused by hormonal and neurochemical changes related to the rate at which glucose enters the bloodstream and its downstream effects on amino acid transport in the central nervous system.
Glycemic index: number associated with a particular type of food that indicates the food's effect on a person's blood glucose (also called blood sugar) level.
Glycemic load: of food is a number that estimates how much the food will raise a person's blood glucose level after eating it. One unit of glycemic load approximates the effect of consuming one gram of glucose.
Ketogenic diet: high-fat, adequate-protein, low-carbohydrate diet that in medicine is used primarily to treat difficult-to-control (refractory) epilepsy in children. The diet forces the body to burn fats rather than carbohydrates. Normally, the carbohydrates contained in food are converted into glucose, which is then transported around the body and is particularly important in fuelling brain-function.


Warburg effect: Plant physiology: decrease of photosynthesis by high oxygen concentrations. Oncology: observation that most cancer cells predominantly produce energy by a high rate of glycolysis followed by lactic acid fermentation in the cytosol, rather than by a comparatively low rate of glycolysis followed by oxidation of pyruvate in mitochondria as in most normal cells.
Warburg hypothesis (Warburg theory of cancer): postulates that the driver of tumorigenesis is an insufficient cellular respiration caused by insult to mitochondria. The Warburg hypothesis was that the Warburg effect was the root cause of cancer. The current popular opinion is that cancer cells ferment glucose while keeping up the same level of respiration that was present before the process of carcinogenesis, and thus the Warburg effect would be defined as the observation that cancer cells exhibit glycolysis with lactate secretion and mitochondrial respiration even in the presence of oxygen.
History of cancer chemotherapy: era of cancer chemotherapy began in the 1940s with the first use of nitrogen mustards and folic acid antagonist drugs.


Category:Health care
Category:Types of healthcare facilities
Category:Mayo Clinic
Mayo Clinic: nonprofit medical practice and medical research group based in Rochester, Minnesota. It is the first and largest integrated nonprofit medical group practice in the world, employing more than 3,800 physicians and scientists and 50,900 allied health staff. The practice specializes in treating difficult cases through tertiary care. It spends over $500 million a year on research.

Cohort studies, longitudinal study[edit]

Category:Cohort studies
Grant Study: part of the Study of Adult Development at Harvard Medical School. It is a 75-year longitudinal study of 268 physically- and mentally-healthy Harvard college sophomores from the classes of 1939–1944. It has run in tandem with a study called "The Glueck Study," which included a second cohort of 456 disadvantaged nondelinquent inner-city youths who grew up in Boston neighborhoods between 1940 and 1945. The subjects were all male, white and of American nationality. The men continue to be studied to this day.
Longitudinal study: correlational research study that involves repeated observations of the same variables over long periods of time — often many decades. It is a type of observational study. Longitudinal studies are often used in psychology to study developmental trends across the life span, and in sociology to study life events throughout lifetimes or generations.

Brave New World[edit]

Intracytoplasmic sperm injection
Designer baby
Human enhancement
Transhumanism: Dehumanization ("Frankenstein complex")
Outline of transhumanism


Evolution as a process during which the fidelity of replication increased several folds of magnitude (RNA world, RNP world / DNA world, protein (the machines, hardware) & DNA (the code, software) world; next step (non-bio): human literature → computer programs & digital storage (copying errors are extremely small compared to human genome replication in digital world))

Speed of reactions catalyzed by these molecules (from the slowest to the fastest): RNA (RNA world) → RNP (early protein + RNA world) → protein (current world of proteins as machines, DNA as storage, mRNA as intermediate remaining as relic & more from the previous "ages"). Human technological evolution: stone → bronze → iron → steel, plastic, silicon, periodic table, all of organic chemistry and biochemistry → speed of light machines running on electricity: computers (→ AI ? )

Modern evolutionary synthesis: 20th c. union of ideas from several biological specialties which provides a widely accepted account of evolution
Evolution: The Modern Synthesis (1942): book by Julian Huxley, one of the most important books of the modern evolutionary synthesis.
Evolution as theory and fact
Punctuated equilibrium: is it a tiny part of the modern evolution synthesis or a huge one? What could tiny/huge mean in terms of genetics and evo-devo?
Arsenic-based life
GFAJ-1: isolated from the shore of Mono Lake, California, USA {highest natural concentrations of arsenic in the world (200 μM)}. On the tree of life, according to the results of 16S rRNA sequencing, the rod-shaped GFAJ-1 nestles in among other salt-loving bacteria in the family Halomonadaceae. When starved of phosphorus, GFAJ-1 can instead incorporate arsenic into its metabolites and macromolecules and continue growing.

Human evolution and extant "cousins"[edit]



Category:Human evolution
Homo sapiens: binomial nomenclature for the only extant human species. Homo is the human genus, which also includes Neanderthals and many other extinct species of hominid; H. sapiens is the only surviving species of the genus Homo. Since 2010, genetic research has led to the emergence of an intermediate position, characterised by mostly recent African origin plus limited admixture with archaic humans.
Neanderthal Genome Project
Chimpanzee genome project
Genes of humans vs non-human apes:
SRGAP2: protein twice duplicated in human genome as compared to chimps and other extant apes. First duplication 3.4 mya, next 2.4 mya (this duplication allows neurons to migrate faster in the human brain).
Baculum: penis bone; absent in humans but present in nearest extant relative the chimpanzee
Population bottleneck: Humans (Toba; 'long bottleneck')
Recent African origin of modern humans: supposition - archaic Homo sapiens evolved to anatomically modern humans solely in Africa, between 200 ka and 150 ka, that members of one branch of Homo sapiens left Africa by between 125 ka and 60 ka, and that over time these humans replaced earlier human populations such as Neanderthals and Homo erectus without interbreeding with them.
Toba catastrophe theory: between 69 ka and 77 ka at Lake Toba (Sumatra, Indonesia); supposed bottleneck in human evolution
Multiregional origin of modern humans: less probable explanation (esp. considering Toba), but maybe the synthesis of both (with majority of modern humans coming from Africa 125 ka - 60 ka, while very small amount survived Toba from the migrations as far back as 2Ma?) is also possible
Template:Human Evolution
Anatomically modern humans vs Archaic humans (includes Homo heidelbergensis, Homo rhodesiensis, Homo neanderthalensis and sometimes Homo antecessor):
Omo remains: 198 ± 14 ka (geologic layer below the fossil), 104 ± 7 ka (geologic layer above the fossil)
Homo sapiens idaltu: ~160 ka
Skhul and Qafzeh hominids: 80 - 120 ka; a few Neanderthal features, but huge resemblance to modern humans
Denisova hominin: ~41 ka mtDNA and genome sequenced; between 4% and 6% of the genome of Melanesians derives from a Denisovan population; mtDNA of the Denisova hominin is distinct from the mtDNAs of Neanderthals and modern humans
Homo erectus soloensis, aka Solo Man: While most subspecies of Homo erectus disappeared from the fossil record roughly 400,000 years ago, H. e. soloensis persisted up until 50,000 years ago in regions of Java and was possibly absorbed by a local Homo sapiens population at the time of its decline.
Researchers: Svante Pääbo
Archaic human admixture with modern humans: through interbreeding of modern humans with Neanderthals, Denisovans, and/or possibly other archaic humans over the course of human history. Neanderthal-derived DNA accounts for an estimated 1–4% of the Eurasian genome, but it is significantly absent or uncommon in the genome of most Sub-Saharan African people. In Oceanian and Southeast Asian populations, there is a relative increase of Denisovan-derived DNA. An estimated 4–6% of the Melanesian genome is derived from Denisovans. Recent noncomparative DNA analyses—as no specimens have been discovered—suggest that African populations have a genetic contribution from a now-extinct archaic African hominin population.
The Descent of Man, and Selection in Relation to Sex (1871): book on evolutionary theory by English naturalist Charles Darwin. The book discusses many related issues, including evolutionary psychology, evolutionary ethics, differences between human races, differences between sexes, the dominant role of women in choosing mating partners, and the relevance of the evolutionary theory to society.

Evolutionary biology, chemistry[edit]

Category:Biological evolution
Category:Evolutionary biology {also q.v. Category:Phylogenetics}
Homology (biology): relationship between a pair of structures, or genes, due to having shared ancestry. Anatomical homology. Sequence homology: Orthology - homologous sequences are orthologous if they are inferred to be descended from the same ancestral sequence separated by a speciation event: when a species diverges into two separate species, the copies of a single gene in the two resulting species are said to be orthologous (orthologs, or orthologous genes); Paralogy - homologous sequences are paralogous if they were created by a duplication event within the genome. Homology between sexes and forms.
Deep homology: growth and differentiation processes are governed by genetic mechanisms that are homologous and deeply conserved across a wide range of species.
Abiogenesis (biopoesis): "how biological life arises from inorganic matter through natural processes, and the method by which life on Earth arose". Early life on earth: at high temperature(?), at high pressure (?), at which concentrations of simple "bio-molecules"? "Primordial soup": Miller–Urey experiment (nowadays: reducing atmosphere, monomer formation); deep sea vent theory; Fox's experiments; Eigen's hypothesis: self-replicating hypercycle; iron–sulfur world theory; radioactive beach hypothesis; RNA world hypothesis...
Last universal ancestor (LUA; last universal common ancestor (LUCA), cenancestor): most recent organism from which all organisms now living on Earth descend; MRCA of all current life on Earth. LUA is estimated to have lived some 3.5-3.8 bya. LUA was a small, single-cell organism; had a cell wall and a ring-shaped coil of DNA floating freely within the cell, like modern bacteria; genetic code was based on DNA; genetic code was expressed via RNA intermediates, which were single-stranded; genetic code was expressed into proteins; proteins were assembled from free amino acids by translation of an mRNA by ribosomes, tRNA and a group of related proteins; ATP was used as an energy intermediate; several hundred protein enzymes which catalyzed chemical reactions that extract energy from fats, sugars, and amino acids, and that synthesize fats, sugars, amino acids, and nucleic acid bases using arbitrary chemical pathways; inside the cell, the concentration of sodium was lower, and potassium was higher, than outside; cell multiplied by duplicating all its contents followed by cellular division.
Evolutionary arms race: prey vs predator, parasite vs host, within the species.
Sexual conflict (sexual antagonism):
Penis fencing: flatworms
Traumatic insemination (hypodermic insemination): bed bugs
Sexual coercion
Sexual cannibalism: primarily by members of arachnid orders as well as several insect orders (mantis).
Love dart (gypsobelum)
Error threshold (evolution): "mutation process places a limit on the number of digits a molecule may have. If a molecule exceeds this critical size, the effect of the mutations become overwhelming and a runaway mutation process will destroy the information in subsequent generations of the molecule." (Eigen, 1971)


Ethology: scientific and objective study of animal behaviour, and is a sub-topic of zoology; animal behaviour under natural conditions, as opposed to behaviourism, which focuses on behavioural response studies in a laboratory setting.


Humans are animals too, but {q.v. #Human medicine and human biology}

Animal (Animalia, Metazoa)
Parazoa {subkingdom}: Sponge (phylum=Porifera) Placozoa (phylum; "flat animals")
Animal sexual behaviour:
Monogamy: social monogamy (90% of bird species are socially monogamous) vs sexual monogamy vs genetic monogamy (very few species show 100% genetic monogamy; out of 180 different species of socially monogamous songbirds, only 10% are sexually monogamous).
Polygamy: polygyny: when a new alpha male arrives, the current embryos and the young are killed/aborted in one of several ways: competitive infanticide (lions, hippopotamuses, some monkeys), harassment to miscarriage (horses, baboons), pheromone based spontaneous abortion (some rodents (e.g. mice): Bruce-Parkes effect).
Promiscuity: chimpanzees and bonobos.
Against Nature?
Sperm whale (cachalot): only living member of genus Physeter, and one of three extant species in the sperm whale family, along with the pygmy sperm whale and dwarf sperm whale of the genus Kogia. Mature males average at 16 metres in length but some may reach 20.5 metres, with the head representing up to one-third of the animal's length. Plunging to 3 kilometres (9,800 ft) for prey, it is the deepest diving mammal. Its clicking vocalization, a form of echolocation and communication, may be as loud as 230 decibels (re 1 µPa at 1 m) underwater, making it the loudest sound produced by any animal; has the largest brain of any animal on Earth, more than five times heavier than a human's; can live for more than 60 years.
Arthropod (Arthropoda)[edit]
  1. Trilobites
  2. Chelicerates
  3. Myriapods
  4. Crustaceans
  5. Hexapods
Phylogenetic relationships of the major extant arthropod groups according to Regier et al. (2010); traditional subphyla in bold
Insects (Insecta), hexapods[edit]
Orthoptera: order of insects includes the grasshoppers, crickets, cave crickets, Jerusalem crickets, katydids, weta, lubber, Acrida, and locusts.
Weta: although they are of an ancient lineage, the present species are quite young, which conflicts with those earlier ideas about dispersal of weta forebears around the Southern Hemisphere (Wallis et al. 2000). Giant, tree, ground, and tusked weta are all members of the family Anostostomatidae (formerly in the Stenopelmatidae, but recently separated (Johns, 1997)). Cave weta are better called tokoriro, and are members of the family Rhaphidophoridae called cave crickets or camel crickets elsewhere, in a different ensiferan superfamily.
From first amniotes to modern animals[edit]
Synapsid: (Greek, 'fused arch'), synonymous with theropsids (Greek, 'beast-face'), are a group of animals that includes mammals and every animal more closely related to mammals than to other living amniotes.
Sauropsida: ("lizard faces") is a group of amniotes that includes all existing reptiles and birds and their fossil ancestors.
Nocturnal bottleneck: hypothesis to explain several mammal traits. The hypothesis states that mammals were mainly or even exclusively nocturnal through most of their evolutionary story, starting with their origin 225 million years ago, and only ending with the demise of the dinosaurs 65 millions years ago. While some mammal groups have later evolved to fill diurnal niches, the 160 million years spent as nocturnal animals has left a lasting legacy on basal anatomy and physiology, and most mammals are still nocturnal.
Carrier's constraint: observation that air-breathing vertebrates which have two lungs and flex their bodies sideways during locomotion find it very difficult to move and breathe at the same time, because the sideways flexing expands one lung and compresses the other, shunting stale air from lung to lung instead of expelling it completely to make room for fresh air.
Sauropsida and Reptilia[edit]
Evolution of reptiles: Reptiles arose about 310–320 million years ago during the Carboniferous period. Reptiles, in the traditional sense of the term, are defined as animals that have scales or scutes, lay land-based hard-shelled eggs, and possess ectothermic metabolisms. So defined, the group is paraphyletic, excluding endothermic animals like birds and mammals that are descended from early reptiles. A definition in accordance with phylogenetic nomenclature, which rejects paraphyletic groups, includes birds while excluding mammals and their mammal-like reptile ancestors. So defined, Reptilia is identical to Sauropsida.
Cladogram of relationships of extant Sauria: 1. Tuatara, 2. Lizards, 3. Snakes, 4. Crocodiles, 5. Birds. "Lizards" are paraphyletic.
Lepidosauria: reptiles with overlapping scales. This subclass includes Squamata and Rhynchocephalia. It is a monophyletic group and therefore contains all descendents of a common ancestor. Squamata includes snakes, lizards, and amphisbaenia. Rhynchocephalia was a widespread and diverse group 220-100 million years ago; however, it is now represented only by the genus Sphenodon, which contains two species of tuatara, native to New Zealand.
Turtle (order: Testudines): characterised by a special bony or cartilaginous shell developed from their ribs and acting as a shield.
Archosaur (Archosauria): group of diapsid amniotes whose living representatives consist of birds and crocodilians. This group also includes all extinct dinosaurs, extinct crocodilian relatives, and pterosaurs. Archosauria, the archosaur clade, is a crown group that includes the most recent common ancestor of living birds and crocodilians.
Pseudosuchia ("false crocodiles"): one of two major divisions of Archosauria and includes living crocodilians and all archosaurs more closely related to crocodilians than to birds (what are often called "crocodilian-line archosaurs").
Avemetatarsalia (Ornithodira): clade name established by British palaeontologist Michael Benton in 1999 for all crown group archosaurs that are closer to birds than to crocodiles.
World distribution of genera and species within family Crocodylidae (C. means Crocodylus).
False gharial
Crocodile (Crocodylinae)
Alligatorinae (many extinct) → Alligator
Caiman (Caimaninae)
Saltwater crocodile: largest of all living reptiles, as well as the largest terrestrial and riparian predator in the world.
Nile crocodile: African crocodile and the second largest extant reptile in the world, after the saltwater crocodile. The Nile crocodile is quite widespread throughout Sub-Saharan Africa, occurring mostly in the central, eastern, and southern regions of the continent and lives in different types of aquatic environments such as lakes, rivers and marshlands. Although capable of living in saline environments, this species is rarely found in saltwater, but occasionally inhabits deltas and brackish lakes. The range of this species once stretched northward throughout the Nile, as far north as the Nile delta. Since a majority of fatal attacks are believed to be predatory in nature, the Nile crocodile can be considered the most prolific predator of humans among wild animals.
Avemetatarsalia: Dinosaurs and birds (aves)[edit]
Evolution of dinosaurs. Typical silhouettes are shown in black. At the bottom of the image red colour shows the differences in the pubis bone.
Dinosaur classification
Feathered dinosaur
Bird (Aves)
Peregrine falcon (Falco peregrinus): widespread bird of prey in the family Falconidae. A large, crow-sized falcon, it has a blue-grey back, barred white underparts, and a black head and "moustache". As is typical of bird-eating raptors, peregrine falcons are sexually dimorphic, females being considerably larger than males. The peregrine is renowned for its speed, reaching over 322 km/h during its characteristic hunting stoop (high speed dive), making it the fastest member of the animal kingdom.
Cretaceous–Paleogene extinction event[edit]
Category:Cretaceous–Paleogene boundary
Cretaceous–Paleogene boundary: geological signature, usually a thin band of rock. The K–Pg boundary marks the end of the Cretaceous Period, the last period of the Mesozoic Era, and marks the beginning of the Paleogene Period, the first period of the Cenozoic Era. Its age is usually estimated at around 66 Ma (million years ago), with radioisotope dating yielding a more specific age of 66.043 ± 0.011 Ma.
Cretaceous–Paleogene extinction event (aka: Cretaceous–Tertiary (K–T) extinction): mass extinction of some three-quarters of plant and animal species on Earth—including all non-avian dinosaurs—that occurred over a geologically short period of time, 66 mya. It marked the end of the Cretaceous period and with it, the entire Mesozoic Era, opening the Cenozoic Era that continues today. K–Pg boundary: high levels of the metal iridium. K–Pg extinction was triggered by a massive comet/asteroid impact.
Chicxulub crater: impact crater buried underneath the Yucatán Peninsula in Mexico. The date of the Chicxulub impactor, which created it, coincides precisely with K–Pg boundary. More than 180 kilometers in diameter and 20 km in depth, making the feature one of the largest confirmed impact structures on Earth; the impacting bolide that formed the crater was at least 10 km in diameter.
Distribution of extant and recently extinct mammal species across orders.
Mammal: any members of a clade of endothermic amniotes distinguished from reptiles and birds by the possession of hair [with a few exceptions, all of them cetaceans], three middle ear bones, mammary glands, and a neocortex (a region of the brain). The mammalian brain regulates body temperature and the circulatory system, including the four-chambered heart. The mammals include the largest animals on the planet, the rorquals and other large whales, as well as some of the most intelligent, such as elephants, some primates, including humans, and some of the cetaceans. The largest group of mammals, the placentals, have a placenta, which enables feeding the fetus during gestation. Mammals range in size from the 30–40 mm (1.2–1.6 in) bumblebee bat to the 33-meter (108 ft) blue whale.
Odd-toed ungulate (Perissodactyla): Equidae (horses...), Tapiridae (tapirs), Rhinocerotidae (rhinoceroses)
Rodent (Rodentia): mammals which are characterized by a single pair of unremittingly growing incisors in each of the upper and lower jaws. ~40% of all mammal species are rodents. Most rodents are small animals with robust bodies, short limbs and long tails. They use their sharp incisors to gnaw food, excavate burrows and defend themselves. Most eat seeds or other plant material, but some have more varied diets.
Rat (Rattus): Rats are typically distinguished from mice by their size. Generally, when someone discovers a large muroid rodent, its common name includes the term rat, while if it is smaller, the name includes the term mouse.
Brown rat (Rattus norvegicus: misnomer): thought to have originated in northern China, this rodent has now spread to all continents except Antarctica, and is the dominant rat in Europe and much of North America—making it by at least this particular definition the most successful mammal on the planet after humans. With rare exceptions, the brown rat lives wherever humans live, particularly in urban areas. Selective breeding of Rattus norvegicus has produced the laboratory rat, a model organism in biological research, as well as pet rats.
Black rat (Rattus rattus): species originated in tropical Asia and spread through the Near East in Roman times before reaching Europe by the 1st century and spreading with Europeans across the world; generalist omnivores.
Comparison of the physique of a black rat (Rattus rattus) with a brown rat (Rattus norvegicus).
Naked mole-rat: lives completely underground and can form colonies of up to eighty individuals. Only one female and up to three males in the colony reproduce, while the rest of the members are smaller, sterile and function as workers. Some individuals are of intermediate size. They help with the rearing of the young and can take the place of a reproductive if one dies.
Damaraland mole-rat: characterized by having a single reproductively active male and female in a colony where the remaining animals are not truly sterile, but only become fertile if they establish a colony of their own.
Rats in New York City
Behavioral sink: John B. Calhoun conducted over-population experiments on rats which culminated in 1962 with the publication of an article in the Scientific American of a study of behavior under conditions of overcrowding.
Bats (Chiroptera)[edit]
Bat: forelimbs form webbed wings, making them the only mammals naturally capable of true and sustained flight. Bats do not flap their entire forelimbs, as birds do, but instead flap their spread-out digits, which are very long and covered with a thin membrane or patagium. Bats are the second largest order of mammals (after the rodents), representing about 20% of all classified mammal species worldwide, with about 1,240 bat species divided into two suborders: the less specialized and largely fruit-eating megabats, or flying foxes, and the highly specialized and echolocating microbats. Most molecular biological evidence supports the view that bats form a single or monophyletic group.
Megabat: have well-developed visual cortices and show good visual acuity; eat fruit, nectar, or pollen (cf microbat).
Microbat: rely on echolocation for navigation and finding prey; use echolocation; lack the claw at the second finger of the forelimb; lack underfur; most microbats eat insects; others may feed on fruit, nectar, pollen, fish, frogs, small mammals, or the blood of animals (cf. megabat).
Soricomorpha (split up)[edit]
Soricomorpha (order): taxon within the class of mammals. In previous years it formed a significant group within the former order Insectivora. However, that order was shown to be polyphyletic and various new orders were split off from it, including Afrosoricida (tenrecs and golden moles), Macroscelidea (elephant shrews), and Erinaceomorpha (hedgehogs and gymnures), leaving just four families as shown here, leaving Insectivora empty and disbanded.
Afrosoricida (order)
Elephant shrew (order: Macroscelididae)
Erinaceidae (order)
Insectivora: now-abandoned biological grouping within the class of mammals. Some species have now been moved out, leaving the remaining ones in the order Eulipotyphla, within the larger clade Laurasiatheria, which makes up one of the most basic clades of placental mammals.
Eulipotyphla: order of mammals suggested by molecular methods of phylogenetic reconstruction, and includes members of the now-invalid order Insectivora except for those in the order Afrosoricida (tenrecs and golden moles), i.e. comprising the solenodons (family Solenodontidae); the order Eulipotyphla includes hedgehogs and gymnures (family Erinaceidae) as well as desmans, moles, and shrew moles (family Talpidae) and the true shrews (family Soricidae). True shrews and talpids are sometimes included in the clade Soricomorpha, which however appears as paraphyletic in some analyses.
Hominoid taxonomy 7.svg
Primate (order Primates): with the exception of humans, who inhabit every continent, most primates live in tropical or subtropical regions of the Americas, Africa and Asia. Primates are characterized by large brains relative to other mammals, as well as an increased reliance on stereoscopic vision at the expense of smell, the dominant sensory system in most mammals. These features are more developed in monkeys and apes and noticeably less so in lorises and lemurs. Three-color vision has developed in some primates.
Haplorhini ("dry-nosed" primates): all lost the function of the terminal enzyme which manufactures vitamin C; haplorhine upper lip, which has replaced the ancestral rhinarium found in strepsirrhines, is not directly connected to their nose or gum, allowing a large range of facial expressions. Their brain to body ratio is significantly greater than the strepsirrhines, and their primary sense is vision.
Simian (infraorder Simiiformes, Anthropoidea): "higher primates"
Catarrhini: catarrhines (from Ancient Greek kata-, "down" and rhin-, "nose") have nostrils which face downwards; never have prehensile tails, and have flat fingernails and toenails, a tubular ectotympanic (ear bone),
Ape (Hominoidea; hominoids): Old World anthropoid catarrhine mammals; apes are native to Africa and SE Asia; the largest primates and the orangutan, an ape, is the largest living arboreal animal. Except for gorillas and humans, hominoids are agile climbers of trees. Their diet is best described as vegetarian or omnivorous, consisting of leaves, nuts, seeds and fruits, including grass seeds, and in most cases other animals, either hunted or scavenged (or farmed in the case of humans), along with anything else available and easily digested. Great apes, including humans, go through a menstrual cycle. History of hominoid taxonomy: Changes in taxonomy
Hominidae (great apes): Physical description: large, tailless primates; degree of sexual dimorphism varies greatly among species; most species are omnivorous, but fruit is the preferred food among all but some human groups; human teeth and jaws are markedly smaller for their size than those of other apes, which may be an adaptation to eating cooked food for more than a million years; gestation: 8-9 months. 4 genera:
Chimpanzee (chimp; genus Pan): Common chimpanzee (Pan troglodytes; W. + C. Africa) + Bonobo (Pan paniscus; DR Congo)
Gorilla: DNA of gorillas is highly similar to that of a human, from 95–99% depending on what is counted, and they are the next closest living relatives to humans after the bonobo and common chimpanzee.
Homo: genus is estimated to be about 2.3 to 2.4 mya.
Orangutan (Pongo): Bornean orangutan (P. pygmaeus) and the Sumatran orangutan (P. abelii); both species had their genomes sequenced and they appear to have diverged around 400,000 years ago. Orangutans diverged from the rest of the great apes 15.7 to 19.3 mya; most arboreal of the great apes and spend most of their time in trees. Most solitary of the great apes, with social bonds occurring primarily between mothers and their dependent offspring, who stay together for the first two years
Old World monkey (Superfamily: Cercopithecoidea; Family: Cercopithecidae): most have tails (the family name means "tailed ape"); tails are never prehensile; distinction of Old World monkeys from apes depends on dentition (the number of teeth is the same in both, but they are shaped differently)
Gibbon: apes in the family Hylobatidae /ˌhaɪlɵˈbeɪtɨdiː/. The family historically contained one genus, but now is split into four genera. Gibbons occur in tropical and subtropical rainforests from eastern Bangladesh and northeast India to southern China and Indonesia (including the islands of Sumatra, Borneo, and Java).
Strepsirrhini: suborder of primates that includes the lemuriform primates, which consist of the lemurs of Madagascar, galagos ("bushbabies") and pottos from Africa, and the lorises from India and southeast Asia.


Common chimpanzee (Pan troglodytes)
Bonobo (Pan paniscus): Behavior: Social behavior: Most studies indicate that females have a higher social status in bonobo society; Sexual social behavior: Sexual activity generally plays a major role in bonobo society, being used as what some scientists perceive as a greeting, a means of forming social bonds, a means of conflict resolution, and postconflict reconciliation.


Western gorilla (Gorilla gorilla)
Eastern gorilla (Gorilla beringei)
Mountain gorilla (Gorilla beringei beringei)
Eastern lowland gorilla (Gorilla beringei graueri)


Bornean orangutan (Pongo pygmaeus)
Sumatran orangutan (Pongo abelii)
Australopithecus is not shown. Genetic distance below the diagram; temporal remoteness above the diagram (MYA).
Carnivora (carnivorans): includes over 280 species of placental mammals. Carnivorans are the most diverse in size of any mammalian order, ranging from the least weasel (Mustela nivalis), at as little as 25 g and 11 cm, to the polar bear (Ursus maritimus), which can weigh up to 1,000 kg, to the southern elephant seal (Mirounga leonina), whose adult males weigh up to 5,000 kg and measure up to 6.9 m in length. Some carnivorans, such as cats and pinnipeds, depend entirely on meat for their nutrition. Others, such as raccoons and bears, depending on the local habitat, are more omnivorous: the giant panda is almost exclusively a herbivore, but will take fish, eggs and insects, while the polar bear subsists mainly on seals. Carnivorans have teeth and claws adapted for catching and eating other animals. Many hunt in packs and are social animals.

NimravidaeHoplophoneus mentalis



Nandiniidae Two-spotted palm civet


PrionodontidaeSpotted linsang


Felidae Ocelot


Viverridae African civet


Hyaenidae Striped hyena

Herpestidae Meller's mongoose

Eupleridae Falanouc


AmphicyonidaeYsengrinia americana

Canidae African golden wolf


HemicyonidaeHemicyon sansaniensis

Ursidae American black bear


EnaliarctidaeEnaliarctos mealsi


Phocidae Common seal


Otariidae California sea lion

Odobenidae Pacific walrus


Ailuridae Red panda


Mephitidae Striped skunk


Procyonidae Common raccoon

Mustelidae European polecat

=Wolves (wolf), dogs, foxes, Canidae=[edit]
Canidae: domestic dogs, wolves, foxes, jackals, dingoes, and many other extant and extinct dog-like mammals. A member of this family is called a canid.

Side-striped jackal Dogs, jackals, wolves, and foxes (Plate XIII).jpg

Black-backed jackal Dogs, jackals, wolves, and foxes (Plate XII).jpg

Dog Dogs, jackals, wolves, and foxes (Plate XXXVII).jpg

Gray wolf Dogs, jackals, wolves, and foxes (Plate I).jpg

Coyote Dogs, jackals, wolves, and foxes (Plate IX).jpg

African golden wolf Dogs, jackals, wolves, and foxes (Plate XI).jpg

Golden jackal Dogs, jackals, wolves, and foxes (Plate X).jpg

Ethiopian wolf Dogs, jackals, wolves, and foxes (Plate VI).jpg

Dhole Dogs, jackals, wolves, and foxes (Plate XLI).jpg

African wild dog Dogs, jackals, wolves, and foxes (Plate XLIV).jpg

Even-toed ungulate (Artiodactyla)[edit]
Even-toed ungulate: Artiodactyla excludes whales (Cetacea), although DNA sequence and anatomical data indicate they share a common ancestor, making the group paraphyletic. The phylogenetically accurate group is called Cetartiodactyla (from Cetacea + Artiodactyla).
Cladogram of Cetacea within Artiodactyla.png
Lagomorpha (order Lagomorpha): two living families: the Leporidae (hares and rabbits) and the Ochotonidae (pikas). ~80 species of lagomorph: 30 species of pika, 20 species of rabbit and cottontail, and 30 species of hare.
Fossil occurrences of leporids and ochotonids and global environmental change (climate change, C3/C4 plants distribution).
Category:Anatomical simulation
Anatomography: interactive website which supports generating anatomical diagrams and animations of the human body.
Zygote Body (formerly: Google Body): web application by Zygote Media Group that rendered manipulable 3D anatomical models of the human body.
Domesticated animals, feral animals[edit]
Category:Domesticated animals
Category:Domesticated birds
Category:Domestic pigs
Category:Feral animals
Category:Feral parrots
Opinion 2027: ruling of the International Commission on Zoological Nomenclature (ICZN) concerning the conservation of 17 species names of wild animals with domestic derivatives. If these wild animals and their domesticated derivatives are regarded as one species, then the scientific name of that species is the scientific name of the wild animal.
Feral parrot: parrot that has adapted to life in an ecosystem to which it is not native. Many are descended from pets that have escaped or been deliberately released.
Red-masked parakeet (Psittacara erythrogenys): medium-sized parrot from Ecuador and Peru. It is popular as a pet and are known in aviculture as the cherry-headed conure or the red-headed conure. They are also considered the best talkers of all the conures.
Rose-ringed parakeet (Psittacula krameri): ring-necked parakeet, is a gregarious tropical Afro-Asian parakeet species that has an extremely large range. Both sexes have a distinctive green colour. Rose-ringed parakeets measure on average 40 cm in length, including the tail feathers, a large portion of their total length. One of the few parrot species that have successfully adapted to living in disturbed habitats, it has withstood the onslaught of urbanisation and deforestation. As a popular pet species, escaped birds have colonised a number of cities around the world; herbivorous and not migratory.
Kingston parakeets: feral rose-ringed parakeets that live in the suburbs around Kingston and Twickenham, South West London, England, numbering at least 6,000, with some estimates suggesting the UK population could be as high as 50,000 individuals.

Botany, plant biology[edit]

Soil plant atmosphere continuum: pathway for water moving from soil through plants to the atmosphere.
Transpiration stream: uninterrupted stream of water and solutes which is taken up by the roots and transported via the xylem vessels to the leaves where it evaporates into the air/apoplast-interface of the substomatal cavity. It is driven by capillary action and in some plants by root pressure. The main driving factor is the difference in water potential between the soil and the substomatal cavity caused by transpiration.
Pressure bomb (pressure chamber, Scholander bomb): instrument with which it is possible to measure the approximate water potential of plant tissues. A leaf attached to a stem is placed inside a sealed chamber and pressurised gas is added to the chamber slowly. As the pressure increases at some point sap will be forced out of the xylem and will be visible at the cut end of the stem. The pressure that is required to do so is equal and opposite to the water potential of the leaf.
Vascular tissue
Vascular bundle
Xylem: transport water from roots to shoot and leaves, but it also transports some nutrients.
Phloem: carries organic nutrients (known as photosynthate), in particular, sucrose, a sugar, to all parts of the plant where needed. Unlike xylem (which is composed primarily of dead cells), the phloem is composed of still-living cells that transport sap.

Plant taxonomy[edit]

Template:List of systems of plant taxonomy
Angiosperm Phylogeny Group: refers to an informal international group of systematic botanists who came together to try to establish a consensus on the taxonomy of flowering plants (angiosperms) that would reflect new knowledge about plant relationships discovered through phylogenetic studies.
APG III system (Angiosperm Phylogeny Group III system)


Buffer strip: area of land maintained in permanent vegetation that helps to control air, soil, and water quality, along with other environmental problems, dealing primarily on land that is used in agriculture. Buffer strips trap sediment, and enhance filtration of nutrients and pesticides by slowing down runoff that could enter the local surface waters.
Riparian buffer: vegetated area near a stream, usually forested, which helps shade and partially protect a stream from the impact of adjacent land uses. It plays a key role in increasing water quality in associated streams, rivers, and lakes, thus providing environmental benefits.


DPANN (Diapherotrites, Parvarchaeota, Aenigmarchaeota, Nanoarchaeota, Nanohaloarchaea): superphylum of Extremophile Archaea.
Archaea: superphylum - TACK - has been proposed that includes the Thaumarchaeota, Aigarchaeota, Crenarchaeota, and Korarchaeota. This superphylum may be related to the origin of eukaryotes.
Proteoarchaeota (TACK): proposed archaeal kingdom.

Bacteriology, bacteria[edit]

Mycobacterium: aerobic and nonmotile bacteria (except: Mycobacterium marinum, which has been shown to be motile within macrophages); characteristically acid-alcohol-fast; lack of an outer cell membrane; all share a characteristic cell wall, thicker than in many other bacteria, which is hydrophobic, waxy, and rich in mycolic acids. Adapt readily to growth on very simple substrates, using ammonia or amino acids as nitrogen sources and glycerol as a carbon source in the presence of mineral salts. Some species can be very difficult to culture, have extremely long reproductive cycles — M. leprae, may take more than 20 days to proceed through one division cycle; availability of genetic manipulation techniques still lags far behind that of other bacterial species
Tuberculosis: common, and in many cases lethal, infectious disease caused by various strains of mycobacteria, usually Mycobacterium tuberculosis; typically attacks the lungs, but can also affect other parts of the body; most infections are asymptomatic and latent, but about one in ten latent infections eventually progresses to active disease which, if left untreated, kills more than 50% of those so infected; classic symptoms of active TB infection are a chronic cough with blood-tinged sputum, fever, night sweats, and weight loss (the latter giving rise to the formerly prevalent term "consumption"); multiple drug-resistant tuberculosis (MDR-TB) infections. 1/3rd of the world's population is thought to have been infected with M. tuberculosis, with new infections occurring in about 1% of the population each year. ~80% of the population in many Asian and African countries test positive in tuberculin tests, while only 5–10% of USA population tests positive. More people in the developing world contract tuberculosis because of compromised immunity, largely due to high rates of HIV infection and the corresponding development of AIDS.
Mycobacterium tuberculosis: most recent common ancestor of the M. tuberculosis complex evolved ~40,000 years ago.
Multi-drug-resistant tuberculosis
Extensively drug-resistant tuberculosis
Totally drug-resistant tuberculosis
Lipoarabinomannan (LAM): glycolipid, and a virulence factor associated with M. tuberculosis; inactivate macrophages and scavenge oxidative radicals
Mycolic acid: long fatty acids found in the cell walls of Mycobacterium sp.; major component of the cell wall
Leprosy (Hansen's disease (HD)): left untreated, leprosy can be progressive, causing permanent damage to the skin, nerves, limbs and eyes. Contrary to folklore, leprosy does not cause body parts to fall off, although they can become numb or diseased as a result of secondary infections; these occur as a result of the body's defenses being compromised by the primary disease
Mycobacterium leprae (Hansen’s coccus spirilly): intracellular, pleomorphic, acid-fast bacterium; culture takes several weeks to mature; obligate intracellular parasite; longest doubling time of all known bacteria, and has thwarted every effort at culture in the laboratory
Mycobacterium lepromatosis: discovered in 2008; species is distinct from Mycobacterium leprae; causes diffuse Lepromatous leprosy (DLL)
Leprosy stigma
Leper colony (leprosarium, lazar house): in 2001, government-run leper colonies in Japan came under judicial scrutiny, leading to the determination that the Japanese government had mistreated the patients, and the District Court ordered Japan to pay compensation to former patients
National Hansen's Disease Museum (Japan)
Bacterial microcompartment
Carboxysome: bacterial microcompartments that contain enzymes involved in carbon fixation; made of polyhedral protein shells about 80 to 140 nm in diameter; thought to concentrate carbon dioxide to overcome the inefficiency of RuBisCO; found in all cyanobacteria and many chemotrophic bacteria that fix carbon dioxide
Escherichia coli: Gram-negative, facultatively anaerobic, rod-shaped bacterium of the genus Escherichia that is commonly found in the lower intestine of warm-blooded organisms (endotherms). Most E. coli strains are harmless, but some serotypes can cause serious food poisoning in their hosts, and are occasionally responsible for product recalls due to food contamination. The harmless strains are part of the normal flora of the gut, and can benefit their hosts by producing vitamin K2, and preventing colonization of the intestine with pathogenic bacteria.
Escherichia coli O104:H4
Escherichia coli O157:H7
Escherichia coli (molecular biology)
Taxon in disguise: in bacteriology, a species, genus or higher unit of biological classification whose evolutionary history reveals has evolved from another unit of similar or lower rank, making the parent unit paraphyletic. This happens when rapid evolution makes a new species appear radically different from the ancestral group, so that it is not (initially) recognised as belonging to the parent phylogenetic group, leaving the latter an evolutionary grade. The bacterial genus Shigella is the cause of bacillary dysentery, a potentially severe infection that claim the lives of over a million people annually. The genus (S. dysenteriae, S. flexneri, S. boydii, S. sonnei) have evolved from the common intestinal bacterium Escherichia coli, rendering that species parephyletic. E. coli itself can also cause serious dysentery, but the difference in the genetic makeup between the E. coli and Shigella causes different medical conditions and symptoms.

Borderline life[edit]

Ultramicrobacteria (0.3-0.2 µm): many, if not all, of these small bacteria are dormant forms of larger cells that allow survival under starvation conditions
Nanobe: tiny filamental structure first found in some rocks and sediments.
Template:Subviral agents
Sputnik virophage
Prion: infectious agent thought to be the cause of the transmissible spongiform encephalopathies (TSEs). It is composed entirely of protein material, called PrP (short for prion protein), that can fold in multiple, structurally distinct ways, at least one of which is transmissible to other prion proteins, leading to disease that is similar to viral infection. This would be in contrast to all other known infectious agents (virus/bacteria/fungus/parasite) which must contain nucleic acids (either DNA, RNA, or both).
PRNP (Major prion protein; PrP): the only known example of a prion protein. In humans, it is encoded by the PRNP gene.
Creutzfeldt–Jakob disease (CJD): degenerative neurological disease that is incurable and invariably fatal. Caused by infectious PRNP. CDC: the defective protein can be transmitted by contaminated harvested human brain products, corneal grafts (in at least one reported case), dural grafts or electrode implants (acquired or iatrogenic form (iCJD)); it can be familial (fCJD); or it may appear for the first time in the patient (sporadic form: sCJD); in the familial form, a mutation occurs in the gene for PrP, PRNP; 10%-15% of CJD cases are familial.
Gerstmann–Sträussler–Scheinker syndrome: very rare, usually familial, fatal neurodegenerative disease that affects patients from 20 to 60 years in age. A change in codon 102 from proline to leucine on chromosome 20, has been found in PRNP of most affected individuals.
Fatal familial insomnia: extremely rare autosomal dominant inherited prion disease of the brain; almost always caused by a mutation to the protein PrPC, but can also develop spontaneously in patients with a non-inherited mutation variant called sporadic fatal insomnia.
Kuru (disease): incurable degenerative neurological disorder endemic to tribal regions of Papua New Guinea. Now widely accepted that kuru was transmitted among members of the Fore tribe of Papua New Guinea via funerary cannibalism. Prion-resistant genetic variant of PRNP G127V.


Non-cellular life: term presumes the phylogenetic scientific classification of viruses as lifeforms
Viral evolution: many viruses, in particular RNA viruses, have short generation times and relatively high mutation rates (on the order of one point mutation or more per genome per round of replication for RNA viruses). Studies at the molecular level have revealed relationships between viruses infecting organisms from each of the three domains of life, and viral proteins that pre-date the divergence of life and thus the last universal common ancestor; genomes of most vertebrate species contain hundreds to thousands of sequences derived from ancient retroviruses
Paleovirology (viral fossils): regions of genomes that originate from ancient germline integration of viral genetic material
Endogenous viral element (EVE): DNA sequence derived from a virus, and present within the germline of a non-viral organism; may be entire viral genomes (proviruses), or fragments of viral genomes.
Endogenous retrovirus (ERV; HERV: Human Endogenous Retrovirus): can play an active role in shaping genomes; long terminal repeat (LTR) sequences that flank ERV genomes frequently act as alternate promoters and enhancers, often contributing to the transcriptome by producing tissue-specific variants. 64% of known LTR-promoted transcription variants are expressed in reproductive tissues. Retroelements in general are largely prevalent in rapidly evolving, mammal-specific gene families whose function is largely related to the response to stress and external stimuli: class I & class II MHC genes. Majority of ERVs that occur in vertebrate genomes are ancient, inactivated by mutation, and have reached genetic fixation in their host species. HERVs comprise: 98,000 ERV elements; fragments make up nearly 8%; no HERVs capable of replication had been identified [2005], containing major deletions or nonsense mutations. HERV-K (HML2) family of viruses has been active since the divergence of humans and chimpanzees; makes up less than 1% of HERV elements but is one of the most studied; has even been active in the past few hundred thousand years, e.g., some human individuals carry more copies of this virus family than others; two members of HERV-K(HML2), HERV-K106 and HERV-K116, were active in the last 800,000 years and that HERV-K106 may have infected modern humans 150kya; absence of known infectious members of the HERV-K(HML2) family, and the lack of elements with a full coding potential within the published human genome sequence, suggests to some that the family is less likely to be active at present
ERVWE1 (HERV-W_7q21.2 provirus ancestral Env polyprotein; syncytin; enverin): in humans, and other mammals, intact env proteins called syncytins are responsible for the formation and function of syncytiotrophoblasts; been suggested that the selection and fixation of these proteins for this function have played a critical role in the evolution of viviparity. Distinct, syncytin-like genes have been identified in primates, rodents, lagomorphs, carnivores, and ungulates, with integration dates ranging from 10-85 million years ago. Syncytins: retroviral envelope proteins have been exapted to produce a protein that is expressed in the placental syncytiotrophoblast, and is involved in fusion of the cytotrophoblast cells to form the syncytial layer of the placenta; syncytiotrophoblast: responsible for maintaining nutrient exchange and protecting the developing fetus from the mother's immune system
Virology: study of viruses; structure, classification and evolution, their ways to infect and exploit host cells for reproduction, their interaction with host organism physiology and immunity, the diseases they cause, the techniques to isolate and culture them, and their use in research and therapy; virology is considered to be a subfield of microbiology or of medicine.
RNA virus: mutation rate about 106 times faster than DNA viruses, "because viral RNA polymerases lack the proof-reading ability of DNA polymerases". ssRNA, sometimes dsRNA. Ribovirus: explicitly excludes retroviruses (DNA intermediate).

Very large viruses:

Pithovirus (genome: ): 1.5 µm in length and 0.5 µm in diameter; infects amoebas; double-stranded DNA virus; viable specimen was found in a 30,000-year-old ice core harvested from permafrost in Siberia.
Mimivirus (genome: 1,181,404 bp)
Pandoravirus (genome: 1.9-2.5 Mb)
Megavirus (genome: 1,259,197 bp)
Subtypes of HIV
History of HIV/AIDS: originated in non-human primates in Sub-Saharan Africa and was transferred to humans during the late 19th or early 20th century. Two types: HIV-1 and HIV-2. The pandemic strain of HIV-1 is closely related to a virus found in the chimpanzees of the subspecies Pan troglodytes troglodytes, which lives in the forests of the Central African nations of Cameroon, Equatorial Guinea, Gabon, Republic of Congo (or Congo-Brazzaville), and Central African Republic. HIV-2 is less transmittable and is largely confined to West Africa, along with its closest relative, a virus of the sooty mangabey (Cercocebus atys atys), an Old World monkey inhabiting southern Senegal, Guinea-Bissau, Guinea, Sierra Leone, Liberia, and western Ivory Coast.
Timeline of early HIV/AIDS cases
Timeline of HIV/AIDS


HIV Rev response element (RRE): highly structured, ~350 nucleotide RNA segment present in the Env coding region of unspliced and partially spliced viral mRNAs; in the presence of the HIV-1 accessory protein Rev, HIV-1 mRNAs that contain the RRE can be exported from the nucleus to the cytoplasm for downstream events such as translation and virion packaging.


{q.v. User:Kazkaskazkasako/Books/Physical sciences#Biogeography}

Classification, taxonomy, systematics[edit]

Category:Scientific classification
Category:Morphology (biology)
Category:Scientific nomenclature
Category:Classification systems
Category:Borderline life
Category:Phylogenetics {also q.v. Category:Evolutionary biology}
Template:Taxonomic ranks: Main ones: Domain, Kingdom, Phylum/Division, Class, Order, Family, Tribe, Genus, Species.
Taxonomy (biology): academic discipline of defining groups of biological organisms on the basis of shared characteristics and giving names to those groups; groups created through this process are referred to as taxa (singular taxon). Father of modern taxonomy: Carolus Linnaeus. Taxonomic descriptions; Classifying organisms: Phylogenetics and cladistics, Phenetics.
Biological classification (scientific classification in biology): method of taxonomy used to group and categorize organisms into groups such as genus or species
Systematics: study of the diversification of living forms, both past and present, and the relationships among living things through time; used to understand the evolutionary history of life on Earth.
Synonym (taxonomy): scientific name that applies to a taxon that (now) goes by a different scientific name, although zoologists use the term somewhat differently. Differences between zoology and botany.
Monophyly: "A satisfactory and comprehensive cladistic definition of a species or genus is in fact impossible, and reflects the impossibility of seamlessly impressing a gradualistic model of continual change over the 'quantum' Linnean model, where species have defined boundaries, and intermediaries between species cannot be accommodated". Then comes paraphyly, polyphyly... Quantum physics vs classical physics; (mathematical) logics vs complete & consistent
Evolutionary grade {q.v. Taxon in disguise}: in alpha taxonomy, a grade refers to a taxon united by a level of morphological or physiological complexity. The term was coined by British biologist Julian Huxley, to contrast with clade, a strictly phylogenetic unit.
Gene Ontology
Structural Classification of Proteins: SCOP, manual classification
CATH: CATH Protein Structure Classification

Organizations and nomenclature:

International Code of Zoological Nomenclature (ICZN or ICZN Code): Principles: Principle of Binominal Nomenclature, Principle of Priority, Principle of Coordination, Principle of the First Reviser, Principle of Homonymy (name of each taxon must be unique), Principle of Typification.
International Commission on Zoological Nomenclature (ICZN)
ZooBank: open access website intended to be the official ICZN (Commission) registry of zoological nomenclature; proposed: 2005; live: 2006.08.10 :: 1.5 mln species. LSIDs
International Code of Nomenclature for algae, fungi, and plants (ICN; before 2011.07: International Code of Botanical Nomenclature (ICBN))

Biological classification[edit]

Species problem: mixture of difficult, related questions that often come up when biologists define the word "species". E.g. what works well for some organism (e.g., birds) will be useless for others (e.g., bacteria). When to recognize a new species, for example when new data indicate that one previously described species actually may include two or more separately evolving groups, each of which could possibly be recognized as a separate species. Jody Hey: "result of two conflicting motivations by biologists: 1) to categorize and identify organisms; 2) to understand the evolutionary processes that give rise to species".
Ring species: connected series of neighboring populations, each of which can interbreed with closely sited related populations, but for which there exist at least two "end" populations in the series, which are too distantly related to interbreed, though there is a potential gene flow between each "linked" species. Such non-breeding, though genetically connected, "end" populations may co-exist in the same region thus closing a "ring". Formally, the issue is that interfertile ("able to interbreed") is not a transitive relation – if A can breed with B, and B can breed with C, it does not follow that A can breed with C – and thus does not define an equivalence relation.
Template:Mammal hybrids: some are through natural and some through artificial insemination.
Bikont ("two flagella")
Plants+HC+SAR megagroup (AH/SAR)
Plants+HC clade
Archaeplastida (Plantae sensu lato): Red algae (Rhodophyta), Glaucophytes (glaucocystophytes), Plantae
Hacrobia (cryptomonads-haptophytes assemblage; CCTH (standing for Cryptophyta, Centrohelida, Telonemia and Haptophyta); "Eukaryomonadae"): proposed monophyletic grouping of chromalveolata that are not included in the SAR supergroup
SAR supergroup
Heterokont (stramenopiles ("S")): major line of eukaryotes currently containing more than 100,000 known species: algae (kelp - diatoms (plankton)), oomycetes (generally parasitic)
Rhizaria: vary considerably in form, but for the most part they are amoeboids with filose, reticulose, or microtubule-supported pseudopods; many produce shells or skeletons, which may be quite complex in structure, and these make up the vast majority of protozoan fossils. Nearly all have mitochondria with tubular cristae.
Excavate (Excavata): major subgroup of unicellular eukaryotes: Discoba or JEH (Euglenozoa, Heterolobosea (Percolozoa), Jakobea), Metamonada or POD (Preaxostyla, Fornicata, Parabasalia)
Apusozoa: comprising several genera of flagellate protozoa; occur in soils and aquatic habitats, where they feed on bacteria; grouped together based on the presence of an organic shell or theca under the dorsal surface of the cell.
Unikont: have a single emergent flagellum, or are amoebae with no flagella
Amoebozoa: pseudopodia are characteristically blunt and finger-like, called lobopodia
Opisthokont (ὀπίσθιος (opísthios) = "rear, posterior" + κοντός (kontós) = "pole" i.e. "flagellum"; "Fungi/Metazoa group")
Holozoa: includes animals and their closest single-celled relatives, but excludes fungi
Mesomycetozoea (DRIP clade, or Ichthyosporea): small group of protists, mostly parasites of fish and other animals
Filozoa: monophyletic grouping; include animals along with their nearest unicellular relatives (those organisms which are more closely related to animals than to fungi or Mesomycetozoa)
Metazoa or "Animalia"
Fungus (pl.: fungi or funguses)
Nucleariid: group of amoebae with filose pseudopods, known mostly from soils and freshwater; distinguished from the superficially similar vampyrellids mainly by having mitochondria with discoid cristae.

Tech and ethics[edit]

Technological singularity

Experiments, research, laboratory[edit]

In vitro
In vivo
In silico: "performed on computer or via computer simulation"
Laboratory (lab)
Wet laboratory (wet lab)
Society for Laboratory Automation and Screening (SLAS): formed in 2010 as a merger between the Association for Laboratory Automation and the Society for Biomolecular Sciences. SLAS is a global organization that exists to provide forums for education and information exchange to encourage the study of, and improve the science and practice of, laboratory automation and screening.
Journal of Laboratory Automation (1996-): bimonthly peer-reviewed scientific journal published by SLAS; covers a wide range of technologies including sample processing (liquid handling, sample storage, sample analysis, and system integration), microfluidics (design, applications, and integration), and informatics (data acquisition and management, electronic laboratory notebooks, and integration).
Journal of Biomolecular Screening: peer-reviewed scientific journal published by SAGE Publications on behalf of SLAS; covers scientific and technical applications and advances in areas such as lab automation and robotics, virtual screening, and high throughput screening.
Operant conditioning chamber (Skinner box): laboratory apparatus used in the experimental analysis of behavior to study animal behavior.

Scientific modeling[edit]

Category:Scientific modeling
Category:Artificial life
OpenWorm: international open science project to simulate the roundworm Caenorhabditis elegans at the cellular level in silico. Although the long term goal is to model all 959 cells of the C. elegans, the first stage is to model the worm's locomotion by simulating the 302 neurons and 95 muscle cells.
WormBase: online biological database about the biology and genome of C. elegans and contains information about other related nematodes. Sequence curation: Genome sequence; Gene structure models (Gene prediction programs give a reasonable set of gene structures, but the best of them only predict about 80% of the complete gene structures correctly. They have difficulty predicting genes with unusual structures, as well as those with a weak translation start signal, weak splice sites or single exon genes. They can incorrectly predict a coding gene model where the gene is a pseudogene and they predict the isoforms of a gene poorly, if at all.);
WormBook: open access, comprehensive collection of original, peer-reviewed chapters covering topics related to the biology of the nematode worm C. elegans.

Software, internet, databases[edit]

Academic, research, science games:

NanoMission: serious game by PlayGen for Wellcome Trust and FEI in order to teach the player about the world of nanomedicine. Advergame


Category:Computational chemistry software
Category:Bioinformatics software {q.v. User:Kazkaskazkasako/Books/All#Process management, workflow}
List of molecular graphics systems
Molecular design software: polymers, peptides, nucleic acids, solvents, partial charges, docking, optimization, molecular mechanics, quantum mechanics, Force Fields
Category:Molecular modelling software: PyMOL, UCSF Chimera, Coot (program)
List of software for nanostructures modeling: more material sciences
Comparison of software for molecular mechanics modeling: MD simulations
Structural alignment software: structure-function
List of sequence alignment software
b:Software Tools For Molecular Microscopy: molecular microscopy or cryo-electron microscopy (cryoEM)
UCSF Chimera

Computations, CS, IT, bioinformatics (BioInfo), computational biology (Comp Bio)[edit]

Critical Assessment of Prediction of Interactions
Critical Assessment of Techniques for Protein Structure Prediction
PHYLIP ((PHYLogeny Inference Package)): free computational phylogenetics package of programs for inferring evolutionary trees (phylogenies).
Open Bioinformatics Foundation: BioPython
Bioconductor: based on statistical R programming language


Genome Reference Consortium (GRC): international collective of academic and research institutes with expertise in genome mapping, sequencing, and informatics, formed to improve the representation of reference genomes. At the time the human reference (Human Genome Project) was initially described, it was clear that some regions were recalcitrant to closure with existing technology. Initially the focus lies with the Human and the Mouse reference genomes, but in mid-late 2010 full maintenance and improvement of the Zebrafish genome sequence was also added to the GRC. The goal of the Consortium is to correct the small number of regions in the reference that are currently misrepresented, to close as many remaining gaps as possible and to produce alternative assemblies of structurally variant loci when necessary. 2015.06 the major assembly release for human, mouse and zebrafish are GRCh38, GRCm38 and GRCz10 respectively.
Multiple sequence alignment (MSA): sequence alignment of three or more biological sequences, generally protein, DNA, or RNA.
Clustal: widely used MSA program. ClustalW: command line; ClustalX: GUI; Clustal Omega: increase in scalability over previous versions, allowing hundreds of thousands of sequences to be aligned in only a few hours (command line, protein-only).
Stockholm format: MSA format used by Pfam and Rfam to disseminate protein and RNA sequence alignments
Chemistry Development Kit (CDK; GNU LGPL; Java): library for Chemoinformatics and Bioinformatics. Wrappers: Python, Ruby.
Pfam: database of protein families that includes their annotations and multiple sequence alignments generated using hidden Markov models.
Rfam: database containing information about ncRNA families and other structured RNA elements. It is an annotated, open access database originally developed at the Wellcome Trust Sanger Institute in collaboration with Janelia Farm, and currently hosted at the EBI. Unlike proteins, ncRNAs often have similar secondary structure without sharing much similarity in the primary sequence. Rfam divides ncRNAs into families based on evolution from a common ancestor. Producing multiple sequence alignments (MSA) of these families can provide insight into their structure and function, similar to the case of protein families. These MSAs become more useful with the addition of secondary structure information

molecular dynamics (MD) & molecular modeling[edit]

Finite element method, FEM, aka finite element analysis (FEA): numerical technique for finding approximate solutions of partial differential equations (PDE) as well as of integral equations.
Gaussian network model, also elastic network models (ENM): representation of a biological macromolecule as an elastic mass-and-spring network to study, understand, and characterize mechanical aspects of its long-scale dynamics.
Anisotropic Network Model: essentially an Elastic Network Model for the Cα atoms with a step function for the dependence of the force constants on the inter-particle distance.

Databases (DBs), classification: phys, chem, bio, ...[edit]

Biocurator (scientific curators, data curators or annotators): professional scientist who collects, annotates, and validates information that is disseminated by biological and model organism databases. Employ shared biomedical ontologies; consistent use of nomenclatures (e.g. HUGO, IUBMB: EC number). International Society for Biocuration (ISB) was founded in 2008.
Bioinformatic Harvester: uses many DBs to gather bio/chem/(phys) data
Enzyme Commission number (EC number; enzyme nomenclature): numerical classification scheme for enzymes, based on the chemical reactions they catalyze; every EC number is associated with a recommended name for the respective enzyme. Strictly speaking, EC numbers do not specify enzymes, but enzyme-catalyzed reactions, if different enzymes (for instance from different organisms) catalyze the same reaction, then they receive the same EC number; through convergent evolution, completely different protein folds can catalyze an identical reaction and therefore would be assigned an identical EC number.
Entrez: federated search engine over many DBs: PubMed (Medline, PubMed Central), OMIM & OMIA, (Nucleotide (SNP, Gene, HomoloGene, Genome), Taxonomy, Protein, Structure), many other
Mendelian Inheritance in Man: OMIM; diseases with genetic component (nature vs. nurture), links to genes in human genome
BLAST: Basic Local Alignment Search Tool. Bio-sequences: protein, nucleotides (DNA (genomic), RNA). Algorithm, scoring matrix, "training" the algorithm.
UniProt (Universal Protein resource; launched in 2003.12): comprehensive, high-quality and freely accessible database of protein sequence and functional information, many of which are derived from genome sequencing projects. It contains a large amount of information about the biological function of proteins derived from the research literature. In 2002, these joined forces as UniProt Consortium: European Bioinformatics Institute (EBI (UK), @EMBL) + the Swiss Institute of Bioinformatics (SIB) + Protein Information Resource (PIR (US)). SIB: ExPASy; PIR (@Georgetown University Medical Center in Washington, DC, USA): Margaret Dayhoff's Atlas of Protein Sequence and Structure, first published in 1965.
UniProtKB (UniProt Knowledgebase):
UniProtKB/Swiss-Prot: contains reviewed, manually annotated entries by biocurators. Aim: to provide all known relevant information about a particular protein.
UniProtKB/TrEMBL: contains unreviewed, automatically annotated entries; introduced in response to increased dataflow resulting from genome projects, as the time- and labour-consuming manual annotation process of UniProtKB/Swiss-Prot could not be broadened to include all available protein sequences.
UniParc (UniProt Archive): comprehensive and non-redundant database, which contains all the protein sequences from the main, publicly available protein sequence databases. Identical sequences are merged, regardless of whether they are from the same or different species. Each sequence is given a stable and unique identifier (UPI), making it possible to identify the same protein from different source databases. UniParc contains only protein sequences, with no annotation.
UniRef (UniProt Reference Clusters): consists of three databases of clustered sets of protein sequences from UniProtKB and selected UniParc records: UniRef100 (identical sequences, 100% sequence identity), UniRef90 (at least 90%), UniRef50 (at least 50% sequence identity). This clustering of sequences enables faster sequence searches and reduces DB size.
UniMes (UniProt Metagenomic and Environmental Sequences): metagenomic and environmental data.
Other UniProt related:
ExPASy: proteomics: sequence (domains), structure (functional sites), protein families, 2D gel electrophoresis analysis. By SIB; collaborates with EMBL-EBI.
NeXtProt: knowledge platform on human proteins; comprehensive resource that provides a variety of types of information on human proteins, such as their function, subcellular location, expression, interactions and role in diseases. Major part of the information obtained from the UniProt Swiss-Prot database, but gradually being complemented by data originating from high-throughput studies with an emphasis on proteomics
BRENDA (BRaunschweig ENzyme DAtabase): enzymes
International HapMap Project: human genomes, SNPs
HUGO Gene Nomenclature Committee (HGNC) {}: approves a unique and meaningful name for every known human gene based on a query of experts. In addition to a long name, the HGNC also assigns an abbreviation (referred to as symbol) to every gene.
Information Hyperlinked over Proteins: (iHOP) genes, proteins, RNA as hyperlinks in PubMed abstracts
KEGG: collection of DBs: genomes, enzymatic pathways , biological chemicals ("pathway intermediates")
WikiPathways: community resource for contributing and maintaining content dedicated to biological pathways. built using MediaWiki software, a custom graphical pathway editing tool (PathVisio) and integrated BridgeDb databases covering major gene, protein, and metabolite systems.
Protein Information Resource: PIR; bioinfo DB: genomic and proteomic (+RNA?)
Ensembl: the ultimate resource to genomes, genomics and genetics. Retrieval of genomic information
Vertebrate and Genome Annotation Project: annotated genomes of human, mouse, zebrafish, pig, dog. Built upon Ensembl
Protein Data Bank (PDB): 3D structural data repository of large (bio)molecules, e.g. DNA, RNA, protein, sugars, lipids (small inorganics are excluded). X-ray, NMR, EM, hybrid data. File format. Classification projects: Gene Ontology, SCOP, CATH.
EM Data Bank (Electron Microscopy Data Bank (EMDB)): from 2011.12.20 EMDB joined PDB archive.
Worldwide Protein Data Bank (wwPDB): organization that maintains the archive of macromolecular structure; mission: to maintain a single PDB Archive of macromolecular structural data that is freely and publicly available to the global community. 4 members: Research Collaboratory for Structural Bioinformatics Protein Database (RCSB PDB), Protein Data Bank in Europe (PDBe), Protein Data Bank Japan (PDBj), Biological Magnetic Resonance Data Bank (BMRB).
Orientations of Proteins in Membranes database (OPM) {}: spatial positions of membrane protein structures with respect to the lipid bilayer. However, structures of many membrane-associated proteins are not included in the database if they can not be computationally predicted.
Ki Database: binding affinities (Ki) of chemical compounds for biomacromolecules (proteins: receptors, transporters, ion channels, enzymes)
OvidSP: health science DBs search interface
InterPro {}: database of protein families, domains and functional sites in which identifiable features found in known proteins can be applied to new protein sequences in order to functionally characterise them; signatures consist of models (simple types, such as regular expressions or more complex ones, such as Hidden Markov models) which describe protein families, domains or sites.
Pfam: database of protein families that includes their annotations and multiple sequence alignments generated using hidden Markov models. {q.v. TrEMBL}
PRINTS: collection of so-called "fingerprints"; provides both a detailed annotation resource for protein families, and a diagnostic tool for newly-determined sequence.
TIGRFAMs: database of protein families designed to support manual and automated genome annotation.
Superfamily database (SUPERFAMILY; {}): database of structural and functional annotation for all proteins and genomes
PROSITE {}: entries describing the protein families, domains and functional sites as well as amino acid patterns, signatures, and profiles in them; manually curated by a team of the Swiss Institute of Bioinformatics and tightly integrated into Swiss-Prot protein annotation
Transporter Classification database (TCDB): IUBMB approved classification system for membrane transport proteins including ion channels; designed to be analogous to the EC number system for classifying enzymes, but it also uses phylogenetic information.
GeneCards: database of human genes that provides genomic, proteomic, transcriptomic, genetic and functional information on all known and predicted human genes; developed and maintained by the Crown Human Genome Center at the Weizmann Institute of Science.
Comparative Toxicogenomics Database (CTD): public website and research tool that curates scientific data describing relationships between chemicals, genes, and human diseases.
Reactome: free online database of biological pathways. There are several Reactomes that concentrate on specific organisms, the largest of these is focused on human biology. The core unit of the Reactome data model is the reaction. Entities (nucleic acids, proteins, complexes and small molecules) participating in reactions form a network of biological interactions and are grouped into pathways. Examples of biological pathways in Reactome include signaling, innate and acquired immune function, transcriptional regulation, translation, apoptosis and classical intermediary metabolism.
Bionumbers: free-access database of quantitative data in biology designed to provide the scientific community with access to the large amount of data now generated in the biological literature. BioNumbers project performs literature-based curation of various sources. It is a regularly updated online resource that contains >6,000 entries from ~1,000 distinct references. Examples of data include transcription and translation rates, organism and organelle sizes, metabolites concentrations and growth rates.
Comprehensive Microbial Resource (CMR): data on publicly available prokaryotic genomes; searches for similarities and differences between genomes.


Proteopedia: Wiki of proteins, RNA, DNA and other molecules. All PDB entries.

Other DBs: arts, humanities, ...[edit]

Publication (article)[edit]

Publication bias: bias with regard to what is likely to be published, among what is available to be published; one problematic and much-discussed bias is the tendency of researchers, editors, and pharmaceutical companies to handle the reporting of experimental results that are positive (i.e. showing a significant finding) differently from results that are negative (i.e. supporting the null hypothesis) or inconclusive, leading to a misleading bias in the overall published literature. The file drawer effect, or file drawer problem, is that many studies in a given area of research may be conducted but never reported, and those that are not reported may on average report different results from those that are reported.
Data publication: practice consisting in preparing certain data or data set(s) for public use thus to make them available to everyone to use as they wish. This practice is an integral part of the open science movement. There is a large and multidisciplinary consensus on the benefits resulting from this practice. The main goal is to elevate data to be first class research outputs.
Data paper: “scholarly publication of a searchable metadata document describing a particular on-line accessible dataset, or a group of datasets, published in accordance to the standard academic practices”. Their final aim being to provide “information on the what, where, why, how and who of the data”.

Repositories for data publication:

Figshare: online digital repository where researchers can preserve and share their research outputs, including figures, datasets, images, and videos. It is free to upload content and free to access, in adherence to the principle of open data. Researchers can upload all of their research outputs to Figshare, thus making them publicly available. Users can upload files in any format and items are attributed a DOI.
Dryad (repository): international disciplinary repository of data underlying scientific and medical publications.
PANGAEA (data library): Data Publisher for Earth & Environmental Science is a digital data library and a data publisher for earth system science. Data can be georeferenced in time (date/time or geological age) and space (latitude, longitude, depth/height).
[ (GIGA)n DB]: repository to host data and tools associated with articles in GigaScience; however, it also includes a subset of datasets that are not associated with GigaScience articles.

Dedicated search engines of published papers[edit]

List of academic databases and search engines: representative list of major databases and search engines useful in an academic setting for finding and accessing articles in academic journals, repositories, archives, or other collections of scientific and other articles.
Microsoft Academic Search: free public search engine for academic papers and literature, developed by Microsoft Research for the purpose of algorithms research in object-level vertical search, data mining, entity linking, and data visualization. Although largely functional, the service is not intended to be a production web site and may be taken offline in the future when the research goals of the project have been met.
ArXiv {physics, mathematics, CS, nonlinear sciences, quantitative bio, statistics}
Social Science Research Network (SSRN): website devoted to the rapid dissemination of scholarly research in the social sciences and humanities. SSRN was founded in 1994 by Michael Jensen and Wayne Marr, both financial economists. Academic papers in PDF can be uploaded directly to the site by authors and are then available for worldwide free downloading. Publishers and institutions can upload papers and charge a fee for readers to download them. In economics, and to some degree in law (especially in the field of law and economics), almost all papers are now first published as preprints on SSRN and/or other paper distribution networks such as Research Papers in Economics (RePEc) before being submitted to an academic journal.
CiteSeer: replaced by CiteSeerX.
Google scholar
JSTOR: originally containing digitized back issues of academic journals, it now also includes books and primary sources, and current issues of journals;
LexisNexis {law} gateway to US government scientific and technical information and research
Scopus (SciVerse Scopus, @Elsevier): bibliographic database containing abstracts and citations for academic journal articles.
Pubget: by Copyright Clearance Center (CCC).
PubMed (1996.01): free database accessing primarily the MEDLINE database of references and abstracts on life sciences and biomedical topics. The United States National Library of Medicine at NIH maintains the database as part of the Entrez information retrieval system. Indexed with MeSH.
PubMed identifier (PMID): unique number assigned to each PubMed record; there is a similar PMCID (PMC). Assignment of a PMID or PMCID to a publication tells the reader nothing about the type or quality of the content. PMIDs are assigned to letters to the editor, editorial opinions, op-ed columns, and any other piece that the editor chooses to include in the journal, as well as peer-reviewed papers. The existence of the identification number is also not proof that the papers have not been retracted for fraud, incompetence, or misconduct. The announcement about any corrections to original papers may be assigned a PMID.
MEDLINE (Medical Literature Analysis and Retrieval System Online, or MEDLARS Online): bibliographic database of life sciences and biomedical information. MEDLARS (Medical Literature Analysis and Retrieval System) is a computerised biomedical bibliographic retrieval system, launched by NLM in 1964.
United States National Library of Medicine (NLM): operated by USA federal government; world's largest medical library; collections include >7 mln. books, journals, technical reports, manuscripts, microfilms, photographs, and images on medicine and related sciences, including some of the world's oldest and rarest works. Institute within NIH.
National Center for Biotechnology Information (NCBI): part of NLM, branch of NIH. NCBI houses a series of databases relevant to biotechnology and biomedicine and an important resource for bioinformatics tools and services. GenBank; PubMed. All these databases are available online through the Entrez search engine. BLAST.
MedlinePlus: online information service produced by US NLM; provides curated consumer health information in English and Spanish
Index Medicus
GoPubMed: mashup; Gene Ontology (GO) and Medical Subject Headings (MeSH) serve as "Table of contents" in order to structure the millions of articles of the MEDLINE database.
PubMed Central: free digital database of full-text scientific literature in biomedical and life sciences. It grew from the online Entrez PubMed biomedical literature search system. PubMed Central was developed by NLM as an online archive of biomedical journal articles.
Europe PubMed Central (Europe PMC; till 2012.11.01: UK PubMed Central): launched in 2007 as the first ‘mirror’ site to PMC
PubMed Central Canada (PMC Canada; 2009-)
Zasshi Kiji Sakuin (雑誌記事索引, "Japanese Periodicals Index"): searchable database of scholarly articles in Japanese
Japanese Historical Text Initiative (JHTI): Japanese historical documents and English translations. It is part of the Center for Japanese Studies at the University of California at Berkeley.
ISI Web of Knowledge: search engine, citation index, who is highly cited and why ("popular research")
Scirus (2001.04.1): comprehensive science-specific search engine

Technical writing styles[edit]

Technical writing:
Style guide R
Template:Styles : writing, formatting, citing, other examples according to defined "standard" styles
Wikipedia:Manual of Style: q.v. User:Kazkaskazkasako/Books/Wikipedia#Manual of Style

Citation, references, SW, reference management[edit]



Parenthetical referencing and Wikipedia:Parenthetical referencing: "author-date" and "author-title"
Comparison of reference management software:
Internet browser integration
Zotero (AGPL; by Roy Rosenzweig Center for History and New Media (CHNM)): Firefox (original add-on); Zotero Standalone can be integrated into Google Chrome, Safari.
Mendeley (on ~2013.04 Elsevier bought): proprietary; main competitor to Zotero. Based on Qt, runs on Windows, Mac, Linux, iOS (iPhone, iPad).
Papers (software) (on ~2012.11 Springer bought): initially only Mac OS X and iOS (iPhone, iPad), in 2012.02.14 on Windows. iTunes-like look & feel.
Social bookmarking of papers/articles: CiteULike, Connotea (NPG)
No integration into Internet browser:
EndNote (Thomson Reuters): the granddaddy of all current reference management software.
Aigaion, JabRef, RefDB, Refbase, BibDesk (Mac OS X)
Template:Reference management software: web-based reference management (OS independent, only browser is needed)
Comparison of notetaking software: Evernote, Microsoft OneNote
Citavi: reference management program for MS Windows. Popular in DE.
Citation Style Language: open XML-based language to describe the formatting of citations and bibliographies. Used by Zotero, Mendeley, Papers.

Publishers (groups), journals, information management[edit]

Category:Academic publishing
Category:Academic journals
Category:Technical communication
Category:Peer review
IMRAD (introduction, methods, results, and discussion)
Academic journal
Review journal
Review article: attempt to summarize the current state of understanding on a topic; analyze or discuss research previously published by others, rather than reporting new experimental results.
Journals and publishing groups:
Template:Reed Elsevier:
Cell Press: imprint of Elsevier
Trends (journals)
Science (journal)
Georg von Holtzbrinck Publishing Group (also: Die Zeit (50%), Handelsblatt, Der Tagesspiegel.):
Nature Publishing Group (NPG)
Macmillan Publishers Ltd (The Macmillan Group)
Proceedings of the National Academy of Sciences (PNAS): by USA NAS
Public Library of Science & Template:PLoS:
Plos one - multidisciplinary, comparable to Nature, Science, PNAS...
Annual Reviews (publisher): reviews of particular topics
Annual Review of Biochemistry: sets the standard for review articles in biological chemistry and molecular biology.
Wiley-Blackwell: Microscopy Research and Technique
Cold Spring Harbor Laboratory Press (1933-): CSH monographs, CSH perspectives
RNA (journal) (1995.03-2003: Cambridge University Press; 2003-: CSHL Press): published on behalf of the RNA Society.
Cambridge University Press (1534- granted letters patent by Henry VIII): world's oldest publishing house, and the second largest university press in the world.
Template:Thomson Reuters: business data provider and was created by the Thomson Corporation's purchase of Reuters Group on 17 April 2008. Owned 53% by Thomson family. Thomson Reuters is Canada's "leading corporate brand".
Thomson Scientific & Healthcare: split in 2006: Thomson Healthcare + Thomson Scientific. In 2008 both were renamed due to the merger and in 2009 both were merged back into Healthcare & Science unit of the Professional Division of Thomson Reuters, now [12/02/09] called IP & Science (includes also: Legal and Tax & Accounting).
Wolters Kluwer: global information services and publishing company. In 1987 formed by friendly merger of Kluwer Publishers and Wolters Samson (to defend against hostile takeover by Elsevier).
Health & Pharma Solutions: Ovid Technologies: access to online (health science) bibliographic databases, journals and other products; once produced MEDLINE; new DB search interface OvidSP in 2007. SilverPlatter (SilverPlatter Information, Inc.): produced commercial reference databases on CD-ROMs; now part of Ovid.
other: Financial & Compliance Services; Legal & Regulatory; Tax & Accounting.
Journal of Visualized Experiments (JoVE; 2006-): publishing biological, medical, chemical, and physical research in video format.
Royal Society of Chemistry: learned society (professional association) in UK with the goal of "advancing the chemical sciences"; formed in 1980 from the merger of the Chemical Society, the Royal Institute of Chemistry, the Faraday Society and the Society for Analytical Chemistry with a new Royal Charter and the dual role of learned society and professional body.
List of Royal Society of Chemistry journals
Lab on a Chip (journal): any aspect of miniaturisation at the micro and nano scale
Faculty of 1000: recent research papers evaluated by "over 2000 biological researchers by interestingness"


VroniPlag Wiki & de:VroniPlag Wiki (2011.03.28-): wiki at Wikia that examines and documents the extent of plagiarism in German theses (Doctoral, MD, Master, Law...).
de:GuttenPlag Wiki: for Karl-Theodor zu Guttenberg's de:Verfassung und Verfassungsvertrag


Scientometrics: science of measuring and analysing science. In practice, scientometrics is often done using bibliometrics which is a measurement of the impact of (scientific) publications. Fathers of scientometrics: Derek J. de Solla Price and Eugene Garfield. One significant finding in the field is a principle of cost escalation to the effect that achieving further findings at a given level of importance grow exponentially more costly in the expenditure of effort and resources. However, new methods in search, machine learning and data mining are showing that is not the case for many information retrieval and extraction based problems (what about robotization?).
Impact factor (IF): measure reflecting the average number of citations to articles published in science and social science journals. Frequently used as proxy for the relative importance of a journal within its field, with journals with higher impact factors deemed to be more important than those with lower ones. Devised by Eugene Garfield, the founder of ISI (now part of Thomson Reuters). Spoofs of IF: "A short history of SHELX" (by University of Göttingen crystallographer George Sheldrick); reviews have much higher per article IF than an article/letter about original research. Articles providing new tools (e.g. software (esp. FOSS), new biochemical method (e.g. SDS-PAGE, Bradford assay)) have much higher IFs than articles about new phys/chem/bio phenomena.
Bibliometrics: set of methods to quantitatively analyze scientific and technological literature. Citation analysis and content analysis. Trying to make automatic tools to make citation indexes and to use these to distribute scientific funding, grant tenures...
Altmetrics: new metrics proposed as an alternative to the widely used Journal Impact Factor; covers not just citation counts, but also other aspects of the impact of a paper, such as how many data and knowledge bases refer to the article, article views, downloads, or mentions in social media and news media. Counting cites in: Wikipedia; saved by users using CiteULike, Mendeley.

Be objective[edit]

Jan Hendrik Schön
Bogdanov Affair

Scientific wikis[edit]

Scholarpedia: English-language online wiki-based encyclopedia that uses the same MediaWiki software as Wikipedia, but has features more commonly associated with open-access online academic journals. Articles are written by invited expert authors and are subject to peer review. Scholarpedia lists the real names and affiliations of all authors, curators and editors involved in an article, however, the peer review process (which can suggest changes or additions, and has to be satisfied before an article can appear) is anonymous. Focus fields: computational neuroscience, dynamical systems, computational intelligence, physics and astrophysics.

Openness and competition[edit]

Open notebook science


Edward Tufte#Criticism of PowerPoint: PowerPoint - useful or not? Handouts and reading vs. only speaking? Q&A session?

Reference works, encyclopedias[edit]

Category:Reference works

{q.v. User:Kazkaskazkasako/Books/All#Science writers, encyclopedists}

Natural History (Pliny): early encyclopedia in Latin by Pliny the Elder, who died in 79 AD. one of the largest single works to have survived from the Roman Empire to the modern day and purports to cover all ancient knowledge; cover topics including astronomy, mathematics, geography, ethnography, anthropology, human physiology, zoology, botany, agriculture, horticulture, pharmacology, mining, mineralogy, sculpture, painting, and precious stones. The work is dedicated to the emperor Titus, son of Pliny's close friend, the emperor Vespasian, in the first year of Titus's reign. It is the only work by Pliny to have survived and the last that he published. He began it in 77, and had not made a final revision at the time of his death during the AD 79 eruption of Vesuvius.
Suda massive 10th-century Byzantine encyclopedia of the ancient Mediterranean world. Encyclopedic lexicon, written in Greek, with 30,000 entries, many drawing from ancient sources that have since been lost, and often derived from medieval Christian compilers. The articles on literary history are especially valuable; these entries supply details and quotations from authors whose works are otherwise lost.
History of the Encyclopædia Britannica: 1st edition (1771); 2nd (1783); 3rd (1797). Piracy of Britannica: Dobson's Encyclopædia (1789-1798) and Moore's Dublin Edition, Encyclopædia Britannica. The 4th (1800-1810), 5th (1817), and 6th (1823) editions are virtually the same as each other. 7th (1827; 1830-1842): new work, first edition to include a general index for all articles. 8th (1860): thorough revision. 9th (1875-1889): W. Robertson Smith addressed the historical interpretation of the Bible; first to include a significant article about women ("Women, Law Relating to"); evolution was listed for the first time, in the wake of Charles Darwin's writings; 8,500 sold in Britain and 45,000 in USA, but in spite of this, several hundred thousand cheaply produced pirated copies were also sold in USA. American editions (10th-14th): 11th (1903-1910). 15th (1st ed.: 1974-1984)
ARKive: "promoting the conservation of the world's threatened species, through the power of wildlife imagery"; locating and gathering films, photographs and audio recordings of the world's species into a centralised digital archive
Encyclopedia of Life (EOL; 2008.02.26-): free, online collaborative encyclopedia intended to document all of the 1.9 million living species known to science
Biodiversity Heritage Library (BHL; 2005-): consortium of natural history and botanical libraries that cooperate to digitize and make accessible the legacy literature of biodiversity held in their collections and to make that literature available for open access and responsible use as a part of a global “biodiversity commons". Since 2009, the BHL has expanded globally.
Integrated Taxonomic Information System (ITIS): partnership designed to provide consistent and reliable information on the taxonomy of biological species
Catalogue of Life: started in 2001.06 by ITIS and Species 2000; planned to become a comprehensive catalogue of all known species of organisms on Earth
Species 2000: federation of database organizations across the world
Urban Dictionary: satirical crowdsourced online dictionary of slang words and phrases that was founded in 1999 as a parody of by then-college freshman Aaron Peckham. Anyone with either a Facebook or Gmail account can make a submission to the dictionary, and it is claimed that all entries are reviewed by volunteers.

Funding (agencies), companies, government, politics, scientific societies, institutes[edit]

Science policy
List of wealthiest charitable foundations (charitable foundations, private foundations and other charitable organizations):
Howard Hughes Medical Institute (HHMI) (endowment=16.1 bln USD)
Janelia Farm Research Campus (opened in 2006)
Wellcome Trust (est. 1936): biomedical research charity based in London, UK; legacies from the pharmaceutical magnate Sir Henry Wellcome to fund research to improve human and animal health. The aim of the Trust is to "achieve extraordinary improvements in health by supporting the brightest minds", and in addition to funding biomedical research it supports the public understanding of science. Endowment of around £18 bln. The Trust has been described by the Financial Times as the United Kingdom's largest provider of non-governmental funding for scientific research and one of the largest providers in the world; in the field of medical research, it is the world's second-largest private funder after the Bill & Melinda Gates Foundation.
Bill & Melinda Gates Foundation (Gates Foundation, BMGF; 2000-; endowment of US$44.3 bln as of 2014.12.31): largest private foundation in the world, founded by Bill and Melinda Gates; largest transparently operated private foundation in the world. Primary aims of the foundation are, globally, to enhance healthcare and reduce extreme poverty, and in USA, to expand educational opportunities and access to information technology.

United States of America[edit]

National Institutes of Health (NIH): agency of United States Department of Health and Human Services; primary agency of the United States government responsible for biomedical and health-related research (Main provider of funds for biomedical research).
National Science Foundation (NSF); fundamental research and education in all the non-medical fields of science and engineering
National Institute of Standards and Technology (NIST): agency of United States Department of Commerce. Very few funds to keep measurement standards.
Non-money giving organization:
United States National Academy of Sciences (NAS): corporation in the United States whose members serve pro bono as "advisers to the nation on science, engineering, and medicine." Publishes PNAS.
American Association for the Advancement of Science (AAAS): council of AAAS has some elected delegates where at least 2 are from US NAS.
Sage Bionetworks: nonprofit organization in Seattle that promotes open science and patient engagement in the research process. Sage Bionetworks was founded in 2009 as a spinout of Merck & Co., who released software, hardware, intellectual property, and staff connected to its Rosetta Inpharmatics unit.
Stephen Friend (1953.12.10-) is an American physician, scientist, entrepreneur and innovator. He is an authority in the field of cancer biology and a pioneer in the field of the genetics of gene expression, integrating system biology approaches to complex diseases. He is the president, co-founder and director of Sage Bionetworks.
Andrew Kasarskis (1972.11.02-): His focus is on improving health outcomes through better data mining, and his research program includes sequencing-based pathogen surveillance; pharmacogenomics; electronic health records; and systems biology of sleep, behavior, and stress. Kasarskis is known for directing the first class that allowed medical and PhD students to fully sequence and analyze their own genomes, along with co-instructors Michael Linderman, George Diaz, Ali Bashir, and Randi Zinberg. He has said that courses like this will be critical for training teams of people capable of performing this type of analysis in a medical setting. He chose whole genome sequencing because he expects the more limited exome sequencing will not be a relevant technological approach in the long term.
Eric Schadt (1965.01.31): Schadt’s work combines supercomputing and advanced computational modeling with diverse biological data to understand the relationship between genes, gene products, other molecular features such as cells, organs, organisms, and communities and their impact on complex human traits such as disease. He is known for calling for a shift in molecular biology toward a network-oriented view of living systems to complement the reductionist, single-gene approaches that currently dominate biology to more accurately model the complexity of biological systems. Demonstrating the ability to infer causal relationships among features in high dimensional data using DNA variation information, Schadt and his colleagues at Merck began reconstructing predictive networks that were shown to be causally associated with disease, leading to the idea of targeting networks, not single genes, to effectively treat common disorders such as Alzheimer’s disease, obesity, and most forms of cancer. A Merck spokesman said that the papers Schadt began publishing based on this genetic network data “changed the way people looked at disease”.
Santa Fe Institute: independent, nonprofit theoretical research institute located in Santa Fe (New Mexico, United States) and dedicated to the multidisciplinary study of the fundamental principles of complex adaptive systems, including physical, computational, biological, and social systems.

European Union[edit]

EU: European Research Area (ERA) ⇒ European Research Council (ERC) similar to NSF: Framework Programmes for Research and Technological Development funds research in ERA.
European Molecular Biology Laboratory (EMBL): established in 1974 by many EU members at that time (Western part of current EU); the main Laboratory in Heidelberg, and Outstations in Hinxton (EBI), Grenoble, Hamburg, and Monterotondo near Rome.
European Bioinformatics Institute (EBI; 1992-): lots of DBs
European Science Foundation (ESF; 1974-): association of 72 member organizations devoted to scientific research in 30 European countries; independent, non-governmental, non-profit organisation that facilitates cooperation and collaboration in European research and development, European science policy and science strategy. Together represent €25 bln funding.
Central European Institute of Technology (CEITEC; Brno, Czech Republic): European centre of excellence in the fields of life sciences and advanced materials and technologies; nanotechnologies and microtechnologies, structural biology, genomics and proteomics going into advanced materials and medicine.
Alfried Krupp von Bohlen und Halbach Foundation & de:Alfried Krupp von Bohlen und Halbach-Stiftung
de:Fonds der Chemischen Industrie
Boehringer Ingelheim Fonds


DE: de:Deutsche Forschungsgemeinschaft (DFG):
Fraunhofer Society: 1/3rd from gov, 2/3rds from contract work, either for government sponsored projects or from industry
Max Planck Society (Max-Planck-Gesellschaft zur Förderung der Wissenschaften Eingetragener Verein, MPG): federal and state (Länder) gov. funding
Forschungszentrum Jülich: Ernst Ruska-Centre does HRTEM (FEI Titan, JEOL TEMs)
Helmholtz Association of German Research Centres:
German Cancer Research Center (Deutsches Krebsforschungszentrum, DKFZ)
DESY (Deutsches Elektronen Synchrotron), collaborates in International Linear Collider (ILC, under planning/building, 2010), European x-ray free electron laser (Eu XFEL) (being built, 2010)
Alfred-Wegener-Institut für Polar- und Meeresforschung (AWI), German Center for Neurodegenerative Diseases (DZNE) [being built, 2010], Max Delbrück Center for Molecular Medicine Berlin-Buch (MDC), Forschungszentrum Dresden-Rossendorf (FZD)

United Kingdom[edit]

Template:Science and technology in the United Kingdom
UK Research councils: Arts and Humanities Research Council (AHRC), Biotechnology and Biological Sciences Research Council (BBSRC), Economic and Social Research Council (ESRC), Engineering and Physical Sciences Research Council (EPSRC), Medical Research Council (MRC), Natural Environment Research Council (NERC), Particle Physics and Astronomy Research Council (PPARC), Science and Technology Facilities Council (STFC)
Royal Society of Chemistry (RSC): learned society (professional association) in UK with the goal of "advancing the chemical sciences." Formed in 1980.


Category:Canada Research Chairs
Canada Research Chair (CRC; 2000-): prestigious Canadian university research professorships created through the Canada Research Chairs Program; created to attract world best scholars in various disciplines to be part of CA university system. $300 million is spent annually to attract and retain outstanding scholars and scientists. Tier 1 Chairs – tenable for seven years and renewable indefinitely, are for outstanding researchers acknowledged by their peers as world leaders in their fields; Tier 2 Chairs – tenable for five years and renewable once, are for exceptional emerging researchers, acknowledged by their peers as having the potential to lead in their field.

Middle East, Western Asia[edit]

King Abdullah University of Science and Technology (KAUST): public research university located in Thuwal, Saudi Arabia; built and operated for the first three years by Saudi Aramco. Focuses exclusively on graduate education and research, using English as the official language of instruction. Biological and Environmental Sciences and Engineering; Computer, Electrical, and Mathematical Sciences and Engineering; and Physical Sciences and Engineering

Scientific societies[edit]


International Association of Academies (IAA; 1899-1913): was an academy designed for the purpose of linking the various Academies around the world, of which the first meeting was held in Paris, FR, in 1900.
Template:International Council for Science (ICSU, formerly International Council of Scientific Unions): formed in 1931; international co-operation in the advancement of science. One of the oldest non-governmental organizations in the world and represents the evolution and expansion of two earlier bodies known as the IAA (1899-1913/14) and the International Research Council (IRC; 1919-1931). Members are national scientific bodies (e.g. academy of science of country X), and international scientific unions.

The international scientific unions (also members of ICSU; [member since]):

IUPAC (1922)
International Astronomical Union (IAU; [1922])
International Mathematical Union (IMU; [1922])
(IUGS; [1922])
International Union of Biological Sciences (IUBS; founded in 1919; [1925]): promotes the biological sciences internationally.
International Union of Crystallography (IUCr; [1947])
International Union of Biochemistry and Molecular Biology (IUBMB; formed as International Union of Biochemistry in [1955])
European Molecular Biology Organization (EMBO); publications: Molecular Systems Biology, EMBO Journal, EMBO Reports
European Life Scientist Organisation (ELSO) absorbed by EMBO, end 2008
Federation of European Biochemical Societies (FEBS); publications: FEBS Journal, FEBS Letters and Molecular Oncology


Pharma (according to size {human count}):
  1. Bayer: chemical and pharmaceutical
  2. Hoffmann–La Roche (aka Roche): pharmaceuticals and diagnostics; holding company: Roche Holding AG
  3. Boehringer Ingelheim

Science hoax[edit]

Dihydrogen monoxide hoax (DHMO; hydroxyl acid, hydrogen oxide)