Mathematical and theoretical biology

From Wikipedia, the free encyclopedia

https://en.wikipedia.org/wiki/Mathematical_and_theoretical_biology 

 

Yellow chamomile head showing the Fibonacci numbers in spirals consisting of 21 (blue) and 13 (aqua). Such arrangements have been noticed since the Middle Ages and can be used to make mathematical models of a wide variety of plants.

Mathematical and theoretical biology or, Biomathematics, is a branch of biology which employs theoretical analysis, mathematical models and abstractions of the living organisms to investigate the principles that govern the structure, development and behavior of the systems, as opposed to experimental biology which deals with the conduction of experiments to prove and validate the scientific theories. The field is sometimes called mathematical biology or biomathematics to stress the mathematical side, or theoretical biology to stress the biological side. Theoretical biology focuses more on the development of theoretical principles for biology while mathematical biology focuses on the use of mathematical tools to study biological systems, even though the two terms are sometimes interchanged.

Mathematical biology aims at the mathematical representation and modeling of biological processes, using techniques and tools of applied mathematics. It can be useful in both theoretical and practical research. Describing systems in a quantitative manner means their behavior can be better simulated, and hence properties can be predicted that might not be evident to the experimenter. This requires precise mathematical models.

Because of the complexity of the living systems, theoretical biology employs several fields of mathematics, and has contributed to the development of new techniques.

History

Early history

Mathematics has been used in biology as early as the 13th century, when Fibonacci used the famous Fibonacci series to describe a growing population of rabbits. In the 18th century Daniel Bernoulli applied mathematics to describe the effect of smallpox on the human population. Thomas Malthus' 1789 essay on the growth of the human population was based on the concept of exponential growth. Pierre François Verhulst formulated the logistic growth model in 1836.

Fritz Müller described the evolutionary benefits of what is now called Müllerian mimicry in 1879, in an account notable for being the first use of a mathematical argument in evolutionary ecology to show how powerful the effect of natural selection would be, unless one includes Malthus's discussion of the effects of population growth that influenced Charles Darwin: Malthus argued that growth would be exponential (he uses the word "geometric") while resources (the environment's carrying capacity) could only grow arithmetically.

The term "theoretical biology" was first used by Johannes Reinke in 1901. One founding text is considered to be On Growth and Form (1917) by D'Arcy Thompson, and other early pioneers include Ronald Fisher, Hans Leo Przibram, Nicolas Rashevsky and Vito Volterra.

Recent growth

Interest in the field has grown rapidly from the 1960s onwards. Some reasons for this include:

• The rapid growth of data-rich information sets, due to the genomics revolution, which are difficult to understand without the use of analytical tools
• Recent development of mathematical tools such as chaos theory to help understand complex, non-linear mechanisms in biology
• An increase in computing power, which facilitates calculations and simulations not previously possible
• An increasing interest in in silico experimentation due to ethical considerations, risk, unreliability and other complications involved in human and animal research

Areas of research

Several areas of specialized research in mathematical and theoretical biology as well as external links to related projects in various universities are concisely presented in the following subsections, including also a large number of appropriate validating references from a list of several thousands of published authors contributing to this field. Many of the included examples are characterised by highly complex, nonlinear, and supercomplex mechanisms, as it is being increasingly recognised that the result of such interactions may only be understood through a combination of mathematical, logical, physical/chemical, molecular and computational models.

Abstract relational biology

Abstract relational biology (ARB) is concerned with the study of general, relational models of complex biological systems, usually abstracting out specific morphological, or anatomical, structures. Some of the simplest models in ARB are the Metabolic-Replication, or (M,R)--systems introduced by Robert Rosen in 1957-1958 as abstract, relational models of cellular and organismal organization.

Other approaches include the notion of autopoiesis developed by Maturana and Varela, Kauffman's Work-Constraints cycles, and more recently the notion of closure of constraints.

Algebraic biology

Algebraic biology (also known as symbolic systems biology) applies the algebraic methods of symbolic computation to the study of biological problems, especially in genomics, proteomics, analysis of molecular structures and study of genes.

Complex systems biology

An elaboration of systems biology to understanding the more complex life processes was developed since 1970 in connection with molecular set theory, relational biology and algebraic biology.

Computer models and automata theory

A monograph on this topic summarizes an extensive amount of published research in this area up to 1986, including subsections in the following areas: computer modeling in biology and medicine, arterial system models, neuron models, biochemical and oscillation networks, quantum automata, quantum computers in molecular biology and genetics, cancer modelling, neural nets, genetic networks, abstract categories in relational biology, metabolic-replication systems, category theory applications in biology and medicine, automata theory, cellular automata, tessellation models and complete self-reproduction, chaotic systems in organisms, relational biology and organismic theories.

Modeling cell and molecular biology

This area has received a boost due to the growing importance of molecular biology.

• Mechanics of biological tissues
• Theoretical enzymology and enzyme kinetics
• Cancer modelling and simulation
• Modelling the movement of interacting cell populations
• Mathematical modelling of scar tissue formation
• Mathematical modelling of intracellular dynamics
• Mathematical modelling of the cell cycle
• Mathematical modelling of apoptosis

Modelling physiological systems

• Modelling of arterial disease
• Multi-scale modelling of the heart
• Modelling electrical properties of muscle interactions, as in bidomain and monodomain models

Computational neuroscience

Computational neuroscience (also known as theoretical neuroscience or mathematical neuroscience) is the theoretical study of the nervous system.

Evolutionary biology

Ecology and evolutionary biology have traditionally been the dominant fields of mathematical biology.

Evolutionary biology has been the subject of extensive mathematical theorizing. The traditional approach in this area, which includes complications from genetics, is population genetics. Most population geneticists consider the appearance of new alleles by mutation, the appearance of new genotypes by recombination, and changes in the frequencies of existing alleles and genotypes at a small number of gene loci. When infinitesimal effects at a large number of gene loci are considered, together with the assumption of linkage equilibrium or quasi-linkage equilibrium, one derives quantitative genetics. Ronald Fisher made fundamental advances in statistics, such as analysis of variance, via his work on quantitative genetics. Another important branch of population genetics that led to the extensive development of coalescent theory is phylogenetics. Phylogenetics is an area that deals with the reconstruction and analysis of phylogenetic (evolutionary) trees and networks based on inherited characteristics Traditional population genetic models deal with alleles and genotypes, and are frequently stochastic.

Many population genetics models assume that population sizes are constant. Variable population sizes, often in the absence of genetic variation, are treated by the field of population dynamics. Work in this area dates back to the 19th century, and even as far as 1798 when Thomas Malthus formulated the first principle of population dynamics, which later became known as the Malthusian growth model. The Lotka–Volterra predator-prey equations are another famous example. Population dynamics overlap with another active area of research in mathematical biology: mathematical epidemiology, the study of infectious disease affecting populations. Various models of the spread of infections have been proposed and analyzed, and provide important results that may be applied to health policy decisions.

In evolutionary game theory, developed first by John Maynard Smith and George R. Price, selection acts directly on inherited phenotypes, without genetic complications. This approach has been mathematically refined to produce the field of adaptive dynamics.

Mathematical biophysics

The earlier stages of mathematical biology were dominated by mathematical biophysics, described as the application of mathematics in biophysics, often involving specific physical/mathematical models of biosystems and their components or compartments.

The following is a list of mathematical descriptions and their assumptions.

Deterministic processes (dynamical systems)

A fixed mapping between an initial state and a final state. Starting from an initial condition and moving forward in time, a deterministic process always generates the same trajectory, and no two trajectories cross in state space.

• Difference equations/Maps – discrete time, continuous state space.
• Ordinary differential equations – continuous time, continuous state space, no spatial derivatives. See also: Numerical ordinary differential equations.
• Partial differential equations – continuous time, continuous state space, spatial derivatives. See also: Numerical partial differential equations.
• Logical deterministic cellular automata – discrete time, discrete state space. See also: Cellular automaton.

Stochastic processes (random dynamical systems)

A random mapping between an initial state and a final state, making the state of the system a random variable with a corresponding probability distribution.

• Non-Markovian processes – generalized master equation – continuous time with memory of past events, discrete state space, waiting times of events (or transitions between states) discretely occur.
• Jump Markov process – master equation – continuous time with no memory of past events, discrete state space, waiting times between events discretely occur and are exponentially distributed. See also: Monte Carlo method for numerical simulation methods, specifically dynamic Monte Carlo method and Gillespie algorithm.
• Continuous Markov process – stochastic differential equations or a Fokker–Planck equation – continuous time, continuous state space, events occur continuously according to a random Wiener process.

Spatial modelling

One classic work in this area is Alan Turing's paper on morphogenesis entitled The Chemical Basis of Morphogenesis, published in 1952 in the Philosophical Transactions of the Royal Society.

• Travelling waves in a wound-healing assay
• Swarming behaviour
• A mechanochemical theory of morphogenesis
• Biological pattern formation
• Spatial distribution modeling using plot samples
• Turing patterns

Mathematical methods

A model of a biological system is converted into a system of equations, although the word 'model' is often used synonymously with the system of corresponding equations. The solution of the equations, by either analytical or numerical means, describes how the biological system behaves either over time or at equilibrium. There are many different types of equations and the type of behavior that can occur is dependent on both the model and the equations used. The model often makes assumptions about the system. The equations may also make assumptions about the nature of what may occur.

Molecular set theory

Molecular set theory (MST) is a mathematical formulation of the wide-sense chemical kinetics of biomolecular reactions in terms of sets of molecules and their chemical transformations represented by set-theoretical mappings between molecular sets. It was introduced by Anthony Bartholomay, and its applications were developed in mathematical biology and especially in mathematical medicine. In a more general sense, MST is the theory of molecular categories defined as categories of molecular sets and their chemical transformations represented as set-theoretical mappings of molecular sets. The theory has also contributed to biostatistics and the formulation of clinical biochemistry problems in mathematical formulations of pathological, biochemical changes of interest to Physiology, Clinical Biochemistry and Medicine.

Organizational biology

Theoretical approaches to biological organization aim to understand the interdependence between the parts of organisms. They emphasize the circularities that these interdependences lead to. Theoretical biologists developed several concepts to formalize this idea.

For example, abstract relational biology (ARB) is concerned with the study of general, relational models of complex biological systems, usually abstracting out specific morphological, or anatomical, structures. Some of the simplest models in ARB are the Metabolic-Replication, or (M,R)--systems introduced by Robert Rosen in 1957-1958 as abstract, relational models of cellular and organismal organization.

Model example: the cell cycle

The eukaryotic cell cycle is very complex and is one of the most studied topics, since its misregulation leads to cancers. It is possibly a good example of a mathematical model as it deals with simple calculus but gives valid results. Two research groups have produced several models of the cell cycle simulating several organisms. They have recently produced a generic eukaryotic cell cycle model that can represent a particular eukaryote depending on the values of the parameters, demonstrating that the idiosyncrasies of the individual cell cycles are due to different protein concentrations and affinities, while the underlying mechanisms are conserved (Csikasz-Nagy et al., 2006).

By means of a system of ordinary differential equations these models show the change in time (dynamical system) of the protein inside a single typical cell; this type of model is called a deterministic process (whereas a model describing a statistical distribution of protein concentrations in a population of cells is called a stochastic process).

To obtain these equations an iterative series of steps must be done: first the several models and observations are combined to form a consensus diagram and the appropriate kinetic laws are chosen to write the differential equations, such as rate kinetics for stoichiometric reactions, Michaelis-Menten kinetics for enzyme substrate reactions and Goldbeter–Koshland kinetics for ultrasensitive transcription factors, afterwards the parameters of the equations (rate constants, enzyme efficiency coefficients and Michaelis constants) must be fitted to match observations; when they cannot be fitted the kinetic equation is revised and when that is not possible the wiring diagram is modified. The parameters are fitted and validated using observations of both wild type and mutants, such as protein half-life and cell size.

To fit the parameters, the differential equations must be studied. This can be done either by simulation or by analysis. In a simulation, given a starting vector (list of the values of the variables), the progression of the system is calculated by solving the equations at each time-frame in small increments.

In analysis, the properties of the equations are used to investigate the behavior of the system depending on the values of the parameters and variables. A system of differential equations can be represented as a vector field, where each vector described the change (in concentration of two or more protein) determining where and how fast the trajectory (simulation) is heading. Vector fields can have several special points: a stable point, called a sink, that attracts in all directions (forcing the concentrations to be at a certain value), an unstable point, either a source or a saddle point, which repels (forcing the concentrations to change away from a certain value), and a limit cycle, a closed trajectory towards which several trajectories spiral towards (making the concentrations oscillate).

A better representation, which handles the large number of variables and parameters, is a bifurcation diagram using bifurcation theory. The presence of these special steady-state points at certain values of a parameter (e.g. mass) is represented by a point and once the parameter passes a certain value, a qualitative change occurs, called a bifurcation, in which the nature of the space changes, with profound consequences for the protein concentrations: the cell cycle has phases (partially corresponding to G1 and G2) in which mass, via a stable point, controls cyclin levels, and phases (S and M phases) in which the concentrations change independently, but once the phase has changed at a bifurcation event (Cell cycle checkpoint), the system cannot go back to the previous levels since at the current mass the vector field is profoundly different and the mass cannot be reversed back through the bifurcation event, making a checkpoint irreversible. In particular the S and M checkpoints are regulated by means of special bifurcations called a Hopf bifurcation and an infinite period bifurcation.

Conscientiousness

From Wikipedia, the free encyclopedia

https://en.wikipedia.org/wiki/Conscientiousness

Conscientiousness is the personality trait of being careful, or diligent. Conscientiousness implies a desire to do a task well, and to take obligations to others seriously. Conscientious people tend to be efficient and organized as opposed to easy-going and disorderly. They exhibit a tendency to show self-discipline, act dutifully, and aim for achievement; they display planned rather than spontaneous behavior; and they are generally dependable. It is manifested in characteristic behaviors such as being neat, and systematic; also including such elements as carefulness, thoroughness, and deliberation (the tendency to think carefully before acting).

Conscientiousness is one of the five traits of both the Five Factor Model and the HEXACO model of personality and is an aspect of what has traditionally been referred to as having character. Conscientious individuals are generally hard-working, and reliable. When taken to an extreme, they may also be "workaholics", perfectionists, and compulsive in their behavior. People who score low on conscientiousness tend to be laid back, less goal-oriented, and less driven by success; they also are more likely to engage in antisocial and criminal behavior.

Personality models

Conscientiousness is one of the five major dimensions in the Big Five model (also called Five Factor Model) of personality, which also consists of extraversion, neuroticism, openness to experience, and agreeableness (OCEAN acronym). Two of many personality tests that assess these traits are Costa and McCrae's NEO PI-R and Goldberg's NEO-IPIP. According to these models, conscientiousness is considered to be a continuous dimension of personality, rather than a categorical 'type' of person.

In the NEO framework, Conscientiousness is seen as having six facets: Competence, Order, Dutifulness, Achievement Striving, Self-Discipline, and Deliberation. Other models suggest a smaller set of two "aspects": orderliness and industriousness form an intermediate level of organization, with orderliness associated with the desire to keep things organized and tidy and industriousness being more associated with productivity and work ethic.

Other personality traits ((Low) extraversion, (high) agreeableness, (low) openness and (low) neuroticism) are linked to high conscientiousness along with impulse control. Behaviorally, low conscientiousness is associated with an inability to motivate one's self to perform tasks that the individual desires to accomplish.

Conscientiousness also appears in other models of personality, such as Cloninger's Temperament and Character Inventory, in which it is related to both self-directedness and persistence. It also includes the specific traits of rule consciousness and perfectionism in Cattell's 16 PF model. It is negatively associated with impulsive sensation-seeking in Zuckerman's alternative five model. Traits associated with conscientiousness are frequently assessed by self-report integrity tests given by various corporations to prospective employees.

Origin

Terms such as 'hard-working,' 'reliable,' and 'persevering' describe desirable aspects of character. Because it was once believed to be a moral evaluation, conscientiousness was overlooked as a real psychological attribute. The reality of individual differences in conscientiousness has now been clearly established by studies of cross-observer agreement. Peer and expert ratings confirm the self-reports that people make about their degrees of conscientiousness. Furthermore, both self-reports and observer ratings of conscientiousness predict real-life outcomes such as academic success.

During most of the 20th century, psychologists believed that personality traits could be divided into two categories: temperament and character. Temperament traits were thought to be biologically based, whereas character traits were thought to be learned either during childhood or throughout life. With the advent of the FFM (Five-Factor Model), behavior geneticists began systematic studies of the full range of personality traits, and it soon became clear that all five factors are substantially heritable. Identical twins showed very similar personality traits even when they had been separated at birth and raised apart, and this was equally true for both character traits and temperament traits. Parents and communities influence the ways in which conscientiousness is expressed, but they apparently do not influence its level.

Measurement

A person's level of conscientiousness is generally assessed using self-report measures, although peer-reports and third-party observation can also be used. Self-report measures are either lexical or based on statements. Deciding which measure of either type to use in research is determined by an assessment of psychometric properties and the time and space constraints of the study being undertaken.

Lexical

Lexical measures use individual adjectives that reflect conscientiousness traits, such as efficient and systematic, and are very space and time efficient for research purposes. Goldberg (1992) developed a 20-word measure as part of his 100-word Big Five markers. Saucier (1994) developed a briefer 8-word measure as part of his 40-word mini-markers. Thompson (2008) systematically revised these measures to develop the International English Mini-Markers which has superior validity and reliability in populations both within and outside North America. Internal consistency reliability of the International English Mini-Markers for the Conscientiousness measure for native English-speakers is reported as .90, that for non-native English-speakers is .86.

Statement

Statement measures tend to comprise more words than lexical measures, so hence consume more research instrument space and more respondent time to complete. Respondents are asked the extent to which they, for example, often forget to put things back in their proper place, or are careful to avoid making mistakes. Some statement-based measures of conscientiousness have similarly acceptable psychometric properties in North American populations to lexical measures, but their generally emic development makes them less suited to use in other populations. For instance, statements in colloquial North American English like Often forget to put things back in their proper place or Am careful to avoid making mistakes can be hard for non-native English-speakers to understand, suggesting internationally validated measures might be more appropriate for research conducted with non-North Americans.

Behavior

Development

Currently, little is known about conscientiousness in young children because the self-report inventories typically used to assess it are not appropriate for that age group. It is likely, however, that there are individual differences on this factor at an early age. It is known, for example, that some children have attention deficit/hyperactivity disorder (ADHD may not go away with age; however it is still unclear how neurodevelopmental disorders such as ADHD and autism relate to the development of conscientiousness and other personality traits), which is characterized in part by problems with concentration, organization, and persistence; traits which are related to conscientiousness. Longitudinal and cross-sectional studies suggest that conscientiousness is relatively low among adolescents but increases between 18 and 30 years of age. Research has also shown that conscientiousness generally increases with age from 21 to 60, though the rate of increase is slow.

Individual differences are also strongly preserved, meaning that a careful, neat, and scrupulous 30-year-old is likely to become a careful, neat, and scrupulous 80-year-old.

Daily life

People who score high on the trait of conscientiousness tend to be more organized and less cluttered in their homes and offices. For example, their books tend to be neatly shelved in alphabetical order, or categorized by topic, rather than scattered around the room. Their clothes tend to be folded and arranged in drawers or closets instead of lying on the floor. The presence of planners and to-do lists are also signs of conscientiousness. Their homes tend to have better lighting than the homes of people who score low on this trait. Recently, ten behaviors strongly associated with conscientiousness were scientifically categorized (the number at the end of each behavior is a correlation coefficient; a negative number means conscientious people were less likely to manifest the behavior):

Academic and workplace performance

Conscientiousness is importantly related to successful academic performance in students and workplace performance among managers and workers. Low levels of conscientiousness are strongly associated with procrastination. A considerable amount of research indicates that conscientiousness has a moderate to large positive correlation with performance in the workplace, and indeed that after general mental ability is taken into account, the other four of the Big Five personality traits do not aid in predicting career success.

Conscientious employees are generally more reliable, more motivated, and harder working. They also have lower rates of absenteeism and counterproductive work behaviors such as stealing and fighting with other employees. Furthermore, conscientiousness is the only personality trait that correlates with performance across all categories of jobs. However, agreeableness and emotional stability may also be important, particularly in jobs that involve a significant amount of social interaction. Of all manager/leader types, top executives show the lowest level of rule-following, a conscientious trait. Conscientiousness is not always positively related to job performance, sometimes the opposite is true. Being too conscientious could lead to taking too much time to making urgent decisions and to working too attached to the rules and lack innovation.

Subjective well-being

In general, conscientiousness has a positive relationship with subjective well-being, particularly satisfaction with life, so highly conscientious people tend to be happier with their lives than those who score low on this trait. Although conscientiousness is generally seen as a positive trait to possess, recent research has suggested that in some situations it may be harmful for well-being. In a prospective study of 9570 individuals over four years, highly conscientious people suffered more than twice as much if they became unemployed. The authors suggested this may be due to conscientious people making different attributions about why they became unemployed, or through experiencing stronger reactions following failure. This finding is consistent with perspectives which see no trait as inherently positive or negative, but rather the consequences of the trait being dependent on the situation and concomitant goals and motivations.

Problematic life outcomes

Low conscientiousness has been linked to antisocial and criminal behaviors, as well as unemployment, homelessness, and imprisonment. Low conscientiousness and low agreeableness taken together are also associated with substance abuse. People low in conscientiousness have difficulty saving money and have different borrowing practices than conscientious people. High conscientiousness is associated with more careful planning of shopping trips and less impulse buying of unneeded items. Conscientiousness has been found to be positively correlated with business and white-collar crime.

Health and longevity

According to an 80-year old and ongoing study started in 1921 by psychologist Lewis Terman on over 1,500 gifted adolescent Californians, "The strongest predictor of long life was conscientiousness." Specific behaviors associated with low conscientiousness may explain its influence on longevity. Nine different behaviors that are among the leading causes of mortality—alcohol use, disordered eating (including obesity), drug use, lack of exercise, risky sexual behavior, risky driving, tobacco use, suicide, and violence—are all predicted by low conscientiousness. Health behaviors are more strongly correlated with the conventionality rather than the impulse-control aspect of conscientiousness. Apparently, social norms influence many health-relevant behavior, such as healthy diet and exercise, not smoking and moderate drinking, and highly conscientious people adhere the most strongly to these norms. Additionally, conscientiousness is positively related to health behaviors such as regular visits to a doctor, checking smoke alarms, and adherence to medication regimens. Such behavior may better safeguard health and prevent disease.

Relationships

Relationship quality is positively associated with partners' level of conscientiousness, and highly conscientious people are less likely to get divorced. Conscientiousness is associated with lower rates of behavior associated with divorce, such as extramarital affairs, spousal abuse, and alcohol abuse. Conscientious behaviors may have a direct influence on relationship quality, as people low in conscientiousness are less responsible, less responsive to their partners, are more condescending, and less likely to hold back offensive comments. On the other hand, more conscientious people are better at managing conflict and tend to provoke fewer disagreements, perhaps because they elicit less criticism due to their well-controlled and responsible behavior.

Intelligence

Conscientiousness significantly correlated negatively with abstract reasoning (−0.26) and verbal reasoning (−0.23).

Large unselected studies, however, have found null relationships, and the negative relationship sometimes found in selected samples such as universities may result from students whose low ability would reduce their chance of gaining entrance, but who have higher conscientiousness, gaining their GPA via hard work rather than giftedness.

A large study found that fluid intelligence was significantly negatively correlated with the order (−0.15), self-discipline (−0.08), and deliberation (−0.09) subfactors of conscientiousness (all correlations significant with p < 0.001.).

Political attitudes and obedience to authority

Conscientiousness has a weak relationship with conservative political attitudes. Although right-wing authoritarianism is one of the most powerful predictors of prejudice, a large scale meta-analysis found that conscientiousness itself is uncorrelated with general prejudice. Rebellion against control is significantly negatively correlated with conscientiousness.

Conscientiousness is associated with rule compliance, obedience and integrity.

Creativity

The orderliness/dependability subfactors (order, dutifulness, and deliberation) of conscientiousness correlate negatively with creativity while the industriousness/achievement subfactors correlate positively. Another study showed that people who score high on the order subfactor of conscientiousness show less innovative behavior. Group conscientiousness has a negative effect on group performance during creative tasks. Groups with only conscientious members have difficulty solving open-ended problems.

Adaptability

A study from 2006 found that those scoring low on conscientiousness make better decisions after unanticipated changes in the context of a task. Specifically, the subfactors order, dutifulness, and deliberation negatively correlated with decision-making quality, but not competence, achievement striving, and self-discipline.

Religiosity

General religiosity was mainly related to Agreeableness and Conscientiousness of the big five traits.

Societal Health

Research comparing countries on personality traits has largely found that countries with high average levels of conscientiousness tend to be poorer, less democratic, and to have lower life expectancy compared to their less conscientious counterparts. Less conscientious nations had higher rates of atheism and of alcohol consumption. As discussed earlier, at the individual level, conscientiousness is associated with valuing security, conformity and tradition. Adherence to such values might be more adaptive under harsh living circumstances than more comfortable and prosperous ones.

Geography

United States

Average levels of conscientiousness vary by state in the United States. People living in the central part, including the states of Kansas, Nebraska, Oklahoma, and Missouri, tend to have higher scores on average than people living in other regions. People in the southwestern states of New Mexico, Utah, and Arizona also have relatively high average scores on conscientiousness. Among the eastern states, Florida is the only one that scores in the top ten for this personality trait. The four states with the lowest scores on conscientiousness on average were, in descending order, Rhode Island, Hawaii, Maine, and Alaska.

Great Britain

A large scale survey of residents of Great Britain found that average levels of all the Big Five, including conscientiousness, vary across regional districts in England, Wales and Scotland. High levels of conscientiousness were found throughout much of Southern England, scattered areas of the Midlands, and most of the Scottish Highlands. Low levels of conscientiousness were observed in London, Wales, and parts of the North of England. Higher mean levels of regional conscientiousness were positively correlated with voting for the Conservative Party, and negatively correlated with voting for the Labour Party, in the 2005 and 2010 elections, and also correlated with a higher proportion of married residents, with higher life expectancy for men and women, fewer long-term health problems, and with lower rates of mortality from stroke, cancer, and heart disease. Higher regional conscientiousness was also correlated with lower median annual income in 2011.

Niche differentiation

From Wikipedia, the free encyclopedia

https://en.wikipedia.org/wiki/Niche_differentiation 

In ecology, niche differentiation (also known as niche segregation, niche separation and niche partitioning) refers to the process by which competing species use the environment differently in a way that helps them to coexist. The competitive exclusion principle states that if two species with identical niches (ecological roles) compete, then one will inevitably drive the other to extinction. This rule also states that two species cannot occupy the same exact niche in a habitat and coexist together, at least in a stable manner. When two species differentiate their niches, they tend to compete less strongly, and are thus more likely to coexist. Species can differentiate their niches in many ways, such as by consuming different foods, or using different areas of the environment.

As an example of niche partitioning, several anole lizards in the Caribbean islands share common diets—mainly insects. They avoid competition by occupying different physical locations. Although these lizards might occupy different locations, some species can be found inhabiting the same range, with up to 15 in certain areas. For example, some live on the ground while others are arboreal. Species who live in different areas compete less for food and other resources, which minimizes competition between species. However, species who live in similar areas typically compete with each other.

Detection and quantification

The Lotka–Volterra equation states that two competing species can coexist when intra-specific (within species) competition is greater than inter-specific (between species) competition (Armstrong and McGehee 1981). Since niche differentiation concentrates competition within-species, due to a decrease in between-species competition, the Lotka-Volterra model predicts that niche differentiation of any degree will result in coexistence.

In reality, this still leaves the question of how much differentiation is needed for coexistence (Hutchinson 1959). A vague answer to this question is that the more similar two species are, the more finely balanced the suitability of their environment must be in order to allow coexistence. There are limits to the amount of niche differentiation required for coexistence, and this can vary with the type of resource, the nature of the environment, and the amount of variation both within and between the species.

To answer questions about niche differentiation, it is necessary for ecologists to be able to detect, measure, and quantify the niches of different coexisting and competing species. This is often done through a combination of detailed ecological studies, controlled experiments (to determine the strength of competition), and mathematical models (Strong 1982, Leibold 1995). To understand the mechanisms of niche differentiation and competition, much data must be gathered on how the two species interact, how they use their resources, and the type of ecosystem in which they exist, among other factors. In addition, several mathematical models exist to quantify niche breadth, competition, and coexistence (Bastolla et al. 2005). However, regardless of methods used, niches and competition can be distinctly difficult to measure quantitatively, and this makes detection and demonstration of niche differentiation difficult and complex.

Development

Over time, two competing species can either coexist, through niche differentiation or other means, or compete until one species becomes locally extinct. Several theories exist for how niche differentiation arises or evolves given these two possible outcomes.

Current competition (The Ghost of Competition Present)

Niche differentiation can arise from current competition. For instance, species X has a fundamental niche of the entire slope of a hillside, but its realized niche is only the top portion of the slope because species Y, which is a better competitor but cannot survive on the top portion of the slope, has excluded it from the lower portion of the slope. With this scenario, competition will continue indefinitely in the middle of the slope between these two species. Because of this, detection of the presence of niche differentiation (through competition) will be relatively easy. It is also important to remember that there is no evolutionary change of the individual species in this case; rather this is an ecological effect of species Y out-competing species X within the bounds of species Y's fundamental niche.

Via past extinctions (The Ghost of Competition Past)

Another way by which niche differentiation can arise is via the previous elimination of species without realized niches. This asserts that at some point in the past, several species inhabited an area, and all of these species had overlapping fundamental niches. However, through competitive exclusion, the less competitive species were eliminated, leaving only the species that were able to coexist (i.e. the most competitive species whose realized niches did not overlap). Again, this process does not include any evolutionary change of individual species, but it is merely the product of the competitive exclusion principle. Also, because no species is out-competing any other species in the final community, the presence of niche differentiation will be difficult or impossible to detect.

Evolving differences

Finally, niche differentiation can arise as an evolutionary effect of competition. In this case, two competing species will evolve different patterns of resource use so as to avoid competition. Here too, current competition is absent or low, and therefore detection of niche differentiation is difficult or impossible.

Types

Below is a list of ways that species can partition their niche. This list is not exhaustive, but illustrates several classic examples.

Resource partitioning

Resource partitioning is the phenomenon where two or more species divides out resources like food, space, resting sites etc. to coexist. For example, some lizard species appear to coexist because they consume insects of differing sizes. Alternatively, species can coexist on the same resources if each species is limited by different resources, or differently able to capture resources. Different types of phytoplankton can coexist when different species are differently limited by nitrogen, phosphorus, silicon, and light. In the Galapagos Islands, finches with small beaks are more able to consume small seeds, and finches with large beaks are more able to consume large seeds. If a species' density declines, then the food it most depends on will become more abundant (since there are so few individuals to consume it). As a result, the remaining individuals will experience less competition for food.

Although "resource" generally refers to food, species can partition other non-consumable objects, such as parts of the habitat. For example, warblers are thought to coexist because they nest in different parts of trees. Species can also partition habitat in a way that gives them access to different types of resources. As stated in the introduction, anole lizards appear to coexist because each uses different parts of the forests as perch locations. This likely gives them access to different species of insects.

Predator partitioning

Predator partitioning occurs when species are attacked differently by different predators (or natural enemies more generally). For example, trees could differentiate their niche if they are consumed by different species of specialist herbivores, such as herbivorous insects. If a species density declines, so too will the density of its natural enemies, giving it an advantage. Thus, if each species is constrained by different natural enemies, they will be able to coexist. Early work focused on specialist predators; however, more recent studies have shown that predators do not need to be pure specialists, they simply need to affect each prey species differently. The Janzen–Connell hypothesis represents a form of predator partitioning.

Conditional differentiation

Conditional differentiation (sometimes called temporal niche partitioning) occurs when species differ in their competitive abilities based on varying environmental conditions. For example, in the Sonoran Desert, some annual plants are more successful during wet years, while others are more successful during dry years. As a result, each species will have an advantage in some years, but not others. When environmental conditions are most favorable, individuals will tend to compete most strongly with member of the same species. For example, in a dry year, dry-adapted plants will tend to be most limited by other dry-adapted plants. This can help them to coexist through a storage effect.

Competition-predation trade-off

Species can differentiate their niche via a competition-predation trade-off if one species is a better competitor when predators are absent, and the other is better when predators are present. Defenses against predators, such as toxic compounds or hard shells, are often metabolically costly. As a result, species that produce such defenses are often poor competitors when predators are absent. Species can coexist through a competition-predation trade-off if predators are more abundant when the less defended species is common, and less abundant if the well-defended species is common. This effect has been criticized as being weak, because theoretical models suggest that only two species within a community can coexist because of this mechanism.

Coexistence without niche differentiation: exceptions to the rule

Some competing species have been shown to coexist on the same resource with no observable evidence of niche differentiation and in “violation” of the competitive exclusion principle. One instance is in a group of hispine beetle species (Strong 1982). These beetle species, which eat the same food and occupy the same habitat, coexist without any evidence of segregation or exclusion. The beetles show no aggression either intra- or inter-specifically. Coexistence may be possible through a combination of non-limiting food and habitat resources and high rates of predation and parasitism, though this has not been demonstrated.

This example illustrates that the evidence for niche differentiation is by no means universal. Niche differentiation is also not the only means by which coexistence is possible between two competing species (see Shmida and Ellner 1984). However, niche differentiation is a critically important ecological idea which explains species coexistence, thus promoting the high biodiversity often seen in many of the world's biomes.

Research using mathematical modelling is indeed demonstrating that predation can indeed stabilize lumps of very similar species. Willow warbler and chiffchaff and other very similar warblers can serve as an example. The idea is that it is also a good strategy to be very similar to a successful species or have enough dissimilarity. Also trees in the rain forest can serve as an example of all high canopy species basically following the same strategy. Other examples of nearly identical species clusters occupying the same niche were water beetles, prairie birds and algae. The basic idea is that there can be clusters of very similar species all applying the same successful strategy and between them open spaces. Here the species cluster takes the place of a single species in the classical ecological models.

Symbiosis

From Wikipedia, the free encyclopedia

https://en.wikipedia.org/wiki/Symbiosis 

In a cleaning symbiosis, the clownfish feeds on small invertebrates that otherwise have potential to harm the sea anemone, and the fecal matter from the clownfish provides nutrients to the sea anemone. The clownfish is protected from predators by the anemone's stinging cells, to which the clownfish is immune. The clownfish emits a high pitched sound that deters butterfly fish, which would otherwise eat the anemone, making the relationship mutualistic.

Symbiosis (from Greek συμβίωσις, sumbíōsis, "living together", from σύν, sún, "together", and βίωσις, bíōsis, "living") is any type of a close and long-term biological interaction between two different biological organisms, be it mutualistic, commensalistic, or parasitic. The organisms, each termed a symbiont, must be of different species. In 1879, Heinrich Anton de Bary defined it as "the living together of unlike organisms". The term was subject to a century-long debate about whether it should specifically denote mutualism, as in lichens. Biologists have now abandoned that restriction.

Symbiosis can be obligatory, which means that one or more of the symbionts entirely depend on each other for survival, or facultative (optional), when they can generally live independently.

Symbiosis is also classified by physical attachment. When symbionts form a single body it is called conjunctive symbiosis, while all other arrangements are called disjunctive symbiosis. When one organism lives on the surface of another, such as head lice on humans, it is called ectosymbiosis; when one partner lives inside the tissues of another, such as Symbiodinium within coral, it is termed endosymbiosis.

Definition

Diagram of the six possible types of symbiotic relationship, from mutual benefit to mutual harm.

The definition of symbiosis was a matter of debate for 130 years. In 1877, Albert Bernhard Frank used the term symbiosis to describe the mutualistic relationship in lichens. In 1878, the German mycologist Heinrich Anton de Bary defined it as "the living together of unlike organisms". The definition has varied among scientists, with some advocating that it should only refer to persistent mutualisms, while others thought it should apply to all persistent biological interactions (in other words, to mutualism, commensalism, and parasitism, but excluding brief interactions such as predation). In the 21st century, the latter has become the definition widely accepted by biologists.

In 1949, Edward Haskell proposed an integrative approach with a classification of "co-actions", later adopted by biologists as "interactions".

Obligate versus facultative

Relationships can be obligate, meaning that one or both of the symbionts entirely depend on each other for survival. For example, in lichens, which consist of fungal and photosynthetic symbionts, the fungal partners cannot live on their own. The algal or cyanobacterial symbionts in lichens, such as Trentepohlia, can generally live independently, and their part of the relationship is therefore described as facultative (optional).

Physical interaction

Alder tree root nodule houses endosymbiotic nitrogen-fixing bacteria.

Endosymbiosis is any symbiotic relationship in which one symbiont lives within the tissues of the other, either within the cells or extracellularly. Examples include diverse microbiomes: rhizobia, nitrogen-fixing bacteria that live in root nodules on legume roots; actinomycetes, nitrogen-fixing bacteria such as Frankia, which live in alder root nodules; single-celled algae inside reef-building corals; and bacterial endosymbionts that provide essential nutrients to about 10%–15% of insects.

Ectosymbiosis is any symbiotic relationship in which the symbiont lives on the body surface of the host, including the inner surface of the digestive tract or the ducts of exocrine glands. Examples of this include ectoparasites such as lice; commensal ectosymbionts such as the barnacles, which attach themselves to the jaw of baleen whales; and mutualist ectosymbionts such as cleaner fish.

Male-male interference competition in red deer

Competition

Competition can be defined as an interaction between organisms or species, in which the fitness of one is lowered by the presence of another. Limited supply of at least one resource (such as food, water, and territory) used by both usually facilitates this type of interaction, although the competition may also exist over other 'amenities', such as females for reproduction (in the case of male organisms of the same species).

Mutualism

Hermit crab, Calcinus laevimanus, with sea anemone.

Mutualism or interspecies reciprocal altruism is a long-term relationship between individuals of different species where both individuals benefit. Mutualistic relationships may be either obligate for both species, obligate for one but facultative for the other, or facultative for both.

Bryoliths document a mutualistic symbiosis between a hermit crab and encrusting bryozoans.

A large percentage of herbivores have mutualistic gut flora to help them digest plant matter, which is more difficult to digest than animal prey. This gut flora is made up of cellulose-digesting protozoans or bacteria living in the herbivores' intestines. Coral reefs are the result of mutualism between coral organisms and various types of algae which live inside them. Most land plants and land ecosystems rely on mutualism between the plants, which fix carbon from the air, and mycorrhyzal fungi, which help in extracting water and minerals from the ground.

An example of mutualism is the relationship between the ocellaris clownfish that dwell among the tentacles of Ritteri sea anemones. The territorial fish protects the anemone from anemone-eating fish, and in turn the stinging tentacles of the anemone protect the clownfish from its predators. A special mucus on the clownfish protects it from the stinging tentacles.

A further example is the goby, a fish which sometimes lives together with a shrimp. The shrimp digs and cleans up a burrow in the sand in which both the shrimp and the goby fish live. The shrimp is almost blind, leaving it vulnerable to predators when outside its burrow. In case of danger, the goby touches the shrimp with its tail to warn it. When that happens both the shrimp and goby quickly retreat into the burrow. Different species of gobies (Elacatinus spp.) also clean up ectoparasites in other fish, possibly another kind of mutualism.

A non-obligate symbiosis is seen in encrusting bryozoans and hermit crabs. The bryozoan colony (Acanthodesia commensale) develops a cirumrotatory growth and offers the crab (Pseudopagurus granulimanus) a helicospiral-tubular extension of its living chamber that initially was situated within a gastropod shell.

Many types of tropical and sub-tropical ants have evolved very complex relationships with certain tree species.

Endosymbiosis

In endosymbiosis, the host cell lacks some of the nutrients which the endosymbiont provides. As a result, the host favors endosymbiont's growth processes within itself by producing some specialized cells. These cells affect the genetic composition of the host in order to regulate the increasing population of the endosymbionts and ensure that these genetic changes are passed onto the offspring via vertical transmission (heredity).

A spectacular example of obligate mutualism is the relationship between the siboglinid tube worms and symbiotic bacteria that live at hydrothermal vents and cold seeps. The worm has no digestive tract and is wholly reliant on its internal symbionts for nutrition. The bacteria oxidize either hydrogen sulfide or methane, which the host supplies to them. These worms were discovered in the late 1980s at the hydrothermal vents near the Galapagos Islands and have since been found at deep-sea hydrothermal vents and cold seeps in all of the world's oceans.

As the endosymbiont adapts to the host's lifestyle, the endosymbiont changes dramatically. There is a drastic reduction in its genome size, as many genes are lost during the process of metabolism, and DNA repair and recombination, while important genes participating in the DNA-to-RNA transcription, protein translation and DNA/RNA replication are retained. The decrease in genome size is due to loss of protein coding genes and not due to lessening of inter-genic regions or open reading frame (ORF) size. Species that are naturally evolving and contain reduced sizes of genes can be accounted for an increased number of noticeable differences between them, thereby leading to changes in their evolutionary rates. When endosymbiotic bacteria related with insects are passed on to the offspring strictly via vertical genetic transmission, intracellular bacteria go across many hurdles during the process, resulting in the decrease in effective population sizes, as compared to the free-living bacteria. The incapability of the endosymbiotic bacteria to reinstate their wild type phenotype via a recombination process is called Muller's ratchet phenomenon. Muller's ratchet phenomenon, together with less effective population sizes, leads to an accretion of deleterious mutations in the non-essential genes of the intracellular bacteria. This can be due to lack of selection mechanisms prevailing in the relatively "rich" host environment.

Commensalism

Commensal mites travelling (phoresy) on a fly (Pseudolynchia canariensis)

Commensalism describes a relationship between two living organisms where one benefits and the other is not significantly harmed or helped. It is derived from the English word commensal, used of human social interaction. It derives from a medieval Latin word meaning sharing food, formed from com- (with) and mensa (table).

Commensal relationships may involve one organism using another for transportation (phoresy) or for housing (inquilinism), or it may also involve one organism using something another created, after its death (metabiosis). Examples of metabiosis are hermit crabs using gastropod shells to protect their bodies, and spiders building their webs on plants.

Parasitism

Head (scolex) of tapeworm Taenia solium is adapted to parasitism with hooks and suckers to attach to its host.

In a parasitic relationship, the parasite benefits while the host is harmed. Parasitism takes many forms, from endoparasites that live within the host's body to ectoparasites and parasitic castrators that live on its surface and micropredators like mosquitoes that visit intermittently. Parasitism is an extremely successful mode of life; about 40% of all animal species are parasites, and the average mammal species is host to 4 nematodes, 2 cestodes, and 2 trematodes.

Mimicry

Mimicry is a form of symbiosis in which a species adopts distinct characteristics of another species to alter its relationship dynamic with the species being mimicked, to its own advantage. Among the many types of mimicry are Batesian and Müllerian, the first involving one-sided exploitation, the second providing mutual benefit. Batesian mimicry is an exploitative three-party interaction where one species, the mimic, has evolved to mimic another, the model, to deceive a third, the dupe. In terms of signalling theory, the mimic and model have evolved to send a signal; the dupe has evolved to receive it from the model. This is to the advantage of the mimic but to the detriment of both the model, whose protective signals are effectively weakened, and of the dupe, which is deprived of an edible prey. For example, a wasp is a strongly-defended model, which signals with its conspicuous black and yellow coloration that it is an unprofitable prey to predators such as birds which hunt by sight; many hoverflies are Batesian mimics of wasps, and any bird that avoids these hoverflies is a dupe. In contrast, Müllerian mimicry is mutually beneficial as all participants are both models and mimics. For example, different species of bumblebee mimic each other, with similar warning coloration in combinations of black, white, red, and yellow, and all of them benefit from the relationship. 

Amensalism

The black walnut secretes a chemical from its roots that harms neighboring plants, an example of antagonism.

Amensalism is an asymmetric interaction where one species is harmed or killed by the other, and one is unaffected by the other. There are two types of amensalism, competition and antagonism (or antibiosis). Competition is where a larger or stronger organism deprives a smaller or weaker one from a resource. Antagonism occurs when one organism is damaged or killed by another through a chemical secretion. An example of competition is a sapling growing under the shadow of a mature tree. The mature tree can rob the sapling of necessary sunlight and, if the mature tree is very large, it can take up rainwater and deplete soil nutrients. Throughout the process, the mature tree is unaffected by the sapling. Indeed, if the sapling dies, the mature tree gains nutrients from the decaying sapling. An example of antagonism is Juglans nigra (black walnut), secreting juglone, a substance which destroys many herbaceous plants within its root zone.

Amensalism is often used to describe strongly asymmetrical competitive interactions, such as between the Spanish ibex and weevils of the genus Timarcha which feed upon the same type of shrub. Whilst the presence of the weevil has almost no influence on food availability, the presence of ibex has an enormous detrimental effect on weevil numbers, as they consume significant quantities of plant matter and incidentally ingest the weevils upon it.

Cleaning symbiosis

Cleaning symbiosis is an association between individuals of two species, where one (the cleaner) removes and eats parasites and other materials from the surface of the other (the client). It is putatively mutually beneficial, but biologists have long debated whether it is mutual selfishness, or simply exploitative. Cleaning symbiosis is well known among marine fish, where some small species of cleaner fish, notably wrasses but also species in other genera, are specialised to feed almost exclusively by cleaning larger fish and other marine animals.

Co-evolution

Leafhoppers protected by meat ants

Symbiosis is increasingly recognized as an important selective force behind evolution; many species have a long history of interdependent co-evolution.

Symbiogenesis

One hypothesis for the origin of the nucleus in eukaryotes (plants, animals, fungi, and protists) is that it developed from a symbiogenesis between bacteria and archaea. It is hypothesized that the symbiosis originated when ancient archaea, similar to modern methanogenic archaea, invaded and lived within bacteria similar to modern myxobacteria, eventually forming the early nucleus. This theory is analogous to the accepted theory for the origin of eukaryotic mitochondria and chloroplasts, which are thought to have developed from a similar endosymbiotic relationship between proto-eukaryotes and aerobic bacteria. Evidence for this includes the fact that mitochondria and chloroplasts divide independently of the cell, and that these organelles have their own genome.

The biologist Lynn Margulis, famous for her work on endosymbiosis, contended that symbiosis is a major driving force behind evolution. She considered Darwin's notion of evolution, driven by competition, to be incomplete and claimed that evolution is strongly based on co-operation, interaction, and mutual dependence among organisms. According to Margulis and her son Dorion Sagan, "Life did not take over the globe by combat, but by networking."

Co-evolutionary relationships

Mycorrhizas

About 80% of vascular plants worldwide form symbiotic relationships with fungi, in particular in arbuscular mycorrhizas.

Pollination is a mutualism between flowering plants and their animal pollinators.

Pollination

A fig is pollinated by the fig wasp, Blastophaga psenes.

Flowering plants and the animals that pollinate them have co-evolved. Many plants that are pollinated by insects (in entomophily), bats, or birds (in ornithophily) have highly specialized flowers modified to promote pollination by a specific pollinator that is correspondingly adapted. The first flowering plants in the fossil record had relatively simple flowers. Adaptive speciation quickly gave rise to many diverse groups of plants, and, at the same time, corresponding speciation occurred in certain insect groups. Some groups of plants developed nectar and large sticky pollen, while insects evolved more specialized morphologies to access and collect these rich food sources. In some taxa of plants and insects, the relationship has become dependent, where the plant species can only be pollinated by one species of insect.

Pseudomyrmex ant on bull thorn acacia (Vachellia cornigera) with Beltian bodies that provide the ants with protein

Acacia ants and acacias

The acacia ant (Pseudomyrmex ferruginea) is an obligate plant ant that protects at least five species of "Acacia" (Vachellia) from preying insects and from other plants competing for sunlight, and the tree provides nourishment and shelter for the ant and its larvae.