This glossary contains a vocabulary used by CPER concerning the overall site, regarding: meaning of scientific words, useful definitions, short explanations of some concepts, and references to reliable external sources of information on the Internet or on paper.
Domestication is the process whereby a population of living
organisms is changed at the genetic level, through generations of
selective breeding, to accentuate traits that ultimately benefit
the interests of humans. A usual by-product of domestication is
the creation of a dependency in the domesticated organisms, so
that they lose their ability to live in the wild. Through
domestication a change in the phenotypical expression and in the
genotype of the animal occurs over generations. A
domesticated species is defined as "a plant- or animal-species in
which the evolutionary process has been influenced by humans to
meet the needs of mankind". Therefore, an important
factor on domestication is Artificial Selection by
Charles Darwin was the first to describe how domestication, selection and evolution are interlinked, and based on natural heritable variation among individual plants and animals. Today we know that such natural variation is caused by mutations in genes coding for these traits, and by new combinations of already existing genetic variation, based on earlier mutations. Darwin described how the process of domestication can involve both unconscious and methodical elements. Routine human interactions with animals and plants create selection pressures that cause adaptation to human presence, use or cultivation. Deliberate selective breeding has also been used to create desired changes, often after initial domestication. These two forces, unconscious natural selection and methodical selective breeding, may have both played roles in the processes of domestication throughout history. Both have been described from human perspective as processes of Artificial Selection. also called Extrinsic Eugenics.
The domestication of wheat
Wild wheat plants fall to the ground to re-seed themselves, when ripened. But domesticated wheat stays upright on the stem, for easier harvesting by man. For a wild wheat plant, this 'uprightness' may not be a clever way of dispersing its seed. There is evidence that this change was possible because of a random mutation that happened in the wild populations at the beginning of wheat cultivation. Wheat plants with this mutation (i.e. a long-lasting erect stem) were harvested more frequently by humans, and thus became the seed for the next crop. Therefore, without realizing, early farmers selected for this mutation, which may otherwise have died out. The result is domesticated wheat, which now relies on farmers for its own reproduction and dissemination.
The domestication of dogs
It is speculated that thousands of years ago, certain wolves which were tamer than the average wolf and less wary of humans, selected themselves as dogs over many generations. Most animals love their freedom or independence, and hunt for their own food. Some wolves may be sick or crippled in a fight, and have to find other ways to get their meal for the day. So they become opportunistic. These wolves were able to thrive by following humans to scavenge for food near camp fires and garbage dumps; this behaviour gave them an advantage over more shy individuals. Eventually a symbiotic relationship developed between people and these 'proto-dogs'. The dogs fed on human food scraps, and humans found that dogs could warn them of approaching dangers, such as large predators or other intruders. Some dogs could help with hunting, act as pets, provide warmth, or supplement the food supply of humans (!). As this relationship progressed, humans eventually began to keep these self-tamed wolves and breed from them the types of dogs that we have today.
Scientific research on artificial selection
In recent times, selective breeding may best explain how continuing processes of domestication often work. Some of the best-known evidence of the power of selective breeding comes from the Farm-Fox Experiment by Russian scientist, Dmitri K. Belyaev, in the 1950s. His team spent many years breeding the domesticated silver fox (Vulpes vulpes) and selecting only those individuals that showed the least fear of humans. Eventually, Belyaev's team selected only those that showed the most positive response to humans. He ended up with a population of grey-coloured foxes whose behaviour and appearance was significantly changed. They no longer showed any fear of humans and often wagged their tails and licked their human caretakers to show affection. Their behaviour was more 'childlike' as if they were mentally stuck in a youngster-phase, but with an adult body (This is called Pedomorphosis: the retention of juvenile characteristics in the adult body). These foxes had floppy ears, smaller skulls, rolled tails and other traits commonly found in dogs. Domesticated foxes had less pronounced stress hormones (cortisol, adrenalin) and higher serotonin levels. It took Belyaev's team some 10 to 30 generations of artificially selecting fox offspring, to wilfully 'steer' the evolution of behaviour in their desired direction!
Selection of animals for visible "desirable" traits may make them unfit in other, unseen, ways. The consequences for the captive and domesticated animals were reduction in size, piebald colour, shorter faces with smaller and fewer teeth, diminished horns, weak muscle ridges, and less genetic variability. Poor joint definition, late fusion of the limb bone epiphyses with the diaphyses, hair changes, greater fat accumulation, smaller brains, simplified behaviour patterns, extended immaturity, and more pathology are a few of the defects of domestic animals. All of these changes have been documented in direct observations of the rat in the 19th century, by archaeological evidence, and confirmed by animal breeders in the 20th century.
Other negative aspects of domestication have been explored. For example: Man substitutes controlled breeding for natural selection; animals are selected for special traits like milk production of passivity [e.g. child-friendly Golden Retriever dog], at the expense of overall fitness and nature-wide relationships. Though domestication broadens the diversity of forms (that is: increases visible polymorphism, for example, the many kinds of sizes and colours dogs have today) it undermines the crisp demarcations that separate wild species. And it cripples our (i.e. modern citizens) recognition of the species as a group. Knowing only domestic animals dulls our understanding of the way in which unity and discontinuity occur as patterns in nature, and substitutes an attention to individuals and breeds. The wide variety of size, colour, shape, and form of domestic horses, for example, blurs the distinction among different species of Equus that once were constant and meaningfully adapted to natural surroundings.
The term Domestication is derived from the Latin word domesticus meaning "of the home".
http://10e.devbio.com/article.php?ch=23&id=223 (Fox breeding).
Second Law of Thermodynamics
According to the second law of thermodynamics the entropy of an
isolated system never decreases. An isolated system will
spontaneously evolve toward thermodynamic equilibrium, the
configuration with maximum entropy.
The idea of "irreversibility" is central to the understanding of
entropy. Most people have an intuitive understanding of
irreversibility (a dissipative process): if one watches a movie
of everyday life running forward and in reverse, it is easy to
distinguish between the two. The movie running in reverse shows
impossible things happening: water jumping out of a glass into a
pitcher above it, smoke going down a chimney, water "unmelting"
to form ice in a warm room, crashed cars reassembling themselves,
and so on.
Entropy as energy dispersal
Entropy can also be described in terms of "energy dispersal" and the "spreading of energy", while avoiding all mention of "disorder", "randomness" and "chaos". In this approach, the second law of thermodynamics is introduced as: "Energy spontaneously disperses from being localized to becoming spread out if it is not hindered from doing so."
This explanation can be used in the context of common experiences such as a rock falling, a hot frying pan cooling down, iron rusting, air leaving a punctured tyre and ice melting in a warm room. Entropy is then depicted as a sophisticated kind of "before and after" yardstick: Measuring how much energy is spread out over time as a result of a process such as heating a system, or how widely spread out the energy is after something happens in comparison with its previous state, in a process such as gas expansion or fluids mixing (at a constant temperature).
The equations are explored with reference to the common experiences, with emphasis that in chemistry the energy that entropy measures as dispersing is the internal energy of molecules.
The second law of thermodynamics, states that a closed system has entropy which may increase or otherwise remain constant. Chemical reactions cause changes in entropy and entropy plays an important role in determining in which direction a chemical reaction spontaneously proceeds.
Systems ecology and Negentropy
Nowadays, many biologists use the term 'entropy of an organism', or its antonym 'negentropy', as a measure of the structural order within an organism.
The term entropy was coined in 1865 by the German physicist Rudolf Clausius, who stated that: “The entropy of the universe tends to a maximum.”.
Unlike many other functions of state, entropy cannot be directly
observed but must be calculated. Entropy can be calculated for a
substance as the standard molar entropy from absolute zero
temperature (also known as absolute entropy).
The arrow of time
Entropy is the only quantity in the physical sciences that seems
to imply a particular direction of progress, sometimes called an
arrow of time. As time progresses, the second law of
thermodynamics states that the entropy of an isolated system
never decreases (but rather will increase). Hence, from this
perspective, entropy measurement is thought of as a kind of clock
(an isolated system has low entopy in the past, and high entropy
in the future).
The term Entropy is derived from the Ancient Greek word
entropía (ἐντροπία) meaning “a turning
In biology, epigenetics is the study of cellular and physiological traits that are not caused by changes in the DNA sequence. Epigenetics describes the study of stable, long-term alterations in the transcriptional potential of a cell. Some of those alterations are heritable. Unlike simple genetics based on changes to the DNA sequence (the genotype), the changes in gene expression or cellular phenotype of epigenetics have other causes, thus use of the term epi-genetics.
The term also refers to the changes themselves: functionally relevant changes to the genome that do not involve a change in the nucleotide sequence. Examples of mechanisms that produce such changes are DNA methylation and histone modification, each of which alters how genes are expressed without altering the underlying DNA sequence. Gene expression can be controlled through the action of repressor proteins that attach to silencer regions of the DNA. These epigenetic changes may last through cell divisions for the duration of the cell's life, and may also last for multiple generations even though they do not involve changes in the underlying DNA sequence of the organism; instead, non-genetic factors cause the organism's genes to behave (or "express themselves") differently.
One example of an epigenetic change in eukaryotic biology is the process of cellular differentiation. During Morphogenesis, totipotent stem cells become the various pluripotent cell lines of the embryo, which in turn become fully differentiated cells. In other words, as a single fertilized egg cell – the zygote – continues to divide, the resulting daughter cells change into all the different cell types in an organism (including neurons, muscle cells, epithelium, endothelium of blood vessels, etc.) by activating some genes while inhibiting the expression of others.
The term Epigenetics is derived from the ancient Greek prefix epi (επί-) meaning "over, outside of, around, on top of" and the word genetics from genesis (γένεσις) meaning "origin", "source", or "birth".
Eugenics is also called Eugenetics.
Eugenics is the theory and practice of improving the genetic quality of the human population. It is a social philosophy advocating the improvement of human genetic traits through the promotion of higher reproduction of people with desired traits (positive eugenics), and reduced reproduction of people with less-desired or undesired traits (negative eugenics).
CPER propagates the fundamental human right of Positive Intrinsic Eugenics (PIE), which belief is based on the following conditions:
Some examples of possible improved outcome (as perceived by the
procreating partners) of intrinsic positive 'breeding'
CPER's definition of PIE (within
Future evolution of mankind:
The term Eugenics is derived from the ancient Greek words eu- (εὖ), meaning "good/well", and -genes (γένος), meaning "born" or "race".
Feedback occurs when outputs of a system are "fed back" as inputs as part of a chain of cause-and-effect that forms a circuit or loop. The system can then be said to "feed back" into itself. The notion of 'cause-and-effect' has to be handled carefully when applied to feedback systems: Simple causal reasoning about a feedback system is difficult because the first system influences the second and second system influences the first, leading to a circular argument. This makes reasoning based upon cause and effect tricky, and it is necessary to analyze the system as a whole. In this context, the term "feedback" has also been used as an abbreviation for:
Positive - Negative
The terms positive and negative feedback are defined in different ways within different disciplines:
Fields of Application
In biological systems such as organisms, ecosystems, or the
biosphere, most parameters must stay under control within a
narrow range around a certain optimal level under certain
Biological systems contain many types of regulatory circuits,
both positive and negative. As in other contexts, positive and
negative do not imply that the feedback causes good or bad
effects. A negative feedback loop is one that tends to slow down
a process, whereas the positive feedback loop tends to accelerate
Feedback is also central to the operations of genes and gene regulatory networks. Repressor (see Lac repressor) and activator proteins are used to create genetic operons, which were identified by Francois Jacob and Jacques Monod in 1961 as feedback loops. These feedback loops may be positive (as in the case of the coupling between a sugar molecule and the proteins that import sugar into a bacterial cell), or negative (as is often the case in metabolic consumption).
On a larger scale, feedback can have a stabilizing effect on
animal populations even when profoundly affected by external
changes, although time lags in feedback response can give rise to
In psychology, the body receives a stimulus from the environment or internally that causes the release of hormones. Release of hormones then may cause more of those hormones to be released, causing a positive feedback loop. This cycle is also found in certain behaviour. For example, "shame loops" occur in people who blush easily. When they realize that they are blushing, they become even more embarrassed, which leads to further blushing, and so on.
The term Genotype, will be explained together with the term Phenotype.
The genotype is the genetic makeup of a cell, an organism, or an
The genotype of an organism is the inherited instructions it carries within its genetic code. Not all organisms with the same genotype look or act the same way because appearance and behavior are modified by environmental and developmental conditions. Likewise, not all organisms that look alike necessarily have the same genotype.
A phenotype is the composite of an organism's observable characteristics or traits, such as its morphology, development, biochemical or physiological properties, phenology, behaviour, and products of behaviour (such as a bird's nest). A phenotype results from the expression of an organism's genes as well as the influence of environmental factors and the interactions between the two. When two or more clearly different phenotypes exist in the same population of a species, the species is called polymorph.
Phenotypic variation (due to underlying heritable genetic variation) is a fundamental prerequisite for evolution by natural selection. It is the living organism as a whole that contributes (or not) to the next generation, so natural selection affects the genetic structure of a population indirectly via the contribution of phenotypes. Without phenotypic variation, there would be no evolution by natural selection.
The interaction between genotype and phenotype has often been
conceptualized by the following relationship:
The smallest unit of replicators is the gene. Replicators cannot be directly selected upon, but they are selected on by their phenotypic effects. These effects are packaged together in organisms. We should think of the replicator as having extended phenotypic effects. These are all of the ways it affects the world, not just the effects the replicators have on the body in which they reside.
This genotype-phenotype distinction was proposed by Wilhelm Johannsen in 1911 to make clear the difference between an organism's heredity and what that heredity produces. The distinction is similar to that proposed by August Weismann, who distinguished between germ plasm (heredity) and somatic cells (the body). The genotype-phenotype distinction should not be confused with Francis Crick's central dogma of molecular biology, which is a statement about the directionality of molecular sequential information flowing from DNA to protein, and not the reverse.
Evolution of genetic traits
The genotype–phenotype distinction is drawn in genetics. "Genotype" is an organism's full hereditary information. "Phenotype" is an organism's actual observed properties, such as morphology, development, or behavior. This distinction is fundamental in the study of inheritance of traits and their evolution.
It is the organism's physical properties which directly determine its chances of survival and reproductive output, while the inheritance of physical properties occurs only as a secondary consequence of the inheritance of genes. Therefore, to properly understand the theory of evolution via natural selection, one must understand the genotype–phenotype distinction. The genes contribute to a trait, and the phenotype is the observable expression of the genes (and therefore the genotype that affects the trait). Say a white mouse had both recessive genes that cause the colour of the mouse to be inactive (so "cc"). Its genotype would be responsible for its phenotype (the white colour).
The mapping of a set of genotypes to a set of phenotypes is sometimes referred to as the genotype–phenotype map.
An organism's genotype is a major influencing factor in the development of its phenotype, but it is not the only one. Even two organisms with identical genotypes normally differ in their phenotypes. One experiences this in everyday life with monozygous (i.e. identical) twins. Identical twins share the same genotype, since their genomes are identical; but they never have the same phenotype, although their phenotypes may be very similar. This is apparent in the fact that their mothers and close friends can always tell them apart, even though others might not be able to see the subtle differences. Further, identical twins can be distinguished by their fingerprints, which are never completely identical.
The term Genotype is derived from the ancient Greek word genes (γένος) meaning "born" or "race", and týpos (τύπος), meaning "type".
The term Phenotype is derived from the ancient Greek word phainein / phainō (φαίνω) meaning "to show, to bring to light, make to appear", and typos, meaning "type".
When can you speak of an 'intelligent organism'?
This is obviously an anthropocentric definition.
Morphogenesis is the biological process that causes an organism to develop its shape. It is one of three fundamental aspects of developmental biology along with the control of cell growth and cellular differentiation. The process controls the organized spatial distribution of cells during the embryonic development of an organism. Morphogenesis can take place also in a mature organism, in cell culture or inside tumor cell masses.
Morphogenesis also describes the development of unicellular life forms that do not have an embryonic stage in their life cycle, or describes the evolution of a body structure within a taxonomic group. Morphogenetic responses may be induced in organisms by hormones, by environmental chemicals ranging from substances produced by other organisms to toxic chemicals or radionuclides released as pollutants, and other plants, or by mechanical stresses induced by spatial patterning of the cells.
The term Morphogenesis is derived from the ancient Greek words morphê (μορφή) meaning "shape" or "form", and genesis (γένεσις) meaning "creation", "origin", "source", or "birth" thus literally: "beginning of the shape".
Negative Feedback Loop
Negative Feedback Loop
Negative feedback occurs when some function of the output of a system, process, or mechanism is fed back in a manner that tends to reduce the fluctuations in the output, whether caused by changes in the input or by other disturbances. Whereas positive feedback tends to lead to instability via exponential growth or oscillation, negative feedback generally promotes stability.
Negative feedback tends to promote a settling to equilibrium, and reduces the effects of perturbations. Negative feedback loops in which just the right amount of correction is applied in the most timely manner can be very stable, accurate, and responsive.
In place of the adjective "Negative" before feedback loop, alternative terms are used, such as: degenerative, self-inhibiting, self-correcting, self-dampening, balancing, discrepancy-reducing, or centripetal.
Negative feedback is widely used in mechanical and electronic engineering, but it also occurs naturally within living organisms, and can be seen in many other fields from chemistry and economics to physical systems such as the climate. General negative feedback systems are studied in control systems engineering.
In organisms, feedback enables various measures (eg body temperature, or blood sugar level) to be maintained within precise desired ranges by homeostatic processes. In many physical and biological systems, qualitatively different influences can oppose each other. For example, in biochemistry, one set of chemicals drives the system in a given direction, whereas another set of chemicals drives it in an opposing direction. If one or both of these opposing influences are non-linear, equilibrium point(s) result.
Figure: Both starting points eventuate in equilibrium, during a negative feedback loop.
Early researchers in the area of cybernetics subsequently generalized the idea of negative feedback to cover any goal-seeking or purposeful behavior. All purposeful behavior may be considered to require negative feed-back. If a goal is to be attained, some signals from the goal are necessary at some time to direct the behavior.
Cybernetics pioneer Norbert Wiener helped to formalize the concepts of feedback control, defining feedback in general as "the chain of the transmission and return of information". Wiener defind negative feedback as the case when: "The information fed back to the control center tends to oppose the departure of the controlled from the controlling quantity...".
Confusion arose after BF Skinner introduced the terms positive and negative reinforcement, both of which can be considered negative feedback mechanisms in the sense that they try to minimize deviations from the desired behavior.
In a similar context, Herold and Greller used the term "negative" to refer to the valence of the feedback: that is, cases where a subject receives an evaluation with an unpleasant emotional connotation.
Differerence in Terminology
In biology, this process (in general, biochemical) is often referred to as homeostasis; whereas in mechanics, the more common term is equilibrium.
In engineering, mathematics and the physical, and biological sciences, common terms for the points around which the system gravitates include: attractors, stable states, eigenstates/eigenfunctions, equilibrium points, and setpoints.
In control theory, negative refers to the sign of the multiplier in mathematical models for feedback. In delta notation, −Δoutput is added to or mixed into the input.
In multivariate systems, vectors help to illustrate how several influences can both partially complement and partially oppose each other.
Some authors, in particular with respect to modelling business systems, use negative to refer to the reduction in difference between the desired and actual behavior of a system.
In a psychology context, on the other hand, negative refers to the valence of the feedback – attractive versus aversive, or praise versus criticism.
Negative versus Positive
Negative feedback is feedback in which the system responds so as
to decrease the magnitude of any particular perturbation, leading
to dampening of the original signal, resulting in stabilization
of the process.
Any system in which there is positive feedback together with a
gain greater than one will result in a runaway situation. Both
positive and negative feedback require a feedback loop to
Fields of application
Examples of the use of negative feedback to control its system are: thermostat control, the phase-locked loop oscillator, the ballcock control of water level, and temperature regulation in animals.
The ballcock or float valve uses negative feedback to control the water level in a cistern of a toilette.
Figure: the ballcock control of water level via negative feedback.
A simple and practical example is a thermostat. When the temperature in a heated room reaches a certain upper limit, the room heating is switched off so that the temperature begins to fall. When the temperature drops to a lower limit, the heating is switched on again. Provided the limits are close to each other, a steady room temperature is maintained. Similar control mechanisms are used in cooling systems, such as an air conditioner, a refrigerator, or a freezer.
Biology and chemistry
Control of endocrine hormones by negative feedback. Some biological systems exhibit negative feedback such as the baroreflex in blood pressure regulation and erythropoiesis. Many biological process (e.g., in human physiology) use negative feedback. Examples of this are numerous, from the regulating of body temperature, to the regulating of blood glucose levels.
The disruption of feedback loops can lead to undesirable results: in the case of blood glucose levels, if negative feedback fails, the glucose levels in the blood may begin to rise dramatically, thus resulting in diabetes.
For hormone secretion regulated by the negative feedback loop:
when gland X releases hormone X, this stimulates target cells to
release hormone Y. When there is an excess of hormone Y, gland X
"senses" this and inhibits its release of hormone X.
Figure: Stress hormone Cortisol dampens its own creation indirectly.
Self-organization is the capability of certain systems "of organizing their own behavior or structure". There are many possible factors contributing to this capacity, and most often positive feedback is identified as a possible contributor. However, negative feedback also can play a role.
In economics, automatic stabilisers are government programs that are intended to work as negative feedback to dampen fluctuations in real GDP. Free market economic theorists claim that the pricing mechanism operated to match supply and demand. However Norbert Wiener wrote in 1948: "There is a belief current in many countries and elevated to the rank of an official article of faith in the United States that free competition is itself a homeostatic process... Unfortunately the evidence, such as it is, is against this simple-minded theory."