## Terminology

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.

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# Practopoiesis

## Explanation

Practopoiesis is an overarching biological theory from Danko Nikolic. The term reflects the fundamental presumption on what the common property is, that can be found across all the different levels of organization of biological systems: to Act.
For example: Gene expression mechanisms act; bacteria act; organs act; organisms as a whole act.

### Cybernetics

Due to this focus on biological action, practopoiesis has a strong cybernetic flavour as it has to deal with the need of acting systems to close feedback loops.

Thus, the theory of practopoiesis builds on the concepts of cybernetics. Cybernetic laws assumes monitor-and-act machinery (either physical or biological):
input → processing → output → feedback (as new input).
In practopoiesis, input is needed to trigger actions and to determine whether more actions are needed. For that reason, the theory is founded in the basic theorems of cybernetics, namely that of Requisite Variety and of Good Regulator Theorem.

The key novelty of practopoiesis is that it introduces the mechanisms explaining how different levels of organization mutually interact. These mechanisms help explain how genes create anatomy of the nervous system, or how anatomy creates behaviour.

### Intelligence

Practopoiesis is a theory on how life organizes into a mind. It proposes the principles by which adaptive systems organize. It is a general theory of what it takes to be biologically intelligent. Being general, the theory is applicable to the brain as much as it is applicable to artificial intelligence (AI) technologies. What makes the theory so general is that it is grounded in the principles of cybernetics (e.g. feedback loops), rather than describing the physiological implementations of those mechanisms (e.g. inhibition/excitation, plasticity, etc.).

In practopoiesis there is no longer a cycle: action → representation → action … . Instead, practopoietic theory works with actions only, which interact and form a hierarchy: One action is in a service of another action. This hierarchy starts with actions of gene expression mechanisms and ends with our overt behavior. Perception and cognition are then understood as emergent properties of those cybernetics-like actions.

The practopoietic theory of Prof. Dr. Danko Nikolic consists of two parts:

1. The first part is the foundation. This is where the basic principles of adaptive systems are formulated. These principles can be applied to various biological processes, not only to the brain. Also, the first part can be applied to non-biological systems, such as AI.
2. The second part applies those principles to human mind and to the mind/body problem. The second part explains the ways in which the mind is special and different from any other adaptive system.

## Linguistic derivation

The term Practopoiesis is derived from Ancient Greek words praxis  (πρᾶξις)) meaning "deed", "act" or "action" + poiesis (ποίησις, ποιέω) which means "to make". Practopoiesis means: creation of actions.

## External Sources

 Keyword(s): Danko Nikolic

# Pseudocode

PseudoCode is a 'language syntax shorthand notation' that uses expressions in between human language and computer programming language. A programmer tries to write down cause-effect actions, using normal human words, so that a laymen (with no programming experience) can read and understand the serie of commands (= algorithms) that execute a specific computer process.

In the category 'Bio-Mental Cybernetics', the term (Bio-)PseudoCode is used to denote the following: To describe in plain language (shorthand notation), mental algorithms based on neuronal mechanisms that form feelings or thoughts, especially in human beings.

Bio-Mental Cybernetics describes the underlying mechanism of certain cause-effect phenomena that emerged during evolution to give rise to brain processes with regard to emotions (feelings) and cognitions (thought).

Mental-pseudocode (also called: neuro-pseudocode) denotes, on the concrete level, the actual thought process as a result of functional neuronal process.

Evo-pseudocode (also called: meta-pseudocode) describes, on a meta level, the way evolution gave birth to processes by which animals obtained the ability to generate brain processes resembling human thought.

 Keyword(s): PseudocodeAlgorithm

# Semi-Science

## Explanation

Semi-Science is an attribute given by scientists to questionable knowledge-findings of certain people or non-objective truth-claims of certain groups. This attribute indicates that the underlying facts are not (yet) properly proven according to scientific rules, or that they are based on half-truths.

CPER's principle:
CPER uses this term to denote the fact that science has the following limitations:

• There are many phenomena that science cannot explain properly because of limited technical means.
• Scientists have not investigated everything there is to investigate yet.
• Some scientists do not do value-free research in order to find the objective truth.
• Scientists avoid to investigate certain tricky phenomena, for example: many scientists refuse to do objective research on the aspect of homosexuality, because of moral or political reasons.
• There is little integration of knowledge from different scientific areas related to cross-domain patterns or phenomena.
• Universities focus more on in-depth research, rather than on expository education.
• Universities are limited in their financial resources, so they choose to invest in research on popular or urgent themes.
• To become famous or to get subsidies, current scientists investigate mainly unexplored new areas. This way, much relatively 'old' knowledge (but still useful for people at home) is not perpetuated in a global popular knowledge base. Useful scientific findings or solutions disappear into the background of daily concerns of society. (Four family generations later, a scientist re-invents the wheel again.)

This means that certain theorems can not be refuted, and should not be ignored by the scientific community, as long as science does not contain 'all answers to everything'.

CPER's vocabulary:
CPER applies the term 'semi-science' to emphasize those statements that may become scientifically proven in the future, by research done under supervision of a university. Thus, these semi-scientific statements, formulations, explanations or descriptions of phenomena are -for now- 'hypotheses': they are set candidacy for proper academic examination, and -who knows- may get included into the accepted repertoire of proven scientific knowledge, some day.

## Linguistic derivation

The prefix Semi is derived from the Latin word semi, meaning "half" and the term Science from Latin scientia, meaning "knowledge".

 Keyword(s): HypothesisObjectivityPhenomenonSemiTruthValue-free Research

# Taxonomy

Taxonomy is the science of defining groups of biological organisms on the basis of shared characteristics and giving names to those groups. Organisms are grouped together into taxa (singular: taxon) and given a taxonomic rank. Groups of a given rank can be aggregated to form a super group of higher rank and thus create a taxonomic hierarchy. The Swedish botanist Carolus Linnaeus is regarded as the father of taxonomy, as he developed a system known as Linnaean classification for categorization of organisms and binomial nomenclature for naming organisms. With the advent of such fields of study as phylogenetics, cladistics, and systematics, the Linnaean system has progressed to a system of modern biological classification based on the evolutionary relationships between organisms, both living and extinct

The term taxonomy is derived from the Ancient Greek word taxis (τάξις) meaning "arrangement" and -nomia (νομία) meaning "method".

Taxon

In biology, a taxon (plural taxa; back-formation from taxonomy) is a group of one or more populations of an organism or organisms seen by taxonomists to form a unit. A taxon is usually known by a particular name and given a particular ranking.

Taxonomic rank

In biological classification, rank is the level (the relative position) in a taxonomic hierarchy. Examples of taxonomic ranks are species, genus, family, and class.
Each rank subsumes under it a number of less general categories.
The rank of species, and specification of the genus to which the species belongs is basic, which means that it may not be necessary to specify ranks other than these.
The International Code of Zoological Nomenclature defines rank as:
The level, for nomenclatural purposes, of a taxon in a taxonomic hierarchy (e.g. all families are for nomenclatural purposes at the same rank, which lies between superfamily and subfamily).

Figure: Example of division terms used in Taxonomic rank.

## Related concepts

Cladistics is an approach to biological classification in which organisms are grouped together. This grouping is based on whether or not organisms have one or more shared unique characteristics that come from the group's last common ancestor and are not present in more distant ancestors. Therefore, members of the same group are thought to share a common history and are considered to be more closely related. When these lineage-branching (with regard to common ancestor) are drawn in a diagram, this is called a cladogram.

The term cladistic is derived from the Ancient Greek word klados (κλάδος) meaning "branch".

### Phylogenetic nomenclature

Phylogenetic nomenclature, often called cladistic nomenclature, is a method of nomenclature for taxa in biology that uses phylogenetic definitions for taxon names. This contrasts with the traditional approach, in which taxon names are defined by a type, which can be a specimen or a taxon of lower rank, and a diagnosis, a statement intended to supply characters that differentiate the taxon from others with which it is likely to be confused. Phylogenetic nomenclature is currently not regulated, but the International Code of Phylogenetic Nomenclature (PhyloCode) is intended to regulate it once it is ratified.

# Vector

## Explanation

CPER: a vector is an abstract reference pointer, that indicates the direction of an evolutionary trend. Within the framework of the theory of CPER, a vector resembles the definition of a mathematical pointer or physical impulse, rather than of a biological carrier.

Mathematics: a vector is a geometric pointer-entity endowed with magnitude and direction as well as a positive-definite inner product. It is an element of an Euclidean vector space that is used to represent physical quantities that have both magnitude and direction (X, Y, Z), such as force, in contrast to scalar quantities, which have no direction. An inner product space is a vector space with an additional structure called an inner product. This additional structure associates each pair of vectors in the space with a scalar quantity known as the inner product of the vectors. Inner products allow the rigorous introduction of intuitive geometrical notions such as the length of a vector or the angle between two vectors. An inner product naturally induces an associated norm, thus an inner product space is also a normed vector space.

Epidemiology: a vector is a carrier-organism, often an invertebrate arthropod, that transmits a pathogen from reservoir to host.

Molecular biology: a vector is a carrier-vehicle used to transfer genetic material to a target cell, such as a plasmid vector.

## Linguistic derivation

The word Vector is derived from the Latin term vehere, which means "to carry".

 Keyword(s): vectorEuclideanInner Product SpaceEpidemiologyMolecular Biology

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