Example of a Geologic map information meta-model, with four types of meta-objects, and their self-references.
A metamodel or surrogate model is a model of a model, and metamodeling is the process of generating such metamodels. Thus metamodeling or meta-modeling is the analysis, construction and development of the frames, rules, constraints, models and theories applicable and useful for modeling a predefined class of problems. As its name implies, this concept applies the notions of meta- and modeling in software engineering and systems engineering. Metamodels are of many types and have diverse applications.
Overview
A
metamodel/ surrogate model is a model of the model, i.e. a simplified
model of an actual model of a circuit, system, or software like entity. Metamodel can be a mathematical relation or algorithm representing input and output relations. A model is an abstraction of phenomena in the real world;
a metamodel is yet another abstraction, highlighting properties of the
model itself. A model conforms to its metamodel in the way that a
computer program conforms to the grammar of the programming language in
which it is written. Various types of metamodels include polynomial
equations, neural network, Kriging,
etc. "Metamodeling" is the construction of a collection of "concepts"
(things, terms, etc.) within a certain domain. Metamodeling typically
involves studying the output and input relationships and then fitting
right metamodels to represent that behavior.
Common uses for metamodels are:
As a schema for semantic data that needs to be exchanged or stored
As a language that supports a particular method or process
As a language to express additional semantics of existing information
As a mechanism to create tools that work with a broad class of models at run time
As a schema for modeling and automatically exploring sentences of a language with applications to automated test synthesis
As an approximation of a higher-fidelity model for use when reducing computational cost is necessary
In software engineering, the use of models
is an alternative to more common code-based development techniques. A
model always conforms to a unique metamodel. One of the currently most
active branch of Model Driven Engineering is the approach named model-driven architecture proposed by OMG. This approach is based on the utilization of a language to write metamodels called the Meta Object Facility or MOF. Typical metamodels proposed by OMG are UML, SysML, SPEM or CWM. ISO has also published the standard metamodel ISO/IEC 24744. All the languages presented below could be defined as MOF metamodels.
Meta-models are closely related to ontologies. Both are often used to describe and analyze the relations between concepts:
Ontologies: express something meaningful within a specified universe or domain of discourse
by utilizing a grammar for using vocabulary. The grammar specifies what
it means to be a well-formed statement, assertion, query, etc. (formal
constraints) on how terms in the ontology’s controlled vocabulary can be
used together.
Meta-modeling: can be considered as an explicit description
(constructs and rules) of how a domain-specific model is built. In
particular, this comprises a formalized specification of the
domain-specific notations. Typically, metamodels are – and always should
follow - a strict rule set. "A valid metamodel is an ontology, but not all ontologies are modeled explicitly as metamodels".
Types of metamodels
For software engineering, several types of models (and their corresponding modeling activities) can be distinguished:
A library of similar metamodels has been called a Zoo of metamodels.
There are several types of meta-model zoos. Some are expressed in ECore. Others are written in MOF 1.4 – XMI 1.2. The metamodels expressed in UML-XMI1.2 may be uploaded in Poseidon for UML, a UMLCASE tool.
Metamodeling software
Surrogate Modeling Toolbox (SMT: https://github.com/SMTorg/smt):
is a Python package that contains a collection of surrogate modeling
methods, sampling techniques, and benchmarking functions. This package
provides a library of surrogate models that is simple to use and
facilitates the implementation of additional methods. SMT is different
from existing surrogate modeling libraries because of its emphasis on
derivatives, including training derivatives used for gradient-enhanced
modeling, prediction derivatives, and derivatives with respect to the
training data. It also includes new surrogate models that are not
available elsewhere: kriging by partial-least squares reduction and
energy-minimizing spline interpolation.
Example of a Method Engineering Process. This figure provides a process-orientedview of the approach used to develop prototype IDEF9 method concepts, a procedure, and candidate graphical and textual language elements.
Method engineering in the "field of information systems is the discipline to construct new methods from existing methods". It focuses on "the design, construction and evaluation of methods, techniques and support tools for information systems development".
Furthermore, method engineering "wants to improve the usefulness of systems development methods by creating an adaptation framework whereby methods are created to match specific organisational situations".
Types
Computer aided method engineering
The meta-process modeling process is often supported through software tools, called computer aided method engineering (CAME) tools, or MetaCASE tools
(Meta-level Computer Assisted Software Engineering tools). Often the
instantiation technique "has been utilised to build the repository of
Computer Aided Method Engineering environments". There are many tools for meta-process modeling.
Method tailoring
In
the literature, different terms refer to the notion of method
adaptation, including 'method tailoring', 'method fragment adaptation'
and 'situational method engineering'. Method tailoring is defined as:
A process or capability in which human agents through
responsive changes in, and dynamic interplays between contexts,
intentions, and method fragments determine a system development
approach for a specific project situation.
Potentially, almost all agile methods are suitable for method tailoring. Even the DSDM method is being used for this purpose and has been successfully tailored in a CMM context.
Situation-appropriateness can be considered as a distinguishing
characteristic between agile methods and traditional software
development methods, with the latter being relatively much more rigid
and prescriptive. The practical implication is that agile methods allow
project teams to adapt working practices according to the needs
of individual projects. Practices are concrete activities and products
that are part of a method framework. At a more extreme level, the
philosophy behind the method, consisting of a number of principles, could be adapted.
Situational method engineering
Situational method engineering is the construction of methods which are tuned to specific situations of development projects. It can be described as the creation of a new method by
selecting appropriate method components from a repository of reusable method components,
tailoring these method components as appropriate, and
integrating these tailored method components to form the new situation-specific method.
This enables the creation of development methods suitable for any
development situation. Each system development starts then, with a
method definition phase where the development method is constructed on
the spot.
In case of mobile business development, there are methods available for specific parts of the business model
design process and ICT development. Situational method engineering can
be used to combine these methods into one unified method that adopts the
characteristics of mobile ICT services.
Method engineering process
The developers of the IDEF
modeling languages, Richard J. Mayer et al. (1995), have developed an
early approach to method engineering from studying common method
engineering practice and experience in developing other analysis and design methods. The following figure provides a process-oriented view of this approach. This image uses the IDEF3
Process Description Capture method to describe this process where boxes
with verb phrases represent activities, arrows represent precedence
relationships, and "exclusive or" conditions among possible paths are
represented by the junction boxes labeled with an "X.".
This image provides a general overview of the IDEF Method engineering process approach.
According to this approach there are three basic strategies in method engineering:
Reuse: one of the basic strategies of methods engineering is reuse. Whenever possible, existing methods are adopted.
Tailormade: find methods that can satisfy the identified
needs with minor modification. This option is an attractive one if the
modification does not require a fundamental change in the basic concepts
or design goals of the method.
New development: Only when neither of these options is viable should method designers seek to develop a new method.
This basic strategies can be developed in a similar process of concept development.
Knowledge engineering approach
A knowledge engineering
approach is the predominant mechanism for method enhancement and new
method development. In other words, with very few exceptions, method
development involves isolating, documenting, and packaging existing
practice for a given task in a form that promotes reliable success among
practitioners. Expert attunements are first characterized in the form
of basic intuitions and method concepts. These are often initially
identified through analysis of the techniques, diagrams, and expressions
used by experts. These discoveries aid in the search for existing
methods that can be leveraged to support novice practitioners in
acquiring the same attunements and skills.
New method development is accomplished by establishing the scope
of the method, refining characterizations of the method concepts and
intuitions, designing a procedure that provides both task accomplishment
and basic apprenticeship support to novice practitioners, and
developing a language(s) of expression. Method application techniques
are then developed outlining guidelines for use in a stand-alone mode
and in concert with other methods. Each element of the method then
undergoes iterative refinement through both laboratory and field
testing.
Method language design process
The
method language design process is highly iterative and experimental in
nature. Unlike procedure development, where a set of heuristics and
techniques from existing practice can be identified, merged, and
refined, language designers rarely encounter well-developed graphical
display or textual information capture mechanisms. When potentially
reusable language structures can be found, they are often poorly defined
or only partially suited to the needs of the method.
A critical factor in the design of a method language is clearly
establishing the purpose and scope of the method. The purpose of the
method establishes the needs the method must address. This is used to
determine the expressive power required of the supporting language. The
scope of the method establishes the range and depth of coverage which
must also be established before one can design an appropriate language
design strategy. Scope determination also involves deciding what
cognitive activities will be supported through method application. For
example, language design can be confined to only display the final
results of method application (as in providing IDEF9 with graphical and
textual language facilities that capture the logic and structure of
constraints). Alternatively, there may be a need for in-process language
support facilitating information collection and analysis. In those
situations, specific language constructs may be designed to help method
practitioners organize, classify, and represent information that will
later be synthesized into additional representation structures intended
for display.
With this foundation, language designers begin the process of
deciding what needs to be expressed in the language and how it should be
expressed. Language design can begin by developing a textual language
capable of representing the full range of information to be addressed.
Graphical language structures designed to display select portions of the
textual language can then be developed. Alternatively, graphical
language structures may evolve prior to, or in parallel with, the
development of the textual language. The sequence of these activities
largely depends on the degree of understanding of the language
requirements held among language developers. These may become clear only
after several iterations of both graphical and textual language design.
Graphical language design
Graphical
language design begins by identifying a preliminary set of schematics
and the purpose or goals of each in terms of where and how they will
support the method application process. The central item of focus is
determined for each schematic. For example, in experimenting with
alternative graphical language designs for IDEF9, a Context Schematic
was envisioned as a mechanism to classify the varying environmental
contexts in which constraints may apply. The central focus of this
schematic was the context. After deciding on the central focus for the
schematic, additional information (concepts and relations) that should
be captured or conveyed is identified.
Up to this point in the language design process, the primary
focus has been on the information that should be displayed in a given
schematic to achieve the goals of the schematic. This is where the
language designer must determine which items identified for possible
inclusion in the schematic are amenable to graphical representation and
will serve to keep the user focused on the desired information content.
With this general understanding, previously developed graphical language
structures are explored to identify potential reuse opportunities.
While exploring candidate graphical language designs for emerging IDEF
methods, a wide range of diagrams were identified and explored. Quite
often, even some of the central concepts of a method will have no
graphical language element in the method.
For example, the IDEF1
Information Modeling method includes the notion of an entity but has no
syntactic element for an entity in the graphical language.8. When the
language designer decides that a syntactic element should be included
for a method concept, candidate symbols are designed and evaluated.
Throughout the graphical language design process, the language designer
applies a number of guiding principles to assist in developing high
quality designs. Among these, the language designer avoids overlapping
concept classes or poorly defined ones. They also seek to establish
intuitive mechanisms to convey the direction for reading the schematics.
For example, schematics may be designed to be read from left to
right, in a bottom-up fashion, or center-out. The potential for clutter
or overwhelmingly large amounts of information on a single schematic is
also considered as either condition makes reading and understanding the
schematic extremely difficult.
Method testing
Each
candidate design is then tested by developing a wide range of examples
to explore the utility of the designs relative to the purpose for each
schematic. Initial attempts at method development, and the development
of supporting language structures in particular, are usually
complicated. With successive iterations on the design, unnecessary and
complex language structures are eliminated.
As the graphical language design approaches a level of maturity,
attention turns to the textual language. The purposes served by textual
languages range from providing a mechanism for expressing information
that has explicitly been left out of the graphical language to providing
a mechanism for standard data exchange and automated model
interpretation. Thus, the textual language supporting the method may be
simple and unstructured (in terms of computer interpretability), or it
may emerge as a highly structured, and complex language. The purpose of
the method largely determines what level of structure will be required
of the textual language.
Formalization and application techniques
As
the method language begins to approach maturity, mathematical
formalization techniques are employed so the emerging language has clear
syntax and semantics. The method formalization process often helps
uncover ambiguities, identify awkward language structures, and
streamline the language.
These general activities culminate in a language that helps focus
user attention on the information that needs to be discovered,
analyzed, transformed, or communicated in the course of accomplishing
the task for which the method was designed. Both the procedure and
language components of the method also help users develop the necessary
skills and attunements required to achieve consistently high quality
results for the targeted task.
Once the method has been developed, application techniques will
be designed to successfully apply the method in stand-alone mode as well
as together with other methods. Application techniques constitute the
"use" component of the method which continues to evolve and grow
throughout the life of the method. The method procedure, language
constructs, and application techniques are reviewed and tested to
iteratively refine the method.
Problem structuring methods (PSMs) are a group of techniques used to model or to map the nature or structure of a situation or state of affairs that some people want to change. PSMs are usually used by a group of people in collaboration (rather than by a solitary individual) to create a consensus about, or at least to facilitate negotiations about, what needs to change. Some widely adopted PSMs include soft systems methodology, the strategic choice approach, and strategic options development and analysis (SODA).
Unlike some problem solving
methods that assume that all the relevant issues and constraints and
goals that constitute the problem are defined in advance or are
uncontroversial, PSMs assume that there is no single uncontested
representation of what constitutes the problem.
PSMs are mostly used with groups of people, but PSMs have also influenced the coaching and counseling of individuals.
History
The term "problem structuring methods" as a label for these techniques began to be used in the 1980s in the field of operations research, especially after the publication of the book Rational Analysis for a Problematic World: Problem Structuring Methods for Complexity, Uncertainty and Conflict. Some of the methods that came to be called PSMs had been in use since the 1960s.
Thinkers who later came to be recognized as significant early contributors to the theory and practice of PSMs include:
In discussions of problem structuring methods, it is common to
distinguish between two different types of situations that could be
considered to be problems. Rittel and Webber's distinction between tame problems and wicked problems (Rittel & Webber 1973) is a well known example of such types.
The following table lists similar (but not exactly equivalent)
distinctions made by a number of thinkers between two types of "problem"
situations, which can be seen as a continuum between a left and right
extreme:
Different types of situations, and thinkers who named them
Tame problems (or puzzles or technical challenges) have
relatively precise, straightforward formulations that are often amenable
to solution with some predetermined technical fix or algorithm. It is
clear when these situations have changed in such a way that the problem
can be called solved.
Wicked problems (or messes or adaptive challenges) have multiple interacting issues with multiple stakeholders and uncertainties and no definitive formulation. These situations are complex and have no stopping rule and no ultimate test of a solution.
PSMs were developed for situations that tend toward the wicked or "soft" side, when methods are needed that assist argumentation about, or that generate mutual understanding of multiple perspectives on, a complex situation.
Other problem solving methods are better suited to situations toward
the tame or "hard" side where a reliable and optimal solution is needed
to a problem that can be clearly and uncontroversially defined.
Characteristics
Problem
structuring methods constitute a family of approaches that have
differing purposes and techniques, and many of them had been developed
independently before people began to notice their family resemblance. Several scholars have noted the common and divergent characteristics among PSMs.
Eden and Ackermann identified four characteristics that problem structuring methods have in common:
The methods focus on creating "a model that is populated with
data that is specific to the problem situation". These cause–effect
models can be analyzed (albeit in different ways by different methods),
and the models are intended to facilitate conversation and negotiation
between the participants.
The methods seek to increase the overall productivity of group
processes. Productivity includes creating better agreements that are
more likely to be implemented, and realizing (to the extent possible in
the given situation) ideals such as communicative rationality and procedural justice.
The methods emphasize that the facilitation
of effective group processes requires some attention to, and open
conversation about, power and politics within and between organizations.
Power and politics can become especially important when major change is
being proposed.
The methods provide techniques and skills for facilitation of group
processes, and they appreciate that such techniques and skills are
essential for effective sensemaking, systems modeling, and participative decision-making. People who use PSMs must pay attention to what group facilitators call process skills (guiding interactions between people through nonlinear applications of the methods) and content skills (helping people build sufficiently comprehensive models of the given situation).
Rosenhead provided another list of common characteristics of PSMs, formulated in a more prescriptive style:
Seek solutions which satisfice on separate dimensions rather than seeking an optimal decision on a single dimension.
Integrate hard and soft (quantitative and qualitative) data with social judgments.
Produce models that are as transparent as possible to and that clarify conflicts of interpretation, rather than hiding conflicts behind neutral technical language.
Consider people to be agents actively involved in the decision-making process, rather than as passive objects to be modeled or ignored.
Facilitate the problem structuring process from the bottom-up as
much as possible, not only top-down from formal organizational
leadership.
Aim to preserve options in the face of unavoidable uncertainty, rather than to base decisions on a prediction of the future.
An early literature review of problem structuring proposed grouping
the texts reviewed into "four streams of thought" that describe some
major differences between methods:
the checklist stream, which is step-by-step technical problem solving (not problem structuring as it came to be defined in PSMs, so this stream does not apply to PSMs),
the definition stream, which is primarily modeling of relationships between variables, as described by Ackoff and others,
the science research stream which emphasizes doing field research and gathering quantitative data, and
the people stream, which "regards the definition of problems as a function of people's perceptions" as described by Checkland, Eden, and others.
Compared to large group methods
Mingers and Rosenhead have noted that there are similarities and differences between PSMs and large group methods such as Future Search, Open Space Technology, and others.
PSMs and large group methods both bring people together to talk about,
and to share different perspectives on, a situation or state of affairs
that some people want to change. However, PSMs always focus on creating a
sufficiently rigorous conceptual model or cognitive map
of the situation, whereas large group methods do not necessarily
emphasize modeling, and PSMs are not necessarily used with large groups
of people.
Compared to participatory rural appraisal
There is significant overlap or shared characteristics between PSMs and some of the techniques used in participatory rural appraisal
(PRA). Mingers and Rosenhead pointed out that in situations where
people have low literacy, the nonliterate (oral and visual) techniques
developed in PRA would be a necessary complement to PSMs, and the
approaches to modeling in PSMs could be (and have been) used by
practitioners of PRA.
Applications
In 2004, Mingers and Rosenhead published a literature review of papers that had been published in scholarly journals and that reported practical applications of PSMs. Their literature survey covered the period up to 1998, which was "relatively early in the development of interest in PSMs",
and categorized 51 reported applications under the following
application areas: general organizational applications; information
systems; technology, resources, planning; health services; and general
research. Examples of applications reported included: designing a
parliamentary briefing system, modeling the San Francisco Zoo, developing a business strategy and information system
strategy, planning livestock management in Nepal, regional planning in
South Africa, modeling hospital outpatient services, and eliciting
knowledge about pesticides.
Technology and software
PSMs are a general methodology and are not necessarily dependent on electronic information technology, but PSMs do rely on some kind of shared display of the models that participants are developing. The shared display could be flip charts, a large whiteboard, Post-it notes on the meeting room walls, and/or a personal computer connected to a video projector.
After PSMs have been used in a group work session, it is normal for a
record of the session's display to be shared with participants and with
other relevant people.
Software programs for supporting problem structuring include Banxia Decision Explorer and Group Explorer, which implement cognitive mapping for strategic options development and analysis (SODA), and Compendium, which implements IBIS for dialogue mapping and related methods; a similar program is called Wisdom.
Such software can serve a variety of functions, such as simple
technical assistance to the group facilitator during a single event, or
more long-term online group decision support systems.
Some practitioners prefer not to use computers during group work sessions because of the effect they have on group dynamics, but such use of computers is standard in some PSMs such as SODA[27] and dialogue mapping, in which computer display of models or maps is intended to guide conversation in the most efficient way.
In some situations additional software that is not used only for
PSMs may be incorporated into the problem structuring process; examples
include spreadsheet modeling, system dynamics software or geographic information systems. Some practitioners, who have focused on building system dynamics simulation models with groups of people, have called their work group model building (GMB) and have concluded "that GMB is another PSM".[32] GMB has also been used in combination with SODA.
A clinical formulation, also known as case formulation and problem formulation,
is a theoretically-based explanation or conceptualisation of the
information obtained from a clinical assessment. It offers a hypothesis
about the cause and nature of the presenting problems and is considered
an adjunct or alternative approach to the more categorical approach of
psychiatric diagnosis. In clinical practice, formulations are used to communicate a hypothesis and provide framework for developing the most suitable treatment approach. It is most commonly used by clinical psychologists and psychiatrists and is deemed to be a core component of these professions. Mental health nurses and social workers may also use formulations.
Types of formulation
Different psychological schools or models utilize clinical formulations, including cognitive behavioral therapy (CBT) and related therapies: systemic therapy, psychodynamic therapy, and applied behavior analysis.
The structure and content of a clinical formulation is determined by
the psychological model. Most systems of formulation contain the
following broad categories of information: symptoms and problems;
precipitating stressors or events; predisposing life events or
stressors; and an explanatory mechanism that links the preceding
categories together and offers a description of the precipitants and
maintaining influences of the person's problems.
A model of formulation that is more specific to CBT is described by Jacqueline Persons.
This has seven components: problem list, core beliefs, precipitants and
activating situations, origins, working hypothesis, treatment plan, and
predicted obstacles to treatment.
A psychodynamic formulation would consist of a summarizing
statement, a description of nondynamic factors, description of core
psychodynamics using a specific model (such as ego psychology, object relations or self psychology), and a prognostic assessment which identifies the potential areas of resistance in therapy.
One school of psychotherapy which relies heavily on the formulation is cognitive analytic therapy (CAT).
CAT is a fixed-term therapy, typically of around 16 sessions. At around
session four, a formal written reformulation letter is offered to the
patient which forms the basis for the rest of the treatment. This is
usually followed by a diagrammatic reformulation to amplify and
reinforce the letter.
Many psychologists use an integrative psychotherapy approach to formulation.
This is to take advantage of the benefits of resources from each model
the psychologist is trained in, according to the patient's needs.
Critical evaluation of formulations
The quality of specific clinical formulations, and the quality of the general theoretical models used in those formulations, can be evaluated with criteria such as:
Clarity and parsimony: Is the model understandable and internally consistent, and are key concepts discrete, specific, and non-redundant?
Comprehensiveness and generalizability: Is the model holistic enough to apply across a range of clinical phenomena?
Utility and applied value: Does it facilitate shared meaning-making between clinician and client, and are interventions based on the model shown to be effective?
Formulations can vary in temporal scope from case-based to
episode-based or moment-based, and formulations may evolve during the
course of treatment.
Therefore, ongoing monitoring, testing, and assessment during treatment
are necessary: monitoring can take the form of session-by-session
progress reviews using quantitative measures, and formulations can be
modified if an intervention is not as effective as hoped.
History
Psychologist George Kelly, who developed personal construct theory in the 1950s, noted his complaint against traditional diagnosis in his book The Psychology of Personal Constructs
(1955): "Much of the reform proposed by the psychology of personal
constructs is directed towards the tendency for psychologists to impose
preemptive constructions upon human behaviour. Diagnosis is all too
frequently an attempt to cram a whole live struggling client into a
nosological category." In place of nosological categories, Kelly used the word "formulation" and mentioned two types of formulation: a first stage of structuralization,
in which the clinician tentatively organizes clinical case information
"in terms of dimensions rather than in terms of disease entities"
while focusing on "the more important ways in which the client can
change, and not merely ways in which the psychologist can distinguish
him from other persons", and a second stage of construction,
in which the clinician seeks a kind of negotiated integration of the
clinician's organization of the case information with the client's
personal meanings.
Psychologists Hans Eysenck, Monte B. Shapiro, Vic Meyer, and Ira Turkat were also among the early developers of systematic individualized alternatives to diagnosis. Meyer has been credited with providing perhaps the first training course of behaviour therapy based on a case formulation model, at the Middlesex Hospital Medical School in London in 1970. Meyer's original choice of words for clinical formulation were "behavioural formulation" or "problem formulation".
Secondary metabolism produces a large number of specialized
compounds (estimated 200,000) that do not aid in the growth and
development of plants but are required for the plant to survive in its
environment. Secondary metabolism
is connected to primary metabolism by using building blocks and
biosynthetic enzymes derived from primary metabolism. Primary metabolism
governs all basic physiological processes that allow a plant to grow
and set seeds, by translating the genetic code into proteins,
carbohydrates, and amino acids. Specialized compounds from secondary
metabolism are essential for communicating with other organisms in
mutualistic (e.g. attraction of beneficial organisms such as
pollinators) or antagonistic interactions (e.g. deterrent against
herbivores and pathogens). They further assist in coping with abiotic
stress such as increased UV-radiation. The broad functional spectrum of
specialized metabolism is still not fully understood. In any case, a
good balance between products of primary and secondary metabolism is
best for a plant’s optimal growth and development as well as for its
effective coping with often changing environmental conditions. Well
known specialized compounds include alkaloids, polyphenols including
flavonoids, and terpenoids. Humans use quite a lot of these compounds,
or the plants from which they originate, for culinary, medicinal and
nutraceutical purposes.
History
Research
into secondary plant metabolism primarily took off in the later half of
the 19th century, however, there was still much confusion over what the
exact function and usefulness of these compounds were. All that was
known was that secondary plant metabolites
were "by-products" of the primary metabolism and were not crucial to
the plant's survival. Early research only succeeded as far as
categorizing the secondary plant metabolites but did not give real
insight into the actual function of the secondary plant metabolites. The
study of plant metabolites is thought to have started in the early
1800s when Friedrich Willhelm Serturner isolated morphine from opium
poppy, and after that new discoveries were made rapidly. In the early
half of the 1900s, the main research around secondary plant metabolism
was dedicated to the formation of secondary metabolites in plants, and this research was compounded by the use of tracer techniques which made deducing metabolic pathways
much easier. However, there was still not much research being conducted
into the functions of secondary plant metabolites until around the
1980s. Before then, secondary plant metabolites were thought of as
simply waste products. In the 1970s, however, new research showed that
secondary plant metabolites play an indispensable role in the survival
of the plant in its environment. One of the most ground breaking ideas
of this time argued that plant secondary metabolites evolved in relation
to environmental conditions, and this indicated the high gene
plasticity of secondary metabolites, but this theory was ignored for
about half a century before gaining acceptance. Recently, the research
around secondary plant metabolites is focused around the gene level and
the genetic diversity of plant metabolites. Biologists are now trying to
trace back genes to their origin and re-construct evolutionary
pathways.
Primary vs. Secondary Plant Metabolism
Primary
metabolism in a plant comprises all metabolic pathways that are
essential to the plant's survival. Primary metabolites are compounds
that are directly involved in the growth and development of a plant
whereas secondary metabolites are compounds produced in other metabolic
pathways that, although important, are not essential to the functioning
of the plant. However, secondary plant metabolites are useful in the
long term, often for defense purposes,
and give plants characteristics such as color. Secondary plant
metabolites are also used in signalling and regulation of primary
metabolic pathways. Plant hormones, which are secondary metabolites, are
often used to regulate the metabolic activity within cells and oversee
the overall development of the plant. As mentioned above in the History
tab, secondary plant metabolites help the plant maintain an intricate
balance with the environment, often adapting to match the environmental
needs. Plant metabolites that color the plant are a good example of
this, as the coloring of a plant can attract pollinators and also defend
against attack by animals.
Types of Secondary Metabolites in plants
There
is no fixed, commonly agreed upon system for classifying secondary
metabolites. Based on their biosynthetic origins, plant secondary
metabolites can be divided into three major groups:
Flavonoids and allied phenolic and polyphenolic compounds,
Terpenoids and
Nitrogen-containing alkaloids and sulphur-containing compounds.
Other researchers have classified secondary metabolites into following, more specific types
Some of the secondary metabolites are discussed below:
Atropine
Atropine is a type of secondary metabolite called a tropane alkaloid. Alkaloids contain nitrogens, frequently in a ring structure, and are derived from amino acids.
Tropane is an organic compound containing nitrogen and it is from
tropane that atropine is derived. Atropine is synthesized by a reaction
between tropine and tropate, catalyzed by atropinase.
Both of the substrates involved in this reaction are derived from
amino acids, tropine from pyridine (through several steps) and tropate
directly from phenylalanine. Within Atropa belladonna atropine synthesis has been found to take place primarily in the root of the plant.
The concentration of synthetic sites within the plant is indicative of
the nature of secondary metabolites. Typically, secondary metabolites
are not necessary for normal functioning of cells within the organism
meaning the synthetic sites are not required throughout the organism.
As atropine is not a primary metabolite, it does not interact specifically with any part of the organism, allowing it to travel throughout the plant.
Flavonoids
Flavonoids are one class of secondary plant metabolites that are also known as Vitamin P or citrin.
These metabolites are mostly used in plants to produce yellow and other
pigments which play a big role in coloring the plants. In addition,
Flavonoids are readily ingested by humans and they seem to display
important anti-inflammatory, anti-allergic and anti-cancer activities.
Flavonoids are also found to be powerful anti-oxidants and researchers
are looking into their ability to prevent cancer and cardiovascular
diseases. Flavonoids help prevent cancer by inducing certain mechanisms
that may help to kill cancer cells, and researches believe that when the
body processes extra flavonoid compounds, it triggers specific enzymes
that fight carcinogens. Good dietary sources of Flavonoids are all
citrus fruits, which contain the specific flavanoids hesperidins, quercitrin,and rutin,
berries, tea, dark chocolate and red wine and many of the health
benefits attributed to these foods come from the Flavonoids they
contain. Flavonoids are synthesized by the phenylpropanoid metabolic pathway where the amino acid phenylalanine is used to produce 4-coumaryol-CoA, and this is then combined with malonyl-CoA to produce chalcones which are backbones of Flavonoids Chalcones
are aromatic ketones with two phenyl rings that are important in many
biological compounds. The closure of chalcones causes the formation of
the flavonoid structure. Flavonoids are also closely related to flavones
which are actually a sub class of flavonoids, and are the yellow
pigments in plants. In addition to flavones, 11 other subclasses of
Flavonoids including, isoflavones, flavans, flavanones, flavanols,
flavanolols, anthocyanidins, catechins (including proanthocyanidins),
leukoanthocyanidins, dihydrochalcones, and aurones.
Cyanogenic glycoside
Many plants have adapted to iodine-deficient terrestrial environment
by removing iodine from their metabolism, in fact iodine is essential
only for animal cells.
An important antiparasitic action is caused by the block of the transport of iodide of animal cells inhibiting sodium-iodide symporter (NIS). Many plant pesticides are cyanogenic glycoside which liberate cyanide, which, blocking cytochrome c oxidase
and NIS, is poisonous only for a large part of parasites and herbivores
and not for the plant cells in which it seems useful in seed dormancy phase.
To get a better understanding of how secondary metabolites play a big
role in plant defense mechanisms we can focus on the recognizable
defense-related secondary metabolites, cyanogenic glycosides. The
compounds of these secondary metabolites (As seen in Figure 1) are found
in over 2000 plant species. Its structure allows the release of cyanide,
a poison produced by certain bacteria, fungi, and algae that is found
in numerous plants. Animals and humans possess the ability to detoxify
cyanide from their systems naturally. Therefore, cyanogenic glycosides
can be used for positive benefits in animal systems always. For example,
the larvae of the southern armyworm consumes plants that contain this
certain metabolite and have shown a better growth rate with this
metabolite in their diet, as opposed to other secondary
metabolite-containing plants. Although this example shows cyanogenic
glycosides being beneficial to the larvae many still argue that this
metabolite can do harm. To help in determining whether cyanogenic
glycosides are harmful or helpful researchers look closer at its
biosynthetic pathway (Figure 2). Past research suggests that cyanogenic
glucosides stored in the seed of the plant are metabolized during
germination to release nitrogen for seedling to grow. With this, it can
be inferred that cyanogenic glycosides play various roles in plant
metabolism. Though subject to change with future research, there is no
evidence showing that cyanogenic glycosides are responsible for
infections in plants.
Phytic acid
Phytic acid is the main method of phosphorus storage in plant seeds, but is not readily absorbed by many animals (only absorbed by ruminant animals). Not only is phytic acid a phosphorus storage unit, but it also is a source of energy and cations, a natural antioxidant for plants, and can be a source of myoinositol which is one of the preliminary pieces for cell walls.
Phytic acid is also known to bond with many different minerals,
and by doing so prevents those minerals from being absorbed; making
phytic acid an anti-nutrient.
There is a lot of concern with phytic acids in nuts and seeds because
of its anti-nutrient characteristics. In preparing foods with high
phytic acid concentrations, it is recommended they be soaked in after
being ground to increase the surface area. Soaking allows the seed to undergo germination which increases the availability of vitamins and nutrient, while reducing phytic acid and protease inhibitors,
ultimately increasing the nutritional value. Cooking can also reduce
the amount of phytic acid in food but soaking is much more effective.
Phytic acid is an antioxidant
found in plant cells that most likely serves the purpose of
preservation. This preservation is removed when soaked, reducing the
phytic acid and allowing the germination and growth of the seed. When
added to foods it can help prevent discoloration by inhibiting lipid
peroxidation.
There is also some belief that the chelating of phytic acid may have potential use in the treatment of cancer.
Gossypol
Gossypol
has a yellow pigment and is found in cotton plants. It occurs mainly
in the root and/or seeds of different species of cotton plants.
Gossypol can have various chemical structures. It can exist in three
forms: gossypol, gossypol acetic acid, and gossypol formic acid. All of
these forms have very similar biological properties. Gossypol is a type
of aldehyde, meaning that it has a formyl group. The formation of
gossypol occurs through an isoprenoid pathway. Isoprenoid pathways are
common among secondary metabolites.
Gossypol's main function in the cotton plant is to act as an enzyme
inhibitor. An example of gossypol's enzyme inhibition is its ability to
inhibit nicotinamide adenine dinucleotide-linked enzymes of Trypanosoma
cruzi. Trypanosoma cruzi is a parasite which causes Chaga's disease.
For some time it was believed that gossypol was merely a waste
product produced during the processing of cottonseed products.
Extensive studies have shown that gossypol has other functions. Many of
the more popular studies on gossypol discuss how it can act as a male contraceptive. Gossypol has also been linked to causing hypokalemic paralysis. Hypokalemic
paralysis is a disease characterized by muscle weakness or paralysis
with a matching fall in potassium levels in the blood. Hypokalemic
paralysis associated with gossypol in-take usually occurs in March, when
vegetables are in short supply, and in September, when people are
sweating a lot. This side effect of gossypol in-take is very rare
however. Gossypol induced hypokalemic paralysis is easily treatable
with potassium repletion.
Phytoestrogens
Plants synthesize certain compounds called secondary metabolites which
are not naturally produced by humans but can play vital roles in
protection or destruction of human health. One such group of metabolites
is phytoestrogens, found in nuts, oilseeds, soy, and other foods. Phytoestrogens are chemicals which act like the hormone estrogen. Estrogen is important for women's bone and heart health, but high amounts of it has been linked to breast cancer. In the plant, the phytoestrogens are involved in the defense system against fungi.
Phytoestrogens can do two different things in a human body. At low
doses it mimics estrogen, but at high doses it actually blocks the
body's natural estrogen.
The estrogen receptors in the body which are stimulated by estrogen
will acknowledge the phytoestrogen, thus the body may reduce its own
production of the hormone. This has a negative result, because there are
various abilities of the phytoestrogen which estrogen does not do. Its
effects the communication pathways between cells and has effects on
other parts of the body where estrogen normally does not play a role.
It has also been found to induce tumor growth of the estrogen receptor
cells in the breast.
But, one role of estrogens which phytoestrogens mimic is its protective
behavior for the heart. So, an intake of phytoestrogens has also been
seen to reduce the risk of cardiovascular disease. Resveratrol,
a phytoestrogen found in grapes is responsible for this. For example,
the French suffer relatively little heart disease despite the average
French diet being relatively high in fat. One proposed reason for this
is the resveratrol found in red wine, which has been linked to decreased
risk of cardiovascular disease.
Carotenoids
Carotenoids are organic pigments found in the chloroplasts and chromoplasts
of plants. They are also found in some organisms such as algae, fungi,
some bacteria, and certain species of aphids. There are over 600 known
carotenoids. They are split into two classes, xanthophylls and carotenes. Xanthophylls are carotenoids with molecules containing oxygen, such as lutein and zeaxanthin. Carotenes are carotenoids with molecules that are unoxygenated, such as α-carotene, β-carotene and lycopene.
In plants, carotenoids can occur in roots, stems, leaves, flowers, and
fruits. Carotenoids have two important functions in plants. First, they
can contribute to photosynthesis. They do this by transferring some of
the light energy they absorb to chlorophylls,
which then uses this energy for photosynthesis. Second, they can
protect plants which are over-exposed to sunlight. They do this by
harmlessly dissipating excess light energy which they absorb as heat. In
the absence of carotenoids, this excess light energy could destroy
proteins, membranes, and other molecules. Some plant physiologists
believe that carotenoids may have an additional function as regulators
of certain developmental responses in plants. Tetraterpenes
are synthesized from DOXP precursors in plants and some bacteria.
Carotenoids involved in photosynthesis are formed in chloroplasts;
Others are formed in plastids. Carotenoids formed in fungi are
presumably formed from mevalonic acid precursors. Carotenoids are formed
by a head-to-head condensation of geranylgeranyl pyrophosphate or
diphosphate (GGPP) and there is no NADPH requirement.
