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Friday, October 7, 2022

Plant evolutionary developmental biology

From Wikipedia, the free encyclopedia
https://en.wikipedia.org/wiki/Plant_evolutionary_developmental_biology

Evolutionary developmental biology (evo-devo) is the study of developmental programs and patterns from an evolutionary perspective. It seeks to understand the various influences shaping the form and nature of life on the planet. Evo-devo arose as a separate branch of science rather recently. An early sign of this occurred in 1999.

Most of the synthesis in evo-devo has been in the field of animal evolution, one reason being the presence of model systems like Drosophila melanogaster, C. elegans, zebrafish and Xenopus laevis. However, since 1980, a wealth of information on plant morphology, coupled with modern molecular techniques has helped shed light on the conserved and unique developmental patterns in the plant kingdom also.

Historical perspective

Before 1900

Johann Wolfgang von Goethe first used the word morphology.

The origin of the term "morphology" is generally attributed to Johann Wolfgang von Goethe (1749–1832). He was of the opinion that there is an underlying fundamental organisation (Bauplan) in the diversity of flowering plants. In his book The Metamorphosis of Plants, he proposed that the Bauplan enabled us to predict the forms of plants that had not yet been discovered. Goethe was the first to make the perceptive suggestion that flowers consist of modified leaves. He also entertained different complementary interpretations.

In the middle centuries, several basic foundations of our current understanding of plant morphology were laid down. Nehemiah Grew, Marcello Malpighi, Robert Hooke, Antonie van Leeuwenhoek, Wilhelm von Nageli were just some of the people who helped build knowledge on plant morphology at various levels of organisation. It was the taxonomical classification of Carl Linnaeus in the eighteenth century though, that generated a firm base for the knowledge to stand on and expand. The introduction of the concept of Darwinism in contemporary scientific discourse also had had an effect on the thinking on plant forms and their evolution.

Wilhelm Hofmeister, one of the most brilliant botanists of his times, was the one to diverge away from the idealist way of pursuing botany. Over the course of his life, he brought an interdisciplinary outlook into botanical thinking. He came up with biophysical explanations on phenomena like phototaxis and geotaxis, and also discovered the alternation of generations in the plant life cycle.

1900 to the present

Arabidopsis thaliana, a flowering plant that has been a model system for most of plant molecular studies

The past century witnessed a rapid progress in the study of plant anatomy. The focus shifted from the population level to more reductionist levels. While the first half of the century saw expansion in developmental knowledge at the tissue and the organ level, in the latter half, especially since the 1990s, there has also been a strong impetus on gaining molecular information.

Edward Charles Jeffrey was one of the early evo-devo researchers of the 20th century. He performed a comparative analyses of the vasculatures of living and fossil gymnosperms and came to the conclusion that the storage parenchyma has been derived from tracheids. His research focussed primarily on plant anatomy in the context of phylogeny. This tradition of evolutionary analyses of plant architectures was further advanced by Katherine Esau, best known for her book The Plant Anatomy. Her work focussed on the origin and development of various tissues in different plants. Working with Vernon Cheadle, she also explained the evolutionary specialization of the phloem tissue with respect to its function.

In 1959 Walter Zimmermann published a revised edition of Die Phylogenie der Planzen. This very comprehensive work, which has not been translated into English, has no equal in the literature. It presents plant evolution as the evolution of plant development (hologeny). In this sense it is plant evolutionary developmental biology (plant evo-devo). According to Zimmermann, diversity in plant evolution occurs though various developmental processes. Three very basic processes are heterochrony (changes in the timing of developmental processes), heterotopy (changes in the relative positioning of processes), and heteromorphy (changes in form processes).

In the meantime, by the beginning of the latter half of the 1900s, Arabidopsis thaliana had begun to be used in some developmental studies. The first collection of Arabidopsis thaliana mutants were made around 1945. However it formally became established as a model organism only in 1998.

The recent spurt in information on various plant-related processes has largely been a result of the revolution in molecular biology. Powerful techniques like mutagenesis and complementation were made possible in Arabidopsis thaliana via generation of T-DNA containing mutant lines, recombinant plasmids, techniques like transposon tagging etc. Availability of complete physical and genetic maps, RNAi vectors, and rapid transformation protocols are some of the technologies that have significantly altered the scope of the field. Recently, there has also been a massive increase in the genome and EST sequences of various non-model species, which, coupled with the bioinformatics tools existing today, generate opportunities in the field of plant evo-devo research.

Gérard Cusset provided a detailed in-depth analysis of the history of plant morphology, including plant development and evolution, from its beginnings to the end of the 20th century. Rolf Sattler discussed fundamental principles of plant morphology.

Organisms, databases and tools

The sampling of the Floral Genome Project

The most important model systems in plant development have been arabidopsis and maize. Maize has traditionally been the favorite of plant geneticists, while extensive resources in almost every area of plant physiology and development are available for Arabidopsis thaliana. Apart from these, rice, Antirrhinum majus, Brassica, and tomato are also being used in a variety of studies. The genomes of Arabidopsis thaliana and rice have been completely sequenced, while the others are in process. It must be emphasized here that the information from these "model" organisms form the basis of our developmental knowledge. While Brassica has been used primarily because of its convenient location in the phylogenetic tree in the mustard family, Antirrhinum majus is a convenient system for studying leaf architecture. Rice has been traditionally used for studying responses to hormones like abscissic acid and gibberelin as well as responses to stress. However, recently, not just the domesticated rice strain, but also the wild strains have been studied for their underlying genetic architectures.

Some people have objected against extending the results of model organisms to the plant world. One argument is that the effect of gene knockouts in lab conditions wouldn't truly reflect even the same plant's response in the natural world. Also, these supposedly crucial genes might not be responsible for the evolutionary origin of that character. For these reasons, a comparative study of plant traits has been proposed as the way to go now.

Since the past few years, researchers have indeed begun looking at non-model, "non-conventional" organisms using modern genetic tools. One example of this is the Floral Genome Project, which envisages to study the evolution of the current patterns in the genetic architecture of the flower through comparative genetic analyses, with a focus on EST sequences. Like the FGP, there are several such ongoing projects that aim to find out conserved and diverse patterns in evolution of the plant shape. Expressed sequence tag (EST) sequences of quite a few non-model plants like sugarcane, apple, barley, cycas, coffee, to name a few, are available freely online. The Cycad Genomics Project, for example, aims to understand the differences in structure and function of genes between gymnosperms and angiosperms through sampling in the order Cycadales. In the process, it intends to make available information for the study of evolution of seeds, cones and evolution of life cycle patterns. Presently the most important sequenced genomes from an evo-devo point of view include those of A. thaliana (a flowering plant), poplar (a woody plant), Physcomitrella patens (a bryophyte), Maize (extensive genetic information), and Chlamydomonas reinhardtii (a green alga). The impact of such a vast amount of information on understanding common underlying developmental mechanisms can easily be realised.

Apart from EST and genome sequences, several other tools like PCR, yeast two-hybrid system, microarrays, RNA Interference, SAGE, QTL mapping etc. permit the rapid study of plant developmental patterns. Recently, cross-species hybridization has begun to be employed on microarray chips, to study the conservation and divergence in mRNA expression patterns between closely related species.[25] Techniques for analyzing this kind of data have also progressed over the past decade. We now have better models for molecular evolution, more refined analysis algorithms and better computing power as a result of advances in computer sciences.

Evolution of plant morphology

Overview of plant evolution

Evidence suggests that an algal scum formed on the land 1,200 million years ago, but it was not until the Ordovician period, around 500 million years ago, that land plants appeared. These began to diversify in the late Silurian period, around 420 million years ago, and the fruits of their diversification are displayed in remarkable detail in an early Devonian fossil assemblage known as the Rhynie chert. This chert preserved early plants in cellular detail, petrified in volcanic springs. By the middle of the Devonian period most of the features recognised in plants today are present, including roots and leaves. By the late Devonian, plants had reached a degree of sophistication that allowed them to form forests of tall trees. Evolutionary innovation continued after the Devonian period. Most plant groups were relatively unscathed by the Permo-Triassic extinction event, although the structures of communities changed. This may have set the scene for the evolution of flowering plants in the Triassic (~200 million years ago), which exploded the Cretaceous and Tertiary. The latest major group of plants to evolve were the grasses, which became important in the mid Tertiary, from around 40 million years ago. The grasses, as well as many other groups, evolved new mechanisms of metabolism to survive the low CO2 and warm, dry conditions of the tropics over the last 10 million years. Although animals and plants evolved their bodyplan independently, they both express a developmental constraint during mid-embryogenesis that limits their morphological diversification.

Meristems

The meristem architectures differ between angiosperms, gymnosperms and pteridophytes. The gymnosperm vegetative meristem lacks organization into distinct tunica and corpus layers. They possess large cells called central mother cells. In angiosperms, the outermost layer of cells divides anticlinally to generate the new cells, while in gymnosperms, the plane of division in the meristem differs for different cells. However, the apical cells do contain organelles like large vacuoles and starch grains, like the angiosperm meristematic cells.

Pteridophytes, like fern, on the other hand, do not possess a multicellular apical meristem. They possess a tetrahedral apical cell, which goes on to form the plant body. Any somatic mutation in this cell can lead to hereditary transmission of that mutation. The earliest meristem-like organization is seen in an algal organism from group Charales that has a single dividing cell at the tip, much like the pteridophytes, yet simpler. One can thus see a clear pattern in evolution of the meristematic tissue, from pteridophytes to angiosperms: Pteridophytes, with a single meristematic cell; gymnosperms with a multicellular, but less defined organization; and finally, angiosperms, with the highest degree of organization.

Evolution of plant transcriptional regulation

Transcription factors and transcriptional regulatory networks play key roles in plant development and stress responses, as well as their evolution. During plant landing, many novel transcription factor families emerged and are preferentially wired into the networks of multicellular development, reproduction, and organ development, contributing to more complex morphogenesis of land plants.

Evolution of leaves

Origins of the leaf

Leaf lamina. The leaf architecture probably arose multiple times in the plant lineage

Leaves are the primary photosynthetic organs of a plant. Based on their structure, they are classified into two types - microphylls, that lack complex venation patterns and megaphylls, that are large and with a complex venation. It has been proposed that these structures arose independently. Megaphylls, according to the telome theory, have evolved from plants that showed a three-dimensional branching architecture, through three transformations: planation, which involved formation of a planar architecture, webbing, or formation of the outgrowths between the planar branches and fusion, where these webbed outgrowths fused to form a proper leaf lamina. Studies have revealed that these three steps happened multiple times in the evolution of today's leaves.

Contrary to the telome theory, developmental studies of compound leaves have shown that, unlike simple leaves, compound leaves branch in three dimensions. Consequently, they appear partially homologous with shoots as postulated by Agnes Arber in her partial-shoot theory of the leaf. They appear to be part of a continuum between morphological categories, especially those of leaf and shoot. Molecular genetics confirmed these conclusions (see below).

It has been proposed that the before the evolution of leaves, plants had the photosynthetic apparatus on the stems. Today's megaphyll leaves probably became commonplace some 360 mya, about 40 my after the simple leafless plants had colonized the land in the early Devonian period. This spread has been linked to the fall in the atmospheric carbon dioxide concentrations in the late Paleozoic era associated with a rise in density of stomata on leaf surface. This must have allowed for better transpiration rates and gas exchange. Large leaves with less stomata would have heated up in the sun's rays, but an increased stomatal density allowed for a better-cooled leaf, thus making its spread feasible.

Factors influencing leaf architectures

Various physical and physiological forces like light intensity, humidity, temperature, wind speeds etc. are thought to have influenced evolution of leaf shape and size. It is observed that high trees rarely have large leaves, owing to the obstruction they generate for winds. This obstruction can eventually lead to the tearing of leaves, if they are large. Similarly, trees that grow in temperate or taiga regions have pointed leaves, presumably to prevent nucleation of ice onto the leaf surface and reduce water loss due to transpiration. Herbivory, not only by large mammals, but also small insects has been implicated as a driving force in leaf evolution, an example being plants of the genus Aciphylla, that are commonly found in New Zealand. The now-extinct moas (birds) fed upon these plants, and the spines on the leaves probably discouraged the moas from feeding on them. Other members of Aciphylla that did not co-exist with the moas were spineless.

Genetic evidences for leaf evolution

At the genetic level, developmental studies have shown that repression of the KNOX genes is required for initiation of the leaf primordium. This is brought about by ARP genes, which encode transcription factors. Genes of this type have been found in many plants studied till now, and the mechanism i.e. repression of KNOX genes in leaf primordia, seems to be quite conserved. Expression of KNOX genes in leaves produces complex leaves. It is speculated that the ARP function arose quite early in vascular plant evolution, because members of the primitive group lycophytes also have a functionally similar gene  Other players that have a conserved role in defining leaf primordia are the phytohormone auxin, gibberelin and cytokinin.

The diversity of leaves

One feature of a plant is its phyllotaxy. The arrangement of leaves on the plant body is such that the plant can maximally harvest light under the given constraints, and hence, one might expect the trait to be genetically robust. However, it may not be so. In maize, a mutation in only one gene called abphyl (abnormal phyllotaxy) was enough to change the phyllotaxy of the leaves. It implies that sometimes, mutational tweaking of a single locus on the genome is enough to generate diversity. The abphyl gene was later on shown to encode a cytokinin response regulator protein.

Once the leaf primordial cells are established from the SAM cells, the new axes for leaf growth are defined, one important (and more studied) among them being the abaxial-adaxial (lower-upper surface) axes. The genes involved in defining this, and the other axes seem to be more or less conserved among higher plants. Proteins of the HD-ZIPIII family have been implicated in defining the adaxial identity. These proteins deviate some cells in the leaf primordium from the default abaxial state, and make them adaxial. It is believed that in early plants with leaves, the leaves just had one type of surface - the abaxial one. This is the underside of today's leaves. The definition of the adaxial identity occurred some 200 million years after the abaxial identity was established. One can thus imagine the early leaves as an intermediate stage in evolution of today's leaves, having just arisen from spiny stem-like outgrowths of their leafless ancestors, covered with stomata all over, and not optimized as much for light harvesting.

How the infinite variety of plant leaves is generated is a subject of intense research. Some common themes have emerged. One of the most significant is the involvement of KNOX genes in generating compound leaves, as in tomato (see above). But this again is not universal. For example, pea uses a different mechanism for doing the same thing. Mutations in genes affecting leaf curvature can also change leaf form, by changing the leaf from flat, to a crinkly shape, like the shape of cabbage leaves. There also exist different morphogen gradients in a developing leaf which define the leaf's axis. Changes in these morphogen gradients may also affect the leaf form. Another very important class of regulators of leaf development are the microRNAs, whose role in this process has just begun to be documented. The coming years should see a rapid development in comparative studies on leaf development, with many EST sequences involved in the process coming online.

Molecular genetics has also shed light on the relation between radial symmetry (characteristic of stems) and dorsiventral symmetry (typical for leaves). James (2009) stated that "it is now widely accepted that... radiality [characteristic of most shoots] and dorsiventrality [characteristic of leaves] are but extremes of a continuous spectrum. In fact, it is simply the timing of the KNOX gene expression!" In fact there is evidence for this continuum already at the beginning of land plant evolution. Furthermore, studies in molecular genetics confirmed that compound leaves are intermediate between simple leaves and shoots, that is, they are partially homologous with simple leaves and shoots, since "it is now generally accepted that compound leaves express both leaf and shoot properties”. This conclusion was reached by several authors on purely morphological grounds.

Evolution of flowers

The pollen-bearing organs of the early flower Crossotheca

Flower-like structures first appear in the fossil records some ~130 mya, in the Cretaceous era.

The flowering plants have long been assumed to have evolved from within the gymnosperms; according to the traditional morphological view, they are closely allied to the gnetales. However, recent molecular evidence is at odds to this hypothesis, and further suggests that gnetales are more closely related to some gymnosperm groups than angiosperms, and that gymnosperms form a distinct clade to the angiosperms. Molecular clock analysis predicts the divergence of flowering plants (anthophytes) and gymnosperms to ~300 mya.

The main function of a flower is reproduction, which, before the evolution of the flower and angiosperms, was the job of microsporophylls and megasporophylls. A flower can be considered a powerful evolutionary innovation, because its presence allowed the plant world to access new means and mechanisms for reproduction.

Origins of the flower

It seems that on the level of the organ, the leaf may be the ancestor of the flower, or at least some floral organs. When we mutate some crucial genes involved in flower development, we end up with a cluster of leaf-like structures. Thus, sometime in history, the developmental program leading to formation of a leaf must have been altered to generate a flower. There probably also exists an overall robust framework within which the floral diversity has been generated. An example of that is a gene called LEAFY (LFY), which is involved in flower development in Arabidopsis thaliana. The homologs of this gene are found in angiosperms as diverse as tomato, snapdragon, pea, maize and even gymnosperms. Expression of Arabidopsis thaliana LFY in distant plants like poplar and citrus also results in flower-production in these plants. The LFY gene regulates the expression of some gene belonging to the MADS-box family. These genes, in turn, act as direct controllers of flower development.

Evolution of the MADS-box family

The members of the MADS-box family of transcription factors play a very important and evolutionarily conserved role in flower development. According to the ABC model of flower development, three zones - A, B and C - are generated within the developing flower primordium, by the action of some transcription factors, that are members of the MADS-box family. Among these, the functions of the B and C domain genes have been evolutionarily more conserved than the A domain gene. Many of these genes have arisen through gene duplications of ancestral members of this family. Quite a few of them show redundant functions.

The evolution of the MADS-box family has been extensively studied. These genes are present even in pteridophytes, but the spread and diversity is many times higher in angiosperms. There appears to be quite a bit of pattern into how this family has evolved. Consider the evolution of the C-region gene AGAMOUS (AG). It is expressed in today's flowers in the stamens, and the carpel, which are reproductive organs. It's ancestor in gymnosperms also has the same expression pattern. Here, it is expressed in the strobili, an organ that produces pollens or ovules. Similarly, the B-genes' (AP3 and PI) ancestors are expressed only in the male organs in gymnosperms. Their descendants in the modern angiosperms also are expressed only in the stamens, the male reproductive organ. Thus, the same, then-existing components were used by the plants in a novel manner to generate the first flower. This is a recurring pattern in evolution.

Factors influencing floral diversity

The various shapes and colors of flowers

How is the enormous diversity in the shape, color and sizes of flowers established? There is enormous variation in the developmental program in different plants. For example, monocots possess structures like lodicules and palea, that were believed to be analogous to the dicot petals and carpels respectively. It turns out that this is true, and the variation is due to slight changes in the MADS-box genes and their expression pattern in the monocots. Another example is that of the toad-flax, Linaria vulgaris, which has two kinds of flower symmetries: radial and bilateral. These symmetries are due to changes in copy number, timing, and location of expression in CYCLOIDEA, which is related to TCP1 in Arabidopsis. 

The large number of petals in roses has probably been a result of human selection.

Arabidopsis thaliana has a gene called AGAMOUS that plays an important role in defining how many petals and sepals and other organs are generated. Mutations in this gene give rise to the floral meristem obtaining an indeterminate fate, and many floral organs keep on getting produced. We have flowers like roses, carnations and morning glory, for example, that have very dense floral organs. These flowers have been selected by horticulturists since long for increased number of petals. Researchers have found that the morphology of these flowers is because of strong mutations in the AGAMOUS homolog in these plants, which leads to them making a large number of petals and sepals. Several studies on diverse plants like petunia, tomato, impatiens, maize etc. have suggested that the enormous diversity of flowers is a result of small changes in genes controlling their development.

Some of these changes also cause changes in expression patterns of the developmental genes, resulting in different phenotypes. The Floral Genome Project looked at the EST data from various tissues of many flowering plants. The researchers confirmed that the ABC Model of flower development is not conserved across all angiosperms. Sometimes expression domains change, as in the case of many monocots, and also in some basal angiosperms like Amborella. Different models of flower development like the fading boundaries model, or the overlapping-boundaries model which propose non-rigid domains of expression, may explain these architectures. There is a possibility that from the basal to the modern angiosperms, the domains of floral architecture have gotten more and more fixed through evolution.

Flowering time

Another floral feature that has been a subject of natural selection is flowering time. Some plants flower early in their life cycle, others require a period of vernalization before flowering. This decision is based on factors like temperature, light intensity, presence of pollinators and other environmental signals. In Arabidopsis thaliana it is known that genes like CONSTANS (CO), FRIGIDA, Flowering Locus C (FLC) and FLOWERING LOCUS T (FT) integrate the environmental signals and initiate the flower development pathway. Allelic variation in these loci have been associated with flowering time variations between plants. For example, Arabidopsis thaliana ecotypes that grow in the cold temperate regions require prolonged vernalization before they flower, while the tropical varieties and common lab strains, do not. Much of this variation is due to mutations in the FLC and FRIGIDA genes, rendering them non-functional.

Many genes in the flowering time pathway are conserved across all plants studied to date. However, this does not mean that the mechanism of action is similarly conserved. For example, the monocot rice accelerates its flowering in short-day conditions, while Arabidopsis thaliana, a eudicot, responds to long-day conditions. In both plants, the proteins CO and FT are present but in Arabidopsis thaliana CO enhances FT production, while in rice the CO homolog represses FT production, resulting in completely opposite downstream effects.

Theories of flower evolution

There are many theories that propose how flowers evolved. Some of them are described below.

The Anthophyte Theory was based on the observation that a gymnospermic family Gnetaceae has a flower-like ovule. It has partially developed vessels as found in the angiosperms, and the megasporangium is covered by three envelopes, like the ovary structure of angiosperm flowers. However, many other lines of evidence show that gnetophytes are not related to angiosperms.

The Mostly Male Theory has a more genetic basis. Proponents of this theory point out that the gymnosperms have two very similar copies of the gene LFY while angiosperms only have one. Molecular clock analysis has shown that the other LFY paralog was lost in angiosperms around the same time as flower fossils become abundant, suggesting that this event might have led to floral evolution. According to this theory, loss of one of the LFY paralog led to flowers that were more male, with the ovules being expressed ectopically. These ovules initially performed the function of attracting pollinators, but sometime later, may have been integrated into the core flower.

Evolution of secondary metabolism

Structure of azadirachtin, a terpenoid produced by the neem plant, which helps ward off microbes and insects. Many secondary metabolites have complex structures.

Plant secondary metabolites are low molecular weight compounds, sometimes with complex structures that have no essential role in primary metabolism. They function in processes such as anti-herbivory, pollinator attraction, communication between plants, allelopathy, maintenance of symbiotic associations with soil flora and enhancing the rate of fertilization. Secondary metabolites have great structural and functional diversity and many thousands of enzymes may be involved in their synthesis, coded for by as much as 15–25% of the genome. Many plant secondary metabolites such as the colour and flavor components of saffron and the chemotherapeutic drug taxol are of culinary and medical significance to humans and are therefore of commercial importance. In plants they seem to have diversified using mechanisms such as gene duplications, evolution of novel genes and the development of novel biosynthetic pathways. Studies have shown that diversity in some of these compounds may be positively selected for. Cyanogenic glycosides may have been proposed to have evolved multiple times in different plant lineages, and there are several other instances of convergent evolution. For example, the enzymes for synthesis of limonene – a terpene – are more similar between angiosperms and gymnosperms than to their own terpene synthesis enzymes. This suggests independent evolution of the limonene biosynthetic pathway in these two lineages.

Mechanisms and players in evolution

While environmental factors are significantly responsible for evolutionary change, they act merely as agents for natural selection. Some of the changes develop through interactions with pathogens. Change is inherently brought about via phenomena at the genetic level – mutations, chromosomal rearrangements and epigenetic changes. While the general types of mutations hold true across the living world, in plants, some other mechanisms have been implicated as highly significant.

Polyploidy is a very common feature in plants. It is believed that at least half plants are or have been polyploids. Polyploidy leads to genome doubling, thus generating functional redundancy in most genes. The duplicated genes may attain new function, either by changes in expression pattern or changes in activity. Polyploidy and gene duplication are believed to be among the most powerful forces in evolution of plant form. It is not known though, why genome doubling is such a frequent process in plants. One possible reason is the production of large amounts of secondary metabolites in plant cells. Some of them might interfere in the normal process of chromosomal segregation, leading to polypoidy.

Top: teosinte; bottom: maize; middle: maize-teosinte hybrid

In recent times, plants have been shown to possess significant microRNA families, which are conserved across many plant lineages. In comparison to animals, while the number of plant miRNA families is less, the size of each family is much larger. The miRNA genes are also much more spread out in the genome than those in animals, where they are found clustered. It has been proposed that these miRNA families have expanded by duplications of chromosomal regions. Many miRNA genes involved in regulation of plant development have been found to be quite conserved between plants studied.

Domestication of plants such as maize, rice, barley, wheat etc. has also been a significant driving force in their evolution. Some studies have looked at the origins of the maize plant and found that maize is a domesticated derivative of a wild plant from Mexico called teosinte. Teosinte belongs to the genus Zea, just as maize, but bears very small inflorescence, 5–10 hard cobs, and a highly branched and spread-out stem.

CauliflowerBrassica oleracea var. botrytis

Crosses between a particular teosinte variety and maize yield fertile offspring that are intermediate in phenotype between maize and teosinte. QTL analysis has also revealed some loci that when mutated in maize yield a teosinte-like stem or teosinte-like cobs. Molecular clock analysis of these genes estimates their origins to some 9000 years ago, well in accordance with other records of maize domestication. It is believed that a small group of farmers must have selected some maize-like natural mutant of teosinte some 9000 years ago in Mexico, and subjected it to continuous selection to yield the maize plant as known today.

Another case is that of cauliflower. The edible cauliflower is a domesticated version of the wild plant Brassica oleracea, which does not possess the dense undifferentiated inflorescence, called the curd, that cauliflower possesses.

Cauliflower possesses a single mutation in a gene called CAL, controlling meristem differentiation into inflorescence. This causes the cells at the floral meristem to gain an undifferentiated identity, and instead of growing into a flower, they grow into a lump of undifferentiated cells. This mutation has been selected through domestication at least since the Greek empire.

Thursday, October 6, 2022

Cascading failure

From Wikipedia, the free encyclopedia
 
An animation demonstrating how a single failure may result in other failures throughout a network.

A cascading failure is a failure in a system of interconnected parts in which the failure of one or few parts leads to the failure of other parts, growing progressively as a result of positive feedback. This can occur when a single part fails, increasing the probability that other portions of the system fail. Such a failure may happen in many types of systems, including power transmission, computer networking, finance, transportation systems, organisms, the human body, and ecosystems.

Cascading failures may occur when one part of the system fails. When this happens, other parts must then compensate for the failed component. This in turn overloads these nodes, causing them to fail as well, prompting additional nodes to fail one after another.

In power transmission

Cascading failure is common in power grids when one of the elements fails (completely or partially) and shifts its load to nearby elements in the system. Those nearby elements are then pushed beyond their capacity so they become overloaded and shift their load onto other elements. Cascading failure is a common effect seen in high voltage systems, where a single point of failure (SPF) on a fully loaded or slightly overloaded system results in a sudden spike across all nodes of the system. This surge current can induce the already overloaded nodes into failure, setting off more overloads and thereby taking down the entire system in a very short time.

This failure process cascades through the elements of the system like a ripple on a pond and continues until substantially all of the elements in the system are compromised and/or the system becomes functionally disconnected from the source of its load. For example, under certain conditions a large power grid can collapse after the failure of a single transformer.

Monitoring the operation of a system, in real-time, and judicious disconnection of parts can help stop a cascade. Another common technique is to calculate a safety margin for the system by computer simulation of possible failures, to establish safe operating levels below which none of the calculated scenarios is predicted to cause cascading failure, and to identify the parts of the network which are most likely to cause cascading failures.

One of the primary problems with preventing electrical grid failures is that the speed of the control signal is no faster than the speed of the propagating power overload, i.e. since both the control signal and the electrical power are moving at the same speed, it is not possible to isolate the outage by sending a warning ahead to isolate the element.

Examples

Cascading failure caused the following power outages:

In computer networks

Cascading failures can also occur in computer networks (such as the Internet) in which network traffic is severely impaired or halted to or between larger sections of the network, caused by failing or disconnected hardware or software. In this context, the cascading failure is known by the term cascade failure. A cascade failure can affect large groups of people and systems.

The cause of a cascade failure is usually the overloading of a single, crucial router or node, which causes the node to go down, even briefly. It can also be caused by taking a node down for maintenance or upgrades. In either case, traffic is routed to or through another (alternative) path. This alternative path, as a result, becomes overloaded, causing it to go down, and so on. It will also affect systems which depend on the node for regular operation.

Symptoms

The symptoms of a cascade failure include: packet loss and high network latency, not just to single systems, but to whole sections of a network or the internet. The high latency and packet loss is caused by the nodes that fail to operate due to congestion collapse, which causes them to still be present in the network but without much or any useful communication going through them. As a result, routes can still be considered valid, without them actually providing communication.

If enough routes go down because of a cascade failure, a complete section of the network or internet can become unreachable. Although undesired, this can help speed up the recovery from this failure as connections will time out, and other nodes will give up trying to establish connections to the section(s) that have become cut off, decreasing load on the involved nodes.

A common occurrence during a cascade failure is a walking failure, where sections go down, causing the next section to fail, after which the first section comes back up. This ripple can make several passes through the same sections or connecting nodes before stability is restored.

History

Cascade failures are a relatively recent development, with the massive increase in traffic and the high interconnectivity between systems and networks. The term was first applied in this context in the late 1990s by a Dutch IT professional and has slowly become a relatively common term for this kind of large-scale failure.

Example

Network failures typically start when a single network node fails. Initially, the traffic that would normally go through the node is stopped. Systems and users get errors about not being able to reach hosts. Usually, the redundant systems of an ISP respond very quickly, choosing another path through a different backbone. The routing path through this alternative route is longer, with more hops and subsequently going through more systems that normally do not process the amount of traffic suddenly offered.

This can cause one or more systems along the alternative route to go down, creating similar problems of their own.

Related systems are also affected in this case. As an example, DNS resolution might fail and what would normally cause systems to be interconnected, might break connections that are not even directly involved in the actual systems that went down. This, in turn, may cause seemingly unrelated nodes to develop problems, that can cause another cascade failure all on its own.

In December 2012, a partial loss (40%) of Gmail service occurred globally, for 18 minutes. This loss of service was caused by a routine update of load balancing software which contained faulty logic—in this case, the error was caused by logic using an inappropriate 'all' instead of the more appropriate 'some'. The cascading error was fixed by fully updating a single node in the network instead of partially updating all nodes at one time.

Cascading structural failure

Certain load-bearing structures with discrete structural components can be subject to the "zipper effect", where the failure of a single structural member increases the load on adjacent members. In the case of the Hyatt Regency walkway collapse, a suspended walkway (which was already overstressed due to an error in construction) failed when a single vertical suspension rod failed, overloading the neighboring rods which failed sequentially (i.e. like a zipper). A bridge that can have such a failure is called fracture critical, and numerous bridge collapses have been caused by the failure of a single part. Properly designed structures use an adequate factor of safety and/or alternate load paths to prevent this type of mechanical cascade failure.

Other examples

Biology

Biochemical cascades exist in biology, where a small reaction can have system-wide implications. One negative example is ischemic cascade, in which a small ischemic attack releases toxins which kill off far more cells than the initial damage, resulting in more toxins being released. Current research is to find a way to block this cascade in stroke patients to minimize the damage.

In the study of extinction, sometimes the extinction of one species will cause many other extinctions to happen. Such a species is known as a keystone species.

Electronics

Another example is the Cockcroft–Walton generator, which can also experience cascade failures wherein one failed diode can result in all the diodes failing in a fraction of a second.

Yet another example of this effect in a scientific experiment was the implosion in 2001 of several thousand fragile glass photomultiplier tubes used in the Super-Kamiokande experiment, where the shock wave caused by the failure of a single detector appears to have triggered the implosion of the other detectors in a chain reaction.

Finance

In finance, the risk of cascading failures of financial institutions is referred to as systemic risk: the failure of one financial institution may cause other financial institutions (its counterparties) to fail, cascading throughout the system. Institutions that are believed to pose systemic risk are deemed either "too big to fail" (TBTF) or "too interconnected to fail" (TICTF), depending on why they appear to pose a threat.

Note however that systemic risk is not due to individual institutions per se, but due to the interconnections. Frameworks to study and predict the effects of cascading failures have been developed in the research literature.

A related (though distinct) type of cascading failure in finance occurs in the stock market, exemplified by the 2010 Flash Crash.

Interdependent cascading failures

Illustration of the interdependent relationship among different infrastructures

Diverse infrastructures such as water supply, transportation, fuel and power stations are coupled together and depend on each other for functioning, see Fig. 1. Owing to this coupling, interdependent networks are extremely sensitive to random failures, and in particular to targeted attacks, such that a failure of a small fraction of nodes in one network can trigger an iterative cascade of failures in several interdependent networks. Electrical blackouts frequently result from a cascade of failures between interdependent networks, and the problem has been dramatically exemplified by the several large-scale blackouts that have occurred in recent years. Blackouts are a fascinating demonstration of the important role played by the dependencies between networks. For example, the 2003 Italy blackout resulted in a widespread failure of the railway network, health care systems, and financial services and, in addition, severely influenced the telecommunication networks. The partial failure of the communication system in turn further impaired the electrical grid management system, thus producing a positive feedback on the power grid. This example emphasizes how inter-dependence can significantly magnify the damage in an interacting network system.

Model for overload cascading failures

A model for cascading failures due to overload propagation is the Motter–Lai model.

Geopolymer cement

From Wikipedia, the free encyclopedia

Geopolymer cement is a binding system that hardens at room temperature.

List of the minerals, chemicals used for making geopolymer cements

It is a more environmentally friendly alternative to conventional Portland cement. It relies on minimally processed natural materials or industrial byproducts to significantly reduce the carbon footprint of cement production, while also being highly resistant to many common concrete durability issues.

Geopolymer cements exist which may cure more rapidly than Portland-based cements.

Production

Production of geopolymer cement requires an aluminosilicate precursor material such as metakaolin or fly ash, a user-friendly alkaline reagent (for example, sodium or potassium soluble silicates with a molar ratio MR SiO2:M2O ≥ 1.65, M being Na or K) and water (See the definition for "user-friendly" reagent below). Room temperature hardening is more readily achieved with the addition of a source of calcium cations, often blast furnace slag.

Geopolymer cements can be formulated to cure more rapidly than Portland-based cements; some mixes gain most of their ultimate strength within 24 hours. However, they must also set slowly enough that they can be mixed at a batch plant, either for precasting or delivery in a concrete mixer. Geopolymer cement also has the ability to form a strong chemical bond with silicate rock-based aggregates. In March 2010, the US Department of Transportation Federal Highway Administration released a TechBrief titled Geopolymer Concrete that states:

The production of versatile, cost-effective geopolymer cements that can be mixed and hardened essentially like Portland cement would represent a game changing advancement, revolutionizing the construction of transportation infrastructure and the building industry.

Geopolymer concrete

There is often confusion between the meanings of the terms 'geopolymer cement' and 'geopolymer concrete'. A cement is a binder, whereas concrete is the composite material resulting from the mixing and hardening of cement with water (or an alkaline solution in the case of geopolymer cement), and stone aggregates. Materials of both types (geopolymer cements and geopolymer concretes) are commercially available in various markets internationally. 

Chemistry: Portland cement vs Geopolymer cement

Portland cement chemistry compared to geopolymerization GP

Left: hardening of Portland cement (P.C.) through hydration of calcium silicate into calcium silicate hydrate (C-S-H) and portlandite, Ca(OH)2.

Right: hardening (setting) of geopolymer cement (GP) through poly-condensation of potassium oligo-(sialate-siloxo) into potassium poly(sialate-siloxo) cross linked network.

If a geopolymer compound requires heat setting it is not called geopolymer cement but rather geopolymer binder.

Alkali-activated materials vs. geopolymer cements.

Geopolymerization chemistry requires appropriate terminologies and notions that are evidently different from those in use by Portland cement experts. The main article geopolymer summarizes how geopolymer cements belong to the category of inorganic polymer. On this matter, the Australian Geopolymer Alliance outlines on its web site the following statement: "Joseph Davidovits developed the notion of a geopolymer (a Si/Al inorganic polymer) to better explain these chemical processes and the resultant material properties. To do so required a major shift in perspective, away from the classical crystalline hydration chemistry of conventional cement chemistry. To date this shift has not been well accepted by practitioners in the field of alkali activated cements who still tend to explain such reaction chemistry in Portland cement terminology.

Indeed, geopolymer cement is sometimes mistaken for alkali-activated cement and concrete, developed more than 50 years ago by V.D. Glukhovsky in Ukraine, the former Soviet Union. They were originally known under the names "soil silicate concretes" and "soil cements". Because Portland cement concretes can be affected by the deleterious Alkali-aggregate reaction, coined AAR or Alkali-silica reaction coined ASR (see for example the RILEM Committee 219-ACS Aggregate Reaction in Concrete Structures), the wording alkali-activation has a negative impact on civil engineers. However, geopolymer cements do not in general show these deleterious reactions (see below in Properties), when an appropriate aggregate is selected - geopolymers can also work in acidic mediums, further disassociating them from AAM. In addition, alkali-activated materials are not polymers, so they cannot be called and mistaken for geopolymers. Indeed, the polymer chemistry is radically different compared to the calcium hydrate or precipitate chemistry. Nevertheless, several cement scientists continue to promote the terminology related to alkali-activated materials or alkali-activated geopolymers. These cements, abbreviated AAM, encompass the specific fields of alkali-activated slags, alkali-activated coal fly ashes, and various blended cementing systems (see RILEM Technical committee 247-DTA).

User-friendly alkaline-reagents

List of user-hostile and user-friendly chemical reagents

Although geopolymerization does not rely on toxic organic solvents but only on water, it needs chemical ingredients that may be dangerous and therefore requires some safety procedures. Material Safety rules classify the alkaline products in two categories: corrosive products (named here: hostile) and irritant products (named here: friendly). The two classes are recognizable through their respective logos.

The table lists some alkaline chemicals and their corresponding safety label. The corrosive products must be handled with gloves, glasses and masks. They are user-hostile and cannot be implemented in mass applications without the appropriate safety procedures. In the second category one finds Portland cement or hydrated lime, typical mass products. Geopolymeric alkaline reagents belonging to this class may also be termed as User-friendly, although the irritant nature of the alkaline component and the potential inhalation risk of powders still require the selection and use of appropriate personal protective equipment, as in any situation where chemicals or powders are handled.

The development of so-called alkali-activated-cements or alkali-activated geopolymers (the latter considered by some to be incorrect terminology), as well as several recipes found in the literature and on the Internet, especially those based on fly ashes, use alkali silicates with molar ratios SiO2:M2O below 1.20, or systems based on pure NaOH (8M or 12M). These conditions are not user-friendly for the ordinary labor force, and require careful consideration of personal protective equipment if employed in the field. Indeed, laws, regulations, and state directives push to enforce for more health protections and security protocols for workers’ safety.

Conversely, Geopolymer cement recipes employed in the field generally involve alkaline soluble silicates with starting molar ratios ranging from 1.45 to 1.95, particularly 1.60 to 1.85, i.e. user-friendly conditions. It may happen that for research, some laboratory recipes have molar ratios in the 1.20 to 1.45 range.

Geopolymer cement categories

Categories of geopolymer cement include:

  • Slag-based geopolymer cement.
  • Rock-based geopolymer cement.
  • Fly ash-based geopolymer cement
    • type 1: alkali-activated fly ash geopolymer.
    • type 2: slag/fly ash-based geopolymer cement.
  • Ferro-sialate-based geopolymer cement.

Slag-based geopolymer cement

Components: metakaolin (MK-750) + blast furnace slag + alkali silicate (user-friendly).

Geopolymeric make-up: Si:Al = 2 in fact solid solution of Si:Al=1, Ca-poly(di-sialate) (anorthite type) + Si:Al =3 , K-poly(sialate-disiloxo) (orthoclase type) and C-S-H Ca-silicate hydrate.

The first geopolymer cement developed in the 1980s was of the type (K,Na,Ca)-poly(sialate) (or slag-based geopolymer cement) and resulted from the research developments carried out by Joseph Davidovits and J.L. Sawyer at Lone Star Industries, USA and yielded the invention of Pyrament® cement. The American patent application was filed in 1984 and the patent US 4,509,985 was granted on April 9, 1985, with the title 'Early high-strength mineral polymer'.

Rock-based geopolymer cement

The replacement of a certain amount of MK-750 with selected volcanic tuffs yields geopolymer cement with better properties and less CO2 emission than the simple slag-based geopolymer cement.

Manufacture components: metakaolin MK-750, blast furnace slag, volcanic tuffs (calcined or not calcined), mine tailings and alkali silicate (user-friendly).

Geopolymeric make-up: Si:Al = 3, in fact solid solution of Si:Al=1 Ca-poly(di-sialate) (anorthite type) + Si:Al =3–5 (Na,K)-poly(silate-multisiloxo) and C-S-H Ca-silicate hydrate.

Fly ash-based geopolymer cements

Later on, in 1997, building on the works conducted on slag-based geopolymeric cements, on the one hand and on the synthesis of zeolites from fly ashes on the other hand, Silverstrim et al. and van Jaarsveld and van Deventer developed geopolymeric fly ash-based cements. Silverstrim et al. US Patent 5,601,643 was titled 'Fly ash cementitious material and method of making a product'.

Presently, there are two types based on siliceous (EN 197) or Class F (ASTM C618) fly ashes:

  • Type 1: alkali-activated fly ash geopolymer (user-hostile):
In many cases requires heat curing at 60–80°C; not manufactured separately as a cement, but rather produced directly as a fly-ash based concrete. NaOH (user-hostile) + fly ash: partially-reacted fly ash particles embedded in an alumino-silicate gel with Si:Al= 1 to 2, zeolitic type (chabazite-Na and sodalite) structures.
  • Type 2: slag/fly ash-based geopolymer cement (user-friendly):
Room-temperature cement hardening. User-friendly silicate solution + blast furnace slag + fly ash: fly ash particles embedded in a geopolymeric matrix with Si:Al= 2, (Ca,K)-poly(sialate-siloxo).

Ferro-sialate-based geopolymer cement

The properties are similar to those of rock-based geopolymer cement but involve geological elements with high iron oxide content. The geopolymeric make up is of the type poly(ferro-sialate) (Ca,K)-(-Fe-O)-(Si-O-Al-O-). This user-friendly geopolymer cement is in the development and commercialization phase.

CO2 emissions during manufacture

According to the Australian concrete expert B. V. Rangan, the growing worldwide demand for concrete is a great opportunity for the development of geopolymer cements of all types, with their lower release of carbon dioxide CO2 during production.

CO2 emissions contrasted

The manufacture of Portland cement clinker involves the calcination of calcium carbonate according to the reactions:

3CaCO3 + SiO2 → Ca3SiO5 + 3CO2
2CaCO3 + SiO2 → Ca2SiO4 + 2CO2

Reactions involving alumina also lead the formation of the aluminate and ferrite components of the clinker.

The production of 1 tonne of Portland clinker directly generates approximately 0.55 tonnes of chemical CO2, directly as a product of these reactions, and requires the combustion of carbonaceous fuel to yield approximately an additional 0.40 tonnes of carbon dioxide, although this is being reduced through gains in process efficiency and the use of waste as fuels. However, in total, 1 tonne of Portland cement leads to the emission of 0.8–1.0 tonnes of carbon dioxide.

Comparatively, Geopolymer cements do not rely on calcium carbonate as a key ingredient, and generate much less CO2 during manufacture, i.e. a reduction in the range of 40% to 80–90%. Joseph Davidovits delivered the first paper on this subject in March 1993 at a symposium organized by the American Portland Cement Association, Chicago, Illinois.

The Portland cement industry reacted strongly by lobbying the legal institutions to deliver CO2 emission numbers that did not include the part related to calcium carbonate decomposition, focusing only on combustion emission. An article written in the scientific magazine New Scientist in 1997 stated that: ...estimates for CO2 emissions from cement production have concentrated only on the former source [fuel combustion]. The UN’s Intergovernmental Panel on Climate Change puts the industry’s total contribution to CO2 emissions at 2.4 %; the Carbon Dioxide Information Analysis Center at the Oak Ridge National Laboratory in Tennessee quotes 2.6 %. Now Joseph Davidovits of the Geopolymer Institute... has for the first time looked at both sources. He has calculated that world cement production of 1.4 billion tonnes a year produces 7 % of [world] current CO2 emissions. Fifteen years later (2012), the situation has worsened with Portland cement CO2 emissions approaching 3 billion tonnes a year.

Comparative energy use

The energy needs and CO2 emissions for regular Portland cement, rock-based geopolymer cements and fly ash-based geopolymer cements. The comparison proceeds between Portland cement and geopolymer cements with similar strength, i.e. average 40 MPa at 28 days. There have been several studies published on the subject that may be summarized in the following way:

Rock-based geopolymer cement manufacture involves:

  • 70% by weight geological compounds (calcined at 700°C)
  • blast furnace slag
  • alkali-silicate solution (industrial chemical, user-friendly).

The presence of blast furnace slag provides room-temperature hardening and increases the mechanical strength.

Energy needs and CO2 emissions for 1 tonne of Portland cement and Rock-based Geopolymer cement
Energy needs (MJ/tonne) Calcination Crushing Silicate Sol. Total Reduction
Portland Cement 4270 430 0 4700 0
GP-cement, slag by-product 1200 390 375 1965 59%
GP-cement, slag manufacture 1950 390 375 2715 43%
CO2 emissions (tonne)




Portland Cement 1.000 0.020
1.020 0
GP-cement, slag by-product 0.140 0,018 0.050 0.208 80%
GP-cement, slag manufacture 0.240 0.018 0.050 0.308 70%

Energy needs

According to the US Portland Cement Association (2006), energy needs for Portland cement is in the range of 4700 MJ/tonne (average). The calculation for Rock- based geopolymer cement is performed with following parameters:

- the blast furnace slag is available as by-product from the steel industry (no additional energy needed);
- or must be manufactured (re-smelting from non granulated slag or from geological resources).

In the most favorable case — slag availability as by-product — there is a reduction of 59% of the energy needs in the manufacture of Rock-based geopolymer-cement in comparison with Portland cement. In the least favorable case —slag manufacture — the reduction reaches 43%.

CO2 emissions during manufacture

In the most favorable case — slag availability as by-product — there is a reduction of 80% of the CO2 emission during manufacture of Rock-based geopolymer cement in comparison with Portland cement. In the least favorable case —slag manufacture — the reduction reaches 70%.

Fly ash-based cements Class F fly ashes

They do not require any further heat treatment. The calculation is therefore easier. One achieves emissions in the range of 0.09 to 0.25 tonnes of CO2 / 1 tonne of fly ash-based cement, i.e. CO2 emissions that are reduced in the range of 75 to 90%.

Workability issues

Generally, one of the main problems with geopolymer binder is its poor workability: Alkali-activated Fly Ash has a much greater plastic viscosity than OPC and is prone to fast setting. In a matter of minutes, it can produce “highly viscous, unmanageable concrete mixtures”.

These problems were faced with Portland cement as well, leading to the development of mix designs and admixtures that increase workability; to a limited extent, those techniques can be applied to geopolymer binder.

File:Slump and Compressive Strength Values for Geopolymer Concrete with Superplasticizer Admixtures

Experimental evidence suggests that there are numerous ways to enhance geopolymer workability:

  • Using different combinations of precursor and activator
  • Adjusting the activator concentration and the ratio of activator to precursor
  • Increasing the water/binder ratio (as in Portland cement, this will increase workability and decrease concrete strength, which can then be counteracted by strength-enhancing measures such as heat curing)
  • Adding certain conventional superplasticizers to certain precursors/activator combinations
  • Adding newly developed superplasticizers for geopolymer binder (such as Alccofine, ground granulated blast-furnace slag, glass powder and rice husk)

Using these techniques, geopolymer binder has been shown to be suitable for both high-strength concrete applications as well as for self-compacting concrete.

Properties for Rock-based geopolymer cement (Ca,K)-poly(sialate-disiloxo)

  • shrinkage during setting: < 0.05%, not measurable.
  • compressive strength (uniaxial): > 90 MPa at 28 days (for high early strength formulation, 20 MPa after 4 hours).
  • flexural strength: 10–15 MPa at 28 days (for high early strength of 10 MPa after 24 hours).
  • Young Modulus: > 2 GPa.
  • freeze-thaw: mass loss < 0.1% (ASTM D4842), strength loss <5 % after 180 cycles.
Alkali-aggregate reaction comparison, Geopolymer cement vs. Portland cement, ASTM C227
  • wet-dry: mass loss < 0.1% (ASTM D4843).
  • leaching in water, after 180 days: K2O < 0.015%.
  • water absorption: < 3%, not related to permeability.
  • hydraulic permeability: 10−10 m/s.
  • sulfuric acid, 10%: mass loss 0.1% per day.
  • hydrochloric acid, 5%: mass loss 1% per day.
  • KOH 50%: mass loss 0.02% per day.
  • ammonia solution: no observed mass loss.
  • sulfate solution: shrinkage 0.02% at 28 days.
  • alkali-aggregate reaction: no expansion after 250 days (−0.01%), as shown in the figure, comparison with Portland cement (ASTM C227). These results were published in 1993. Geopolymer binders and cements even with alkali contents as high as 10%, do not generate any dangerous alkali-aggregate reaction when used with an aggregate of normal reactivity.

The need for standards

In June 2012, the institution ASTM International (former American Society for Testing and Materials, ASTM) organized a symposium on Geopolymer Binder Systems. The introduction to the symposium states: When performance specifications for Portland cement were written, non-portland binders were uncommon...New binders such as geopolymers are being increasingly researched, marketed as specialty products, and explored for use in structural concrete. This symposium is intended to provide an opportunity for ASTM to consider whether the existing cement standards provide, on the one hand, an effective framework for further exploration of geopolymer binders and, on the other hand, reliable protection for users of these materials.

The existing Portland cement standards are not adapted to geopolymer cements. They must be created by an ad hoc committee. Yet, to do so, requires also the presence of standard geopolymer cements. Presently, every expert is presenting his own recipe based on local raw materials (wastes, by-products or extracted). There is a need for selecting the right geopolymer cement category. The 2012 State of the Geopolymer R&D, suggested to select two categories, namely:

  • Type 2 slag/fly ash-based geopolymer cement: fly ashes are available in the major emerging countries;
and
  • Ferro-sialate-based geopolymer cement: this geological iron rich raw material is present in all countries throughout the globe.
and
  • the appropriate user-friendly geopolymeric reagent.

File manager

From Wikipedia, the free encyclopedia
https://en.wikipedia.org/wiki/File_manager

A file manager or file browser is a computer program that provides a user interface to manage files and folders. The most common operations performed on files or groups of files include creating, opening (e.g. viewing, playing, editing or printing), renaming, copying, moving, deleting and searching for files, as well as modifying file attributes, properties and file permissions. Folders and files may be displayed in a hierarchical tree based on their directory structure.

Features

File transfer

Graphical file managers may support copying and moving of files through "copy and paste" and "cut and paste" respectively, as well as through drag and drop, and a separate menu for selecting the target path.

While transferring files, a file manager may show the source and destination direcotires, transfer progress in percentage and/or size, progress bar, name of the file currently being transferred, remaining and/or total number of files, numerical transfer rate, and graphical transfer rate. The ability to pause the file transfer allows temporarily granting other software full sequential read access while allowing to resume later without having to restart the file transfer.

Some file managers move multiple files by copying and deleting each selected file from the source individually, while others first copy all selected files, then delete them from the source afterwards, as described in computer file § Moving methods.

Conflicting file names in a target directory may be handled through renaming, overwriting, or skipping. Renaming is typically numerical. Overwriting may be conditional, such as when the source file is newer or differs in size. Files could technically be compared with checksums, but that would require reading through the entire source and target files, which would slow down the process significantly on larger files.

User interface

Some file managers contain features analogous to web browsers, including forward and back navigational buttons, an address bar, tabs, and a bookmark side bar.

Networking

Some file managers provide network connectivity via protocols, such as FTP, HTTP, NFS, SMB or WebDAV. This is achieved by allowing the user to browse for a file server (connecting and accessing the server's file system like a local file system) or by providing its own full client implementations for file server protocols.

Directory editors

A term that predates the usage of file manager is directory editor. An early directory editor, DIRED, was developed circa 1974 at the Stanford Artificial Intelligence Laboratory by Stan Kugell.

A directory editor was written for EXEC 8 at the University of Maryland, and was available to other users at that time. The term was used by other developers, including Jay Lepreau, who wrote the dired program in 1980, which ran on BSD. This was in turn inspired by an older program with the same name running on TOPS-20. Dired inspired other programs, including dired, the editor script (for emacs and similar editors), and ded

File-list file manager

The Alto Neptune file manager program

File-list file managers are lesser known and older than orthodox file managers.

One such file manager was neptune. It ran on the Xerox Alto in the 1973-1974 time frame. It had some of the same features that would end up in orthodox file managers.

Another such file manager is flist, which was introduced sometime before 1980 on the Conversational Monitor System. This is a variant of FULIST, which originated before late 1978, according to comments by its author, Theo Alkema.

The flist program provided a list of files in the user's minidisk, and allowed sorting by any file attribute. The file attributes could be passed to scripts or function-key definitions, making it simple to use flist as part of CMS EXEC, EXEC 2 or XEDIT scripts.

This program ran only on IBM VM/SP CMS, but was the inspiration for other programs, including filelist (a script run via the Xedit editor), and programs running on other operating systems, including a program also called flist, which ran on OpenVMS, and FULIST (from the name of the corresponding internal IBM program), which runs on Unix.

Orthodox file managers

Midnight Commander, an orthodox file manager with a text-based user interface

Orthodox file managers (sometimes abbreviated to "OFM") or command-based file managers are text-menu based file managers, that commonly have three windows (two panels and one command line window). Orthodox file managers are one of the longest running families of file managers, preceding graphical user interface-based types. Developers create applications that duplicate and extend the manager that was introduced by PathMinder and John Socha's Norton Commander for DOS. The concept dates to the mid-1980s—PathMinder was released in 1984, and Norton Commander version 1.0 was released in 1986. Despite the age of this concept, file managers based on Norton Commander are actively developed, and dozens of implementations exist for DOS, Unix, and Microsoft Windows. Nikolai Bezroukov publishes his own set of criteria for an OFM standard (version 1.2 dated June 1997).

Features

An orthodox file manager typically has three windows. Two of the windows are called panels and are positioned symmetrically at the top of the screen. The third is the command line, which is essentially a minimized command (shell) window that can be expanded to full screen. Only one of the panels is active at a given time. The active panel contains the "file cursor". Panels are resizable and can be hidden. Files in the active panel serve as the source of file operations performed by the manager. For example, files can be copied or moved from the active panel to the location represented in the passive panel. This scheme is most effective for systems in which the keyboard is the primary or sole input device. The active panel shows information about the current working directory and the files that it contains. The passive (inactive) panel shows the content of the same or another directory (the default target for file operations). Users may customize the display of columns that show relevant file information. The active panel and passive panel can be switched (often by pressing the tab key).

The following features describe the class of orthodox file managers.

  • They present the user with a two-panel directory view with a command line below. Either panel may be selected to be active; the other becomes passive. The active panel becomes the working area for delete and rename operations, while the passive panel serves as a target for copy and move operations. Panels may be shrunk, exposing the terminal window hidden behind them. Normally, only the last line of the terminal window (the command line) is visible.
  • They provide close integration with an underlying OS shell via command line, using the associated terminal window that permits viewing the results of executing shell commands entered on the command line (e.g., via Ctrl-O shortcut in Norton Commander).
  • They provide the user with extensive keyboard shortcuts.
  • The file manager frees the user from having to use the mouse.
  • Users can create their own file associations and scripts that are invoked for certain file types and organize these scripts into a hierarchical tree (e.g., as a user script library or user menu).
  • Users can extend the functionality of the manager via a so-called User menu or Start menu and extensions menu.

Other common features include:

  • Information on the "active" and "passive" panels may be used for constructing commands on the command line. Examples include current file, path to left panel, path to right panel, etc.
  • They provide a built-in viewer for (at least) the most basic file types.
  • They have a built-in editor. In many cases, the editor can extract certain elements of the panels into the text being edited.
  • Many support virtual file systems (VFS) such as viewing compressed archives, or working with files via an FTP connection.
  • They often have the word commander in the name, after Norton Commander.
  • Path: shows the source/destination location of the directory in use
  • Information about directory size, disk usage and disk name (usually at the bottom of the panels)
  • Panel with information about file name, extension, date and time of creation, last modification, and permissions (attributes).
  • Info panel with the number of files in directory, and the sum of the sizes of selected files.
  • Tabbed interface (usually in GUI file managers)
  • Function keys: F1–F10 have all the same functions under all orthodox file managers. Examples: F5 always copies file(s) from the active to the inactive panel, while F6 moves the file.

Tabbed panels

The introduction of tabbed panels in some file managers (for example Total Commander) made it possible to manipulate more than one active and passive directory at a time.

Portability

Orthodox file managers are among the most portable file managers. Examples are available on almost any platform, with both command-line and graphical interfaces. This is unusual among command line managers in that something purporting to be a standard for the interface is published. They are also actively supported by developers. This makes it possible to do the same work on different platforms without much relearning of the interface.

Dual-pane managers

Sometimes they are called dual-pane managers, a term that is typically used for programs such as the Windows File Explorer (see below). But they have three panes including a command line pane below (or hidden behind) two symmetric panes. Furthermore, most of these programs allow using just one of the two larger panes with the second hidden. Some also add an item to the Context Menu in Windows to "Open two Explorers, side by side".

Notable ones include:

Navigational file manager

File Manager in Windows 10, displaying the contents of partition X:
 

A navigational file manager is a newer type of file manager. Since the advent of GUIs, it has become the dominant type of file manager for desktop computers.

Typically, it has two panes, with the filesystem tree in the left pane and the contents of the current directory in the right pane. For macOS, the Miller columns view in Finder (originating in NeXTStep) is a variation on the navigational file manager theme.

The Miller Column browser from GNUstep is a type of Navigational file manager.

Concepts

  • The window displays the location currently being viewed.
  • The location being viewed (the current directory) can be changed by the user by opening directories, pressing a back button, typing a location, or using the additional pane with the navigation tree representing all or part of the filesystem.
  • Icons represent files, programs, and directories.

The interface in a navigational file manager often resembles a web browser, complete with back and forward buttons, and often reload buttons. Most also contain an address bar into which the file or directory path (or URI) can be typed.

Most navigational file managers have two panes, the left pane being a tree view of the filesystem. This means that unlike orthodox file managers, the two panes are asymmetrical in their content and use.

Selecting a directory in the Navigation pane on the left designates it as the current directory, displaying its contents in the Contents pane on the right. However, expanding (+) or collapsing (-) a portion of the tree without selecting a directory will not alter the contents of the right pane. The exception to this behavior applies when collapsing a parent of the current directory, in which case the selection is refocused on the collapsed parent directory, thus altering the list in the Contents pane.

The process of moving from one location to another need not open a new window. Several instances of the file manager can be opened simultaneously and communicate with each other via drag-and-drop and clipboard operations, so it is possible to view several directories simultaneously and perform cut-and paste operations between instances.

File operations are based on drag-and-drop and editor metaphors: users can select and copy files or directories onto the clipboard and then paste them in a different place in the filesystem or even in a different instance of the file manager.

Notable examples of navigational file managers include:

Spatial file manager

The Nautilus file manager had a spatial mode, which was removed with the arrival of GNOME (and with it Nautilus) version 3.x. Each of these windows displays an open directory.

Spatial file managers use a spatial metaphor to represent files and directories as if they were actual physical objects. A spatial file manager imitates the way people interact with physical objects.

Some ideas behind the concept of a spatial file manager are:

  1. A single window represents each opened directory
  2. Each window is unambiguously and irrevocably tied to a particular directory.
  3. Stability: files, directories, and windows go where the user moves them, stay where the user puts them ("preserve their spatial state"), and retain all their other "physical" characteristics (such as size, shape, color and location).
  4. The same item can only be viewed in one window at a time.

As in navigational file managers, when a directory is opened, the icon representing the directory changes—perhaps from an image showing a closed drawer to an opened one, perhaps the directory's icon turns into a silhouette filled with a pattern—and a new window is opened to represent that directory.

Examples of file managers that use a spatial metaphor to some extent include:

Dysfunctional spatial file managers:

  • Windows Explorer in Windows 95 was set as a spatial file manager model by default; because it also worked as a navigational file manager, directories could be opened in multiple windows, which made it fail all the above criteria. Later versions gradually abandoned the spatial model.
  • Apple's Finder in macOS was designed with a similar integration of spatial and navigational modes, meaning that the spatial mode did not actually work.

3D file managers

File System Visualizer, one example of a 3D file manager
 
In Cubix, files sharing the same attributes are represented by cubes in a 3D environment.

Some projects have attempted to implement a three-dimensional method of displaying files and directory structures. Three-dimensional file browsing has not become popular; the exact implementation tends to differ between projects, and there are no common standards to follow.

Examples of three-dimensional file managers include:

  • fsn, for Silicon Graphics' IRIX systems, notably featured prominently in one scene from the film Jurassic Park, as a representation of Unix systems.
  • File System Visualizer, or fsv, an open-source clone of fsn for modern Unix-like systems.
  • tdfsb, an open-source 3D file browser, where one enters directories by flying into them (using WASD). Runs on Linux, FreeBSD and BeOS.
  • BumpTop, a file manager using a three-dimensional representation of a desktop with realistic physics, intended for use with a stylus and touchscreen.
  • Real Desktop, a desktop replacement with similarities to BumpTop.
  • Cubix 3D Filer is a Windows file manager which organizes files according to different attributes.
  • GopherVR, a 3D visualisation of networked Gopher resources.

Web-based file managers

Web-based file managers are typically scripts written in either PHP, Ajax, Perl, ASP or another server-side language. When installed on a local server or on a remote server, they allow files and directories located there to be managed and edited, using a web browser, without the need for FTP Access.

More advanced, and usually commercially distributed, web-based file management scripts allow the administrator of the file manager to configure secure, individual user accounts, each with individual account permissions. Authorized users have access to documents stored on the server or in their individual user directories anytime, from anywhere, via a web browser.

A web-based file manager can serve as an organization's digital repository. For example, documents, digital media, publishing layouts, and presentations can be stored, managed, and shared between customers, suppliers, and remote workers, or just internally.

Web-based file managers are becoming increasingly popular due to the rise in popularity of dynamic web content management systems (CMS) and the need for non-technical website moderators to manage media on their websites powered by these platforms.

An example is net2ftp, a PHP- and JavaScript-based FTP client.

File picker

Operating systems typically ship a file picker, which allows specifying in which location to save a file (usually accessed through the "Save as" option in software), and where to open a file from. Sometimes, a folder is selected instead of a file or destination path.

Some file pickers also allow file management to some degree, such as searching, moving, copying, renaming, and copying the path to clipboard.

Some software might have a customized file picker.

Introduction to entropy

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