bluuebunny/crossref_metadata_2025 huggingface dataset:
Introduction
Authors: Cook Peter J. , Carleton Chris M.
Published: November 2020

As pointed out in the Foreword, the United Nations Convention on the Law of the Sea (the Convention) is, by any measure, a remarkable document, which for the first time provides a comprehensive framework of governance for a large part of the world ocean. It covers such issues as delimitation, environmental impact and management, scientific research, economic and commercial issues, and technology transfer and provides a regime for the peaceful settlement of disputes. The resolution of disputes is especially important, given that there are 151 coastal States, all with sovereign rights to the adjacent seas and shelf. Under the Convention, those rights cover a total area of about 60 million km2 or around 20% of the world ocean within the 200-nauticalmile (M) limit. But there is perhaps an additional 5% (15 million km2) which lies beyond the 200-M limit, to which sovereign rights may also extend under the terms of the Convention. Up to 54 coastal States may be able to claim extensions of their continental shelf beyond 200 M (figure 1.1). What is intended is that over the next 10 years or so, nations will document and lay claim to an area of around 75 million km2, equal to more than half the Earth's land surface. Viewed against the background of human history and land conquest extending over thousands of years, the magnitude of the undertaking is extraordinary. What is also remarkable is the key role that science and technology will play. Science and technology have always played a role in exploration and documentation of the oceans in the past. The development of an accurate chronometer by Harrison in the 18th century was critical to developing an accurate means of establishing longitude (Sobel, 1995). This in turn made it possible to accurately chart the oceans for the first time, which then enabled nations to lay claim to newly explored areas, establish trade routes, document marine hazards, and exploit ocean resources. Parts of the world's territorial sea baselines are and will continue to be based on 19th-century data. As will be evident from this book, such data are sufficiently important in some areas that we have felt it necessary to document just how those "historical data" were gathered so that we can establish their reliability.
Historical Methods of Depth Measurement
Authors: Shipman Steve , Laughton Anthony
Published: November 2020

In establishing the limits of the continental shelf, there are two aspects to the use of depth data. Shallow water depths are used to determine the low-water or drying line and hence the baseline from where the measurement of the various limits begin. Deepwater depths are used to determine the foot of continental slope and the 2500-m isobath, which in turn will help to decide where these limits should end. While the principle focus of this book is the delimitation of the outer limit of the continental shelf, some aspects of depth measurement are applicable to both shallow and deepwater measurements, and therefore, in order to provide a complete picture, all aspects will be considered in this chapter. For as long as people have ventured out to sea in boats, they have been interested in obtaining a knowledge of the depth of water and the position of underwater obstructions in order to avoid damaging and possibly losing their vessels. Information was valuable, and having been obtained by ships' captains, either by purchasing it from others or by carrying out their own surveys, it was not readily divulged to other people. It was the formation of national hydrographic offices in the 18th century that started the coordinated collection and wide dissemination of hydrographic data. The earliest methods of measuring depth involved the lowering of a weighted line over the side of the vessel until it hit the seabed or in the case of very shallow water, the use of a graduated pole. Measurements were restricted to shallow water until the latter part of the 18th century. Captain Phipps in HMS Racehorse recorded a depth of 683 fathoms in the Norwegian Sea in 1773. Measuring such depths was a very slow, weatherdependent process, but with the growing interest in the oceans, especially the desire to lay underwater telegraph cables in the second half of the 19th century, the techniques were improved. By 1855, Matthew Fountaine Maury of the U.S. Naval Observatory had accumulated sufficient depths to publish a first attempt at a contour chart of the Atlantic Ocean. In 1904, the first global set of such charts was published by GEBCO.
Present-Day Methods of Depth Measurement
Authors: Clarke John Hughes
Published: November 2020

Bathymetric data are needed to derive the morphological criteria that define the extent of the juridical continental shelf. Two features in particular, the '"foot of slope" and the 2500-m contour, must be defined. The previous chapter considered historical methods of determining bathymetry. This chapter will cover the present day methods that can be used to better meet the need for accurate bathymetry. In order to satisfy the demands of UNCLOS, bathymetric data are required in depths ranging from about 200 m to more than 5000 m. Shallower depths, while useful for demonstrating the morphology of the physical continental shelf, do not bear any relevance to the delineation of juridical continental shelf boundaries, other than where they are required to establish the baseline. Alternate methods to derive bathymetry other than using sound are available. Those involving airborne electromagnetic methods (e.g., electromagnetic induction, red-green lasers, and inversion of sea surface radar images) are not capable of determining depths much in excess of 40 m. The only other method potentially useful for deriving deeper water bathymetry is through inversion of sea surface altimetry obtained from satellites. This will be discussed at the end of this chapter. The optimal method thus remains acoustic. The traditional approach has been to use single-beam echo sounders (see previous chapter). This chapter discusses the more modern '"swath" sonar techniques, which are becoming widely used. The great majority of historic bathymetry has been collected using the single-beam sounding approach. As discussed in chapter 9, this method has a number of limitations, three of the most critical of which are i. incomplete coverage; ii. uncertainty about the exact location of the first arrival of the acoustic pulse; and iii. distortion of short-wavelength topography. In order to achieve more complete coverage, better echo location, and higher spatial resolution, methods were devised to project acoustic energy both within narrower solid angles (figure 10.1) and while deriving this information over angular sectors extending further out from the side of the survey vessel. All the methods commonly applied involved scanning the seabed orthogonal to the ship heading. Sequential scans, accumulated as the ship progresses, form a corridor (or swath) of seabed information (figure 10.2).
Seismic Reflection and Refraction Methods
Authors: Kasuga Shigeru , Katsura Tadahiko
Published: November 2020

In order to establish the outer limit of the continental shelf, as defined by article 76 of the Convention (UNDOALOS, 1993), it is necessary for the coastal State to determine the foot of the slope and to know the thickness of the sediments beneath the ocean floor. Geophysical surveys, using seismic techniques, have been extensively used for mapping of subsurface geological structures. In seismic surveys, seismic waves are generated by near-surface artificial explosions at a series of sites; the resulting waves are then recorded digitally and as an analogue record. The regional geological structure and sediment thickness can then be deduced from analysis of the travel times of identifiable wave groups. This chapter briefly outlines the various seismic survey methods with special emphasis on seismic reflection and refraction surveys. It also discusses the most commonly used techniques for determining the subsurface structure, including determination of the velocities of sediments using seismic waves. Seismic reflection surveys have been extensively used for mapping structures in sedimentary sequences, especially as part of exploration programs for oil and gas. Two seismic reflection methods are widely used: singlechannel and multichannel seismic profiling systems. Although the former typically used an analogue recording system with a single receiver, digital recording is now commonly employed. The single-channel method is often employed during shallow reconnaissance exploration or in offshore engineering surveys because it is relatively cheap. But this advantage of the single-channel system is countered by the fact that the maximum depth of penetration of the single-channel system is rather shallow, and it usually does not give information on the deep geological structure or on the seismic velocity of the sedimentary layers. The multichannel method is characterized by digital recording and multiple receivers in a long multichannel streamer cable. Most marine seismic reflection profiling has now shifted from analogue recording of singlechannel data to digital recording of multichannel data, largely because digital recording and processing of large amounts of data improve the signal-to-noise ratio and provide high-quality seismic records. A data acquisition system for reflection profiling consists of three basic subsystems: the energy source, the receiving unit, and the digital recording system.
The Practical Realization of the Continental Shelf Limit
Authors: Carleton Chris M. , Monahan David
Published: November 2020

The first steps in establishing the case for a possible continental shelf claim beyond 200 nautical miles (M) were covered in the previous chapter. The requirement for an initial assessment of existing data and information before proceeding with the practical stage of new data acquisition and assessment to determine the actual legal limit of the continental margin is clear. This chapter deals with the three possible cases: (case A) no extended continental shelf, (case B) foot of the slope plus 60 M, and (case C) limits based on the foot of the slope and sediment thickness. Finally, the chapter deals with the delimitation of the two possible outer limit lines that are required to be implemented by coastal States, provided their continental margins extend up to or beyond those two limiting lines. Figure 17.1 illustrates how those limits could be combined to form a coastal State's continental shelf limit. . . . The continental shelf of a coastal State comprises the sea-bed and subsoil of the submarine areas that extend beyond its territorial sea throughout the natural prolongation of its land territory to the outer edge of the continental margin, or to a distance of 200 nautical miles (M) from the baselines from which the breadth of the territorial sea is measured where the outer edge of the continental margin does not extend up to that distance. . . . This provision, in principle, provides every coastal State with a continental shelf extending at least 200 M seaward. In practice, there are a number of constraints which result in the situation where a coastal State's entitlement to a continental shelf does not extend beyond 200 M. Let us therefore consider the procedure that each coastal State should follow to enable it to reach this conclusion. If a coastal State's entitlement to a continental shelf does not extend beyond 200 M measured from the territorial sea baseline, it can be assumed that the maritime zone calculated out to that distance will be subsumed within an exclusive economic zone regime, provided the coastal State claims such a zone, under part V of UNCLOS.
Introduction
Authors: Kemeny P. C.
Published: November 2020

Princeton versus Harvard: this 1886 “battle of the Titans,” as one reporter described it, was not an athletic contest, and more was at stake than college pride. At a wintry February meeting of the Nineteenth Century Club at the American Art Gallery in New York City, a “large and fashionable” audience gathered to hear two combatants debate the question, “What place should religion have in a college?” Specifically, the question concerned the role of religious instruction and worship in collegiate education. Princeton College President James McCosh represented the denominational college and his counterpart at Harvard College, Charles W. Eliot, the neutral or nondenominational institution. Each president read his paper with a politeness befitting the Victorian sensibilities of the audience, yet beneath the decorum lay two very different understandings of the nature and role of religion in American collegiate education. McCosh had history on his side, but Eliot had the future on his. “Nearly all the older colleges, such as Harvard, Yale, and Princeton,” McCosh explained, “were founded in the fear of God, with the blessing of heaven invoked; they gave religious instruction to the students, and had weekly and daily exercises of praise and prayer to Almighty God.” Compulsory religious instruction and worship, McCosh insisted, were essential to the intellectual and moral well-being of students—America’s future leaders—and so, ultimately, to the welfare of the nation. Princeton, as with many other institutions established before the Civil War, was officially a nondenominational college chartered in 1746 to serve the general public. In reality, however, Princeton, was a de facto denominational college that met the educational needs and upheld the intellectual ideas of Presbyterians and the larger Protestant community. Because the older American colleges promoted a nonsectarian Protestantism, which would not give offense to any evangelical denomination, McCosh reasoned, they upheld the faith of most Americans and performed a public service. At Princeton, this traditional approach was still readily evident in the late nineteenth century.
The Travails of Becoming a University, 1888-1902
Authors: Kemeny P. C.
Published: November 2020

In bringing the College of New Jersey to the brink of university status, McCosh stood on the verge of the promised land. As the nineteenth century was coming to a close, alumni, professors, and trustees in Princeton, like those at many other American colleges and universities, were eager to see the institution position itself so that it would be better able to meet society’s need for moral and thoughtful leaders, practical knowledge, and scientific expertise once the nation entered the twentieth century. With the future direction of the institution hanging in the balance, the choice of who should succeed McCosh divided the college community along the same lines as had emerged earlier over both the alumni’s attempt to secure direct representation on the Board of Trustees and McCosh’s failed attempt to make the college a university. Whereas McCosh harmoniously upheld the college’s dual mission through the breadth of his scholarly interests, the warmth of his evangelical piety, and the force of his personality, the two candidates who vied for the presidency after his resignation possessed only a portion of McCosh’s qualities and appealed to only one part of the Princeton community. Francis L. Patton appealed to those primarily, though not exclusively, interested in preserving Princeton’s heritage as an evangelical college. According to McCosh, the “older men” among the trustees, faculty, and alumni “want a minister,” and on these grounds, the forty-five-year-old Patton seemed like a natural successor to McCosh. A native of Bermuda, Patton had graduated from University College of the University of Toronto; had attended Knox College, also of the University of Toronto; and had graduated from Princeton Theological Seminary in 1865. Ordained that same year in the Old School Presbyterian church, he served as pastor of a church in New York City. Cyrus H. McCormick (1809-1884), the farming machine magnate and patron of conservative Presbyterian causes, persuaded Patton to accept a position as the Professor of Didactic and Polemical Theology at the Presbyterian Seminary of the Northwest (later McCormick Theological Seminary) in Chicago in 1873.
Use of Soil Surveys for Landscape Architecture
Authors: Keefer Robert F.
Published: November 2020

Modern soil survey reports, published since about 1959, have a wealth of information that could be useful for landscape architects. Characteristics of each specific soil are detailed in the text of the soil survey. Distinct kinds of soils for a specific site can be identified from the soil designation on the aerial photographs at the back of the report. Considerable specific information is provided in tables, including data on temperature, precipitation, freeze dates in spring and fall, woodland management and productivity, recreational development capabilities, wildlife habitat potentials, building site development possibilities, sanitary disposal potentials, engineering properties, value of materials for construction, water management limitations, physical and chemical properties of specific soils, and soil and water features. Modern soil survey reports consist of text, tables, soil maps, and often a glossary. These reports are available free to the public and are usually found in county extension services offices, soil conservation district offices, or state agricultural colleges. The text of a soil survey report describes the general nature of the county as to location in the state, climate, physiography, relief and drainage, geology, farming, natural resources, industries, history of settlement, and how the survey was conducted. Soil associations and individual soils are described in detail. Formation of soils is usually discussed in relation to the factors of soil formation. A glossary of terms is often provided for the nonscientific person. The whole county or counties in the report is shown on a soil association map, which is designed to be used to compare the suitability of large areas for general land use. The county is divided into large areas, each of which contains an association of several soils grouped by similar management. Usually from 5 to 15 soil associations are shown with a legend describing each of the specific associations. This type of information could be used for zoning purposes, county management, or other governmental activities. Aerial photos are provided on sheets showing the location of each individual soil in the county. Comprising about half of the soil survey report, this is one of the most useful sections.
Nature of Soil Erodibility
Authors: Keefer Robert F.
Published: November 2020

Inherent properties of a soil determine the extent to which that soil will erode. These properties are soil texture, soil structure, soil permeability, and the amount of soil organic matter. Soil texture consists of a mixture of soil particle sizes of sand, silt, and clay. Soil texture is also related to water movement into the soil [infiltration] and water movement through a soil (permeability). Sand grains are large and difficult to move; however, they are easily detached. Clay particles often stick together and therefore are difficult to detach; however, once detached the clays remain suspended and are easily carried and separated from the original soil mass by water. Silt is intermediate in size between sand and clay, but silt is both easily detached and easily transported. Thus, any soil that has large amounts of silt will erode easily. Infiltration. Water moves into and within a soil through the large macropores and only a very limited amount in the small micropores. Sandy soils have many large pores allowing water to move into the soils by infiltration. Conversely, clay soils have many microspores through which water passes only very slowly. Therefore, during a moderate storm, runoff and erosion would be greater from a soil with more fine textured clays than from a soil where coarse texture dominates. Permeability. Once water enters a soil, it flows within the soil. The extent of internal movement of water in a soil is the permeability of that soil. A soil aggregate is a soil granule or soil crumb consisting of a number of soil grains, that is, silt or clay, held together by a cementing substance. Aggregation is the condition of a soil having many individual aggregates. Soils that have many large stable aggregate are more permeable and are difficult to detach and erode. An aggregate has stability when it is not broken easily by water. Soil aggregates help keep the soil receptive to rapid infiltration of water and keep water from moving over the soil and eroding it.
Chemical Properties of Soils for Growing Plants
Authors: Keefer Robert F.
Published: November 2020

Soil reaction is the amount of acids (acidity) or bases (alkalinity) present in a soil and is indicated by a term called “pH”. By definition, pH is the logarithm of the reciprocal of the hydrogen ion (H+) concentration, or When a number has a smaller superscript number with it, the number is raised to that power which is called the “logarithm.” Raising a number to a power means multiplying that number by itself the number of times indicated by the superscript. . . . Examples: 102 means 10 x 10 = 100; 103 means 10 x 10 x 10 = 1,000. The logarithm (log) is 2 for the first example and 3 for the second. . . . Logarithms are used as these are more convenient in expressing the amount of hydrogen ions present. Under neutral solutions the pH is 7.0. Any pH that is less than 7 is acid and any pH above is alkaline. When changing from a pH of 7 to a pH of 6, the H ion concentration increases ten times, and when going from a pH of 7 to a pH of 5, the H ion concentration increases 100 times because pH uses a geometric scale and not an arithmetic scale. Thus, pH changes by steps of ten times the next adjacent number. The logarithmic scale used for pH is the same type, but opposite in direction, as that used to measure earthquakes. For each larger number of earthquake, the severity increases ten times; for each smaller number of pH, the acidity increases ten times. Some plants can tolerate very low pH (4.5) and others can withstand a pH of 8.3, but the optimum range for growth of most plants and microbes is between 6 and 7. Availability of most nutrients is affected by pH changes. Charts have been constructed to show this relationship. On these charts the pH at which most nutrients are readily available is from 6 to 7. At extremes of pH, availability of nutrients to plants often is reduced considerably.
Soil Organic Matter
Authors: Keefer Robert F.
Published: November 2020

Soil organic matter (SOM) is probably the most important constituent of soils. The effect of SOM on soil properties far exceeds the relative percentage of this material in soils. The small amount of organic matter in soils, usually from 1 to 5%, is very important in providing a reserve food source for microorganisms and higher plants. Almost all properties of SOM are beneficial for plant growth. Soil organic matter can be defined as a complex, heterogeneous mixture of plant and animal remains in various stages of decay, microbial cells—both living and dead—microbially synthesized compounds, and derivatives of all of the above through microbial activity. Soil organic matter is probably the most complex of all naturally occurring substances. Some compounds in SOM are distinctive to soil and are not present in plants or animals. By examining the composition of SOM, one can see why it is such a complex material. The following compounds have been isolated from chemical SOM extracts: . . . 1. Carbohydrates (sugars, polysaccharides)—about 75% of dry weight 2. Lignin (a plant polymer of phenyl propane units) 3. Proteins (combinations of amino acids) 4. Hydrocarbons—fats, waxes, resins, and oils 5. Tannins (phenolic substances) 6. Pigments (chlorophyll) 7. Organic acids (many in the biochemical Krebs cycle) 8. Miscellaneous compounds—includes organic P, organic S, polynuclear hydrocarbons, nucleic acid derivatives, alcohols, aldehydes, esters, etc. . . . Whenever organic materials are added to a soil the physical properties of soil structure, water-holding capacity, and soil color are changed. The extent of change in these properties depends on the amount and type of organic material added, the soil microorganisms present in the soil, and the speed at which decomposition occurs. Aggregation and granulation (crumb formation) is increased by polysaccharides produced by microorganisms during decomposition. This improves soil tilth (ability to work the soil) and helps stabilize the soil crumbs. The ability of a soil to hold water is greatly increased by addition of SOM. This results in greater infiltration (water moving into the soil) and adsorption of water by the SOM, with consequently less erosion and loss of soil particles and fertility.
Attitude-Specific Population Models: Dynamic Custom Evolution
Authors: Chu C. Y. Cyrus
Published: November 2020

In the predator-prey model introduced in chapter 7, two types of individuals interact with each other. The key features are that the reproduction rate of each type depends on the size of both types and that each individual’s welfare depends on his or her interaction with other individuals. Besides the predator-prey interaction described above, there are several other well-known two-type interactions in economic literature. Hardin’s (1968) classic paper on “tragedy of the commons” is a typical example. The scenario of decision interaction Hardin considered is as follows: there is a pasture open to all, and each herdsman considers whether to add an animal to his herd. The benefit of adding an animal goes to each individual, but the social (overgrazing) cost is born by all herdsmen. Thus, it is a dominant strategy for each herdsman to add more cattle, which, however, leads to a Pareto-inferior overgrazing result, If we consider the interaction between any two herdsmen as a 2 × 2 game, then the game Hardin had in mind is similar to the “prisoners’ dilemma.” When the concern with herd size is replaced by the concern with population size, the problem becomes one of population/environment interaction. This kind of decision interaction will be discussed in chapter 14. In this chapter we will study another kind of two-type population interaction, the critical-mass model proposed by Schelling (1978). In the critical-mass setup, people can choose different behavior types in different periods, and their choice depends on the overall behavioral pattern in the previous period. The key idea is described in the following example. Suppose we use the [0,1] interval to characterize the behavioral pattern of the population. When the behavioral pattern is close to 0, then the rational decisions of most people will sustain 0 as a stable equilibrium. When the overall pattern exceeds a certain critical mass, the tide turns; as people gradually change their micro decisions, the macro behavioral pattern eventually changes to 1, which is another stable equilibrium. Schelling (1978) proposed many empirical examples that have the above-mentioned critical-mass property.
Demographic Transition and Economic Development
Authors: Chu C. Y. Cyrus
Published: November 2020

Demographic transition refers to a shift in reproductive behavior from a state of high birth and death rates to a state of low birth and death rates. This transition takes place because of advances in agricultural technology and medical science or improvement in hygiene environment, all of which result in corresponding declines in the mortality rate. In this first phase of the demographic transition, population growth rises because the decline in mortality rate has not been coupled with any significant change in parents’ fertility decisions. Then, in the second phase of the transition, parents begin to reduce their fertility as they realize that their ideal number of children can be more easily achieved with fewer births. The widespread use of contraceptive techniques facilitates parents’ attempts to reduce fertility, which in turn causes a decline in the population growth rate. Eventually, the population growth rate converges to a new level, which may be higher or lower than in the pretransitional stage. To facilitate comparison, we can use figure 11.1 to characterize the time and process of the transition. In figure 11.1, Tα marks the apparent starting point of a continuous decline in mortality. Tβ, which normally occurs later than Tα, refers to the time at which the fertility rate begins to decline. Tγ, is the point of lasting return, with an average rate of natural increase equal to or less than that of the period preceding the date of Tα. The convention is to define D = Tγ - Tα as the duration of the transition period. Chesnais (1992) separated the observations of world demographic transition into several types. The first type includes developed countries in Europe and Japan; the second type consists of countries with immigrant European populations, such as the United States, Australia, and Argentina; late-developing countries, such as India. South Korea, and Jamaica, belong to the third type. For countries of the first type, the mortality decline process is closely related to the development of medical technology, which was gradual and spread out over time; hence, the demographic transition is also long. Late-developing countries and those with large immigrant populations were able to adopt the already-developed medical technology from the advanced countries at one time.
Population Size and Early Development
Authors: Chu C. Y. Cyrus
Published: November 2020

The Malthusian theory hypothesizes that the natural environment imposes various capacity constraints on human population growth and that population size has been and will be checked by these constraints. In such a classical theory, which was presumably motivated by observations of the ancient world, population might be the most important dynamic variable, although its role is rather passive: population is a variable that would be affected by, but would not affect, the environment. Boserup (1981), however, sees the role of population in the development of human economy as more consequential. She gave many persuasive examples that showed that, at least for the period up to the mid-twentieth century, population size might be a variable which actively spurred technological progress. This is also the viewpoint held by Lee (1986) and Pryor and Maurer (1982). After the Industrial Revolution, the role of population in economic dynamics, along with the reduction of mortality fluctuations and the increasing control of female fertility, evidently became secondary. The key variable that dominates the analysis of economic dynamics in the neoclassical growth theory along the lines of Solow (1956) is capital (or per capita capital). In Solow’s growth model, the role of population is minimal in the steady state: neither the level nor the growth rate of the steady-state per capita consumption has anything to do with the size of a population; only the steady-state per capita income level will be affected by the population growth rate. The growth pattern in the latter half of the twentieth century is markedly different. A key feature of our recent growth experience is the rapid innovation of new technologies. Modern growth theory has embraced the concept of increasing returns to explain such a unique growth pattern. However, various versions of the theory of increasing returns turn out to be necessarily linked to population. The hypothesis of learning by doing implies that growth in productivity is an increasing function of aggregate production, which is itself positively related to the size of population.
Plasticity
Authors: West-Eberhard Mary Jane
Published: November 2020

A phenotype-centered view of evolution needs to start with a solid idea about the nature of the phenotype. This chapter and the next are devoted to two universal properties of phenotypes, plasticity, or responsiveness to environmental inputs; and modularity, or subdivision into semi-independent and dissociable parts (chapter 4). Of these two properties, plasticity is probably the more fundamental, for the ability to replicate, which distinguishes organic from inorganic nature, requires molecules which are interactive and precisely responsive— adaptively plastic. So plasticity must have been an early universal property of living things. The universality of modularity is a secondary, or “emergent” result of the universality of plasticity (see Wilczek, 2002, on emergent universality in physics). Any organism whose size, whether due to accretion or growth, is large enough to create internal environmental differences, such as those between the inner and the outer regions of a clump of material, has the potential for regional internal differentiation. As differentiation evolves to produce specialized parts and an internal division of labor, internal heterogeneity gives rise to conditional switches between developmental pathways. The result is a stucture characterized by somewhat discrete parts—modularity. Thus, given plasticity as a universal property of living matter, modularity follows. The present chapter describes some of the remarkable mechanisms of phenotypic plasticity. One reason to focus on mechanisms is to indicate the material basis for the evolution of plasticity, which is a product of concrete devices that are subject to genetic variation and selection. A cursory look at these mechanisms, however incomplete, by itself suggests the importance of plasticity in development and evolution, for the mechanisms of plasticity include some of the most ingenious and widely conserved creations of nature. Mechanisms of plasticity are further discussed in chapter 23, which describes how organisms assess environmental conditions when they adaptively switch between alternative developmental pathways. Phenotypic plasticity has already been defined as the ability of an organism to react to an environmental input with a change in form, state, movement, or rate of activity.
Cross-sexual Transfer
Authors: West-Eberhard Mary Jane
Published: November 2020

Distinctive male and female traits are perhaps the most familiar of all divergent specializations within species. In cross-sexual transfer, discrete traits that are expressed exclusively in one sex in an ancestral species appear in the opposite sex of descendants. An example is the expression of brood care by males in a lineage where ancestral females are the exclusive caretakers of the young, as in some voles (Thomas and Birney, 1979). Despite the prominence of sexual dimorphism and sex reversals in nature, and an early explicit treatment by Darwin, discussed in the next section, cross-sexual transfer is not often recognized as a major factor in the evolution of novelty (but see, on animals, Mayr, 1963, pp. 435-439; Mayr, 1970, p. 254; on plants, Iltis, 1983). When more widely investigated, cross-sexual transfer may prove to rival heterochrony and duplication as an important source of novelties in sexually dimorphic lineages. For this reason, I devote more attention here to cross-sexual transfer than to these other, well-established general patterns of change. The male and female of a sexually dimorphic species may be so different that it is easy to forget that each individual carries most or all of the genes necessary to produce the phenotype of the opposite sex. Sex determination, like caste determination and other switches between alternative phenotypes, depends on only a few genetic loci or, in many species, environmental factors (Bull, 1983). There is considerable flexibility in sex determination and facultative reversal in some taxa. Among fish, for example, there is even a species wherein sex is determined by juvenile size at a critical age (Francis and Barlow, 1993). The sex determination mechanism, whatever its nature, leads to a series of sex-limited responses, often coordinated by hormones and not necessarily all occurring at once. A distinguishing aspect of sexually dimorphic traits in adults is that there is often a close homology between the secondary sexual traits that are differently modified in the two sexes.
Divergence without Speciation
Authors: West-Eberhard Mary Jane
Published: November 2020

Part II discussed the developmental origins of novelty in terms of how the phenotype is reorganized during evolution. It did not deal extensively with the problem of adaptedness during evolutionary transitions. How are we to explain transitions from one well-adapted state to another? Many still-influential discussions of adaptive shifts, such as Simpson’s (1944) treatment of quantum evolution and Wright’s (1932) discussion of shifting balance, associate change with fitness cost. Speciational theories of change depict change as dependent upon reproductively isolated populations in new environments. This chapter discusses divergence without reproductive isolation of novel forms, where the presumed cost of change is sidestepped because of the presence of adaptive options in the population undergoing change. Darwin’s solution to the problem of maladaptation during change was strict gradualism in monomorphically adapted populations. Darwin (1859 [1966]) reasoned that transitions between specialized adaptive states need not be disruptive if they were to occur by a series of small steps. Wright’s (1932) shifting balance is another solution to the same problem, but in Wright’s theory, change is initiated by a chance combination of genes that happens to suit a population to a new adaptive mode. Without a gradual adaptive change or a lucky gene combination, a shift between two peaks on Wright’s adaptive landscape would imply passing through a valley of inferior adaptedness. Alternative phenotypes offer a third kind of solution, one that requires neither strict gradualism in a monomorphic population nor chance genetic events. In species with alternative phenotypes, a recurrent novelty that happens to prove advantageous to some individuals or in some circumstances can be refined via gradual genetic accommodation as an optional trait. Since this involves developmental diversification, not transformation or loss of existing traits, the new option develops as a new specialization alongside old ones. Shapiro notes that conditional expression of alternative phenotypes is a way of having two adaptive specializations “without carrying a genetic load,” or a cost of genotypes that oblige expression of phenotypes less favorable than the fittest one.
Maintenance without Equilibrium
Authors: West-Eberhard Mary Jane
Published: November 2020

The old question of the maintenance of alternative phenotypes appears in a new light when seen from a developmental point of view. In the past, alternatives were treated as genetic polymorphisms and explained in terms of genetic equilibria. During the synthesis of genetics and evolutionary theory in the early twentieth century, single-locus and linkagegroup genetic polymorphisms were seen as maintained in three different ways: by heterosis (heterozygote advantage), by frequency-dependent selection, and by balancing selection in a spatially heterogeneous environment (summarized in Dobzhansky, 1970). Later models showed how alternative behavioral and morphological tactics in theory could be maintained as “evolutionary stable strategies” (ESSs; see summary and history in Parker, 1984a). ESS models treat the maintenance of alternatives not as a problem in genetics but as a problem in game theory. This chapter views the maintenance of alternative phenotypes as a problem in the evolution of regulation, where the genes responsible for the maintenance of alternatives influence regulation at condition-sensitive, polygenic developmental decision points whose thresholds can be adjusted upward and downward under selection. These adjustments affect the ratio of alternatives observed. Regulation may sometimes be determined by a small number of alleles, but even then, insofar as most readily observed alternative phenotypes are concerned, they are alleles that influence a polygenic switch (see chapter 6). Rephrased in developmental terms, the question of maintenance of alternative phenotypes, whether genotype specific or conditional, becomes: What selective factors can influence the evolution of regulatory mechanisms so as to preserve the expression of two or more alternative traits rather than just one? Along with the rest of this book, this chapter focuses on the importance of developmental plasticity for evolutionary interpretations. It describes three types of regulation that have been assumed by theoretical models, and argues that two of them—genotype-specific and stochastic regulation— are relatively uncommon in nature, even though common in theoretical research. I then discuss reasons for the superior stability of the third, conditional type of regulation and argue that the properties of complex adaptive alternative phenotypes may help explain the maintenance of genetic polymorphisms.
Punctuation
Authors: West-Eberhard Mary Jane
Published: November 2020

In punctuated evolution (Eldredge and Gould, 1972) periods of relatively little change (“stasis”) are punctuated by episodes of relatively rapid change in the rate of evolution of a quantitative morphological trait, as seen in the fossil record of morphology. According to Simpson (1984), the term quantum evolution, refers to the same thing. Like Eldredge and Gould, Simpson contrasted quantum evolution with phyletic change, or sustained directional evolution without branching; considered that it could be associated with speciation (though also with phyletic evolution; p. 206); and even mentioned interrupted equilibra “In phyletic evolution equilibrium of the organism-environment system is continuous, or nearly so, although the point of equilibrium may and usually does shift. In quantum evolution equilibrium is lost, and a new equilibrium is reached”. I use the term “punctuation” rather than “quantum” because it less ambiguously describes change in rate of evolution. In its original meaning (from the Latin quantus), quantum means quantity. But quantum change, as mentioned by Simpson, is identified with the “quanta” of physics, which are discrete units of energy. This could encourage mistaken identification of punctuated change with the origin of discrete novelties, not the intended meaning of punctuated evolution, which is periodically altered rate of change in a continuously variable, quantitative trait. Mayr, Eldredge, Gould, and others (e.g., Stanley, 1979, 1981) explain stasis and punctuation in terms of speciation. Speciational punctuation hypotheses see stasis as due to the characteristics of established biological species, such as gene flow within interbreeding populations, large population size, heterogeneity of the species environment that retards directional change, developmental integration, canalization, coadapted genomes, stabilizing selection, and frequently reversing evolution over time within established species (Eldredge and Gould, 1997). These factors have been summarized by the term “gene-pool cohesiveness” (Mayr, 1989) or “developmental coherences” (Gould, 1989b), though the causes of stasis under the speciational hypothesis are admittedly vague and debatable (for reviews of other possible causes of stasis, see Williamson, 1987; Coyne and Charlesworth, 1997; Van Valen, 1982a; Spicer, 1993).
Enzymes and Catalytic Mechanisms
Authors: Frey Perry A. , Hegeman Adrian D.
Published: November 2020

Enzymes catalyze the biochemical reactions in cells of all organisms. These reactions constitute the chemical basis of life. Most enzymes are proteins—a few are ribonucleic acids or ribonucleoproteins—and the catalytic machinery is located in a relatively small active site, where substrates bind and are chemically processed into products. Illustrations of the molecular structure of chymotrypsin, a typical enzyme, and the location of its active site appear in figs. 1-1A and B. The polypeptide chain is shown as a ribbon diagram, and the active site is the region in which an inhibitor, the black ball-and-stick model, is bound. The gray ball-and-stick structures are amino acid side chains at the active site that participate in catalysis. The ribbon diagram shows the individual chains and the α-helices and β-strands as if there were vacant spaces between them; however, very little free space exists in the interior of an enzyme. The packing density in the interior of a protein is typically 0.7 to 0.8, meaning that 70% to 80% of the space is filled and only 20% to 30% is interstitial space (Richards, 1974). That the packing density in hexagonally closest packed spheres is 0.75, similar to a protein, conveys a concept of the interior. The free space inside a protein is so little that in a space-filling model, the polypeptide chain cannot be discerned, and interactions between active sites and substrate or inhibitors cannot be seen. For this reason, we display structures as ribbon diagrams to facilitate the discussion of ligand binding interactions within an active site. Chymotrypsin is the most widely studied and one of the best-understood enzymes. It catalyzes the hydrolysis of proteins at the carboxamide groups of hydrophobic amino acid residues, principally phenylalanyl, tyrosyl, and tryptophanyl residues. It also catalyzes the hydrolysis of small substrates, such as acetyltyrosine ethyl ester (ATEE) or acetyltyrosine p-nitroanilide (ATNA). These reactions are practically irreversible, their rates can be measured spectrophotometrically, and they behave kinetically as one-substrate enzymatic reactions. The overall reaction of ATEE can be written as ATEE → Acetyltyrosine + Ethanol, where the participation of water as a substrate is understood.
Nitrogen and Sulfur Transferases
Authors: Frey Perry A. , Hegeman Adrian D.
Published: November 2020

Unlike other group transfer reactions in biochemistry, the actions of nitrogen transferring enzymes do not follow a single unifying chemical principle. Nitrogen-transferring enzymes catalyze aminotransfer, amidotransfer, and amidinotransfer. An aminotransferase catalyzes the transfer of the NH2 group from a primary amine to a ketone or aldehyde. An amidotransferase catalyzes the transfer of the anide-NH2 group from glutamine to another group. These reactions proceed by polar reaction mechanisms. Aminomutases catalyze 1,2-intramolecular aminotransfer, in which an amino group is inserted into an adjacent C—H bond. The action of lysine 2,3-aminomutase, described in chapter 7, is an example of an aminomutase that functions by a radical reaction mechanism. Tyrosine 2,3-aminomutase also catalyzes the 2,3-amino migration, but it does so by a polar reaction mechanism. In this chapter, we consider NH2-transferring enzymes that function by polar reaction mechanisms. Transaminases or aminotransferases are the most extensively studied pyridoxal-5'-phosphate (PLP)–dependent enzymes, and many aminotransferases catalyze essential steps in catabolic and anabolic metabolism. In the classic transaminase reaction, aspartate aminotransferase (AAT) catalyzes the fully reversible reaction of L-aspartate with α-ketoglutarate according to fig. 13-1 to form oxaloacetate and L-glutamate. Like all aminotransferases, AAT is PLP dependent, and PLP functions in its classic role of providing a reactive carbonyl group to function in facilitating the cleavage of the α-H of aspartate and the departure of the α-amino group of aspartate for transfer to α-ketoglutarate (Snell, 1962). PLP in the holoenzyme functions in essence to stabilize the α-carbanions of L-aspartate or L-glutamate, the major biological role of PLP discussed in chapter 3. The functional groups of the enzyme catalyze steps in the mechanism, such as the 1,3-prototropic shift of the α-proton to C4' of pyridoxamine 5'-phosphate (PMP). The steady-state kinetics corresponds to the ping pong bi bi mechanism shown at the bottom of fig. 13-1. This mechanism allows L-aspartate to react with the internal aldimine, E=PLP in fig. 13-1, to produce an equivalent of oxaloacetate, with conversion of PLP to PMP at the active site (E.PMP), the free, covalently modified enzyme in the ping pong mechanism.