bluuebunny/crossref_metadata_2025 huggingface dataset:
Patterns of Net Primary Production in Chihuahuan Desert Ecosystems
Authors: Huenneke Laura F. , Schlesinger William H.
Published: November 2020

The Jornada Basin of southern New Mexico has long been an important location for the study of productivity in desert ecosystems. Researchers have studied the magnitude and sustainability of plant production since the founding of the USDA Jornada Experimental Range (JER) in 1912. The consistent administration and research focus of the JER and of the Chihuahuan Desert Rangeland Research Center (CDRRC) have facilitated a number of long-term studies of vegetation dynamics and productivity. These long-term data sets are especially critical for understanding arid ecosystems, where interannual and decadal scale variation in climate is great and plant performance is strongly constrained by the physical environment. Long-term data, including the net primary productivity (NPP) data that are the focus of this chapter, are also essential for understanding the progression or rather, degradation of ecosystem structure that has been called desertification. Through the years a variety of approaches have been used to evaluate plant production in the Jornada Basin. These approaches span the range from applied or management-oriented techniques, focused primarily on assessing patterns of palatable forage production, to more basic empirical studies based on dimension analysis or similar measurements of plant growth, to estimates based on photosynthetic measurements, to remote sensing and modeling approaches. NPP was a particular focus of the work performed during the International Biological Programme or IBP (1970s) and is still a major emphasis in the Long-Term Ecological Research (LTER) era. Thus, the Jornada provides a unique opportunity to compare the strengths and weaknesses of different approaches applied to a complex system. Ecosystem science has provided a set of general hypotheses about the factors regulating NPP in arid and semiarid ecosystems (reviewed by Noy-Meir 1973; Hadley and Szarek 1981; Ludwig 1986, 1987). These premises include the following: 1. Plant productivity is low relative to that of other ecosystems (Lieth 1975). 2. NPP is regulated primarily by localized water availability and hence should be correlated closely with precipitation (Le Houerou 1984; Le Houerou et al. 1988). This premise is related to Noy-Meir’s (1973) definition of deserts as “water-controlled ecosystems with infrequent, discrete, and largely unpredictable water inputs.”
Resources of the Continental Margin and International Law
Authors: Prescott Victor
Published: November 2020

As discussed in chapters 2 and 3, the continental margin has been defined in article 3 of the United Nations Convention on the Law of the Sea (the Convention) as comprising "the submerged prolongation of the land mass of the coastal State, and consists of the seabed and subsoil of the shelf, slope and rise. It does not include the deep ocean floor with its oceanic ridges and subsoil thereof." Article 76 allows States to claim the outer edge of the margin with two major qualifications: If the margin is narrower than 200 nautical miles (M), States may claim the seabed to a distance of 200 M from the baselines from which the territorial sea is measured. Such a claim is identical with the area secured when a country claims an exclusive economic zone. If the margin is wider than 200 M, then claims must be made according to precise formulas and absolute limits and must be approved by the Commission on the Limits of the Continental Shelf (the Commission) (see chapter 3). The relationship of a claim to the continental margin with other maritime claims is shown in figures 5.1 and 5.2. In these figures, the contiguous zone, which is concerned with protection of the territorial sea rather than issues of sovereign economic rights, has been omitted. This zone lies between the outer limit of the territorial sea and a line composed of intersecting arcs drawn with a radius of 24 M from the baseline from which the territorial seas are measured. Figure 5.1 shows the situation when the margin is narrower than 200 M wide. In this situation, the State has sovereignty over the territorial sea and the airspace above those waters and the seabed and subsoil beneath them. The exclusive economic zone is bounded by the outer limit of the territorial sea and a line composed of intersecting arcs with a radius of 200 M, drawn from the baseline from which the territorial sea is measured. In this case the landward limits of the high seas coincide with the limits of all seas not included in the exclusive economic zone, territorial waters, and internal waters of a State and the archipelagic waters of archipelagic States, and the limits of the Area, which is all the seabed and subsoil outside national jurisdiction.
Geodetic Techniques
Authors: Dodson Alan , Moore Terry
Published: November 2020

Establishing a claim to the continental shelf is very much dependent on being able to establish base lines, locations, distances and water depth with a high degree of accuracy. Although this has always been the case, it has become much more significant with the increasing accuracy of measurement instrumentation, the introduction of global (satellite) positioning systems, and the need for international collaboration and agreement. This chapter outlines the measurements or calculations relating to position on the surface of the Earth, the geodetic principles underlying the concepts of coordinates and their reference systems, and the level of accuracy with which positions can be determined. Until the advent of satellite positioning and navigation systems, and in particular the Global Positioning System (GPS), geodetic coordinate systems were of little interest to many of the users of coordinate position information. Indeed, many of today's problems stem from historical misunderstanding of the true complexity of systems of coordinates (Ashkenazi, 1986). The first section of this chapter describes a number of common types of coordinate representation, their implementation in the definition of coordinate systems, and the interpretation of these systems with reference data. Examples of typical local, regional, and geocentric data are outlined as illustration of the general principles. In order to combine coordinates based on differing systems, be it the combination of different national systems or of a national and a geocentric system, it is also necessary to understand the methods of transforming coordinates from one system to another. Details of these methods are presented. Coordinate values within the described systems will usually have been obtained through geodetic observation of national (or international) control networks, with subsequent measurement of detail referenced to those network stations. The chapter therefore gives a brief description of geodetic networks before discussing in some detail the theory of errors and related accuracy analysis which is required in order that realistic accuracy estimates can be ascribed to positional information. The final section presents the definitions and calculation algorithms relating to geodetic distance determination on the Earth's surface, with emphasis on the geodesic— the shortest line between points on an ellipsoidal reference surface, and therefore the line that all distances in article 76 are referred to.
Historical Methods of Positioning at Sea
Authors: Kerr Adam J.
Published: November 2020

In the previous chapter, geodesy and modern geodetic techniques were reviewed in some detail. Obviously, in establishing a claim to an extension of the continental shelf, countries will, where possible, use the best and most modern techniques available. But in many cases, it will be necessary to use all existing data, including historical data. But the quality of all bathymetry and other data will be influenced by the accuracy with which the vessel collecting it was geographically positioned. Therefore, in reviewing data from charts and maps, particularly those of a historic nature, it is necessary to have a knowledge of the positioning methods used and hence the likely positional accuracy. This chapter reviews the development of the science and technology of navigating at sea and hence the positional accuracy possible. It also traces the development of the technology over the last 200 years, from the introduction of the sextant and chronometer to modern differential techniques using satellite observations. Against this background, it traces the continually improving ability to position vessels accurately at sea and out of sight of land. The bathymetry of most maps and charts available today was collected over a lengthy period, sometimes extending back beyond the turn of the century. This certainly applies to the General Bathymetric Chart of the Oceans (GEBCO) and to most small-scale nautical charts. Accordingly, the data may be of variable quality, as the technology both of measuring the depths and of geographically positioning the data has undergone significant improvements. Few bathymetric charts have been compiled purely from one set of homogeneous and recent data. In evaluating the quality and reliability of the bathymetry and its consequent use for developing offshore boundaries, it is important that the historical development of offshore positioning technology and marine navigation and their limitations with respect to accuracy be understood in order that the quality of the data used to compile the maps and charts can be properly assessed. Until the development of electronic positioning systems during World War II, the positioning of vessels out of sight of land was carried out primarily by observations of celestial bodies and dead reckoning between observations.
Data Sources, Management, and Presentation
Authors: Holcolmbe Troy L. , Moore Carla J.
Published: November 2020

In the previous chapters, the various techniques for delimiting the continental shelf have been outlined. However many continental shelf claims will be developed largely on the basis of existing information. Therefore, a coastal state should begin its article 76 implementation by assembling and reviewing all available information that is relevant for determining the outer limit of the continental shelf, and for assessing the resource potential beyond 200 nautical miles (M). Data compilation activities tend to be labor-intensive, and the amount of time needed for their successful execution depends to a large extent upon the quantity and condition of the data sets, the skill and experience of the compilation staff, and the data-handling facilities at their disposal. However, it is reasonably safe to assume that almost any compilation of existing data will be less expensive than mobilizing and executing a field program for collecting new data, so it is usually more cost-effective to begin with a compilation. Even if the data compilation operation serves primarily to demonstrate the inadequacy of existing data, it will serve a useful purpose by identifying specifically where and what kind of new information is needed. To satisfy the requirements of article 76, and to provide a foundation for an understanding of the resources within the continental shelf, we are concerned primarily with data in the fields of hydrography, geodesy, geology, geophysics, and geochemistry and their subdisciplines. Such data are usually characterized by their spatial variations, in two or three dimensions, which are of a far greater magnitude than any temporal changes, as for example in the case of gravity anomaly data. However, the temporal variation of some geoscience parameters is becoming increasingly important as an indicator of environmental change. Because of the importance of their spatial changes with respect to the delineation of the continental shelf, the traditional form of presentation of geoscience data has been as maps. Whereas maps provide an excellent visualization of the data field, they may not be sufficient to carry out the analysis needed to satisfy article 76, and increasingly, digital data, profiles, and other data forms are becoming necessary.
Deep Sea Fan Issues
Authors: Taft George , Haq Bilal
Published: November 2020

Deep sea fans occur along many continental margins. The Bengal Fan is the world's largest elongated submarine fan area, occupying over 3 x 106 km2 of seafloor in the Bay of Bengal. The Bay of Bengal is bordered by Sri Lanka, India, Bangladesh, Myanamar, the Andaman and Nicobar Islands, and Sumatra. The fan spans an area that is 2800-3000km in length and 830-1430 km in width. At the northern end of the Bay, the sediment cover is estimated to be more than 16 km in thickness (Curray and Moore, 1971, 1974, Moore et al., 1974). Recent drilling on the distal part of the fan just south of the equator during Ocean Drilling Program Leg 116 cored nearly 1 km of sediment without reaching hardrock basement (Cochran et al., 1990). The submarine feature of the Ninetyeast Ridge divides the fan into two major lobes, the main Bengal Fan and the eastern lobe, also known as the Nicobar Fan (Curray and Moore, 1974) (figure 19.1). The fan extends from 20°N latitude and, based on recent sedimentological and channel-system studies, to beyond 9°S latitude (Stow et al., 1990; Hübscher et al., 1997). The great size of the Bengal Fan is related to the history of the collision of the Indian tectonic plate with Eurasia and the subsequent uplift of the Himalayas. The first encounter of the northward-moving Indian Plate with the Asian mainland occurred around 50 million years (my) ago in the early Eocene Epoch (Haq, 1985). The first collision caused the initial uplift in the Himalayan region. Sedimentation in the bay is inferred to have started after this first collision, but extensive sedimentation probably did not begin until the early Miocene (ca. 17 my ago) after a major uplift in the Himalayas (Haq, 1985). Weathering and denudation of the Himalayas has furnished huge volumes of sediments that have built the Bengal Fan, supplied through the Ganges and Brahmaputra Rivers and their delta (figure 19.2). Sediments are transported largely by turbidity currents across the submerged continental terrace in the proximal part of the fan through a major delta-front canyon, also known as the Swatch-of-No-Ground. Currently, this canyon discharges its load into a single active channel that supplies sediment to the entire length of the fan.
Introduction to Critical Phenomena in Fluids
Authors: Chimowitz Eldred H.
Published: November 2020

Introduction to Critical Phenomena in Fluids encompasses the fundamentals of this relatively young field, as well as applications in the fields of chemical engineering, analytical chemistry, and environmental remediation processing. The exercises in the text have been developed in a way that makes the book suitable for graduate courses in chemical engineering thermodynamics and physical chemistry.
Solvation in Supercritical Fluids
Authors: Chimowitz Eldred H.
Published: November 2020

The use of supercritical fluids as solvent media is driven mainly by the need to reduce the use of organic and halogenated solvents in chemical processes. In the future, one of the main aims of research in this area will be to supplant organic solvent use in many of these processes with solvents such as supercritical carbon dioxide, environmentally a much more acceptable alternative. One of the most common engineering requirements in this area is the need to predict solubility, and other thermodynamic behavior, in high-pressure mixtures where the solvent is close to its critical point and contains nonvolatile solute species of large molecular weight present in small amounts. In this chapter, we address this problem focusing upon solvation in organic solid–supercritical fluid systems which are among the most technologically interesting. The extension of the analyses presented here to situations where the condensed phase may be a mixture of miscible liquids, for example, is straightforward and left to a problem in the additional exercises.
Fluctuations and Critical Behavior
Authors: Chimowitz Eldred H.
Published: November 2020

An important historical result with the Ising model was the achievement of an exact analytical solution by Onsager for the two-dimensional case. It is one of the few statistical-mechanical models for which an exact solution is available, and yields insight into the role played by thermodynamic fluctuations in determining critical behavior. We know that mean-field approaches, for example, which ignore the effects of fluctuations, do not predict the correct scaling exponents in the critical region. Also, we showed in the previous chapter that a mean-field analysis of the Ising model showed its specific heat CH to have a discontinuity at Tc remaining finite on either side of Tc , namely for T > Tc and T < Tc .
Scaling Theory and Computer Simulation
Authors: Chimowitz Eldred H.
Published: November 2020

In this chapter, we investigate the concept of scaling, in particular the scaling hypothesis that has proved so important in the development of the modern theory of critical phenomena. Scaling refers to the way in which properties such as the susceptibility behave in the critical region as they approach infinity (or zero). In this discussion, it is important to be specific about the thermodynamic field variables used to represent the system as well as the direction in which the critical point is approached. A useful schematic in this regard is shown in figure 9.1, which shows phase coexistence diagrams for both an Ising-type magnet and a typical fluid. The fields for the magnet are (H, T ) while for the fluid they are (μ, T ). We note immediately from this figure that the magnet’s coexistence curve is coincident with the H = 0 axis and symmetric about the M = 0 axis. However, these features do not reflect in the corresponding diagrams for the fluid, with important implications for a scaling analysis in this system, which we take up later in this chapter. We illustrate the basic critical scaling laws using the Ising (magnet) system; however, the fact that similar scaling laws also apply to fluids is an important consequence of critical-point universality, a topic we have often alluded to in this text and which is discussed in more detail in chapter 10 dealing with the renormalization-group method.
Pattern Discovery and Classification in Biosequences
Authors: Wang Jason T. L. , Marr Thomas G.
Published: November 2020

With the significant growth of the amount of biosequence data, it becomes increasingly important to develop new techniques for finding “knowledge” from the data. Pattern discovery is a fundamental operation in such applications. It attempts to find patterns in biosequences that can help scientists to analyze the property of a sequence or predict the function of a new entity. The discovered patterns may also help to classify an unknown sequence, that is, assign the sequence to an existing family. In this chapter, we show how to discover active patterns in a set of protein sequences and classify an unlabeled DNA sequence. We use protein sequences as an example to illustrate our discovery algorithm, though the algorithm applies to sequences of any sort, including both protein and DNA. The patterns we wish to discover within a set of sequences are regular expressions of the form *X1 * X2 * ... . The X1,X2,... are segments of a sequence, that is, subsequences made up of consecutive letters, and * represents a variable length don’t care (VLDC). In matching the expression *X1 * X2 * ... with a sequence S, the VLDCs may substitute for zero or more letters in S at zero cost. The dissimilarity measure used in comparing two sequences is the edit distance, that is, the minimum cost of edit operations used to transform one subsequence to the other after an optimal and zero-cost substitution for the VLDCs, where the edit operations include insertion, deletion, and change of one letter to another (Wagner and Fischer, 1974; K. Zhang et al., 1994). That is, we find a one-to-one mapping from each VLDC to a subsequence of the data sequence and from each pattern subsequence to a subsequence of the data sequence such that the following two conditions are satisfied, (i) The mapping preserves the left-to-right ordering (if a VLDC at position i in the pattern maps to a subsequence starting at position i1 and ending at position i2 in the data sequence, and a VLDC at position j in the pattern maps to a subsequence starting at position j1 and ending at position j2 in the data sequence, and i < j, then i2 < j2).
Religion and University Aspirations, 1868-188
Authors: Kemeny P. C.
Published: November 2020

“I have hitherto discouraged all proposals to make Princeton College a university,” President McCosh told the trustees in June of 1885. “I am of the opinion,” he went on to announce, “that the time has now come for considering the question.” Seizing the momentum from what many in Princeton considered a victorious debate with Harvard’s Charles W. Eliot, McCosh launched a formal campaign to make the College of New Jersey a university. He promised that his forthcoming paper, “What an American University Should Be,” would fully explain how and why the board should take this next logical “step” in the institution’s development. Although this was the first time that he officially broached the subject with the trustees, McCosh had long been laying the groundwork to build what he considered would be the crowning achievement of his presidency. With regard to this ambition, the trustees’ minutes preceding this announcement reveal a calculated plan by McCosh to convince the board that the college was making exceptional progress toward becoming a university. He would begin by winning the board’s approval for a particular reform or a new program on the grounds that it was essential if the institution was to advance its civic mission like its rivals, Harvard and Yale. Then, within a year or two, he would proclaim the reform or program a remarkable educational success and a major benefit to American society. The reorganization of biblical instruction in 1876 illustrates this process. Although McCosh had promised the Princeton community in his inaugural address that he harbored no plans to “revolutionize your American colleges or to reconstruct them after a European model,” the College of New Jersey experienced a gradual evolution toward becoming a university under McCosh’s leadership. Spurring consistent improvements in the faculty, curricula, and campus, McCosh led the college out of its antebellum educational doldrums, and, by 1885, he was ready, like his peers at Harvard and Yale, to lead his college into the promised land of American universities.
Micronutrients
Authors: Keefer Robert F.
Published: November 2020

Micronutrients needed by plants are Cu, Fe, Mn, Zn, B, Mo, Cl, Ni, Co, V, Si, and Na. The required amounts of each of these elements is very small but still essential for desirable plant growth and reproduction. These elements must be applied to soils cautiously for the range between deficient and toxic is very small. It is unwise to use a fertilizer containing all of these micronutrients. Any one of them may already be high enough in soils to cause toxicity from that particular element. If a micronutrient is suspected of being deficient, it would be wise to get soil tests and plant tissue tests to corroborate your suspicions. If a micronutrient is deficient, one should apply only the amount recommended but no more. Sometimes a toxicity of an element is more difficult to correct than a deficiency. Copper, iron, manganese, cobalt, and zinc can be present in soils as (a) several types of precipitates, (b) adsorbed onto the surface of soil particles, (c) present in primary minerals (rocks) and secondary minerals (clays), and (d) present as complex ring compounds. These forms may or may not be available to plants. Precipitates of Cu, Fe, Mn, or Zn often form in soils at high pH (after liming Fig. 14.1). This may occur in soils near buildings from the lime used in the mortar. Soil acids dissolve the lime into Ca++ or Mg++ that migrate into the soil raising the pH and cause these micronutrients to precipitate. Often an Fe deficiency is evident, particularly on acid-loving plants, such as azaleas, rhododendrons, or hollies. If this is extensive, the soil near the buildings may need to be replaced. With limited areas, the soil can be acidified by adding elemental S near the plants affected. The elements Cu, Fe, Mn, and Zn can exist as soluble forms or precipitates, depending on the pH of the soil. The soluble forms as cations are present when soils have poor internal drainage (poorly drained soils), whereas the oxides of these elements are present where the soil is well aerated.
Fertilizers
Authors: Keefer Robert F.
Published: November 2020

Fertilizers for soil on which plants grow come in a variety of forms, such as organic, inorganic, single nutrient, double nutrient, complete fertilizer (contains N, P, and K in that order), speciality fertilizers, composts, and manures. Information about each of these forms follows. Most of the N used in fertilizers is derived from a synthetic process developed by Europeans called the “Claude-Haber process.” This process uses nitrogen gas (N2) from the atmosphere along with hydrogen gas (H2) from natural gas in a device where pressure can be increased and temperature can be raised. The reaction is accelerated using an iron catalyst and removing the product (NH3) as it is formed. The Fe catalyst is subject to poisoning from impurities, such as As, Co, P, or S. Anhydrous ammonia has the highest percentage of N and the cheapest per unit of N since no processing is involved. Anhydrous (without water) ammonia is a gas but when compressed changes to a liquid. For application to soils a pressurized tank is required with a device to inject the liquid ammonia into the soil. Upon release of pressure, the liquid changes back to a gas; however, the ammonia gas reacts with the moisture in the soil to form NH4+ that is available for plants. One problem with ammonia is that NH3 gas is toxic to seedlings and growing plants, so must be applied prior to planting. This limits its use for landscape projects. Salt solutions of aqua ammonia are obtained by dissolving ammonia gas, ammonium nitrate, or urea in water. The amount dissolved will vary the concentration of N in the final product. This can be used in landscape projects, but care must be used as this material can salt out and plug up orifices when sprayed onto a soil. There is no real difference between liquid or solid fertilizers, provided the percentage of N is the same. Ammonia Nitrate [NH4NO3] (33.5% N) Ammonium nitrate is formed by ammonia gas reacting with nitric acid: . . . NH3 + HNO3 → NH4NO3 . . . This material is hygroscopic (absorbs water from the air) and requires moisture-proof bags for storage.
Satellite Imaging, Laser Technology, and Computer Programs
Authors: Keefer Robert F.
Published: November 2020

management, and development planning. Two examples of this are: GIS could allow emergency planners to easily calculate emergency response times during natural disasters; or GIS could be used to find wetlands that need protection from pollution. A Geographic Information System (GIS) is an organized collection of computer hardware, software, geographic data and personnel designed to capture, manipulate, analyze, and display all forms of geographically referenced information (Allender, 1998). A more simplified definition would he: a computer system capable of holding and using data, describing places on the earth’s surface, for the purpose of spatial analysis. It is also “intelligent graphics” to aid in the analysis and depiction of complex data sets. Components of GIS include ARC/INFO:GIS software by ESRI (Environmental Systems Research Institute), ARC—graphical features of points, lines/arcs, and polygons, INFO—the relational database component of tables of data of any attribute that ties to a graphical component.
Relations between Model Classes
Authors: Pearson Ronald K.
Published: November 2020

Chapter 2 has provided a brief review of some of the important characteristics of linear models, and Chapters 3 through 6 have introduced and discussed a number of specific classes of nonlinear models. The focus of this chapter is on the relationships that exist between these different model classes. Some of these relationships have already been discussed briefly in isolated places in earlier chapters, but this chapter attempts to give a much broader overview of how different model classes relate. In particular, it is useful to note that many popular model classes are included as proper subsets of other, larger classes. In more subtle cases, one class will be “almost included” in another, larger class, but a portion of the first class will fail to satisfy this inclusion. As a specific example, it was noted in Chapter 4 that the class of Hammerstein models is a proper subset of the class of additive NARMAX models. In contrast, it was also shown in Chapter 4 that Wiener models are not members of the additive NARMAX class except in the two degenerate cases where Wiener and Hammerstein models coincide: linear dynamic models and static nonlinearities. This chapter begins with a summary of these inclusion and exclusion results in Sec. 7.1, including both results assembled from previous chapters and a few new ones. Of particular interest are questions concerning the relationship between structurally-defined model classes and behaviorally-defined classes since these questions are directly related to the practical problem of initial model structure selection for empirical modeling, a topic considered further in Chapter 8. One of the principal objectives of this chapter is to illustrate the utility of category theory in characterizing relations between different classes of dynamic models. Essentially, category theory is a branch of mathematics whose aim is to elucidate relations between different classes of mathematical objects in extremely general terms. More specifically, category theory deals with mathematical objects (in fact, called objects) and transformations between objects (called morphisms), requiring only that these transformations be “well behaved” with respect to successive application (called composition of morphisms).
Developmental Plasticity and Evolution
Authors: West-Eberhard Mary Jane
Published: November 2020

The first comprehensive synthesis on development and evolution: it applies to all aspects of development, at all levels of organization and in all organisms, taking advantage of modern findings on behavior, genetics, endocrinology, molecular biology, evolutionary theory and phylogenetics to show the connections between developmental mechanisms and evolutionary change. This book solves key problems that have impeded a definitive synthesis in the past. It uses new concepts and specific examples to show how to relate environmentally sensitive development to the genetic theory of adaptive evolution and to explain major patterns of change. In this book development includes not only embryology and the ontogeny of morphology, sometimes portrayed inadequately as governed by "regulatory genes," but also behavioral development and physiological adaptation, where plasticity is mediated by genetically complex mechanisms like hormones and learning. The book shows how the universal qualities of phenotypes--modular organization and plasticity--facilitate both integration and change. Here you will learn why it is wrong to describe organisms as genetically programmed; why environmental induction is likely to be more important in evolution than random mutation; and why it is crucial to consider both selection and developmental mechanism in explanations of adaptive evolution. This book satisfies the need for a truly general book on development, plasticity and evolution that applies to living organisms in all of their life stages and environments. Using an immense compendium of examples on many kinds of organisms, from viruses and bacteria to higher plants and animals, it shows how the phenotype is reorganized during evolution to produce novelties, and how alternative phenotypes occupy a pivotal role as a phase of evolution that fosters diversification and speeds change. The arguments of this book call for a new view of the major themes of evolutionary biology, as shown in chapters on gradualism, homology, environmental induction, speciation, radiation, macroevolution, punctuation, and the maintenance of sex. No other treatment of development and evolution since Darwin's offers such a comprehensive and critical discussion of the relevant issues. Developmental Plasticity and Evolution is designed for biologists interested in the development and evolution of behavior, life-history patterns, ecology, physiology, morphology and speciation. It will also appeal to evolutionary paleontologists, anthropologists, psychologists, and teachers of general biology.
Heterotopy
Authors: West-Eberhard Mary Jane
Published: November 2020

Heterotopy is the spatial analogue of heterochrony: it is evolutionary change in the site of expression of a phenotypic trait. Gould (1977) attributes the word “heterotopy” to Haeckel, who used it in a more specialized way, to mean evolutionary change in the germ layer from which an organ differentiates. Wray and McClay (1989, p. 810) list several examples of heterotopy, including the origin of muscles in tetrapod forelimbs from different somites, the origin of vertebrate primordial germ cells from different germ layers, and homeotic “heterotopic” mutations that transfer appendages from one body segment to another. A broad definition of heterotopy extends the concept to include spatial patterning, not only transposition from one location to another, but spatial organization of quantitative processes such as growth (Zellditch et al., 1992) or the location of precursors during the development of homologous traits (Wray and McClay, 1988, p. 313). As in other categorizations of transitions, heterotopies could as well be classified in other ways, such as duplication. Severtzoff signaled a general relationship between heterochrony and heterotopy when he wrote that “heterochrony in development is a means of topographic coordination; i.e., new adaptation of the parts to each other.” Many morphological heterochronies in plants produce heterotopic change, since the morphological ontogeny of a plant is recorded in its adult architecture. Thus, changes in timing of expression of juvenile and adult leaf forms result in heterotopic change in architecture of the mature plant, with the juvenile leaves appearing high on the stem, rather than only basally as before. A clear and oft-described example of environmentally mediated heterotopic change was demonstrated in early experiments on melanization in the Himalayan rabbit (Sturtevant, 1913; Iljin, 1927; Iljin and Iljin, 1930; see discussions in Schmalhausen, 1949 [1986]; Huxley, 1942; Levinton, 1988). In the Himalayan rabbit, as in the Siamese cat, pigment normally develops only in the extremities, where skin temperature is below the general body temperature. Individuals raised at temperatures above 30°C develop white extremities.
Speciation
Authors: West-Eberhard Mary Jane
Published: November 2020

In sexually reproducing organisms, speciation is lineage branching—the origin of reproductive isolation between sister populations descended from a single interbreeding parent population. Obviously, speciation is a process of fundamental importance in evolution. In sexually reproducing organisms, every persistent branching point of a phylogenetic tree, whether between very similar species or higher taxa, reflects a speciation event. Because complete reproductive isolation means the end of gene flow between populations, there is no doubt that it can facilitate genetic and phenotypic divergence. So speciation is a major cause of the diversification of living things. In nonsexual or uniparental populations, isolation between divergent populations may also be called speciation, but reduced gene flow can play no role. Such populations may become genetically distinctive and divergent due to differences in mutation, selection, and drift and thereby qualify as species under some definitions (see M. B. Williams, 1992, for a discussion of the species concept in asexual organisms). This chapter deals only with speciation in sexually reproducing organisms. By the usual view of speciation, some barrier to interbreeding comes first, followed or accompanied by genetic and phenotypic divergence. Reproductive isolation leads to divergence. Here I argue that the reverse may sometimes occur—that divergence, mediated by developmental plasticity and selection, may sometimes originate first and contribute to the evolution of reproductive isolation. As discussed in part III, evolution by disruptive and frequencydependent selection can produce a developmental switch between alternative phenotypes rather than loss of intermediate genotypes. This is particularly well documented in insects, often leading to misidentification of intraspecific morphs as species. Since polymorphic insects may have host-associated morphs, host shifts accompanied by distinctive morphology cannot be assumed to represent sympatric speciation or host-race formation, and sympatric speciation hypotheses need to decisively eliminate the possibility of a role for sympatric divergence in the form of polymorphism or behavioral and physiological plasticity. Such intraspecific host shifts may contribute to speciation, whether sympatric or allopatric, as discussed further below.
Macroevolution
Authors: West-Eberhard Mary Jane
Published: November 2020

Macroevolution, or trans-specific evolution, refers to two different things in the literature on evolution. In discussions of phylogeny, it means phylogenetic branching pattern, or trends, seen at relatively high taxonomic levels (e.g., Stanley, 1979; Brooks and McLennan, 1991; Sober, 1993)—”any patterns that transcend species boundaries” (Lynch, 1991)—such as births and deaths of species and higher taxa and the shapes and diversity of radiations (Valentine, 1990). In discussions of evolutionary phenotypic transitions like those of part II, it means major phenotypic change (Lincoln et al., 1982). Rensch (1960) defined macroevolution as “evolution above the species level.” Microevolution, by contrast, is evolution below the species level, such as adaptive phenotypic and genetic change within populations, and geographic variation within a species. According to Simpson (1953a), the terms “macroevolution” and “microevolution” were invented by Goldschmidt (1940 [1982]), who also claimed that they involve different kinds of evolution. This problematic idea dates back to antiquity (see Rensch, 1960, for a concise review). The macroevolution problem, with emphasis on phylogenesis, was among other things (see Vuilleumier, 1984) behind the skepticism regarding Darwinism promoted by the enormously respected and influential French zoologist P.-P. Grassé. Grassé was convinced that the neo-Darwinian approach, with its emphasis on microevolution, cannot account for the primary features of evolution, namely, the large-scale diversification of life into major phylogenetic branches separated by unbridged gaps (e.g., see Grassé, 1973). This challenge echoes in the writings of many other critics of neo-Darwinism (e.g., Ho and Saunders, 1984; Gould and Eldredge, 1977; Gould, 1994; see also below), especially those who wish to contrast multilevel selection (including species selection) with microevolutionary theories (see Gould, 1999). The two macroevolution concepts, like the homology concepts discussed in chapter 25, are used interchangeably without sufficient attention to potential confusions. The result is needless controversy. The phylogenetic definition, for example, implies that macroevolution cannot, by definition, occur within species, for it refers exclusively to patterns above the species level. The phenotypic, major-change definition, on the other hand, can include processes within species.
Kinetics of Enzymatic Reactions
Authors: Frey Perry A. , Hegeman Adrian D.
Published: November 2020

At some point in characterizing an enzymatic reaction mechanism, kinetic information is required. This may range from the evaluation of the substrate specificity through comparison of Michaelis-Menten kinetic parameters Km and Vm for various substrates to the elucidation of the complete kinetic mechanism and evaluation of rate constants for all the steps. In this chapter, we outline the theory and methods of enzyme kinetics and show for a few simple cases the mechanistic information that can be derived. The steady-state kinetic analysis of enzymatic reactions nearly always entails the measurement of initial rates as a function of varying concentrations of a substrate at a fixed enzyme concentration. An initial rate best represents enzyme activity because it is the rate at time zero, before any of the many factors that can decrease enzyme activity come into play. These factors include inhibition by products, changes in pH, denaturation of the enzyme and so forth. In chemical kinetics, a large fraction of the time course for the reaction is usually measured to obtain a large number of data points to determine the kinetic order of the reaction. No problems with denaturation and product inhibition complicate such measurements. In contrast, the progress curve for an enzymatic reaction is generally sensitive to the accumulation of products, which are inhibitory and have to be taken into account. Moreover, the activity of an enzyme sometimes changes because of instability or environmental factors. However, accurate and reproducible initial rates can generally be obtained. It is possible to follow the full course of an enzymatic reaction by measuring the progress curve, as in conventional chemical kinetics. By fitting the curves to the integrated rate equations the steady-state kinetic parameters for an enzyme can be obtained from a single progress curve (Duggleby, 1995). This method has a number of advantages in principle. In practice, however, the many complications mentioned earlier, especially enzyme stability under reaction condition, have led kineticists to favor the measurement of initial rates at varying substrate concentrations in steady-state kinetic analysis.
Coenzymes II: Metallic Coenzymes
Authors: Frey Perry A. , Hegeman Adrian D.
Published: November 2020

The original coenzymes were small organic molecules that activated enzymes and participated directly in catalyzing enzymatic reactions. Most of them were derived from vitamins and were known as biologically “activated” forms of vitamins such as niacin, riboflavin, thiamine, and pyridoxal. Heme was in a separate category, perhaps because of its widespread biological role as an oxygen carrier, and because it was not a vitamin, it was not widely regarded as a coenzyme. However, heme was clearly an enzymatic prosthetic group in enzymes such as peroxidases and catalase, and it was known to participate in catalysis. Today, heme takes its place among the coenzymes. Other, more recently discovered metallic cofactors round out this chapter on metallocoenzymes. Most of the detailed mechanisms of metallocoenzyme-dependent reactions are not known. Hypothetical mechanisms can often be written, and some of them are supported by a few experiments. Emerging principles are emphasized here for several of the more extensively studied metallocoenzymes. In other cases, the detailed mechanisms that we include in figures and schemes must be regarded as conjectural. We do not regard them as fanciful, but they have not been proved and are referred to as “a mechanism for” in recognition that other possible mechanisms have not been excluded. Space does not permit all conceivable mechanisms to be aired, and we hope that those shown here will stimulate discussion and experimentation. Vitamin B12 coenzymes may be regarded as transitional from traditional coenzymes, in that the parent cyanocobalamin is a true vitamin, and its biologically activated forms adenosylcobalamin and methylcobalamin, with their covalent cobalt-carbon bonds, are organometallic compounds. For these reasons, we begin by discussing the vitamin B12 coenzymes. The structure in fig. 4-1 is that of adenosylcobalamin, the first B12 coenzyme to be discovered. The molecule consists of the tetradentate corrin ring, cobalt in its 3+ oxidation state held within the corrin ring, the lower axial dimethylbenzimidazole α-ribotide ligand linked by a phosphodiester group to the corrin, and the 5'-deoxyadenosyl moiety covalently bonded to cobalt. The corrin ring is structurally and biosynthetically related to heme, but it differs in a number of respects, including that it is more highly reduced and incorporates extensive stereochemistry.
Decarboxylation and Carboxylation
Authors: Frey Perry A. , Hegeman Adrian D.
Published: November 2020

Decarboxylation is an essential process in catabolic metabolism of essentially all nutrients that serve as sources of energy in biological cells and organisms. The most widely known biological process leading to decarboxylation is the metabolism of glucose, in which all of the carbon in the molecule is oxidized to carbon dioxide by way of the glycolytic pathway, the pyruvate dehydrogenase complex, and the tricarboxylic acid cycle. The decarboxylation steps take place in thiamine pyrophosphate (TPP)–dependent α-ketoacid dehydrogenase complexes and isocitrate dehydrogenase. The latter enzyme does not require a coenzyme, other than the cosubstrate NAD+. Many other decarboxylations require coenzymes such as pyridoxal-5'-phosphate (PLP) or a pyruvoyl moiety in the peptide chain. Biological carboxylation is the essential process in the fixation of carbon dioxide by plants and of bicarbonate by animals, plants, and bacteria. Carboxylation by enzymes requires the action of biotin or a divalent metal cofactor, and it requires ATP when the carboxylating agent is the bicarbonate ion. The most prevalent enzymatic carboxylation is that of ribulose bisphosphate carboxylase (rubisco), which is responsible for carbon dioxide fixation in plants. The basic chemistry of decarboxylation is illustrated by mechanisms A to D in fig. 8-1. The mechanisms all require some means of accommodation for the electrons from the cleavage of the bond linking the carboxylate group to the α-carbon. In mechanism A, an electron sink at the β-carbon provides a haven for two electrons. Acetoacetate decarboxylase functions by this mechanism (see chap. 1), as well as PLP- and TPP-dependent decarboxylases (see chap. 3). In mechanism B, a leaving group at the β-carbon departs with two electrons. Mevalonate-5-diphosphate decarboxylate functions by mechanism B and is discussed in a later section. In mechanism C, a leaving group replaces the α-carbon and departs with a pair of electrons. A biological example is formate dehydrogenase, in which the leaving group is a hydride that is transferred to NAD+. In mechanism D, a free radical center is created adjacent to the α-carbon and potentiates the homolytic scission of the bond to the carboxylate group. Mechanism D requires secondary electron transfer processes to create the radical center and quench the formyl radical.