bluuebunny/crossref_metadata_2025 huggingface dataset:
Biogeochemical Fluxes across Piedmont Slopes of the Jornada Basin
Authors: Abrahams Athol D. , Neave Melissa
Published: November 2020

This chapter is an overview of recent studies of the movement of water, sediment, and nutrients across a principle piedmont slope, or bajada, of the Jornada Basin. Bajadas are extensive, gently sloping surfaces formed by the coalescence of alluvial fans and are a major landscape component of the basin and range province. Over the past four decades a considerable body of research has elucidated the form and function of alluvial fans (Bull 1977; Blair and McPherson 1994; Harvey 1997), but less attention has been paid to bajadas. In particular, the bajadas most neglected are those where channels converge and diverge at irregular intervals downslope. This type of bajada is found at the base of Summerford Mountain, the northernmost peak of the Doña Ana Mountains on the western edge of the Jornada Basin. For convenience, this bajada is hereafter referred to as the Summerford bajada. The research has involved rainfall simulation experiments on small plots, monitoring of two small watersheds on this bajada, and computer modeling of the processes operating in these watersheds and over the bajada as a whole. A detailed understanding of the hydrology and hydraulics of overland flow on this bajada requires a numerical model of the rainfall-runoff process. The objective of this chapter is to detail the model and draw conclusions from model simulations about hydrologic transports of sediment and nutrients across this bajada. Because these piedmonts are important surfaces in this desert (chapter 2) an understanding of their hydrologic and biogeochemical dynamics is crucial to understanding landscape dynamics in the basin and throughout arid regions. Summerford Mountain is a steep-sided, rocky inselberg (i.e., isolated mountain) that rises 380 m above the surrounding bajada to an elevation of 1,780 m. The mountain is composed of monzonite porphyry of Oligocene age (Seager et al. 1976) and has a fringing bajada on its northern and eastern sides. This study focuses on the bajada to the east, which extends 2.5 km to the basin floor at an average gradient of 4%.
Eolian Processes on the Jornada Basin
Authors: Gillette Dale , Curtis Monger H.
Published: November 2020

In arid and semiarid lands, soil erosion by wind is an important process that affects both the surface features and the biological potential of the ecosystem. The eolian flux of soil nutrients into or out of an ecosystem results in enrichment or impoverishment of its biological potential. In the Jornada Basin, wind erosion is the only significant mechanism for the net loss of soil materials because fluvial processes do not remove materials from the basin. Vigorous wind erosion leads to topographic changes, altering the growing conditions for plants and animals. Examples of such changes in topography are the formation of sand dunes or the removal of whole soil horizons. Our goal in this chapter is to describe the construction of a mathematical model for wind erosion and dust production for the Jornada Basin. The model attempts to answer the following questions: 1. Which soils are affected by wind erosion? 2. How does wind erosion occur on Jornada soils? 3. Does changing vegetation cover lead to a change in the source/sink relationship? 4. Is the Jornada a source or sink of eolian materials? If it is a source, what materials are lost? 5. How does wind erosion change the soil-forming process? We will provide provisional answers for the questions and outline work that will more clearly define these answers. Airborne dust has a significant residence time in the atmosphere and acts to modify the radiative properties of the atmosphere, mainly by back-scattering the incoming solar radiation (Andreae 1996). Changing land uses in arid and semiarid areas (e.g., overgrazing and cultivation) can drastically alter the dust emissions to the atmosphere (Tegen et al. 1996). The climatic effects of soil-derived dust were investigated in an experiment in central Asia (Golitsyn and Gillette 1993). Using measured size distributions for emitted dust (Sviridenkov et al. 1993) and various real and imaginary indices of refraction (Sokolik et al. 1993), Sokolik and Golitsyn (1993) calculated climatic effects. Atmospheric dust decreased the total radiative balance of the underlying surface and at the same time induced general warming of the underlying surface–atmosphere system due to a decrease in the system albedo over the arid zones.
Scaling Near the Critical Point in Mixture
Authors: Chimowitz Eldred H.
Published: November 2020

The critical point of mixtures requires a more intricate set of conditions to hold than those at a pure-fluid critical point. In contrast to the pure-fluid case, in which the critical point occurs at a unique point, mixtures have additional thermodynamic degrees of freedom. They, therefore, possess a critical line which defines a locus of critical points for the mixture. At each point along this locus, the mixture exhibits a critical point with its own composition, temperature, and pressure. In this chapter we investigate the critical behavior of binary mixtures, since higher-order systems do not bring significant new considerations beyond those found in binaries. We deal first with mixtures at finite compositions along the critical locus, followed by consideration of the technologically important case involving dilute mixtures near the solvent’s critical point. Before taking up this discussion, however, we briefly describe some of the main topographic features of the critical line of systems of significant interest: those for which nonvolatile solutes are dissolved in a solvent near its critical point. The critical line divides the P–T plane into two distinctive regions. The area above the line is a one-phase region, while below this line, phase transitions can occur. For example, a mixture of overall composition xc will have a loop associated with it, like the one shown in figure 4.1, which just touches the critical line of the mixture at a unique point. The leg of the curve to the “left” of the critical point is referred to as the bubble line; while that to the right is termed the dew line. Phase equilibrium occurs between two phases at the point where the bubble line at one composition intersects the dew line; this requires two loops to be drawn of the sort shown in figure 4.1. A question naturally arises as to whether or not all binary systems exhibit continuous critical lines like that shown. In particular we are interested in the situation involving a nonvolatile solute dissolved in a supercritical fluid of high volatility.
Overview: A System for Tracking and Managing the Results from Sequence Comparison Programs
Authors: Yee David P. , Hunkapiller Tim
Published: November 2020

The Human Genome Project was launched in the early 1990s to map, sequence, and study the function of genomes derived from humans and a number of model organisms such as mouse, rat, fruit fly, worm, yeast, and Escherichia coli. This ambitious project was made possible by advances in high-speed DNA sequencing technology (Hunkapiller et al., 1991). To date, the Human Genome Project and other large-scale sequencing projects have been enormously successful. The complete genomes of several microbes (such as Hemophilus influenzae Rd, Mycoplasma genitalium, and Methanococcus jannaschii) have been completely sequenced. The genome of bacteriophage T4 is complete, and the 4.6-megabase sequence of E. coli and the 13-megabase genome of Saccharomyces cerevisiae have just recently also been completed. There are 71 megabases of the nematode Caenorhabditis elegans available. Six megabases of mouse and 60 megabases of human genomic sequence have been finished, which represent 0.2% and 2% of their respective genomes. Finally, more than 1 million expressed sequence tags derived from human and mouse complementary DNA expression libraries are publicly available. These public data, in addition to private and proprietary DNA sequence databases, represent an enormous information-processing challenge and data-mining opportunity. The need for common interfaces and query languages to access heterogeneous sequence databases is well documented, and several good systems are well underway to provide those interfaces (Woodsmall and Benson, 1993; Marr, 1996). Our own work on database and program interoperability in this domain and in computational chemistry (Gushing, 1995) has shown, however, that providing the interface is but the first step toward making these databases fully useful to the researcher. (Here, the term “database” means a collection of data in electronic form, which may not necessarily be physically deposited in a database management system [DBMS]. A scientist’s database could thus be a collection of flat files, where the term “database” means “data stored in a DBMS” is clear from the context.) Deciphering the genomes of sequenced organisms falls into the realm of analysis; there is now plenty of sequence data. The most common form of sequence analysis involves the identification of homologous relationships among similar sequences.
Basic Information About Soils and Plants
Authors: Keefer Robert F.
Published: November 2020

All higher plants require the following factors for growth: . . . 1. Light 2. Heat* 3. Water* 4. Carbon Dioxide* 5. Oxygen* 6. Nutrients* 7. Mechanical Support* * Supplied by Soil or Soil Substitute. Except for light, all of these requirements are supplied by soil or a soil substitute; however, they must be supplied in the proper combination for best plant growth. Whichever of these is supplied below the optimum level will limit plant growth. Landscape architects need to determine which factor or factors limit growth and take measures to correct it. . . . WHAT IS SOIL? . . . “The soil” is a general term for the layer of the earth’s crust above the bedrock that has been weathered (physically and biochemically) by destructive and synthetic sources. “A soil” denotes a specific well-defined part of “the soil” with recognized properties and characteristics. There are thousands of different kinds of soils, and each individual soil has its own characteristics and responds to specific management. The name of a soil is associated with specified soil properties within stated limits. A few examples are Cecil clay loam, Marshall silt loam, and Norfolk sand. A number of factors have been involved in the formation of the soil and also of individual soils. The type of soils that have been formed depend on the nature of parent material (rocks and minerals), topography (lay of the land), climate (temperature and precipitation) whether or not living organisms are present, and geological time for formation. A change in any one or more of these soil-forming factors can have a profound effect on the specific “soil” that is formed. Is it any wonder that many diverse kinds of soil have been formed? In fact, branches of soil science called soil genesis and soil classification delve into this diversity in great detail. Soil Parent Material. Most soils are derived from the weathering of rocks and minerals. Exceptions to this are man-made soils and organic soils that are almost exclusively developed from organic matter.
Physical Properties of Soils
Authors: Keefer Robert F.
Published: November 2020

Soil texture can be defined as the size and proportion of the soil particles—sand, silt, and clay—that are present in a soil. . . . Sand is the largest—from 0.05 to 2mm—and considered coarse texture; consists of angular spheres or cubes. Silt is intermediate—from 0.002 to 0.05mm—and considered medium texture; consists of properties between sand and clay. Clay is the smallest, being less than 0.002mm, and considered fine texture; appears as plate-like or flakes. . . . Any individual soil can be placed on the soil textural diagram when relative amounts of sand, silt, and clay are specified. As a general rule, the type of soil can be determined by feel when squeezed between the fingers. If the soil feels harsh and gritty it would be classified as a sandy soil. One that feels smooth and not sticky or plastic would be a silt soil, and one that is sticky or plastic would be a clay. Another way to distinguish between soils is their ability to form a ribbon. Soils that will not form a ribbon are sands. Those that form a fragile ribbon are loams; those that easily form a thick ribbon are clay loams; and those that easily form a long, thin, flexible ribbon are clays. . . . To be classified a sand, the soil must have more than 45% sand. To be classified a clay, the soil must have more than 20% clay. Loam is a mixture of sand, silt, and clay in about equal proportions. It is considered “ideal” for growing plants. . . . Weight of the soil solids is called “particle density.” For most common mineral soils (soils in which organic matter is usually less than 20%), particle density is about 2.65 g/cm3. Organic soils (where organic matter is greater than 20%) are usually about half as heavy, with particle density between 1.1 to 1.4 g/cm3. This measurement would be an important factor to consider if much material was to be transported for topsoiling.
Occupation-Specific Population Models: Population and Dynastic Cycles
Authors: Chu C. Y. Cyrus
Published: November 2020

As Lee (1987) pointed out, vital rates of the human population are often determined by forces such as culture, institutions, technology, and individual rationality, forces that have little to do with density pressure or prior growth. Perhaps most people also expect “rational” human practice to weaken the biological responses of both fertility and mortality to density pressure, while strengthening the nonbiological response through institutional regulations. But can human institutional designs and rational responses really reduce the impact of natural checks? As we study the pattern of population dynamics in ancient China, we can provide some viewpoints different from the general opinion. The long-term relationship between human institutional designs and natural checks is discussed in chapter 14. The books by Ho (1959) and Chao and Hsieh (1988; hereinafter C&H) contain the most thorough research on the history of Chinese population. The data summarized in C&H have presented us with a time-population diagram, shown in figure 9.1. From this figure, as well as other related literature, the following “stylized facts” of population dynamics in Chinese history can be summarized: 1. Population declines often coincided with dynasty changes (C&H; Ho, 1959). 2. Population declines were often drastic in a rather short period of time. 3. Natural checks such as famine and epidemics did not independently reduce the population surplus (Ho, 1959); rather, population declines were often the direct and indirect results of internecine wars. 4. There are obvious peaks and troughs in the population data, but no regular cyclical patterns (C&H). The fact that no serious population decline appears to have been independently due to famines and epidemics seems to suggest a weak pattern of density-dependency for ancient Chinese populations, a pattern consistent with the observation of Lee mentioned in the beginning of this chapter. However, as noted by many historians (see, e.g., Ho, 1959, and C&H 1988), the frequent clashes between soldiers and rebellious peasants in Chinese history were often initiated by famine or density pressure. As such, the originally weak natural checks on population were often magnified by war, and such magnified “institutional checks” caused very drastic population changes.
Linear Multimodels
Authors: Pearson Ronald K.
Published: November 2020

This chapter briefly discusses the class of linear multimodels, which are globally nonlinear dynamic models, obtained by “piecing together” several local, linear dynamic models. The motivation behind this approach to model development is the observation that an approximate model’s complexity generally increases with the range of operation over which it must be valid. In particular, it has been noted repeatedly that linear models are often adequate approximations of process dynamics over a sufficiently narrow operating range. Thus, if the total operating range can be decomposed into small enough subsets, it is reasonable to expect that linear models will provide reasonable characterizations of process dynamics over these local regimes. The process of piecing these local models together may be approached in a number of different ways, and the details of this process are important, as subsequent examples illustrate. The principal issues that must be addressed in developing linear multimodels are illustrated with the example of a batch fermentation reactor, described in Sec. 6.1. Three possible definitions of discrete-time linear multimodels are presented in Secs. 6.2.1 through 6.2.3. The first of these definitions is based on Johansen and Foss (1993), whereas the second definition represents an apparently slight variation on the first that can lead to fundamentally different qualitative behavior. The third definition of linear multimodels is a special case of the first, described in Tong (1990) under the name open-loop threshold autoregressive models. The primary difference between Tong’s definition and that of Johansen and Foss is whether the regions of local model validity can overlap: they can in the models of Johansen and Foss, but they cannot in Tong’s model. An extremely important practical issue is the criterion by which local models are selected. The primary focus here is on Tong’s class of linear multimodels where each local model completely describes the global model dynamics over some specified operating range. If this operating range is defined entirely in terms of the input sequence {u(k)} , these models will be designated input-selected, whereas if the operating range is defined entirely in terms of the output sequence {y(k)}, they will be called output-selected; if both inputs and outputs are involved, the term generally selected will be used.
Development
Authors: West-Eberhard Mary Jane
Published: November 2020

Any comprehensive theory of adaptive evolution has to feature development. Development produces the phenotypic variation that is screened by selection. For a mutation to affect evolution, it must first affect development. In order to understand phenotypic change during evolution, one has to understand phenotypic change during development, as well as how to relate that change to selection and gene-frequency change (evolution). The evolution of the phenotype is synonymous with the evolution of development. The genotype-phenotype problem addressed by the metaphors of chapter 2 is fundamentally a problem of development. Genetic programming, the canalized epigenetic landscape, and the recipes and blueprints contained in the genes—all are metaphors for development. Development is the missing link between genotype and phenotype, a place too often occupied by metaphors in the past. The task of this chapter is to outline a concept of development that connects it to mechanisms, on the one hand, and natural selection and evolution on the other, without a potentially misleading metaphorical crutch. The portrait of development provided by developmental biology is not adequate to this task. Evolutionary developmental biology extensively treats the genomic correlates of gross morphological variation across phyla, with little or no discussion of behavior, physiology, life histories, and the kind of variation within populations that is required for natural selection to work. Some progress toward a population approach has been made in plant developmental biology (e.g., see Lawton-Rauh et al., 2000). But a strong emphasis on the genome means that environmental influence is systematically ignored. If you begin with DNA and view development as “hard-wired” (e.g., Davidson, 2000), you overlook the flexible phenotype and the causes of its variation that are the mainsprings of adaptive evolution. I begin instead with the observation that DNA activity—gene expression—is universally condition sensitive and dependent upon materials from the environment. This implies connections between a DNA-centered approach and conventional insights about adaptive evolution in variable environments. The genome affects development at nearly every turn, so genes obviously play an important role in any theory of development and evolution.
The Nature and Analysis of Phenotypic Transitions
Authors: West-Eberhard Mary Jane
Published: November 2020

Part II is about origins: how do new traits arise from old phenotypes? People of all ages are fascinated by the question of origins. Origins are the common concern of evolutionists and creationists, of ethnic historians, of Mormon geneologists and the Daughters of the American Revolution, of adopted children searching for their biological parents— indeed, of all who have wondered where Johnny got his patience, his sense of humor, or his big nose. Darwin was a clever publicist when he titled his most famous book The Origin of Species. He touched deep human chords by discussing not only the origin of species but the origin of marvellously complex morphological and psychological traits—specialized limbs, sexual behavior, intelligence, heroism, and the vertebrate eye, to mention just a few. Research on selection and adaptation may tell us why a trait persisted and spread, but it will not tell us where a trait came from. This is why evolutionary biology inevitably intersects with developmental biology, and why satisfactory explanations of ultimate (evolutionary) causation must always include both proximate causes and the study of selection. Novel traits originate via the transformation of ancestral phenotypes during development. This transformational aspect of evolutionary change has been oddly neglected in modern evolutionary biology, even though it is an integral part of human curiosity about origins in other fields. From classical mythology to modern-day childrens’ books, origins are explained in terms of transformations of the phenotype, alongside attention to developmental mechanisms and adaptive functions. Consider this excerpt from The Apeman’s Secret (Dixon, 1980), a Hardy Boys adventure book: . . . [T]he Apeman hated cruelty of any kind. Whenever he saw crooks or villians do something nasty to a helpless victim, he would fly into a rage. This would change his body chemistry and cause him to revert to the savage state. . . .
Duplication
Authors: West-Eberhard Mary Jane
Published: November 2020

Duplication occurs at all levels of phenotypic organization. It was among the first developmental phenomena to attract the attention of biologists interested in phenotypic transitions during evolution. Duplication and repetition of similar segments, or metamerism, appeared in the writings of Aristotle, Cuvier, Owen, and Darwin, and many early twentieth-century authors discussed it (reviewed in Lauder, 1981). More recently it has become a major theme in discussions of genetic diversification (e.g., Ohno, 1970; Weiss, 1990). Nijhout (1991a) considers iteration or redundancy of parts followed by divergence of the replicates “the major principle of morphological evolution.” But it is not easy to rank modes of origin in order of their importance, because it is so easy to reclassify examples from different points of view. Just as heterochrony can be emphasized by focusing on the timing aspect of any regulatory change (as discussed in chapter 13), duplication can be emphasized by focusing on the iterative aspect of repeated expression at different times, places, or contexts. Phenotypic recombinations classified in these chapters as heterotopy, heterochrony, cross-sex transfers, or correlated shifts could be reclassified as duplications, since many are reexpressions of the same trait in a new place or context without loss of the original trait. Similarly, pleiotropy can be described as the duplicated expression of genes (Hamburger, 1980). This chapter focuses mainly on adjacent duplications that result in serial repetitions—serial homologues, or “iteration” (Nijhout, 1991a). Heterotopy, or nonadjacent duplication within the same individual and life stage, is discussed in chapter 14, even though the separation is somewhat arbitrary. The differences in position and surroundings that result in differences in phenotypic pattern are, in their effects, regulatory differences, and it is just such local differences that cause developmental processes to diverge. It is a difference in regulation, then, that causes duplicates to diverge phenotypically and ultimately renders them subject to diverging selection and divergent evolution. One could reason from this that divergence between duplicates is virtually inevitable given enough time, because the local developmental environments on all sides of duplicate parts would rarely be absolutely identical over long periods.
Quantitative Shifts and Correlated Change
Authors: West-Eberhard Mary Jane
Published: November 2020

Preceding chapters have discussed evolutionary transitions as changes in the expression of discrete, modular traits. This chapter discusses transitions that are due to shifts in the magnitude, rather than the time, place, or repetition, of trait expression. Especially, it considers examples where environmental extremes induce quantitative change in the expression of continuously variable plastic traits. Quantitative shifts can produce novel extremes, novel combinations of extremes, or simultaneously opposite shifts due to negative correlations between traits, as in trade-offs. As pointed out by Brien (1969; see also chapter 7), correlated adaptive shifts can produce major changes in which large steps are not lethal because the usual adaptive plasticity of the organism accommodates the kind of change that occurs when “a new type of organization is born”. The same developmental plasticity that is responsible for phenotypic accommodation and homeostatic stability (see chapter 3) can produce correlated change as well. Correlations among the environmental responses of plastic traits mean that several quantitative traits can change at once, if they respond simultaneously to the same mutation or environmental factor. The two-legged goat described in chapter 3 shows how the multidimensional plasticity of the phenotype can produce a strikingly novel form that, lacking intermediates, appears to be a qualitative change—a change in kind, not merely degree. The fact that the same plasticity-mediated changes would occur whether the cause of shortened front legs were due to a mutation or to an environmental effect early in development illustrates the interchangeability of genetic and environmental factors in inducing correlated change. Raff and Kaufman (1983, p. 202) called correlated effects due to developmental relationships among continuously variable traits “relational pleiotropy.” Positive relational pleiotropy can result when numerous positively correlated traits respond in unison to a single stimulus or condition, such as variation in size. Negative relational pleiotropy can give rise to trade-offs, or negative fitness effects among traits such that an increase in the magnitude of one means a decrease in the magnitude of one or more others.
Phenotypic Recombination Due to Learning
Authors: West-Eberhard Mary Jane
Published: November 2020

Learning, like consciousness, is something that everybody can recognize and no one can define without provoking controversy. Perhaps this is why some important books dedicate hundreds of pages to learning without defining it (e.g., Mackintosh, 1974; Marler and Terrace, 1984). In one unusually candid book, the indexed page that promised a definition of learning proved to be completely blank. That stimulated me to make my own definition, something that is easier for a person who is not an expert in the field: learning is a change in the nervous system manifested as altered behavior due to experience (based on discussions in Marler and Terrace, 1984; Bell, 1991; Mackintosh, 1974, 1983; Papaj, 1994). Most people, including most biologists, probably underestimate the importance of learning in the biology of nonhuman animals. But there have been important exceptions, for example, in the writings of Baldwin (1902), Hinde (1959), Partridge (1983), Roper (1983a,b), Slater (1983,1986), Shettleworth (1984), Davey (1989), Wcislo (1989), Real (1993, 1994), Dyer (1994), Morse (1980), Marler (1998), and others (see Marler and Terrace, 1984). Some form of learning, whether habituation, associative learning (Pavlovian conditioning, in which a reward or punishment is associated with some cue such a color, odor, or sound), aversive learning, or trial and error learning (operant conditioning, in which a rewarded behavior is repeated or a punished one stopped), seems to occur in all animal groups where there is enough versatility in movement to allow it to be recognized. The venerable animal psychology text by Maier and Schneirla (1935 [1964]) gives many interesting examples from a time when researchers sought to demonstrate learning in a wide variety of organisms. They found it even in protists. In more recent research in areas such as foraging behavior and kin recognition (e.g., see Heinrich, 1979; Fletcher and Michener, 1987), learning has proven to be important but is a sidelight to research more concerned with optimization and adaptation. So learning itself has not always received the attention it deserves as a phenomenon of general evolutionary interest.
Homology
Authors: West-Eberhard Mary Jane
Published: November 2020

Homology—similarity due to common descent—is the cornerstone of comparative evolutionary research. Wake (1994) calls it “the central concept for all of biology”. Yet homology, like “fitness” or “species,” is an elusive concept. There is unceasing debate within evolutionary biology regarding its meaning and use. Combinatorial evolution and the extensive recurrence of similar traits revealed by modern phylogenetic study (see chapter 19) compel biologists to reconsider many ideas about homology. This is already becoming apparent in recent discussions of homology in relation to developmental variation (e.g., Wagner, 1989a,b; Hall, 1994). The traditional idea of homology visualizes a linear series of changes whereby an ancestral trait has been transformed into a descendent one (see discussion by Cartmill, 1994). By this idea different homologues may appear differently modified on different phylogenetic branches, but each descendant homologous trait has at its core a single ancestral trait. If two characters are homologous, that means that each is the modified descendant of a single ancestral trait of a shared common ancestor, and characters can be homologized in simple two-member pairs. Combinatorial evolution raises the possibility that derived traits may often contain elements of more than one ancestral trait, and that what was formerly seen as a de novo modification actually involves the recombined expression of preexisting traits. Homology may involve not just different degrees of similarity, due to divergent modification, but may be “mixed.” The maize ear, for example, combines features of both male and female ancestral inflorescences (see chapter 15), and the insect head evolved by the fusion of six ancestral body segments (Kukalova-Peck, 1997). Tracing mixed homologies requires separately homologizing pairs or series of ancestral and derived states for different elements of the same descendent trait, not just lineal comparisons focusing on the modifications of a single ancestral form. Other problems are raised for the homology concept by the fact that “the same” feature may be conserved via different developmental pathways, and by the frequent and evolutionarily important occurrence of duplication and modification (see chapter 8, on duplication), producing “serial” or “iterative” homology (“homonomy”) and positional shifts (see chapter 12, on heterotopy) of similar and historically related structures (for discussions of these problems, see Roth, 1984, 1988).
Enzymatic Reaction Mechanisms
Authors: Frey Perry A. , Hegeman Adrian D.
Published: November 2020

Books dealing with the mechanisms of enzymatic reactions were written a generation ago. They included volumes entitled Bioorganic Mechanisms, I and II by T.C. Bruice and S.J. Benkovic, published in 1965, the volume entitled Catalysis in Chemistry and Enzymology by W.P. Jencks in 1969, and the volume entitled Enzymatic Reaction Mechanisms by C.T. Walsh in 1979. The Walsh book was based on the course taught by W.P. Jencks and R.H. Abeles at Brandeis University in the 1960's and 1970's. By the late 1970's, much more could be included about the structures of enzymes and the kinetics and mechanisms of enzymatic reactions themselves, and less emphasis was placed on chemical models. Walshs book was widely used in courses on enzymatic mechanisms for many years. Much has happened in the field of mechanistic enzymology in the past 15 to 20 years. Walshs book is both out-of-date and out-of-focus in todays world of enzymatic mechanisms. There is no longer a single volume or a small collection of volumes to which students can be directed to obtain a clear understanding of the state of knowledge regarding the chemicals mechanisms by which enzymes catalyze biological reactions. There is no single volume to which medicinal chemists and biotechnologists can refer on the subject of enzymatic mechanisms. Practitioners in the field have recognized a need for a new book on enzymatic mechanisms for more than ten years, and several, including Walsh, have considered undertaking to modernize Walshs book. However, these good intentions have been abandoned for one reason or another. The great size of the knowledge base in mechanistic enzymology has been a deterrent. It seems too large a subject for a single author, and it is difficult for several authors to coordinate their work to mutual satisfaction. This text by Perry A. Frey and Adrian D. Hegeman accomplishes this feat, producing the long-awaited replacement for Walshs classic text.
Acyl Group Transfer: Proteases and Esterases
Authors: Frey Perry A. , Hegeman Adrian D.
Published: November 2020

Acyl group transfer processes are plentiful in enzymatic reactions. Examples may be found in ATP-dependent ligation in chapter 11, carbon-carbon bond formation in chapter 14, and fatty acid biosynthesis in chapter 18. In this chapter, we begin by presenting the basic chemistry of acyl group transfer. We then consider four major classes of proteases that catalyze acyl group transfer in the hydrolysis of peptide bonds. Acyl group transfer is so common in organic and biochemistry that the chemistry by which it occurs is often taken for granted. Early studies provided evidence for a mechanism initiated by nucleophilic addition of the acyl group acceptor to the carbonyl group to form a tetrahedral intermediate, analogous to the reversible addition of a nucleophilic molecule to the carbonyl group of an aldehyde or ketone. A mechanism of this type is shown in scheme 6-1 for acyl group transfer from a group :X to a nucleophile :G catalyzed by a general base. This mechanism is drawn from a larger family of possible mechanisms involving specific acid-base, general acid, general base, or concerted general acid-base catalysis of nucleophilic addition to an acyl carbonyl group to form a tetrahedral intermediate, followed by the elimination of :X–H to produce the new acyl compound. In enzymatic reactions the nucleophilic atom G in scheme 6-1 is normally nitrogen, oxygen, sulfur, or a carbanionic species. An acyl carbonyl group is less polar and correspondingly less reactive toward nucleophilic addition than an aldehyde or ketone. The reason is the effect on the heteroatom of nonbonding electrons, which reside in p orbitals that overlap the π orbital of the carbonyl group. The consequent delocalization of electrons stabilizes the carbonyl group and attenuates its reactivity with nucleophiles. Other factors being equal, the order of reactivity is thioester > ester > amide, which is the inverse of the degree of delocalization. Delocalization is least in thioesters because of the high energy of the sulfur p orbitals, which reside in the next higher principal quantum number relative to oxygen in the acyl carbonyl group.
Alkyltransferases
Authors: Frey Perry A. , Hegeman Adrian D.
Published: November 2020

A number of enzymes catalyze alkylation reactions, most of which are reactions of S-adenosyl-L-methionine (SAM) as a methylating agent in the biosynthesis of hormones, modification of DNA, and methyl esterification of proteins involved in signal transduction. Other examples of enzymatic alkylation include prenyl transfer reactions, adenosyltransfer from ATP to methionine in the biosynthesis of SAM, and adenosyltransfer from ATP to cob(I)alamin in the biosynthesis of adenosylcobalamin. Methyl group transfer is also the essential step in the reaction of methionine synthase, which uses 5-methyltetrahydrofolate as an alkylating agent. In an analogous reaction, an analog of 5-methyltetrahydrofolate is the methyl group donor in the methylation of coenzyme M to form methyl coenzyme M, the proximate precursor of methane in methanogenesis (see chap. 4). Glysosyl transfer is an alkylation reaction catalyzed by a large class of enzymes, the glycosyltransferases and glycosidases. The special nature of the glycosyl compounds and their potential for undergoing glycosyltransfer places them in their own class in biochemistry (see chap. 12). The reactivity of glycosyl compounds can be attributed to the contribution of the oxygen atom directly bonded to the glycosyl carbon, the locus of alkylation. In this chapter, we consider other enzymatic alkylations. Alkylation consists of the transfer of a carbon from a leaving group to a nucleophilic acceptor, as in eq.15-1, where R is H or an organic group. The rate is controlled by the reactivity of the nucleophile X:, the stability of the leaving group Y:, and the electrophilic reactivity of the central carbon atom. Alkylation may be regarded as one of the simplest organic chemical reactions because there are few complications in the mechanism. It is the reaction of a nucleophilic molecule with an electrophilic molecule to displace a leaving group. Enzymatic alkylations proceed by polar and not radical mechanisms. In organic chemistry, polar alkylation can occur either by an associative or one-step mechanism, as in fig. 15-1A, or by a dissociative or two-step mechanism through a carbocationic intermediate, as in fig. 15-1B. The chemical nature of the alkylating agent, the propensity of the leaving group to leave, and the polarity of the solvent determine the mechanism.
A Vision for Parenting and Educational Practice
Authors: Berk Laura E.
Published: November 2020

Vygotsky’s sociocultural theory is an empowering perspective for parents and teachers. In underscoring the role of adult–child dialogues in children’s development, it offers a balanced resolution to the dichotomy between adult directiveness and child-centeredness that has, for decades, permeated American parenting advice and educational practice. Consistent with a wealth of current research, sociocultural theory stresses that children contribute actively to their own development, etching their unique imprint on everything they learn. To implement sociocultural concepts of child rearing and teaching, parents and teachers must have a firm grasp of children’s temperaments, interests, knowledge, skills, and strengths and weaknesses. Yet each ingredient of effective dialogue—the shared understanding essential for genuine communication, the sensitive guidance inherent in scaffolding, the narrative conversation that builds the child’s cultural worldview, and the meaningful activities that spark learning of all kinds—requires that adults and children join forces. To create the “zone”—the dynamic region in which children acquire cognitive and social competencies and the capacity to use thought to guide behavior—children and important adults in their lives must collaborate. Adults are leaders in this collaborative process. Through dialogues, they fashion the child’s lifeline with humanity. Weaken or sever that line, and no matter how well endowed children are genetically, they become less than they otherwise could be. Although not the sole influence, adult-child togetherness through the give-and-take of communication indelibly affects children’s development. Dialogues with parents, teachers, and other significant adults transform the child’s mind, connecting it with other minds and transferring to it a wealth of understandings and skills. From the sociocultural perspective, parents help children realize their potential by making a long-term commitment to sensitivity, consistency, and richness of interaction, not by offering brief bursts of attention interspersed with little involvement. This means that good parenting is possible only through great investments of time. Early in this book, I cited evidence indicating that contemporary parents—even those with demanding careers who claim the greatest time scarcity—have ample time for generous involvement in their children’s lives.
Saturated Flow
Authors: Warrick Arthur W.
Published: November 2020

Saturated conditions generally exist below a water table, either as part of the permanent groundwater system (aquifer) or in the vadose zone as perched water. For isotropic and steady-state conditions, such systems can be modeled by Laplace’s equation. Because it is linear, Laplace’s equation is much easier to solve than the variably saturated forms of Richards’ equation and, hence, provides a convenient place to begin. Analyses of water flow for drainage and groundwater systems borrow heavily from the classical (and old!) work in heat conduction, hydrodynamics, and electrostatics. This section presents analytical solutions for subsurface drainage and well discharge in fully penetrating confined aquifers (the solutions are the same). Included are the definition of stream functions and demonstrations of the Cauchy–Riemann relations. A comparable numerical solution is presented, and also for the ponded drainage and well discharge, and the results compared with the analytical solutions. A more complex example is then presented concerning drainage below a curved water table. These results are followed by travel-time calculations relevant to solute movement from the soil surface to a drainage system. A short section covering analytical techniques with three-dimensional images is then given, followed by a section covering additional topics, which includes a complex image example (two dimensional) and some relationships for Fourier series. Consider a point source in a two-dimensional x—y plane, as in figure 3-1. The origin corresponds to a source that is assumed to be an infinite line perpendicular to the x—y plane. If the steady flow rate is Q, then the conservation of mass results in . . . Q = Jr(2πr) (3-1) . . . where Jr is the Darcian flow in the r direction and evaluated at a polar radius r. The dimensions of Q are [L2T-1] corresponding to a volume of flow per unit time from a unit length of the line perpendicular to the x—y plane. Values of Q are taken to be positive for water entering the system.
One-Dimensional Absorption
Authors: Warrick Arthur W.
Published: November 2020

In this chapter we address one-dimensional absorption. Absorption denotes movement of water (or other liquid) into a soil under the influence of capillarity without the effects of gravity. Although important for horizontal flow conditions, there is more interest in the results and principles relevant to the early stage of infiltration and in general relationships descriptive of the physical principles for all unsaturated systems. At the outset, two simplified systems will be considered. Included is the classical problem of linear diffusion into a semi-infinite domain. Then the Boltzmann similarity transform will be applied, confirming results from the simplified solutions and leading to methods for finding soil-water diffusivity and Philip’s quasi-analytical solution. Finally, simultaneous water flow will be considered as a two-phase process. Figure 4-1 shows water introduced into a horizontal column of soil at a matric potential hwet. The value of hwet is maintained as zero or negative by the “mariotte” device to the left. The initial condition is that the matric potential is hdry with hdry < hwet ≤ 0. A porous plate at x = 0 allows water to come into the system but prevents air from flowing from the soil back into the water supply. The right-hand end allows air to freely escape the system as the water displaces the air. Vertical movement in the soil column is ignored. We make key simplifying assumptions that the conductivity is a constant K = Kwet in the wet part of the column and K = 0 for the dry part. Furthermore, we assume a sharp division between the wet and dry part at xf. On the supply side of the column (0 < x < xf), the water content is a constant (θ = θwet) and, to the dry side, the initial value is maintained (θ = θdry). These are equivalent to the “Green–Ampt” assumptions used in chapter 5, when gravity will be included as a driving force.
Fathers of Academically Successful Daughters The Fathers’ Voices
Authors: Hrabowski Freeman A. , Maton Kenneth I. , Greene Monica , Greif Geoffrey L.
Published: November 2020

These two fathers’ quotes encapsulate three central themes for African American fathers. The first reflects an experience common to many fathers, regardless of race—that a father’s participation in child-rearing is not as important as a mother’s. Fathers are often made to feel uncomfortable when they do express an interest. A second theme relates to the dangers in the community of associating with the “wrong crowd” and the pressure on these young women to become sexually active and have babies at a very young age. The second father speaks to the third theme, the challenges he sees his daughter facing as she grows up and tries to compete in an unjust world. This is a refrain that we heard throughout the interviews with the fathers. This chapter presents the stories of the fathers. They are an important part of the tapestry that has produced their academically successful daughters. They have often been a counterweight to the mothers by offering education about the male world and by providing a male perspective. It is they who assume a protective stance (often along with mothers) as they warn about relations with men. And it is they, along with the mothers, who set the achievement bar high. How did they learn the values they impart, and how do they help their daughters prepare for the future? We asked them what messages they received about education and about being Black when they grew up, and how these messages influenced their parenting style. We asked specifically about their daughters’ abilities and interests in math and science. We were interested in who the fathers believed had been helpful to their daughters along the way. We particularly focused on adolescence and the thorny issues that arise regarding emotional and physical development, dating, and growing up Black. Finally, we asked for their wisdom—what do they recommend to other parents who want to engender academic excellence in their children? Many have a certain picture of the African American father, particularly those fathers who are poor.