bluuebunny/crossref_metadata_2025 huggingface dataset:
Western Grego-Roman Cities
Authors: Crouch Dora P.
Published: November 2020

The polity of Rhodes, with Cretan assistance, founded Gela on the south coast of Sicily in 688 B.C.E. (Herodotus, VII, 153) and assisted in the foundation of Akragas/ Agrigento farther northwest on the same coast in 580 B.C.E. Akragas’s foundation was part of the second wave of Greek city building in Sicily, about 150 years after the founding of Syracuse and other east coast settlements. Much of the Rhodian situation was replicated in the new cities. Settlers found familiar terrain like Gela, on a steep ridge facing the sea, surrounded by generous plains. At Gela, the acropolis at the east end is near the River Gelas, which waters the plains. Agrigento is bracketed by two rivers with plains to the south, and its lower ridge is visually equivalent to the site of Gela. An irrigation system of the Greek period like that known a little to the east at Camarina could have facilitated growing food in the alluvial soil between the two rivers, to the south of the temple ridge (Di Vita 1996: 294). If we notice geological similarities and extrapolate too freely from them to architectural similarities, we may introduce chronological fuzziness to our study. The island-wide Rhodian tradition of dealing with water resources was carried to Sicily by the colonists along with other aspects of the culture. Exchange of ideas continued during the centuries between the founding of Akragas and the synoecism of Rhodes City centuries later. For instance, the grottoes of the acropolis of the city of Rhodes are “cut into the bioclastic limestones of the Rhodes formation, with, in some cases, the floor cut down into clayey and marly units that correspond to a line of seepage” (E. Rice, personal communication). At Akragas as at Rhodes, the builders cut down through the stone to the impermeable clay and marl units, to tap the line of seepage. With similar geology, it is not surprising that many elements of the water system of the two places were similar, developed indepen dently from the old tradition. New concepts of water management were carried from place to place by expert builders, from the seventh through the fifth century B.C.E.
Eastern Grego-Roman Cities
Authors: Crouch Dora P.
Published: November 2020

Only since the last two decades of the twentieth century have professional geologists been working specifically at Miletus, investigating the shiny white limestone on top at KalabakHill; the limestone of Theater Hill and Humei Hill; and the limestone of Zeytin Hill (at the west of the hill called Degirmen, west of Kalabak), with sandstone and tuff to the east. The stratigraphy at Miletus is as follows, beginning with the topmost modern layer: . . . Iron deposits in mountains east of Miletus and both iron and brown coal at Mt. Mykale (today Samsun Dag) north of the Meander River valley. Volcanic tuff. Soluble limestone: 200 m of Yatagan or Balat strata of marble with tufa, sand, and gravel from which springs emerge. Early Pliocene limestone, shiny white limestone cap 60–100 m thick, karstified but with few on-site springs, forming ridges, hills, and a thick layer of scree. Miocene marls, sandstones, conglomerates, and clays with springs. Pink-yellow sandstone, sometimes with tuff, around sides of hills. Older clayey limestone deposited in a lake environment. Former large bay, now a swampy river plain with rich alluvial soil. . . . Prof. B. Schröder and his team have done geological research in the area (1990–94) and published their findings swiftly, which I acknowledge with gratitude. Suspected faults run north and south of Kalabak Hill (recognized in C. Schneider 1997). The town of Akköy to the south, where the German archaeological house is located well above the mosquitoes of the archaeological site in the swampy plain, sits on limestone that forms a peninsular ridge, surrounded on three sides by sandstone with tuff. The west coast of Asia Minor is subject to strong relief, steep gradients, and high precipitation; the high amount of energy available allows rapid change in topography (Gage 1978: 621). In Ionia, on average, the sea has risen or the land has sunk 1.75 m since antiquity (Bintliff 1977: 24; 1992). The Greek cities of Asia Minor were without exception built on or next to karst terrain (V. Klemes, 1988, personal communication when he was president of the International Association for Karst Hydrology).
Keeping the Customer Satisfied: Field Service and the Art of Automation
Authors: Salzman Harold , Rosenthal Stephen R.
Published: November 2020

The “Maytag repairman” is the familiar image of field service. When servicing electronic equipment such as computers, however, the job is significantly more demanding than fixing washing machines. Not only are computers more complex than most other machines, they are also more central to the ongoing operations of an organization. Increasingly, everything an organization does depends upon electronic equipment in some way. Large computer systems are often expected to run 24 hours a day, 365 days a year. When computers are such an integral part of an organization’s operations, maintaining the equipment is tantamount to keeping a person’s heart beating and blood circulating. Thus, unlike the idle television caricature, field service engineers are increasingly viewed as the paramedics for electronics who can quickly and ably respond to system crashes. At the same time that field service has become more demanding, the complexity of the job has increased. The “machinery” of the modern organization is less often composed of gears turning, typewriters clattering, and paper being shuffled. Instead, the sights and sounds of the modern organization consist of screens glowing, keys clicking, and, to the uninitiated, an assemblage of opaque, “black boxes.” Inside these boxes is a miniature world that gives no clue as to the nature of its inner workings. The field service engineer’s (FE) job and function have been growing while the size of the technology itself has been shrinking. His or her skill is less often exercised as a skilled craftworker in the repair of a part and more often as a skilled analyst who can understand the abstract workings and nature of electronics to identify the problem and trace it to the malfunctioning component. The required manual skills are often minimal, just enough dexterity to swap out a bad part for a good one usually suffices. At the same time, the scope of field service has expanded from just repairing worn and broken or defective parts to collecting information about design defects and debugging equipment that may have been released prematurely.
Danebury Revisited: A English Iron Age Hillfort in a Digital Landscape
Authors: Lock Gary R. , Harris Trevor M.
Published: November 2020

The doyen of British field archaeology, O. G. S. Crawford, noted that “The surface of England is a palimpsest, a document that has been written on and erased over and over again“ (Crawford 1953: 51). Many centuries of detailed observation and recording of the English landscape have resulted in a wealth of archaeological data, covering many thousands of years of human habitation. The need to record and decipher these extensive field data has led to the adoption of methods and techniques developed in other disciplines, including that of geography. Geographic information systems are the latest tools to be adopted in the quest for effective methods of field recording and archaeological analysis (for introductory GIS texts, see Aronoff 1989; Burrough 1986; Star and Estes 1990; Tomlin 1990). The applications of GIS in archaeology can be differentiated according to scale and type, although relatively few mature applications currently exist. Studies that have been undertaken range from intrasite to intersite analyses, and from research-driven applications to inventorying and cultural resource management (see for example Allen et al. 1990; Gaffney and Stancic 1991, 1992; Harris and Lock 1992; Larsen 1992; Lock and Harris 1991). This regional study, based on the Iron Age hillfort of Danebury in England represents a contribution to this growing literature and to the development of GIS use in archaeological analysis. This paper has two main aims. First, it seeks to identify and examine the archaeology of the Danebury region within the context of existing archaeological theory and to refine and add to these interpretations where applicable. Second, the paper seeks to undertake this analysis within a GIS environment. Our goal here is to illustrate how GIS can contribute to archaeological analysis, shed new light on existing knowledge, and enhance our understanding of the prehistoric use of the landscape. In landscape archaeology, there are several well-established themes that are strengthened and augmented by the data handling and analytical capabilities of GIS. This paper elaborates and develops these themes in the context of the ongoing archaeological study of the Danebury hillfort region.
Information Modeling: The EXPRESS Way
Authors: Schenck Douglas , Wilson Peter
Published: November 2020

Information modeling technology--the open representation of information for database and other computing applications--has grown significantly in recent years as the need for universal systems of information coding has steadily increased. EXPRESS is a particularly successful ISO International Standard language family for object-flavored information modeling. This cogent introduction to EXPRESS provides numerous, detailed examples of the language family's applicability to a diverse range of endeavors, including mechanical engineering, petroleum exploration, stock exchange asset management, and the human genome project. The book also examines the history, practicalities, and implications of information modeling in general, and considers the vagaries of normal language that necessitate precise communication methods. This first-ever guide to information modeling and EXPRESS offers invaluable advice based on years of practical experience. It will be the introduction that students as well as information and data modeling professionals have been waiting for.
Integration and specialization
Authors: Schenck Douglas , Wilson Peter
Published: November 2020

The major topic of this Chapter is modeling in the large. By this we mean looking at methods to integrate several different models into a single cohesive whole, and also examining the inverse problem of extracting a small specialized model from a larger one. Before we can sensibly discuss these, though, we need to look more closely at two aspects of EXPRESS, namely subtyping and schema interfacing. EXPRESS has a concept of Supertype and Subtype which taken together enable a type lattice to be constructed. A Subtype-Supertype relationship is typically called an ‘Isa’ relationship in data modeling terms. That is, a Subtype is a kind of its Supertype(s). For example, if we define an entity pet and also define two subtypes of this called cat and goldfish then an instance of cat is also an instance of pet, and similarly for a goldfish. The relationship, though, is asymmetrical, as a pet may be something other than a cat or goldfish; for instance a pet may also be a dog. A Subtype is a more specialized kind of thing than its Supertype and, conversely, a Supertype is a generalization of its Subtypes. A Subtype inherits all the attributes and constraints of its Supertype(s). In EXPRESS an entity is a Subtype of another entity if it declares its Supertype entity within its Subtype declaration. A Supertype does not declare its Subtypes. In general, an instance of a Subtype requires an instantiation of each of its Supertypes, while an instance of a Supertype does not require instantiation of its Subtypes. This later behavior may be modified by declaring the Supertype to be an Abstract Supertype, in which case an instance of the Supertype does require instantiation of at least one of its Subtypes. In most data modeling and Object Oriented languages that support similar notions to Subtyping, if an instance of a Supertype requires instantiation of a Subtype, then one and only one Subtype can be instantiated. EXPRESS does not have this restriction. Unless otherwise constrained, an instance of a Supertype may be accompanied by one instance of each of its Subtypes.
Beyond Numbers: A Broader Perspective on Risk Perception and Risk Communication
Authors: Slovic Paul
Published: November 2020

In a bold and insightful speech before the National Academy of Sciences at the beginning of his second term as the administrator of the Environmental Protection Agency (EPA), William Ruckelshaus called for a governmentwide process for managing risks that involved the public. Arguing that the government must accommodate the will of the people, he quoted Thomas Jefferson's famous dictum to the effect that "if we think [the people] not enlightened enough to exercise their control with a wholesome discretion, the remedy is not to take it from them, but to inform their discretion" (Ruckelshaus 1983, p. 1028). Midway into his tenure as the EPA administrator, Ruckelshaus's experiences in attempting to implement Jefferson's philosophy led him to a more sober evaluation: "Easy for him to say. As we have seen, informing discretion about risk has itself a high risk of failure" (Ruckelshaus, 1984, p. 160). This chapter attempts to illustrate why the goal of informing the public about risk issues—which in principle seems easy to attain—is surprisingly difficult to accomplish. To be effective, risk communicators must recognize and overcome a number of obstacles that have their roots in the limitations of scientific risk assessment and the idiosyncrasies of the human mind. Doing an adequate job of communicating means finding comprehensible ways of presenting complex technical material that is clouded by uncertainty and inherently difficult to understand. Greater awareness of the nature of risk perceptions, the fundamental values and concerns that underlie those perceptions, and the difficulties of communicating about risk should enhance the chances of designing an environment in which all parties can cooperate in solving the common problems of risk management. Risk assessment is a complex discipline, not fully understood by its practitioners, much less by the lay public. At the technical level, there is still much debate over terminology and techniques, and technical limitations and disagreements among experts inevitably affect communication in the adversarial climate that surrounds many risk issues. Those conveying these issues to the public must be aware of the strengths and limits of the methods they use to generate this information. In particular, such risk communicators need to understand that risk assessments are constructed from theoretical models that are based on assumptions and subjective judgments.
Computation, Dynamics, and Cognition
Authors: Giunti Marco
Published: November 2020

Currently there is growing interest in the application of dynamical methods to the study of cognition. Computation, Dynamics, and Cognition investigates this convergence from a theoretical and philosophical perspective, generating a provocative new view of the aims and methods of cognitive science. Advancing the dynamical approach as the methodological frame best equipped to guide inquiry in the field's two main research programs--the symbolic and connectionist approaches--Marco Giunti engages a host of questions crucial not only to the science of cognition, but also to computation theory, dynamical systems theory, philosophy of mind, and philosophy of science. In chapter one Giunti employs a dynamical viewpoint to explore foundational issues in computation theory. Using the concept of Turing computability, he precisely and originally defines the nature of a computational system, sharpening our understanding of computation theory and its applications. In chapter two he generalizes his definition of a computational system, arguing that the concept of Turing computability itself is relative to the kind of support on which Turing machine operate. Chapter three completes the book's conceptual foundation, discussing a form of scientific explanation for real dynamical systems that Giunti calls "Galilean explanation." The book's fourth and final chapter develops the methodological thesis that all cognitive systems are dynamical systems. On Giunti's view, a dynamical approach is likely to benefit even those scientific explanations of cognition which are based on symbolic models. Giunti concludes by proposing a new modeling practice for cognitive science, one based on "Galilean models" of cognitive systems. Innovative, lucidly-written, and broad-ranging in its analysis, Computation, Dynamics, and Cognition will interest philosophers of science and mind, as well as cognitive scientists, computer scientists, and theorists of dynamical systems. This book elaborates a comprehensive picture of the application of dynamical methods to the study of cognition. Giunti argues that both computational systems and connectionist networks are special types of dynamical systems. He shows how this dynamical approach can be applied to problems of cognition, information processing, consciousness, meaning, and the relation between body and mind.
Discovery and Design
Authors: Blum Bruce I.
Published: November 2020

This book is about a paradigm shift in the development of software; a move to a new era of design for software (and, for that matter, all manufactured artifacts). The goal of Part I is to lay out the scientific and technological foundations for this new era of design. In the chapter just concluded, we have seen how the Legend of science has become tarnished. During the stored-program computer’s brief history, we observe the general perceptions of science and scientific knowledge undergoing a fundamental change. I have focused on the philosophy of science because that tells us something about the theoretical limits of science; it suppresses the details of the day-to-day conduct of science that make it such a successful enterprise. This reassessment of science, of course, has been independent of the growth of computing; indeed, my examination has been free of any technological considerations. From the perspective of computer science, much of this revolution has gone unnoticed. Many still walk in the pathways first laid out in the era of the Legend; some even try to fit computer science into the framework of the Received View. If the conclusions of Chapter 2 are valid, however, such approaches cannot be sustained indefinitely. Therefore, any response to the evolving understanding of science ultimately must lead to a reexamination of computer science. If we are to shift the software design paradigm, we must expect modifications to the underlying principles embedded in computer science. How will these changes take place? will there be new scientific findings that alter the technology, or will a shift in the technology modify what the computer scientists study? To gain insight into the answers to these questions, this chapter addresses the relationship between science and technology and, in particular, between computer science and software engineering. As in the previous chapter, I conduct a broadly based, general review. The traditional relationship between science and engineering normally is described as being causal. Science creates knowledge, and technology consumes knowledge. This has been depicted as an assembly line: “Put money into pure science at the front end of the process.
Adaptive Design
Authors: Blum Bruce I.
Published: November 2020

Finally, I am about to report on my own research. In the material that preceded this chapter I have tried to present the work of others. My role has been closer to that of a journalist than a scientist. Because I have covered so much ground, my presentations may be criticized as superficial; the chapters left more unanswered than they have answered. Nevertheless, by the time the reader has reached this point, we should have a shared perception of the design process and its rational foundations. Perhaps I could have accomplished this with fewer pages or with greater focus. I did not choose that path because I wanted the reader to build a perspective of her own, a perspective in which my model of adaptive design (as well as many other alternative solutions) would seem reasonable. The environment for adaptive design that I describe in this chapther is quite old. work began on the project in 1980, and the environment was frozen in 1982. My software engineering research career began in 1985. Prior to that time I was paid to develop useful software products (i.e., applications that satisfy the sponsor’s needs). Since 1985 I have been supported by research funds to deliver research products (i.e., new and relevant knowledge). Of course, there is no clear distinction between my practitioner and research activities, and my research—despite its change in paradigm—has always had a strong pragmatic bias. Many of my software engineering research papers were published when I was developing applications, and my work at the Johns Hopkins Medical Institutions was accepted as research in medical informatics (i.e., how computer technology can assist the practice of medicine and the delivery of care). The approach described in this chapter emerged from attempts to improve the application of computers in medicine, and this is how I finally came to understand software development—from the perspective of complex, life-critical, open interactive information systems. There is relatively little in this chapter that has not already been published. The chapter integrates what is available in a number of overlapping (and generally unreferenced) papers. I began reporting on my approach before it was fully operational (Blum 1981), but that is not uncommon in this profession.
Computational Model
Authors: Smith Ronnie W. , Hipp D. Richard
Published: November 2020

This chapter describes the computational model that has evolved from the theory of integrated dialog processing presented in the previous chapter. The organization of this chapter follows. 1. A high-level description of the basic dialog processing algorithm. 2. A detailed discussion of the major steps of the algorithm. 3. A concluding critique that evaluates the model’s effectiveness at handling several fundamental problems in dialog processing. The system software that implements this model is available via anonymous FTP. Details on obtaining the software are given in appendix C. Figure 4.1 describes the basic steps of the overall dialog processing algorithm that is executed by the dialog controller. By necessity, this description is at a very high level, but specifics will be given in subsequent sections. The motivation for these steps is presented below. Since the computer is providing task assistance, an important part of the algorithm must be the selection of a task step to accomplish (steps 1 and 2). Because the characterization of task steps is a function of the domain processor, the dialog controller must receive recommendations from the domain processor during the selection process (step 1). However, since a dialog may have arbitrary suspensions and resumptions of subdialogs, the dialog controller cannot blindly select the domain processor’s recommendation. The relationship of the recommended task step to the dialog as well as the dialog status must be considered before the selection can be made (step 2). Once a task step is selected, the dialog controller must use the general reasoning facility (i.e. the interruptible theorem prover, IPSIM) in step 3 to determine when the task step is accomplished. Whenever the theorem prover cannot continue due to a missing axiom, the dialog controller uses available knowledge about linguistic realizations of utterances in order to communicate a contextually appropriate utterance as well as to compute expectations for the response. After the response is received and its relationship to the missing axiom determined, the dialog controller must decide how to continue the task step completion process.
The Wealth of Nature
Authors: Worster Donald
Published: November 2020

Whoever made the dollar bill green had a right instinct. There is a connection, profound and yet so easy to ignore, between the money in our pocket and the green earth, though the connection is more than color. The dollar bill needs paper, which is to say it needs trees, just as our wealth in general derives from nature, from the forest, the earth and waters, the soil. That these are all limited and finite is easy to see, and so also must be wealth; it can never be unlimited, though it can be expanded and multiplied by human ingenuity. Somewhere on the dollar bill that message might be printed, a warning that you hold in your hand a piece of the limited earth that should be handled with respect: “In God we trust; on nature we must depend.” The public is beginning to understand that connection in at least a rudimentary way and to realize that taking better care of the earth will cost money, will lower the standard of living as it is conventionally defined, and will interfere with freedom of enterprise. By the evidence of opinion polls, something like three out of four Americans say they are ready to accept those costs, a remarkable development in our history. The same can be said for almost every other nation on earth, even the poorest, who are learning that, in their own long-term self-interest, the preservation of nature is a cost they ought to pay, though they may demand that the rich nations assume some of the cost. Having money in one’s pocket, no matter how green its color, is no longer the unexamined good it once was. Many have come to realize that wealth might be a kind of poverty. The human species, according to a team of Stanford biologists, is now consuming or destroying 40 percent of the net primary terrestrial production of the planet: that is nearly one half of all the energy fixed by photosynthesis on the land. We are harvesting it, drastically reorganizing it, or losing it through urbanization and desertification in order to support our growing numbers and even faster growing demands.
Biological Diversity
Authors: Norton Bryan G.
Published: November 2020

As a philosopher who has written on the subject of endangered species policy, I am asked from time to time to join a panel discussion on “the value of biological diversity.” Consider a representative example: At the National Forum on Biodiversity, a 1986 conference organized by the Smithsonian Institution and the National Academy of Sciences, I shared the platform with three resource economists and one ecologist. Everyone on the platform agreed that biological diversity has great value; the discussion focused on the question, can that value be quantified in dollar terms? I quickly perceived that I was in the middle of a polarized situation. The economists were there to demonstrate the efficacy of their methods for representing the value of wild species as dollars; the ecologist scoffed at these attempts as irrelevant at best and, at worst, as a symptom of moral depravity. Hovering in the background of discussions like this are celebrated examples such as that of the snaildarter and the Tellico Dam. In that case, the Supreme Court halted work on an almost-completed dam because it would have flooded the only known habitat of the snaildarter, a three-inch member of the perch family. The politically tortured case of the tiny snaildarter illustrates the dilemma environmentalists face in defending biological resources. Environmentalists initially opposed the Tennesee Valley Authority’s plans to dam one of the last free-flowing stretches of the Little Tennessee River because it would destroy white-water canoeing, flood natural ecological systems, and destroy anthropologically important Indian burial sites. Environmentalists made little headway, initially, as the bureaucratic processes ground forward and construction of the dam was begun. Then, in early 1976, in a dramatic development, biologists discovered a hitherto unknown species, the snaildarter, living in the waters upstream from the dam. Since the snaildarter spawned in shallow, fast-moving waters, the dam threatened to wipe out a distinctive form of life. Environmental economists, anxious to use their quantificational tools, saw the Tellico Dam as a case in which assigning a dollar value to a threatened species might tip the scales in an aggregation of costs and benefits of proposed projects.
Interspecific Ethics
Authors: Norton Bryan G.
Published: November 2020

What makes deep ecology deep? This is perhaps the most perplexing question about the much-discussed but little-understood deep ecology movement. Its spokespersons, who are mostly West Coast and Australian academics, all cite, with some degree of affirmation, Norwegian philosopher Arne Naess’s 1974 article, “The Shallow and the Deep Ecology Movement.” But nobody, not even Naess himself, still accepts the seven principles of deep ecology that were outlined in the original paper. There seems to be agreement, however, that the movement gains its unity and identity from a shared belief that nature has value independent of its uses for human purposes. To put their point critically, movement proponents all believe that our current environmental policies are in a profound sense “unjust” to other species. Most simply, the deep ecology movement has clearly defined itself in opposition to “shallow ecologists,” or as some of them put it less pejoratively, “reform environmentalists,” who are taken to include all of the mainline environmental groups. Deep ecology, given its self-proclaimed opposition to all “shallow” approaches, represents a modern version of the idea that environmentalists sort themselves into two broad classifications based on opposed motives. More precisely, we can understand deep ecologists’ characterization of two opposition groups as a theory intended to explain the behavior of contemporary environmentalists: Environmentalists pursue two opposed approaches to environmental problems because some believe, while others do not, that elements of nature have independent value. Some environmentalists, according to this theory, are interested only in conserving natural resources for future human use; others, deep ecologists, act to protect nature for its own sake. If indeed deep ecologists are offering such an explanatory theory, it is important to ask exactly what behavioral phenomena are to be explained: Do reform environmentalists pursue policies that differ significantly from those pursued by deep ecologists? Or do they pursue the same policies, but employ importantly different strategies and tactics in these pursuits? These two questions will be the subject of the next two sections, respectively. Along the way, we can also assess the strengths and weaknesses of the deep ecologists’ contribution to environmental goals.
Variations in Solar Brightness
Authors: Hoyt Douglas V. , Shatten Kenneth H.
Published: November 2020

In the last chapter we saw that sunspots, aurorae, and geomagnetic disturbances vary in an 11-year cycle. So do many other solar features, including faculae and plages, which are bright regions seen in visible and monochromatic light, respectively. If both bright faculae and dark sunspots follow 11-year cycles, does this mean the sun’s total light output varies? Or are these two contrasting features balanced so that the sun’s output of light remains constant? The light output of the sun is often discussed in two different ways: either as the solar luminosity, which is the sun’s omnidirectional radiant output, or as the solar constant, the output seen in the direction of the Earth. In this chapter, we explore the variable solar light output that has been the subject of vigorous discussions. The total solar irradiance or solar constant is defined as the total radiant power passing through a unit area at Earth’s mean orbital distance of 1 astronomical unit. Today the most common units of solar irradiance are watts per square meter (W/m2). Power is defined as energy per unit time, so the solar irradiance can also be expressed in calories per square centimeter per minute. Modern experiments indicate that the sun’s radiant output is about 1367 W/m2, with an uncertainty of about 4 W/m2. About 150 years of effort by many people have been required to establish the value to this accuracy. The sun’s radiant output is not an easy quantity to measure, and we will discuss some of the struggles required to measure it. In the late 1800s, many scientists considered the solar total irradiance or solar irradiance to be constant. Oceanographers Dove and Maury vigorously supported this viewpoint, so the solar irradiance was called the solar constant. For the next century, virtually every paper concerning the sun’s radiant output used the term solar constant. No physical justification for this nomenclature existed, only a philosophical bias. Yet by the 1950s this bias proved so strong and so prevalent that support for individuals who wished to measure variations in the solar constant became almost nonexistent.
The Thermodynamics of Liquid Solutions
Authors: Fawcett W. Ronald
Published: November 2020

Chemistry in the laboratory very often involves the use of liquid solutions. This is especially true in chemical analysis, where the amount of analyte is easily manipulated when it is dissolved in a solution. Solutions are often the medium for chemical reactions which form the basis of titrations. Other simple analytical procedures are based on absorption spectroscopy, which is used to determine the concentrations of an analyte in solution. Most liquid solutions, also called liquid mixtures, are non-ideal. This follows from the fact that the components are in intimate contact with one another, and that the forces between the various species are usually not the same. As a result, the physical properties of the solution, for example, the vapor pressure of a given component, are usually not simply related to its concentration. This non-ideality leads to the concept of the activity of a solution component. As far as the analytical chemist is concerned, only concentration is ultimately of interest. Thus, if an analysis is based on the measurement of a physical property which in turn depends on the activity of a component, it is very important that the relationship between activity and concentration be understood for the system in question. Activity and its relationship to concentration is defined within the context of chemical thermodynamics. Using the laws which govern phase equilibria and the laboratory observations relating to these processes one can develop a detailed understanding of this relationship. In this chapter the macroscopic concepts of chemical thermodynamics which are relevant to solutions are reviewed. In addition, some simple models based on molecular concepts are discussed. The examples chosen are mainly limited to non-electrolyte solutions, especially those involving polar molecules. Concentration of one component in a two-component system can be expressed in several ways: as a weight/weight ratio, as a volume/volume ratio, or as a weight/volume ratio. Physical chemists clearly prefer to express concentration as a weight/weight ratio because then one has the possibility of estimating the number of moles of both components in the solution. In this case, solution composition is independent of temperature and pressure. On the other hand, the analytical chemist prefers to use a weight/volume ratio.
Polar Solvents
Authors: Fawcett W. Ronald
Published: November 2020

Polar solvents are those liquids whose relative permittivity is sufficiently high that electrolytes can be dissolved in them. The best-known example of such a liquid is water. The oxygen end of this simple molecule is electron-rich and can stabilize cations. The hydrogen atoms are electron-poor and thus are involved in the solvation of anions. The structure of pure water is very much influenced by the hydrogen bonding between the negative end of the molecular dipole at oxygen and a hydrogen atom on an adjacent molecule. The special properties of water as a solvent for electrolytes are the central reason for its importance in living systems. There are many other solvents which can be classified as polar. Some of them, such as the alcohols, have the same polar group as the water molecule, namely, the hydroxyl group –OH. These solvents are also involved in hydrogen bonding, and are generally classified as protic. Other examples of protic solvents are simple amides such as formamide and acetamide. In these systems, the protic group is –NH2, the hydrogen atom being involved in hydrogen bonding with the oxygen atom in the carbonyl group on an adjacent molecule. There are other polar solvents which are not protic. These involve liquids with large dipole moments. Some examples are acetonitrile, propylene carbonate, and dimethylsulfoxide. In each case, the solvent molecule possesses an electronegative group which is rich in electrons. The opposite end of the molecule is electron deficient but does not have acidic hydrogen atoms which can participate in hydrogen bonding. This class of solvents is called aprotic. In this chapter, the properties of polar solvents are discussed, especially as they relate to the formation of electrolyte solutions. Polar solvents are arbitrarily defined here as those liquids with a relative permittivity greater than 15. Solvents with zero dipole moment and a relative permittivity close to unity are non-polar. These include benzene, carbon tetrachloride, and cyclohexane. Solvents with relative permittivities between 3 and 5 are weakly polar, and those with values between 5 and 15 are moderately polar. The latter systems are not considered in the discussion in this chapter.
Early Days of Biochemical NMR
Authors: Shulman R.G.
Published: November 2020

It was my pleasure to participate in Oleg’s 65th birthday celebration and to reminisce about the early days of Biochemical NMR. Oleg was always there. I remember in the summer in the early 1960s sitting on lawn chairs at a Gordon Conference and discussing the need for a meeting on biochemical NMR. This was to convene those with common interests, and out of this grew the 1964 meeting in Boston, which was the first International Conference on Magnetic Resonance in Biological Systems. In organizing the 1964 meeting Oleg was stalwart, in charge of the local arrangements at the old mansion, home of the American Academy of Arts and Sciences. The venue was much appreciated by the more than 100 attendees, and the smooth arrangements and elegant, although somewhat dowdy locale, contributed to the sense, generated by the meeting, that the field had a coherent scientific core and a meaningful future. In the early days of the 1960s the field of magnetic resonance in biological systems, brought together biannually by the society, had a coherence that was nurtured by the society. In those days the NMR and ESR methods were much less developed than they soon became, so that any reasonably competent spectroscopist could understand all the methods employed. Additionally, because the earlier studies concentrated upon the better understood biological molecules or processes, the breadth of the applications did not baffle a slightly informed biochemist. The rapid advances in definite understanding were thrilling to practitioners in the field, and individual efforts were motivated by a sense that the field was going to grow. By that time NMR was firmly established as a quantitative method in chemistry, solid state physics, and other material sciences so that with the results in hand it was logical to extrapolate to a future in which magnetic resonance could be central to biological research. These high hopes, however, required considerable confidence in extrapolation, because the individual findings were sometimes slight when compared to the exciting cutting edges of biological research.
Heteronuclear Strategies for the Assignment of Larger protein/DNA complexes: Application to the 37 kDa trp Represser-Operator Complex
Authors: Revington M.J. , Lee W.
Published: November 2020

The sequence-specific DNA binding function of many proteins is recognized as one of the central mechanisms of regulating transcription and DNA replication and repair. The ability of these proteins to select a short (usually 10 to 20 basepair) sequence out of the entire genome with which to form a stable complex is a prime example of molecular recognition. Atomic resolution structural studies using NMR and X-ray crystallography have emerged as essential techniques in understanding the basis of specificity and stability in these systems. While NMR studies of small DNA-binding domains of proteins have become almost routine (see Kaptein, 1993 for a review) relatively few NMR studies of protein-DNA complexes have been reported. These include the lac repressor headpiece complex (Chuprina et al., 1993). the Antennapedia homeodomain complex (Billetere et al., 1993), the GATA-1 complex (Omichinski et al., 1993). and the Myb DNA binding domain complex (Ogata et al., 1993); all of these complexes are smaller than 20 kDa. In most cases, size limitations have meant that only the DNA binding domain of the protein in complex with a single binding element have been studied. In vivo, however, most DNA binding proteins are much larger than these domains and often function as oligomers. The decrease in quality and increase in complexity of spectra as the molecular weight of the sample increases, limits the number of systems amenable to study using NMR and influences the decision to focus on single domains of multidomain proteins. However, since many DNA-binding proteins are regulated by the binding of ligands, other proteins or phosphorylation, often at sites distal from the DNA-binding domain, it is preferable to study as much of the intact protein as possible in order to characterize allosteric and regulatory mechanisms (Pabo and Sauer, 1992). E. coli trp repressor is a 25 kDa homodimer that regulates operons involved in tryptophan biosynthesis. The dimer is one of the smallest intact proteins that binds sequence specifically to DNA and whose affinity is modulated by an effector (L-tryptophan).
A Solid-State NMR Approach to Structure Determination of Membrane-Associated Peptides and Proteins
Authors: Opella S.J. , Chirlian L.E.
Published: November 2020

Structural biology relies on detailed descriptions of the three-dimensional structures of peptides, proteins, and other biopolymers to explain the form and function of biological systems ranging in complexity from individual molecules to entire organisms. NMR spectroscopy and X-ray crystallography, in combination with several types of calculations, provide the required structural information. In recent years, the structures of several hundred proteins have been determined by one or both of these experimental methods. However, since the protein molecules must either reorient rapidly in samples for multidimensional solution NMR spectroscopy or form high quality single crystals in samples for X-ray crystallography, nearly all of the structures determined up to now have been of the soluble, globular proteins that are found in the cytoplasm and periplasmof cells and fortuitously have these favorable properties. Since only a minority of biological properties are expressed by globular proteins, and proteins, in general, have evolved in order to express specific functions rather than act as samples for experimental studies, there are other classes of proteins whose structures are currently unknown but are of keen interest in structural biology. More than half of all proteins appear to be associated with membranes, and many cellular functions are expressed by proteins in other types of supramolecular complexes with nucleic acids, carbohydrates, or other proteins. The interest in the structures of membrane proteins, structural proteins, and proteins in complexes provides many opportunities for the further development and application of NMR spectroscopy. Our understanding of polypeptides associated with lipids in membranes, in particular, is primitive, especially compared to that for globular proteins. This is largely a consequence of the experimental difficulties encountered in their study by conventional NMR and X-ray approaches. Fortunately, the principal features of two major classes of membrane proteins have been identified from studies of several tractable examples. Bacteriorhodopsin (Henderson et al., 1990), the subunits of the photosynthetic reaction center (Deisenhofer et al., 1985), and filamentous bacteriophage coat proteins (Shon et al., 1991; McDonnell et al., 1993) have all been shown to have long transmembrane hydrophobic helices, shorter amphipathic bridging helices in the plane of the bilayers, both structured and mobile loops connecting the helices, and mobile N- and C-terminal regions.
Selective Chemical Deuteration of Aromatic Amino Acids: A Retrospective
Authors: Matthews K.S. , Matthews R.
Published: November 2020

In 1970 when we began post-doctoral work in the laboratory of Professor Oleg Jardetzky, selective deuteration of proteins to limit the number of protons present in the system for subsequent analysis was a newly developed and effective technique for NMR exploration of protein structure (Crespi et al., 1968; Markley et al., 1968). This approach allowed more facile assignment of specific resonances and generated the potential to follow the spectroscopic behavior of protons for a specific amino acid sidechain over a broad range of conditions. The primary method for labeling at that time involved growth of microorganisms (generally bacteria or algae) in D2O, followed by isolation of the deuteratedamino acids from a cellular protein hydrolysate. The amino acids isolated were, therefore, completely deuterated. Selective deuteration of a target protein was achieved by growing the producing organism on a mixture of completely deuterated and selected protonated amino acids under conditions that minimized metabolic interconversion of the amino acids. In one-dimensional spectra, aromatic amino acid resonances occur well downfield of the aliphatic resonances, and this region can therefore be examined somewhat independently by utilizing a single protonated aromatic amino acid to simplify the spectrum of the protein. However, the multiple spectral lines generated by aromatic amino acids can be complex and overlapping, precluding unequivocal interpretation. To address this complication, chemical methods were developed to both completely and selectively deuterate side chains of the aromatic amino acids, thereby avoiding the costly necessity of growing large volumes of microorganisms in D2O and subsequent tedious isolation procedures. In addition, selective deuteration of the amino acids simplified the resonance patterns and thereby facilitated assignment and interpretation of spectra. The methods employed were based on exchange phenomena reported in the literature and generated large quantities of material for use in growth of microorganisms for subsequent isolation of selectively labeled protein (Matthews et al., 1977a). The target protein for incorporation of the selectively deuterated aromatic amino acids generated by these chemical methods was the lactose repressor protein from Escherichia coli, and greatly simplified spectra of this 150,000 D protein were produced by this approach.