bluuebunny/crossref_metadata_2025 huggingface dataset:
Brown’s Half Light
Authors: Bell Derrick
Published: November 2020

The Evening Of May 17, 954, was a night for celebration. An office full of ecstatic NAACP workers in Manhattan, as well as black people throughout the country, were doing just that as they hailed the bright new era all assumed would arrive with the landmark decision in Brown v. Board of Education handed down by the Supreme Court earlier that day. The case was not easily won. It was the culmi­nation of two decades of planning and litigation. At the very least, a party was in order. The NAACP staff hailed the high court’s opinion with cheers, toasts, and impromptu dancing, but according to one report, Thurgood Marshall, one of the chief architects of the litigation wandered morosely through the happy throng frowning. “You fools go ahead and have your fun,” he said, “but we ain’t begun to work yet.” Marshall’s prediction was both prophetic and a highly accurate commentary on the black experience. Even so, the staff had reason to celebrate. The orga­nization was doing what its founders had intended. The National Association for the Advancement of Colored People (NAACP)was founded in 1909. Its founders, an interracial group of liberal lawyers and socialists, concerned with the nonenforcement of the Four­teenth and Fifteenth Amendments, saw the need for an organization that would effectively press for political, legal, and educational rights. They sought an end to segregation, the right to work, and the right to protec­tion from violence and intimidation. The need for the NAACP was clear. In the previous year, in addition to the several dozen blacks lynched each year, thousands of whites rioted in Springfield, Illinois. They killed six blacks, two by lynching, and burned and destroyed black homes and businesses. Two thousand blacks left the city but none of the alleged riot leaders were punished, although the city obtained indictments following the restoration of order. The white community launched a political and economic boycott to drive out the remaining black residents. After its founding, the NAACP established a legal redress com­mittee, and in the next decades several of its cases reached the Supreme Court.
The Racial-Sacrifice Covenants
Authors: Bell Derrick
Published: November 2020

In Prehistoric Times, a people fearing that they had irritated their gods would seek to make amends by sacrificing a lamb, a goat, or sometimes a young virgin. Somehow, the shedding of innocent blood effected a renewed connection between the people and their gods. A similar though seldom recognized phenomenon has occurred throughout American racial history. To settle potentially costly differences between two opposing groups of whites, a compromise is effected that depends on the involuntary sacrifice of black rights or interests. Even less recog­nized, these compromises (actually silent covenants) not only harm blacks but also disadvantage large groups of whites, including those who support the arrangements. Examples of this involuntary racial-sacrifice phenomenon abound and continue. Afew of the more important are: the slavery understandings, the Constitution, universal white male suffrage, the Dred Scott v. Sandford case, the Hayes-Tilden compromise, and the southern disenfranchisement compromise. Contemporary sacrifices of black rights and interests underlie policies on the death penalty, drug-penalty sentencing rules, and reliance on standardized test scores in college and graduate school admissions procedures. Historian Edmund Morgan explains that plantation owners in the early seventeenth century recognized that they needed a stable work force to grow and profit from tobacco. Because Native Americans woulde scape or die, and the indentures of whites came to an end, the solution, over a decade or so, was to sentence African laborers to slavery indenture for life. The landowners convinced working class whites to support African enslavement as being in their interests, eventhough these yeoman workers could never compete with wealthy land owners who could afford slaves. Slaveholders appealed to working-class whites by giving them the chance to vote and by urging them, owing to their shared whiteness, to unite against the threat of slave revolts or escapes. The strategy worked. Wealthy whites retained all their former prerogatives, but the creation of a black subclass enabled poor whites to identify with and support the policies of the upper class. With the safe economic advantage provided by their slaves, large landowners were willing to grantpoor whites a larger role in the political process. Thus, paradoxically, slavery for blacks led both to greater freedom for poor whites and aneconomic structure that would keep them poor.
Searching for Effective Schools in the Post-Brown Era
Authors: Bell Derrick
Published: November 2020

In 1980 I Had Resigned My Faculty Position at the Harvard University Law School in order to accept the deanship at the University of Oregon’s law school. Following the public announcement, I received an urgent request from Ron Herndon, a militant black leader in Portland, Oregon. Herndon explained that the school board there was resisting the black community’s efforts to interpret Brown as requiring improve­ments in the mainly black schools rather than integrating them under a plan blacks feared would close many of them and reassign their children to white schools where they did not wish them to go. Herndon urged me to speak for the black community’s position at an upcoming school board meeting. I wondered about the propriety of myself—the new and, probably of some significance, the first black dean of the state’s only public law school—appearing on one side of a heated racial debate. I decided that, appropriate or not, I would appear, and did so. My defense of the black communities’ position gave pause to the school board’s members and much satisfaction to the black community. It was a reprise of my hear­ings in southern courtrooms years before, more theater than substance, but perhaps of some value. While the school board’s meeting was covered on television and in the local papers, I don’t recall that anyone at the law school ever mentioned my appearance. The more telling point is that as a veteran of the efforts to implement the Brown decision, I found myself opposing the school board’s efforts to use Brownprecisely as I had urged beforedozens of courts several years earlier. Now, tardily, having abandonedmy integrationist idealism, I recognized my obligation to supportblack parents’ efforts to provide effective schooling for their children.Where, I wondered, had Brownor our understanding and expectations for Browngotten derailed? Disenchantment with desegregation as a means of solving educational inequalities led to alternative means of achieving effective schooling for those not able to escape to the suburbs or enroll inexpensive private schools. Two major directions are worth examining. One is the effort, now three decades old, to eliminate or reduce the serious disparities in funding school districts within a particular state.
Introduction
Authors: Berner Robert A.
Published: November 2020

The cycle of carbon is essential to the maintenance of life, to climate, and to the composition of the atmosphere and oceans. What is normally thought of as the “carbon cycle” is the transfer of carbon between the atmosphere, the oceans, and life. This is not the subject of interest of this book. To understand this apparently confusing statement, it is necessary to separate the carbon cycle into two cycles: the short-term cycle and the long-term cycle. The “carbon cycle,” as most people understand it, is represented in figure 1.1. Carbon dioxide is taken up via photosynthesis by green plants on the continents or phytoplankton in the ocean. On land carbon is transferred to soils by the dropping of leaves, root growth, and respiration, the death of plants, and the development of soil biota. Land herbivores eat the plants, and carnivores eat the herbivores. In the oceans the phytoplankton are eaten by zooplankton that are in turn eaten by larger and larger organisms. The plants, plankton, and animals respire CO2. Upon death the plants and animals are decomposed by microorganisms with the ultimate production of CO2. Carbon dioxide is exchanged between the oceans and atmosphere, and dissolved organic matter is carried in solution by rivers from soils to the sea. This all constitutes the shortterm carbon cycle. The word “short-term” is used because the characteristic times for transferring carbon between reservoirs range from days to tens of thousands of years. Because the earth is more than four billion years old, this is short on a geological time scale. As the short-term cycle proceeds, concentrations of the two principal atmospheric gases, CO2 and CH4, can change as a result of perturbations of the cycle. Because these two are both greenhouse gases—in other words, they adsorb outgoing infrared radiation from the earth surface—changes in their concentrations can involve global warming and cooling over centuries and many millennia. Such changes have accompanied global climate change over the Quaternary period (past 2 million years), although other factors, such as variations in the receipt of solar radiation due to changes in characteristics of the earth’s orbit, have also contributed to climate change.
Popular Audiences on the Web
Authors: Boyle Alan
Published: November 2020

Let's face it: We're all Web journalists now. You might be working for a newspaper or magazine, a television or radio outlet, but your story is still likely to end up on the Web as well as in its original medium. You or your publication may even provide supplemental material that appears only on the Web—say, a behind-the-scenes notebook, an interactive graphic, or a blog. Or you might even be a journalist whose work appears almost exclusively on the Web—like me. I worked at daily newspapers for 19 years before joining MSNBC, a combined Web/television news organization. So I still tend to think of the Web as an online newspaper, with a lot of text, some pictures, and a few extra twists. But with the passage of time, online journalism is gradually coming into its own—just as TV started out as radio with pictures, but soon became a distinct news medium. To my mind, the principles of online journalism—having to do with fairness, accuracy, and completeness—are the same as the principles of off-line journalism. But the medium does shape the message, as well as the qualities that each medium considers most important. Wire-service reporters value getting the story out fast; newspapers value exclusive sources; magazines value in-depth coverage; radio and TV look for sounds and pictures that will help tell the story. All these factors are important for the Web as well, but one thing makes online journalism unique: Web writers are looking for ways to tell the story using software. Let's take a closer look at how one multimedia story unfolded, then get into how the tools and toys of the trade can be used in your own work. News coverage of space shuttle launches and landings usually follows a familiar routine: From MSNBC's West Coast newsroom in Redmond, Washington, I would update the landing-day story continuously, starting with the de-orbit burn, just as a wire service reporter might do. On February 1, 2003, however, the shuttle's landing was scheduled for a Saturday morning, one of the lightest times of the week for Web traffic.
Narrative Writing
Authors: Shreeve Jamie
Published: November 2020

“The universe is made of stories, not of atoms,” wrote poet Muriel Rukeyser. While some physicists may not agree, the power of narrative to grip a listener's attention is certainly ubiquitous in human society, and its roots run deep into prehistory—perhaps as far back as language itself. There is even some evidence that the brain is hard-wired to remember information better if it is transmitted in narrative form. As a science writer, you should exploit this propensity whenever the opportunity arises. At its simplest, a narrative is a sequence of events with a beginning, a middle, and an end. In this sense, narrative is endemic to science itself—the creation of the universe, the life history of a butterfly, and the action of an antibody on a pathogen are all essentially narrative events. Broadly speaking, a scientific paper is also a narrative, with a hypothesis (the beginning) determining methods (a middle) that lead to results and conclusions (the end). You may, in fact, have occasion to structure a story by tracing the unfolding of some natural process, or by following the protocol of some specific experiment. In most cases, however, good narrative requires something more than just a beginning, middle, and end: notably characters, and some scenic context for them to interact in, and some implicit tension—a conflict between two scientific teams after the same prize, for instance, or the heartbeat-by-heartbeat progress of an experimental surgical procedure with a life at stake. Developing character and building tension require space, which is why most narrative science writing is to be found in magazine articles, newspaper feature stories, and books. But a journalist on a shorter deadline can still incorporate narrative elements into his or her story, especially in the lead as a hook, or sprinkled into the body of the story to leaven the density of the science under discussion. Whatever the dimensions of your story, tempt readers with a compelling beginning, or they will never make it to your middle or end. Your opening is the rabbit hole through which the reader falls out of reality and into your narrative world. You want to create a disequilibrium in the mind, an itch that can only be resolved by burrowing deeper into the story.
Climate
Authors: McFarling Usha Lee
Published: November 2020

If you plan to cover climate change, thicken your skin. The topic is one of the most highly politicized areas in science journalism today. It's not surprising, given that so much is at stake. Environmentalists fear for the very future of the planet, while conservative politicians and energy industry leaders dread pollution controls that could threaten the nation's prosperity. As with all controversial issues, stakeholders on both sides are quick to attack reports—and reporters—that do not promote their point of view. I have been criticized by conservative think tanks for overplaying the potential dangers of climate change and scolded by environmentalists for downplaying those same dangers. It gives me solace to think that if I am aggravating both sides, then I am being fair. Critics of climate change coverage are right to some extent. The area, in my opinion, is among the most poorly covered in science journalism. This is because politically motivated campaigns of misinformation muddy the issue and because the science of climate—both highly complex and uncertain—is difficult to convey. Much climate change coverage exaggerates potential problems or greatly oversimplifies the issues. Reports are spotty at best, coming in droves when a particularly large piece of ice breaks off of Antarctica or there is a heat wave on the East Coast, but evaporating with the cool of autumn. Events from malaria outbreaks to species declines are attributed to climate change without adequate proof. Climate change coverage too often falls through the cracks between beats. Climate is not only a science story. It is a political story, a foreign story, and a business story as well. It would be best if climate were covered from all of these myriad angles; more commonly, no one takes ownership of it. Science writers, with their technical expertise, ability to translate jargon, and patience with details, are in prime position to be on the front lines of climate coverage—perhaps with occasional forays into political and economic terrain when necessary. The topic, with its interminable feedback loops and references to past epochs, can be intimidating.
Government Agencies
Authors: Henrichsen Colleen
Published: November 2020

A medical resident was on duty at New York Hospital one night in 1979 when a 27-year-old security guard was admitted with a rare form of pneumonia. As inexperienced as the resident was, he knew that this very rare condition was usually diagnosed only in people with a history of cancer, organ transplantation, or other conditions involving immune system suppression. This otherwise healthy young man had none of those. Weeks later, when the resident presented this case at inner-city rounds, a number of hands shot up. These clinicians had seen similar cases. The resident's report of this New York City outbreak was one of three that formed the basis for the first published report of the disease we would come to know as AIDS. Three years later, this physician, Dr. Henry Masur, arrived at the National Institutes of Health where he joined established NIH researchers already anxiously trying to understand this deadly new condition. At key communications offices on the NIH campus, phones were ringing incessantly. Reporters all around the world wanted to know what NIH was doing about it. As public communicators, we were learning about the disease along with the researchers. Why did it seem to disproportionately affect gay men? Why were people with the disease dying from ordinary infections? We were learning the answers to these questions as they unfolded, translating what we learned into plain English, and getting the information out to the public. A prominent AIDS researcher came into the office of one of my colleagues, sat next to her, and made a simple drawing of how immune cells appeared to be affected by the new virus, explaining it to her at the same time scientists themselves were just beginning to understand it. Dr. Masur is now chief of the Critical Care Medicine Department of the NIH Clinical Center. I covered his account of his first meeting with an AIDS patient for an NIH employee newsletter when he delivered the NIH Astute Clinician Lecture in 2002, which honors scientists who observe and investigate unusual clinical occurrences.
Patriotism and the Reconstruction of Washington, D.C., after the British Invasion of 1814
Authors: Pitch Anthony S.
Published: November 2020

Symbols are the choicest targets for those who would make war or instill terror. Destroying the symbolic center of a nation or culture destroys the spirit of its people—or so it would seem. This chapter examines the British invasion of Washington, D.C., during the War of 1812 and reveals how the attackers carefully chose to torch a set of buildings symbolically important for the upstart republic. In the wake of the attack, Washington nearly lost its raison d’être, as Philadelphia, Georgetown, Lancaster, and other cities vied for the honor of becoming the national capital. Invoking the memory of General George Washington himself, the city’s proponents finally convinced Congress to stay put. By hastily reconstructing the edifices of government, Congress effectively sealed the decision to remain and assured the recovery of Washington, D.C. The program of surgical destruction calls to mind the events of September 11, 2001, when another set of symbols—the Pentagon and the World Trade Center—was similarly targeted and, in the case of the WTC, destroyed. But rather than wreck the country’s spirit, both actions instead galvanized the nation and strengthened its commitment to unity, freedom, and democracy. Washington in 1814 was a steamy southern backwater with a population of only 8,000 residents, one-sixth of whom were slaves. The attorney general at the time, Richard Rush, described it as “a meager village, with a few bad houses and extensive swamps.” Nonetheless, it was the capital of the young republic, and capitals, however meager, have symbolic import. The British raided Washington in 1814 partly because they wanted to humiliate and demoralize the Americans, and they calculated that razing public buildings in the nascent capital would accomplish this in the most direct way. After all, Americans had done much the same in the Canadian capital of York the year before, when they torched and plundered public buildings before raiding villages on the Niagara frontier the following year. To retaliate, the British admiral George Cockburn pressed for the seizure of Washington, arguing that the fall of a capital was “always so great a blow to the government of a country.” By this time the countries had been at war for two years.
Resilient Tokyo: Disaster and Transformation in the Japanese City
Authors: Hein Carola
Published: November 2020

Natural disasters have destroyed, in whole or in part, Japan’s cities on numerous occasions. Human action, whether internal warfare or the air raids of the Second World War, has been the cause of further devastation. But regardless of the origin of the destructive force, Japan has always rebuilt its cities, and usually with astonishing speed. This chapter argues that while urban disasters can bring about an opportunity for changes in the built environment, they do not appear to induce innovation per se. Many times, the Japanese rebuilt their cities much the same as they were before, innovating only slightly on building codes or urban form. At times of ongoing political, economic, and social transformation, however, the leadership sponsored urban change in the wake of destruction. These interventions, instead of responding to post-disaster conditions, were often pared-down versions of predisaster concepts, constrained by limited finances, the lack of appropriate planning tools, the strictures of land ownership, and the needs and desires of private initiatives that called for rapid reconstruction and the preservation of traditional urban form. Societal transformation by itself has promoted the large-scale demolition and urban transformation of Japanese cities far beyond the areas touched by natural or human-made disasters. Rapid industrialization, urbanization, modernization, andWesternization, following the Meiji restoration of 1868 and the establishment of modern Japan, in particular buffeted Japanese cities on a grand scale. The repeated destruction of the capital, Tokyo (or Edo, as the city was called until 1868), and its rapid reconstruction provide an especially compelling means to examine disaster and rebuilding in Japanese cities. A focus on Tokyo permits comparison of reconstruction following both sudden, natural destruction and human-inflicted attack, as well as analysis of urban change in the absence of disaster. Earthquakes rattle Japan regularly; typhoons are frequent visitors; and tidal waves as well as tsunami have wiped out many settlements along the coasts. Rivers are highly susceptible to flooding, and inundation along major rivers in Edo resulted in the affluent abandoning the lowlands to the poor and lower classes and building their villas on the highlands. Traditional Japanese architecture has responded to such threats in a variety of ways. Wood construction, for example, provides flexibility in the event of tremors, and heavy roofing helps to stabilize houses buffeted by typhoon-strength winds.
More Molecules, More Mud, and the Isotopic Dimension: Ancient Environments Revealed
Authors: Gaines Susan M. , Eglinton Geoffrey , Rullkötter Jürgen
Published: November 2020

Throughout the 1980s, while the molecule collectors were busy exploring the ocean sediments, tracking their finds into the past, and learning to read the messages hidden in the carbon skeletons, one analytical chemist cum geochemist at Indiana University was finding that important elements of the lexicon lay not only in the molecular structures, stereochemistry, and distributions of the carbon skeletons, but in the carbon atoms themselves. John Hayes had done his graduate work at MIT in the mid-1960s under Klaus Biemann, one of the doyens of mass spectrometry who, like Carl Djerassi, was interested in natural products with biomedical applications. When Hayes told Biemann he wanted to do his doctoral thesis on the organic constituents in meteorites, Biemann was uninterested, to say the least. Forty years later, Hayes can still quote the eminent scientist’s response to his proposal, replete with thick Austrian accent: “Don’t talk to me about zat junk.” Biemann walked away from the discussion without another word, and Hayes was so mortified by his own foolishness that he couldn’t bring himself to tell his wife about the incident. When he went into the lab the next day, he was convinced that his graduate career was over—but Biemann had done some homework and had a change of heart. “It seems we can get lots of money for zat junk!” he exclaimed as soon as he saw Hayes. NASA was, at the time, offering generous funding for such projects. For all his skepticism, Biemann was eventually seduced by the extraterrestrial “junk” and even ended up designing the mass spectrometer for the Viking Mars mission. Hayes remembers him commenting, a couple of years into the meteorite project, that it was actually “much more interesting than the thousandth alkaloid in the thousandth tree,” though Hayes himself says his doctoral thesis was unexceptional, completed before the Murchison meteorite fell and things really got interesting.
Constraint Satisfaction by Survey Propagation
Authors: Braunstein Alfredo , Mézard Marc
Published: November 2020

Methods and analyses from statistical physics are of use not only in studying the performance of algorithms, but also in developing efficient algorithms. Here, we consider survey propagation (SP), a new approach for solving typical instances of random constraint satisfaction problems. SP has proven successful in solving random k-satisfiability (k -SAT) and random graph q-coloring (q-COL) in the “hard SAT” region of parameter space [79, 395, 397, 412], relatively close to the SAT/UNSAT phase transition discussed in the previous chapter. In this chapter we discuss the SP equations, and suggest a theoretical framework for the method [429] that applies to a wide class of discrete constraint satisfaction problems. We propose a way of deriving the equations that sheds light on the capabilities of the algorithm, and illustrates the differences with other well-known iterative probabilistic methods. Our approach takes into account the clustered structure of the solution space described in chapter 3, and involves adding an additional “joker” value that variables can be assigned. Within clusters, a variable can be frozen to some value, meaning that the variable always takes the same value for all solutions (satisfying assignments) within the cluster. Alternatively, it can be unfrozen, meaning that it fluctuates from solution to solution within the cluster. As we will discuss, the SP equations manage to describe the fluctuations by assigning joker values to unfrozen variables. The overall algorithmic strategy is iterative and decomposable in two elementary steps. The first step is to evaluate the marginal probabilities of frozen variables using the SP message-passing procedure. The second step, or decimation step, is to use this information to fix the values of some variables and simplify the problem. The notion of message passing will be illustrated throughout the chapter by comparing it with a simpler procedure known as belief propagation (mentioned in ch. 3 in the context of error correcting codes) in which no assumptions are made about the structure of the solution space. The chapter is organized as follows. In section 2 we provide the general formalism, defining constraint satisfaction problems as well as the key concepts of factor graphs and cavities, using the concrete examples of satisfiability and graph coloring.
Phase Transitions for Quantum Search Algorithms
Authors: Hogg Tad
Published: November 2020

Phase transitions have long been studied empirically in various combinatorial searches and theoretically in simplified models [91, 264, 301, 490]. The analogy with statistical physics [397], explored throughout this volume, shows how the many local choices made during search relate to global properties such as the resulting search cost. These studies have led to a better understanding of typical search behaviors [514] and improved search methods [195, 247, 261, 432, 433]. Among the current research questions in this field are the range of algorithms exhibiting the transition behavior and the algorithm-independent problem properties associated with the difficult instances concentrated near the transition. Towards this end, the present chapter examines quantum computer [123, 126, 158, 486] algorithms for nondeterministic polynomial (NP) combinatorial search problems [191]. As with many conventional methods, they exhibit the easy-hard-easy pattern of computational cost as the degree of constraint in the problems varies. We describe how properties of the search space affect the algorithms and identify an additional structural property, the energy gap, motivated by one quantum algorithm but applicable to a variety of techniques, both quantum and classical. Thus, the study of quantum search algorithms not only extends the range of algorithms exhibiting phase transitions, but also helps identify underlying structural properties. Specifically, the next two sections describe a class of hard search problems and the form of quantum search algorithms proposed to date. The remainder of the chapter presents algorithm behaviors, relevant problem structure, arid an approximate asymptotic analysis of their cost scaling. The final section discusses various open issues in designing and evaluating quantum algorithms, and relating their behavior to problem structure. The k-satisfiability (k -SAT) problem, as discussed earlier in this volume, consists of n Boolean variables and m clauses. A clause is a logical OR of k variables, each of which may be negated. A solution is an assignment, that is, a value for each variable, TRUE or FALSE, satisfying all the clauses. An assignment is said to conflict with any clause it does not satisfy.
Conclusion
Authors: Posner Richard A.
Published: November 2020

To summarize very briefly: The risks of global catastrophe are greater and more numerous than is commonly supposed, and they are growing, probably rapidly. They are growing for several reasons: the increasing rate of technological advance—for a number of the catastrophic risks are created or exacerbated by science and its technological and industrial applications (including such humble ones as the internal combustion engine); the growth of the world economy and world population (both, in part, moreover, indirect consequences of technological progress); and the rise of apocalyptic global terrorism. And the risks are, to a degree, convergent or mutually reinforcing. For example, global warming contributes to loss of biodiversity, an asteroid collision could precipitate catastrophic global warming and cause mass extinctions, and cyberterrorism could be employed to facilitate terrorist attacks with weapons of mass destruction. Each catastrophic risk, being slight in a probabilistic sense (or seeming slight, because often the probability cannot be estimated even roughly) when the probability is computed over a relatively short time span, such as a year or even a decade, is difficult for people to take seriously. Apart from the psychological difficulty that people have in thinking in terms of probabilities rather than frequencies, frequencies normally provide a better grounding for estimating probabilities than theory does; frequent events generate information that enables probabilities to be confirmed or updated. The fact that there have been both nuclear attacks and, albeit on a very limited scale, bioterrorist attacks—which, however, resemble natural disease episodes, of which the human race has a long experience—has enabled the public to take these particular risks seriously. The general tendency, however, is to ignore the catastrophic risks, both individually and in the aggregate. Economic, political, and cultural factors, including the religious beliefs prevalent in the United States, reinforce the effect of cognitive factors (including information costs) in inducing neglect of such risks. The neglect is misguided. The expected costs of even very-low-probability events can be huge if the adverse consequences should the probability materialize are huge, or if the interval over which the probability is estimated is enlarged; the risk of a catastrophic collision with an asteroid is slight in the time span of a year, but not so slight in the time span of a hundred years.
Experimental Test of the Pulse Perturbation Method for Determining Causal Connectivities of Chemical Species in a Reaction Network
Authors: Ross John , Schreiber Igor , Vlad Marcel O.
Published: November 2020

For an experimental test of the pulse perturbation method we choose a part of glycolysis shown in fig. 6.1. There are similarities and some differences between the model in fig. 5.12 and the reaction system in fig. 6.1. The reaction system has reactants, enzymes, and some effectors. One point of interest in choosing this system is the test of detecting and identifying the split of the reaction chain, from glucose to F1,6BP, at the aldolase reaction into two chains, one terminating at G3P and the other at 3PG. The experiments were run in a continuous-flow stirred tank reactor (CSTR) with the reaction system at a nonequilibrium stationary state, such that the reactions run spontaneously from glucose to G3P and 3PG. The concentrations of the species at this state are close to those of physiological conditions. The metabolites G6P, F6P, F1,6BP, DHAP, G3P, and 3PG were detected and analyzed by capillary electrophoresis. Typical relative errors were 4% for G6P, 11% for F6P, 15% for F1,6BP, 9% for DHAP, 6% for 3PG, and 3% for G3P. Figure 6.3 shows the responses of the species to a pulse of G6P, in a plot of relative concentrations versus. time during the relaxation, after the pulse, back to the stationary state. Complete relaxation took about half an hour. As seen from the amplitudes of the responses in the plot, the temporal order of propagation of the pulse is: G6P, F6P, DHAP, G3P, and 3PG. The time ordering of the maximum deviations agrees with this ordering except perhaps for G3P and 3PG. In some experiments, as in this one, the species F1,6BP could not be measured adequately and is not shown. It is possible to extract qualitative information on rates but difficult to derive quantitative information. Following a pulse of F1,6BP, the temporal order of propagation in the maximum relative concentrations is F1,6BP, DHAP, and with similar amplitudes G6P (slightly higher), G3P, 3PG, and F6P (slightly lower). These small differences were within errors of measurement and are therefore not significant. In this experiment the measurements of F1,6BP are reliable.
Correlation Metric Construction: Theory of Statistical Construction of Reaction Mechanisms
Authors: Ross John , Schreiber Igor , Vlad Marcel O.
Published: November 2020

In chapter 5, we studied the responses of chemical species in a reaction system to pulse perturbations and showed the deduction of direct, causal connectivities by chemical reactions—the reaction pathway—and the reaction mechanism from such measurements. The causal connectivites give the information on how the chemical species are connected by chemical reactions. In this chapter we turn to another source of information about chemical species in a reaction system, that of correlations among the species. Correlations of concentrations are measures of the statistical dependence of the concentration of one species on that of one or more of the other species in the system. Such correlations can be determined from measurements of time series of concentrations collected around a stationary state (nonequilibrium or equilibrium). We shall show that from concentration correlations it is possible to construct a skeletal diagram of the reaction system that gives a graphical measure of strong control and regulatory structure in reaction networks, gives some information on connectivity, leads to information on the reaction pathway and mechanism, and may simplify the analysis of such networks by identifying possible, nearly separable subsystems. We begin with the demonstration and explanation of this approach by analyzing some abstract reaction models. In chapter 8 we show the utility of this “correlation metric construction” (CMC) with application to time-series measurements on a part of glycolysis, and in chapter 13 on an extensive genome study. Consider a chemical system as shown in fig. 7.1. Mechanisms of this type are common in biochemical networks. For example, the subnetwork of fig. 7.1 containing S3 to S5 is based on a simple model of fructose interconversion in glycolysis and the subnetwork composed of S6 to S7 is similar to the phosphorylation/dephosphorylation cycles found in cyclic cascades. As an aside, this mechanism performs the function of a biochemical NAND gate, another example of a chemical computational function (see chapter 4).
Applications of Genetic Algorithms to the Determination of Reaction Mechanisms
Authors: Ross John , Schreiber Igor , Vlad Marcel O.
Published: November 2020

The mathematical computational method of genetic algorithms is frequently useful in solving optimization problems in systems with many parameters, for example, a search for suitable parameters of a given problem that achieves a stated purpose. The method searches for these parameters in an efficient parallel way, and has some analogies with evolution. There are other optimization methods available, such as stimulated annealing, but we shall use genetic algorithms. We shall present three different problems that give an indication of the diversity of applications. We begin with a very short primer on genetic algorithms, which can be omitted if the reader has some knowledge of this subject. Genetic algorithms (GAs) work with a coding of a parameter set, which in the field of chemical kinetics may consist of a number of parameters, such as rate coefficients; variables and constraints, such as concentrations; and other quantities such as chemical species. Binary coding for a parameter is done as follows. Suppose we have a rate coefficient = 9.08 × 10−7; then if we write that rate coefficient as 10−P , with −10 ≤ P ≤ 10, a binary coding with string length of 16 bits is given by . . . P = 10 − 20 R /(216 − 1) (10.1) . . . where 0 ≤ R ≤ 216 − 1. Since P = 6.04 we have R = 12,971, or R = 0011001010101010 to the base 2. Thus the value of the rate coefficient is encoded in a single bit string, called a chromosome. For the solution of a given problem an optimization criterion must be chosen. With a given choice of parameters this criterion is calculated; the comparison of that calculation with the goal set for the criterion gives a fitness value for that set of parameters. If the fitness is adequate but not sufficient, when both are selected by prior choice, for any individual, then retain that individual for the next generation. Reject individuals below that choice. Select individuals for the next generation with a probability proportional to the fitness value from a roulette wheel on which the slot size is proportional to the fitness value. Notice that genetic algorithms use probabilistic, not deterministic, transition rules.
Genetics, Behavior, and Behavioral Phenotypes
Authors: Harris James C.
Published: November 2020

Geneticists and specialists working with individuals with intellectual disability now recognize that genetic syndromes may have characteristic physical phenotypes and behavioral features that may be linked to a specific genetic syndrome. These patterns of behavior are referred to as behavioral phenotypes. This chapter utilizes a developmental perspective to provide a definition and characterization of behavioral phenotypes in neurodevelopmental disorders and to discuss etiology, methodologies to understand underlying mechanisms, and the natural history of the disorder. Neurogenetic disorders with behavioral phenotypes include (1) Down syndrome, (2) Velocardiofacial syndrome, (3) Smith-Magenis syndrome, (4) Turner syndrome, (5) Rett’s disorder, (6) Lesch-Nyhan syndrome, (7) Prader-Willi and Angelman syndromes, (8) fragile X syndrome, and (9) Williams syndrome. Each of these neurogenetic disorders involves a different genetic mechanism and provides a portal to understand neurodevelopment. A disorder that is environmentally induced, fetal alcohol syndrome, is also discussed and it, too, may provide a key to understanding aspects of the developing brain (Ikonomidou et al., 2000). The first description of behavior associated with an intellectual disability syndrome was by Down (1887). In describing the syndrome that bears his name, Down observed that “They have considerable powers of imitation, even bordering on being mimics. Their humorousness and a lively sense of the ridiculous often color their mimicry.” Later, he added: “Several patients who have been under my care have been wont to convert their pillow cases into surplices (vestments) and to imitate, in tone and gesture, the clergymen or chaplain which they have recently heard.” He also commented on personality traits, saying that “Another feature is their great obstinacy—they can only be guided by consummate tact.” Although these stereotypes were not confirmed in subsequent studies (Gath and Gumley, 1986; Gunn, Berry, and Andrews, 1981), the prospect of linking behavior and genetics was introduced in this first description of a neurogenetic disorder. Subsequent early clinical descriptions, such as that of tuberous sclerosis complex by Critchley and Earl (1932), identified peculiar, and severe, behavioral problems in children and adult with that condition.
The Lisbon Earthquake and the Age of Reason
Authors: Hough Susan Elizabeth , Bilham Roger G.
Published: November 2020

An individual’s response to any catastrophic event, including the capacity for rebound, surely depends a great deal on one’s expectations before the event. In a short-term sense, earthquakes remain as utterly unpredictable and abrupt as they have been since the dawn of time. Looking back through history, however, it becomes apparent that some earthquakes were more unexpected— and seemingly more mercurial—than others. In the middle of the 18th century, earthquake science had barely reached its infancy. Earthquakes had fascinated, and posed a challenge to, the best minds since at least the day of Aristotle. Aristotle, Pliny the Elder, St. Thomas Aquinas—whether they viewed earthquakes as acts of God or not, they and other philosophers approached the subject with a decidedly naturalist bent. Aristotle and Pliny interpreted earthquakes as the result of subterranean winds or subterranean storms. St. Thomas Aquinas argued in favor of the scholastic approach, supporting Aristotle’s scientific views over later, more theologically oriented interpretations. During the 17th century, earthquakes continued to be the source of scientific speculation. Galileo argued that the earth had a dense, solid core. In 1680 Robert Hooke published Discourse on Earthquakes, arguably the first significant book dealing with earthquakes as a natural phenomenon. In 1750 a series of earthquakes was widely felt throughout England. During this “year of earthquakes,” shocks were felt in London on February 19 and March 29, in Portsmouth and the Isle of Wight on March 29, in northwest England and northeast Wales on April 18, and in and around Northamptonshire on October 11. These shocks are now estimated to have been no larger than mid-magnitude-4: the first two events were quite small, felt strongly in London only because their epicenters were within city limits. But pound for pound—or, rather, magnitude unit for magnitude unit—the impact of these earthquakes far outstripped their literal reverberations within the earth.
The 1886 Charleston, South Carolina, Earthquake
Authors: Hough Susan Elizabeth , Bilham Roger G.
Published: November 2020

By 1886 the population of the United States had grown to over 50 million people. Both the East Coast and the Midwest were by this time well populated with bustling towns and cities. Railroads had sprung up as well, greatly facilitating land travel, which in turn helped spark further migration and trade. The tide of westward expansion had long since steamrolled over whatever reservations the New Madrid earthquakes might have caused. By 1886 the gold rush was already several decades old, and San Francisco had grown into a lively urban center with a population of 35,000—about 5,000 more than the population of Chicago. A number of notable earthquakes had occurred in California by the end of the 19th century. While the massive Fort Tejon earthquake of 1857 occurred too early in the state’s history to leave a lasting impression on the collective psyche, large earthquakes along the eastern Sierras in 1872 and on the Hayward fault in 1872 had begun to suggest that California might be earthquake country. Still, as of the late 1800s people had nothing approaching a modern understanding of earthquakes—neither their underlying physical processes nor their fundamental characteristics. As the 19th century drew to a close, scientists did not have any way to gauge the overall size of an earthquake, for scales had been developed only to rank the severity of shaking from a particular earthquake at a particular location. Whereas scientists today can easily rank temblors in terms of their overall size, or energy release, in earlier times people could only gauge an earthquake’s overall effects, an assessment that can sometimes prove misleading. For example, the overall reach of earthquake shaking depends on the nature of the rocks through which the waves travel. As noted in chapter 5, waves travel especially efficiently in central and eastern North America, and especially inefficiently in California. Thus an earthquake of a given magnitude will pack a disproportionately heavy punch in the former region.
City of Angels or Edge City?
Authors: Hough Susan Elizabeth , Bilham Roger G.
Published: November 2020

Although this book focuses on societal response to earthquake disasters, many common threads can be found in societal response to other types of disasters. Some regions seem especially prone to disasters of all shapes and sizes, perhaps none more so than southern California, which can be star-studded and star-crossed in equal measure. This chapter steps away from the specific responses of societies to one type of disaster to instead consider the response of one society to myriad disasters. In southern California, disasters sometimes seem to pile up like, well, cars on a southern California freeway. During one memorably miserable week in October 2003, for example, firestorms laid waste to almost 700,000 acres in the region—2,000 homes, 24 lives, and a staggering $2 billion in property damage. It was a little like an earthquake in slow motion. The 1989 Loma Prieta earthquake had claimed about three times more lives (63) and total property damage ($6 billion), but the number of homes rendered uninhabitable by that powerful temblor was lower (1,450) than the number destroyed by the firestorms of 2003. That the disaster played out slowly, over the span of several days rather than several tens of seconds, was a curse as well as a blessing. Advance warning kept the death toll from climbing higher; it also generated high anxiety among tens of thousands who would not lose their homes as well as the few thousand who would. Fires are less kind than earthquakes in another critical respect as well: they can reduce an entire house and its contents to ash, whereas much can often be salvaged from even a severely earthquake-ravaged home. Fires can even have their own aftershocks, after a fashion: heavy Christmas Day rains turned parts of two burn areas into torrents of fast-moving debris that swept through two campgrounds and claimed 16 lives, most of them children. Even heavier rains in early 2005 caused a more massive landslide in the coastal community of La Conchita.