bluuebunny/crossref_metadata_2025 huggingface dataset:
Sexual selection and speciation
Authors: Ligon J David
Published: November 2023

As mentioned briefly in Chapter 2, not long after Darwin elucidated the theory of sexual selection, and for many years thereafter, it was an ignored issue. West-Eberhard (1983) refers to this period as ‘The forgotten era of sexual selection’. During this time, most of the leading students of evolutionary theory focused on issues related to speciation. Thus, this neglect of the topic of sexual selection occurred during the same period that the phenomenon of speciation-the key concern of neo-Darwinism-was receiving intensive study and thought. With the benefit of hindsight, it is a bit puzzling to realize that so many of the foremost students of speciation almost completely ignored sexual selection and apparently made no connection between the two phenomena.
Social monogamy
Authors: Ligon J David
Published: November 2023

Social monogamy, by far the most common mating system in the Class Aves (Lack 1968), can be recognized by the apparently exclusive association of one female and one male as mates over some definable period of time, such as a nesting cycle, a breeding season, or even a lifetime. In birds, monogamy is usually closely associated with biparental care. (Although biparental care and monogamy actually refer to two distinct suites of behaviour-parental care and mating system, respectively-the two terms are so closely linked that they are often used interchangeably.) As noted previously, unlike any other group of vertebrates, social monogamy is the prevalent mating system in birds, with well over 90 per cent of all species estimated to exhibit this form of male-female association (Lack 1968). In view of its rarity in other classes of vertebrates, the frequency of monogamy in birds is striking and is a key behavioural-reproductive characteristic that sets this group apart from all other vertebrate taxa.
Extra-pair copulations and their evolutionary significance
Authors: Ligon J David
Published: November 2023

As discussed in Chapter 11, monogamy is the social mating system practised by the vast majority of birds. This chapter deals with the subject of copulations and fertilizations carried out by individual males and females that are not members of a social mateship. These phenomena are widely referred to as extra-pair copulation (EPC) and extra-pair fertilization (EPF), respectively. Extra-pair paternity (EPP) refers to chicks sired by a male other than the social mate. EPCs may occur with or without EPF, due, for example, to sperm competition. Because EPC is usually recognized by the detection of chicks in a brood that had not been sired by their apparent father, this term is commonly used to refer to extra-pair copulations that lead to fertilization of eggs, and this is the convention followed here.
Lek mating systems
Authors: Ligon J David
Published: November 2023

Lekking behaviour is one of the most interesting issues in sociobiology. Lek mating systems are characterized by clusters of males, often at a ‘traditional’ site, which females visit for mating. In contrast to the territorial behaviour of most male birds during the breeding season, males of typical lekking species come together and conduct their courtship activities in close proximity. Thus, the central question posed by lek mating systems is, why do males congregate at a single site? Lekking behaviour is also interesting because it is thought that ‘The potential for sexual selection reaches full expression in species with lek mating systems’ (Trail 1990, p. 1837). The clustering of males, which leads to high variance in male reproductive success and thus to intense sexual selection, is the reason that lek systems have been so attractive to students of sexual selection.
Environmental variations in the south Turkana ecosystem
Authors: Little Michael A , Dyson-Hudson Rada , Dyson-Hudson Neville , Winterbauer Nancy L
Published: November 2023

Although the dry savanna Turkana environment is often characterized as cyclic in its seasonal and longer-range patterns of rainfall, actual rainfall and its corresponding effects are difficult to predict. The outlines of the Turkana climate and ecosystem have been presented in Chapter 3. In this chapter, we discuss the influences that rainfall variation have on Turkana vegetation and water resources, on the livestock, and on the behavior and biology of the people. As noted in Chapter 1, Turkana strategies in response to the low predictability of the dry savanna environment are opportunistic, but individuals have considerable environmental knowledge on which to base their actions. Their behavior reflects contingent responses of the people at a variety of social levels to the environmental conditions they encounter (see Chapter 1). There is also good evidence that the Turkana deal with the low predictability of temporal variation in rainfall by exploiting the great spatial variation in rainfall and resources that exists in South Turkana.
Damage to Needles and Leaves
Authors: Butin Heinz
Published: November 2023

Frost damage on conifers can cause various symptoms, depending on the time of year and the age of the needles. If temperatures below 0°C occur in May, when the new needles have begun to expand, the result is sudden wilting and-a day or two later-browning of most of the new flush. As a rule, only the newly forming needles are harmed by these ‘late frosts, ‘ whereas winter cold can affect older ones, especially those of the previous year ‘s growth. This ‘winter frost damage, ‘ as the term implies, is the result of freezing injury during the dormant season. It usually occurs over much of the crown, and the affected needles typically show a marked pale or medium brown discoloration either at their tips or along their entire length. They may remain attached until some time during the following summer. This kind of damage can be seen on spruces, Silver fir, pines, Douglas fir, and also on cedars.
Epiphytes, Symbionts, and Parasitic Flowering Plants
Authors: Butin Heinz
Published: November 2023

Epiphytes are organisms which use trees or other plants exclusively as support, without parasitizing them. Some are capable of synthesizing their own organic nutrients (e.g. algae and lichens), while others (mainly fungi) live saprotrophically on dead or non-living material accumulated on the bark. Although epiphytes are not parasitic on trees, there are some (e.g. Athelia, Trichonectria) which are nevertheless ‘parasitic, ‘ attacking other organisms that live on the tree bark. Among the epiphytes which occur in Europe, there are a few which attract the attention of the forester, or of others with an interest in trees because they are either economically important or have a particularly striking appearance.
Sustainable transport: how the Royal Commission sees the future
Authors: Houghton John
Published: November 2023

Sir John Houghton, CBE, FRS, has since 1992 been Chairman of the Royal Commission on Environmental Pollution, whose report, Transport and the environment, was published while this series of lectures was in progress. He took his first degree, and in 1955 was awarded his DPhil, as a member of Jesus College, Oxford, where he was elected to a Fellowship in 1960. After spending 3 years on the staff of the Royal Aerospace Establishment, Sir John was appointed to a Lectureship, and subsequently to a Readership, in Atmospheric Physics at Oxford University; in 1976 he became Professor in that subject. After four years as Deputy Director and then Director (Appleton) of the Rutherford Appleton Laboratory, he was appointed Director-General of the Meteorological Office and held this post from 1983 until 1991. Sir John is co-chairman of the Scientific Assessment Working Group of the interGovernmental Panel for Climate Change and a member of the UK Government Panel for Sustainable Development. He is the author of several books on atmospheric physics, including Global warming: the complete briefing (1994), and numerous scientific papers on atmospheric radiation, spectroscopy, and climate change.
The Channel Tunnel, fixed link and
positive choice
Authors: Morton Alastair
Published: November 2023

Sir Alastair Morton was educated at Witwatersrand University, Johannesburg, South Africa and took an MA degree as a member of Worcester College, Oxford; he is now an Honorary Fellow of the College. After holding a succession of senior positions in finance and industry, Sir Alastair became the first Managing Director of the British National Oil Corporation ( BNOC) in 1976. In 1982, he was appointed Chief Executive and subsequently Chairman of the Guinness Peat Group. Five years later, Sir Alastair began his involvement in the project with which his name will always be associated, the Channel Tunnel: he has been the Co-Chairman of Eurotunnel pie since 1987 and was also Group Chief Executive of the company from 1990 to 1994. If, against current expectation, the Channel Tunnel achieves financial success to complement its undoubted status as an engineering triumph, this will be very much Sir Alastair’s personal achievement. He has always taken an active interest in technical and vocational training: he has been Chairman of the Kent Training and Enterprise Council since 1990.
Airlines, aviation, and the environment
Authors: Somerville Hugh
Published: November 2023

Dr Hugh Somerville took his first degree, in chemistry, at the University of Edinburgh and a PhD in microbiology at the University of Shefjzeld. He undertook post-doctoral research at the University of California, Los Angeles before spending a year as an Assistant Professor at the University of California, Berkeley. Dr Somerville then joined Shell Research and was appointed Head of the Microbiology Research Division. He has held environmental posts with Shell in Houston, The Hague, and Aberdeen as well as with Occidental Petroleum. In 1989, he joined British Airways to take up the newly created post of Head of Environment, which he still holds. He has been active in a number of environmental groups and is currently ( August 1995) Chair of the International Air Transport Association ( IA TA) Environment Task Force.
Microregional tumour blood flow: heterogeneity and therapeutic significance
Authors: Chaplin David J , Trotter Martin J , Dougherty Graeme J
Published: November 2023

The continued proliferation of tumour cells depends on an adequate supply of oxygen and nutrients and removal of the waste products of cellular metabolism. These ‘services’ are provided by blood vessels. Thus, expansion of a solid tumour requires the acquisition of a vascular supply. There is evidence that tumours can acquire their vascularity, at least in part, by incorporation of existing host vessels, particularly arteriolar vessels (1-3). However, it is now evident that the majority of tumour vessels are acquired by angiogenesis and that this process is a prerequisite for the continued rapid growth of solid tumours beyond a size of I mm3 (4,5).
Mechanisms of stress-induced angiogenesis in tumours
Authors: Keshet Eli , Stein Ilan , Neeman Michal
Published: November 2023

abstract

Tumour angiogenesis is generally viewed as the consequence of an ‘angiogenic switch’, i.e. a genetic event that endows the tumour with the ability to recruit blood vessels from the neighbouring tissue. Whether the up-regulation of angiogenesis stimulators (]) or the down-regulation of angiogenesis inhibitors (2), the ‘angiogenic switch’ is conceived as a stochastic event in the succession of genetic hits that underlie tumour progression.
The biphasic effects of transforming growth factors in angiogenesis
Authors: Madri Joseph A , Sankar Sabita
Published: November 2023

Angiogenesis is a dynamic process which can be defined as the formation of new vessels. Angiogenesis is known to occur during development, in response to injury and tumour angiogenic factors and is thought to be controlled by many diverse, complex factors acting in concert in local environments over finite time periods. The principal cells involved in the process of angiogenesis are microvascular endothelial cells, which are distinct from endothelial cells lining the larger vessels of the circulatory system in their physiological functions as well as in their responses to injury, although both large vessel and microvascular endothelial cells are derived from the same stem cells (1-5). The differences between large vessel and microvascular endothelial cells are clearly noted when one compares their responses with injury. Large vessel endothelia respond to denudation injury caused by angioplasty, endarterectomy, and synthetic and autologous bypass grafting by undergoing sheet migration which is modulated, in part, by soluble factors and the existing and newly synthesized extracellular matrix components. In many instances re-endothelization is incomplete and the affected endothelial cells exhibit altered metabolic and adhesive behaviours which contribute to the development of stenotic lesions and ultimately compromise blood flow (2-4). In contrast, following injury microvascular endothelial cells initiate an angiogenic process also modulated by both existing and newly synthesized extracellular matrix components and soluble factors (6-9). This process consists of local disruption of the basement membrane investing the affected endothelial cells, migration of the endothelial cells into the local interstitial stroma, cell proliferation, new vessel formation, and stabilization.
Tumour necrosis factor α and angiogenesis
Authors: Fajardo L.G. Luis F , Allison Anthony C
Published: November 2023

Tumour necrosis factor (TNF) a (cachectin) is a cytokine synthesized mainly by cells of the monocyte-macrophage lineage (I). Other sources are mast cells, T lymphocytes (CD4, CDS), natural killer cells, neutrophils, glial cells, and some tumour cells (1-3). The gene encoding TNF-a is located in chromosome 6, near the gene of a related cytokine, lymphotoxin, or TNF-f3 (2,4). Various stimuli induce the production of TNF, especially bacterial lipopolysaccharide (LPS). In fact TNF is a major effector of toxic shock induced by LPS (1,2,5,6). The primary gene product, pro-TNF-a, is a 26 kDa type II integral membrane protein which can be localized to plasma membrane fractions (7). Proteolytic cleavage of pro-TNF at a specific site releases 17 kDa TNF, which binds to both TNF receptors and induces a variety of responses in many cell types. More than 95% of the TNF synthesized by rnonocytes in response to LPS is processed and secreted. Some metalloproteinase inhibitors block pro-TNF cleavage, but the converting enzyme has not been fully characterized (8). The three-dimensional structure of TNF, determined by X-ray crystallography, shows it to be a trimer of the 17 kDa form, each subunit consisting of an anti-parallel f3-sandwich (9). This cytokine, described in 1975 (10), has been sequenced, cloned, and produced by recombinant techniques: human in 1985, mouse in 1986 (11,12).
Endothelial cells transformed by polyomavirus middle T oncogene: a model for haemangiomas and other vascular tumours
Authors: Pepper Michael S , Cottier Fabienne Tacchini , Sabapathy T Kanaga , Montesano Roberto , Wagne Erwin F
Published: November 2023

The establishment of a functional vascular system is an absolute requirement for the growth of normal and neoplastic tissues. However, like all other systems in the living organism, cells of the vascular system are susceptible to genetic and epigenetic changes which may ultimately lead to tumour formation. Recent studies on the endothelial cell-specific transforming ability of the polyoma virus middle T oncogene have defined a model for the study of endothelial cell tumours. The purpose of this chapter is to summarize these studies, and to place them in the context of what is known about the pathogenesis of vascular tumours in humans.
The biological background
Authors: Fogg G E
Published: November 2023

This chapter deals with the effects of polar conditions on living systems in general, the ways in which microorganisms, plants, and animals are able to adapt to the stresses imposed, and how they come to be in these habitats. Stress is a difficult concept to define in precise physiological terms. Radical change in photoperiod is one stress but cold—both in itself and through its secondary effects—is the factor which we think of first as inflicting greatest stress in polar habitats. The impact is rather different on small organisms, termed ectotherms, whose internal temperature conforms to that of their environment, and on larger plants, which to a limited extent can achieve higher temperatures than their surroundings, and warm-blooded animals.
Mankind in polar habitats
Authors: Fogg G E
Published: November 2023

Only recently have the enormous areas around the poles been invaded by mankind (Sugden 1982; Ives and Sugden 1995). The Arctic, being nearer to centres of population and approachable by land, was the first to suffer intrusion. This came via the unglaciated lowland of northeast Siberia and the Beringia peninsula (p. 47) which was occupied by groups of people hunting mammoth, bison, and caribou with stone-tipped spears and living in winter in semi-subterranean dwellings. This Palaeo-Arctic culture persisted until around 7000 BP but long before, perhaps 20 000 BP, it had spread across the then existing land bridge to North America. About 11 000BP the climate became warmer, ice caps melted, and the land connection with Asia was cut by the rising sea, leaving the primitive Arctic hunters to evolve in isolation. Those that remained in coastal areas lived on sea mammals, muskoxen, and caribou, and gave rise to the palaeo-Eskimo who reached northern Greenland about 3000 years BP. Another group, the Dorset culture, with the same origin, moved to the eastern Canadian Arctic and developed the building of ice houses (igloos), boats (umiaks and kayaks), and efficient harpoon technology for hunting on ice. This exploitation of sea mammals was the key to successful occupation of the high Arctic.
Life at the Bottom
Authors: Herring Peter
Published: November 2023

The organisms furthest away from the surface productivity are, of course, those at the bottom of the ocean. The title of this chapter recognizes that this special fauna includes those that live on, in, and just above the seafloor. The first two categories comprise the benthos (cf. plankton and nekton), and respectively describe what are technically known as the epifauna and the infauna.
On being efficient
Authors: Herring Peter
Published: November 2023

In open water food is often reliably available in particular regions or seasons (e.g. in many coastal regions and/or springtime). In these circumstances animals are neither constrained to get the last calorie out of their diet nor is energy conservation a high priority. One frequent result is fast-swimming, solidly muscular animals with skeletons to match. Another is ‘messy’ feeding, in which carnivores scatter scraps of prey and herbivores eat more than they can process, allowing a considerable portion of the ingested phytoplankton to pass through the gut unabsorbed.
Chemical Messages
Authors: Herring Peter
Published: November 2023

The oceanic habitat is awash with organic compounds released deliberately or accidentally by the organisms that live within it. Seawater not only bathes the outer surface of an organism but in most multicellular animals it also travels through it, down the gut lumen. Every living organism is effectively a leaky bag of organic molecules, with survival being dependent upon achieving the right balance of molecular input and output, both qualitatively and quantitatively.
Seeing in the Dark
Authors: Herring Peter
Published: November 2023

Vision is our main remote sensing system. 40% of the sensory connections to the human cortex are those from the visual system. The sun illuminates our environment during the day and at night we sleep, or turn on our own artificial light sources (a strategy matched in the deep sea by bioluminescence, Chapter 9).
Introductory comments: Xenopus as a laboratory animal
Authors: Gurdon J B
Published: November 2023

Xenopus laevis, the South African clawed frog, has come to be, together with the mouse and the chick, the vertebrate species most widely used for research in the areas of developmental, cell and molecular biology. This somewhat surprising situation arose from the use of X. laevis about 50 years ago as an assay for pregnancy in humans; the injection of a few millilitres of urine from a pregnant woman under the female frog’s skin, into the dorsal lymph sac, causes it to lay eggs. From around the 1950s, this was replaced by a more convenient form of pregnancy test, but it was apparent that Xenopus can be induced to mate and provide fertile embryos by the gonadotrophic hormones (primarily luteinizing hormone) of other vertebrate species. This characteristic is not shared by Rana species in which the same result requires the injection of homogenized pituitary glands from several adults, a procedure that is very laborious and extremely wasteful of animals. Even then, fertile eggs can be obtained from Rana only during certain months of the year, as is also true of other amphibians such as newts and salamanders (Triturus) which were favourite objects of research for great names in the field of experimental embryology including Spemann, Holtfeter, etc.
Historical constraints and morphological novelties in the evolution of the skeletal system of pipid frogs (Anura: Pipidae)
Authors: Trues Linda
Published: November 2023

IPipid frogs of the genera Xenopus, Silurana, Hymenochirus, Pseudhymenochirus and Pipa are dissimilar to all other living anurans and highly derived rather than primitive. Among living pipids, Xenopus is the most primitive-i.e., the most similar to the hypothesized ancestor of the Pipidae. Nonetheless, the adults of this taxon possess many morphological features that distinguish them from their closest living non-pipid relatives, Rhinophrynus dorsalis (Rhinophrynidae) and the pelobatoid frogs. Many of the morphological novelties seem to be associated with the evolution of an aquatic anuran from a terrestrial saltatorial ancestor. The sprawled, laterally positioned limbs and dorsoventral compression of the body in pipids that facilitate their swimming inhibit their hopping or jumping and are correlated with modifications of the thigh musculature and structures of the pectoral and pelvic girdles. Movement of the trunk is limited to anterior-posterior shifts of the pelvic girdle on the sacrum; dorsal-ventral rotation of the posterior trunk, which is critical to saltatorial locomotion, is not possible. Many cranial modifications in Xenopus seem to be associated with its mode of feeding without a tongue, but little is known about the feeding mechanism. The mandible is robust, whereas the upper jaw is weak and suspended from the skull by a modified suspensory apparatus. The hyolaryngeal apparatus is highly modified. The plectra! apparatus is hypertrophied and the tympanic annulus is ossified and in synostosis with the dermal squamosal medially. The orbital region of the braincase is depressed and formed by membrane, rather than endochondral, bone.
Molecular approaches to the phylogeny of Xenopus
Authors: Graf Jean-Daniel
Published: November 2023

Comparative molecular studies of Xenopus species have addressed four main ques¬tions: (1) the monophyly or polyphyly of the genus Xenopus, (2) the subdivisions of the genus and the relationships among species groups, (3) the age of major splitting events within the genus, (4) the age of polyploidization events. The first question has been examined in two studies, based on immunological distances and ribosomal DNA sequences, which strongly suggest that the genus Xenopus, including X. tropicalis, is monophyletic with respect to Hymenochirus. The second question has been considered in several studies using electrophoresis of proteins, peptide mapping of albumin or restriction mapping of mtDNA. Different criteria produce different classifications, although some consensus is obtained on the existence of a tropicalis group, a fraseri group and a laevis group. A partial answer to the third question has been provided by a comparison of nucleotide sequences of globin genes: the divergence between the two most distant species groups, i.e. the tropicalis group and the rest of the genus, is estimated to be about 120 million years old. The same study has produced a tentative answer to the fourth question: the divergence time between the homoeologous globin genes of the tetraploid-derived X. laevis is estimated at about 40 to 60 million years ago. However, if tetraploidy resulted from allopolyploidization, then this estimate corresponds to the age of the diploid parental species, and not to the date of polyploidization, which remains unknown.
Adaptations to life in running waters
Authors: Giller Paul S , Malmqvist Björn
Published: November 2023

From one perspective, terrestrial and aquatic habitats are similar in that they consist of a fluid (gaseous atmosphere or liquid water) overlying a solid (land surface or river or lake bed sediments). However, the greater density of water provides mechanical support that allows a vast array of aquatic organisms to live ‘free from contact with the ground’ suspended in the fluid medium, particularly in the oceans and lakes. It also means that any movement of the denser water is also or much greater and more immediate importance for aquatic organisms than air movements arc for terrestrial ones. The challenges to life in streams and rivers arc therefore going to be different from those in terrestrial systems, and as a consequence, we find unique adaptations among the lotic biota, some of’ which we explore in this chapter.
Community patterns, diversity, and biogeography
Authors: Giller Paul S , Malmqvist Björn
Published: November 2023

Freshwater biologists have traditionally lagged somewhat behind their terrestrial colleagues in studying the structure and function of communities, but in the recent past this situation has changed and there is now a considerable literature developing. However, this is not an ecology book and as such we cannot delve too deeply into this burgeoning literature. we have discussed various aspects of lotic communities elsewhere in this book, including longitudinal patterns and the River Continuum Concept (pp. 165-9) and the role of species interactions (pp. 182-92). we have also seen how various physical and chemical factors and disturbances influence aquatic communities and the distribution and abundance of species in Chapter 3. So, here, we will concentrate on a few other important community patterns and processes including resource partitioning, succession, persistence, trophic structure, and food webs, then turn to a consideration of species diversity in streams and rivers and finally to the larger scale biogeographic distribution patterns.
Systematics of sea snakes: a critical review
Authors: Rasmussen Arne Redsted
Published: November 2023

The taxonomy of elapid sea snakes is reviewed. There is no general agreement on generic and suprageneric relationships. The problematic genera are reviewed on the basis of published data and personal observations. Sea snakes form a group of aquatic snakes with a vertically flat paddle-like tail, which is not found in any other terrestrial or aquatic snakes. Sea snakes belong to the same group as terrestrial elapids; they are all characterized by the anterior position of the poison-fangs on the maxillary bone (proteroglyphous) (McCarthy 1985).
Evolution of viperine snakes
Authors: Herrmann Hans-Werner , Joger Ulrich
Published: November 2023

A quantitative immunological determination of serum albumin differences between 41 viperid species was used to reconstruct the phylogenesis of this group.
Systematics of the Bothrops atrox complex: new insights from multivariate analysis and mitochondrial DNA sequence information
Authors: Wuster W , Salomao G M , Thorpe R S , Puorto G , Furtado M F D , Hoge S A , Theakston R D G , Warrell D A
Published: November 2023

We use multivariate analysis of morphological characters and comparative sequencing of a 520 bp fragment of the cytochrome b gene (mitochondrial DNA) to investigate patterns of geographic variation in the Bothrops atrox species complex, and the population phylogeny of the group in parts of South America. Populations conventionally assigned to B. atrox and B. moojeni constitute morphologically distinct groupings, with a zone of phenetically intermediate specimens where their ranges meet. Bothrops marajoensis, B. isabelae, B. leucurus and B. pradoi are poorly differentiated or undifferentiated from B. atrox and each other. Phylogenetic analysis of the cytochrome b sequence information reveals that B. caribbaeus constitutes an outgroup to the South American populations of the B. atrox complex. Within the South American radiation, the conventional species, as generally understood, largely lack historical reality. Two well-corroborated basal dades are revealed: one includes the populations from the lower Amazon and Tocantins-Araguaia drainages, as well as Marajo Island. The other comprises two further basal clades within it, the first consisting of the populations conventionally assigned to B. moojeni, the other a number of populations from the eastern coast of Brazil, various places in western and central Amazonia and western Venezuela. Mantel matrix correlation tests show morphological variation among the populations of the complex to be most strongly associated with vegetation type. This suggests that morphological variation represents primarily an adaptation to current selection pressures, probably for crypsis, and not a reflection of population phylogeny.
Moas and kiwis
Authors: Davies S J J F , Bamford Michael J , Loomes Danika
Published: November 2023

The moas inhabited New Zealand, probably surviving into the nineteenth century. None ,were collected from life by Europeans but sub-fossil remains have been extensively studied. Anderson (1989) has provided a comprehensive recent review of the group and the information given at appropriate places in the introductory chapters of this book is based on his work. It remains only to provide a formal classification. which follows Bock and Biihler (1988) for the higher categories and Anderson (1989) and Brodkorb (1963) for the lower ones.
An introduction to reefs
Authors: Wood Rachel
Published: November 2023

The term ‘reef’ derives from the Old Norse nautical term rif,meaning a hazardous ‘rib’ of rock, sand, or biological material that lies close to the surface of the sea. But as organic constructions of calcium carbonate, the term reef has evolved different scientific meanings from its original nautical usage, such that now no definition is universally accepted by ships’ captains, biologists, and geologists. Consider the diversity of the following four examples.1. Living coral reefs grow to sea level in clear, tropical waters and may cover many square kilometres. They are constructed by large, heavily calcified organisms (mainly corals and coralline algae) whose growth is driven by photosynthesis. Such reefs show mechanical resistance to all but the most vigorous currents and storms, and often form steep walls in the face of severe wave impact.
Molecular Structure And Its change
Authors: Bader Richard F W
Published: November 2023

The essential understanding and original intent associated with the notion of structure in chemistry is that it be a generic property of a system. Structure originally implied the existence of a particular network of bonds, which was presumed to persist over a range of nuclear displacements until some geometrical parameter attained a critical value at which point bonds were assumed to be broken and/or formed to yield a new structure. However, the word ‘structure’ has over the years acquired a duality of meanings. This has occurred for two reasons. The first was a result of our inability to unambiguously assign a network of bonds to a given system. The second was a result of our ever-increasing ability to experimentally measure the geometrical parameters which characterize the minimum energy nuclear configuration of a system within the Born—Oppenheimer model. Thus, if one references the heading ‘molecular structure’ in early books on descriptive chemistry, one finds a discussion of valency and bonding and of models for assigning a network of bonds. Referenced under the same heading in present-day physical chemistry or spectroscopy texts are discussions of the experimental methods used to determine the bond lengths and bond angles which are used to characterize an equilibrium geometrical structure.
The Action Principle For A Quantum Subsystem
Authors: Bader Richard F W
Published: November 2023

It has been demonstrated in Chapter 5 that Schrodinger’s original derivation of the wave equation can be generalized to provide a quantum description of an atom in a molecule. His derivation uses the calculus of variations as applied to an energy functional of Ψ and its extension to an atom in a molecule entails two essential steps: the introduction of a particular type of operator through its identification with the variation of the state function and a variation of the surface bounding the atomic subsystem.
Notation
Authors: Altmann Simon L
Published: November 2023

Whereas no chemist would these days treat, say, molecular vibrations without using the vocabulary of group theory, there is, unfortunately, no elementary introduction to the band theory of solids which adopts this approach. There are, of course, excellent books on the group theory of the solid state, but they are all at a rather rigorous level and are not suitable as an introduction to band theory. Almost twenty years ago I wrote such an introduction in which I made much use of the concept of symmetry, but I could not employ the vocabulary of group theory since undergraduates in the physical sciences were not exposed to this subject in those days. Finite group theory is now the lingua franca of chemistry and many undergraduate courses in physics include some group theory. I felt, therefore, that the time had now come to have a book which would bridge the gap between the current elementary texts on band theory and the more advanced treatments of the group theory of solid state.
Symmetry and group theory: a revision
Authors: Altmann Simon L
Published: November 2023

A lump of metal was considered in Chapter 1 as if it had no internal structure at all, the surface of the metal acting as the walls of a container inside which a free-electron gas is to be found. Even in this case we did find a degeneracy which arises from the isotropy of the space in which the electrons move: the pair of free-electron states corresponding to the values k and - k of the wave vector must be degenerate. (See§1–3.) We shall want in the rest of this book, of course, to introduce the effect of the crystal structure on the electron states and we must expect many more, and more complicated, symmetries which, as we shall see, will lead also to more complicated degeneracies. The study of these degeneracies is essential: if we did not know, for example, that the level 2p of the free sodium atom is six-fold degenerate, we would get the electronic structure of this atom hopelessly wrong. As we shall remind ourselves in this chapter, the study of degeneracy is very much simplified by using some simple ideas of group theory. We shall expect the reader to have some familiarity with these ideas, as treated for instance in the well-known textbook of physical chemistry by Atkins (1990, Chapter 15).
Space groups
Authors: Altmann Simon L
Published: November 2023

We have learnt in Chapter 2 how group theory allows us to classify the degeneracies of a physical system, as long as we know its symmetry group. Symmetry groups of crystals are substantially more involved than those of molecules and they are called space groups. We must learn some of their properties in order to be able to study those of the energy eigenvalues in crystals.
The reciprocal lattice and the Fourier series
Authors: Altmann Simon L
Published: November 2023

A crystal pattern is periodic in the translation lattice, that is, it is obtained in its (infinite) entirety by repeated translations of the unit cell, these translations thus providing periodicity along each of the corresponding directions. As a result, many functions of physical importance in the crystal will be periodic .functions which, once defined inside the unit cell, are then known throughout the crystal by the periodicity condition. An important example of this situation is the crystal potential, but we shall see that various other periodic functions play a very important part in the study of bands in crystals.
Bloch functions and Brillouin zones
Authors: Altmann Simon L
Published: November 2023

We have proved in § 1–3 that, in free space, the momentum eigenfunctions are eigenfunctions of the energy (see eqn 1–3.6), and these momentum eigenfunctions have just been written as the plane waves I k> in (4–10.2), labelled by a propagation vector k in the reciprocal lattice. We want to consider in this chapter the electrons moving in the crystal not just as free particles but rather under the influence of the crystal potential field. In these circumstances, we cannot expect the energy eigenfunctions to continue being the plane waves I k >, although, when we obtain their general form, we shall see that they are deeply related to them. (It is in fact for this reason that we have paid so much attention to these plane waves.)
Brillouin zones and energy bands
Authors: Altmann Simon L
Published: November 2023

We shall start this chapter by considering a three-dimensional Brillouin zone, which will serve us as an example in order to study the properties of the Brillouin zone faces. After this, we shall go back to a one-dimensional example so as to be able to discuss in detail various schemes which are used in order to plot energy bands and Fermi surfaces in k space.
Phonons and conductivity
Authors: Altmann Simon L
Published: November 2023

We have already used more than once the idea that electrical conductivity is due to the fact that the electric field promotes electrons which are near the Fermi level to unoccupied levels above it. We have then assumed that the size of the Fermi surface is a determining factor in conductivity, a point which we shall confirm and refine in § 1. Once this is done we shall see that, because the electric field provides a constant acceleration to the Fermi electron sea, a mechanism must be found which prevents this process from continuing indefinitely, since otherwise a steady state of conduction by the electrical carriers would never be achieved. We must therefore discover in what way the electrons may be scattered and thus slowed down. There are two ways in which this may happen. One is through electron-electron collisions, but this, of course, cannot affect the energy of the electron sea as a whole, whereas it is this energy which we must ensure does not run up to infinity. A second possible mechanism is by collisions between the electrons and the crystal structure. We shall see, though, that a perfect, that is, a rigid crystal cannot exchange energy with the electron sea. It is only a vibrating crystal that can do this, as we shall discover when we study crystal vibrations, which will lead us to the important concept of the phonon.
Wannier functions and Lowdin orbitals
Authors: Altmann Simon L
Published: November 2023

Plane waves and Bloch functions, which have so far been our tools for describing electron states in solids, are delocalized functions which extend throughout the crystal. When dealing with localized phenomena, such as impurities or surface states, it is useful to replace the Bloch functions or the plane waves by functions which are, as far as possible, localized. This means that whereas the Bloch functions are labelled by the different k vectors of the Brillouin zone, the functions we seek, which are called the Wannier functions, must be labelled in terms of the different primitive cells of the crystal. This does not mean that they are entirely localized within each cell but, because each function is associated with one primitive cell, a degree of localization might be achieved, as we shall see later on (§ 2) is in fact the case.
Solutions to the problems
Authors: Altmann Simon L
Published: November 2023

Problem 3

The first two eigenstates correspond to the values shown in Table 1. Follow on in the same manner.

Problem 4

Use the values of h and of the energy equivalent of the electron mass shown in the table on the inside back cover.
How do they do it?—Making oxygen
Authors: Milgrom Lionel R
Published: November 2023

Why is grass green and blood red? Put another way, why is chlorophyll photoactive, beginning the process of photosynthesis, while the closely related heme performs a whole range of transport and redox functions that are non-photochemical in origin and depend on the protein that it is embedded in? To begin to answer these questions we need to know something about the chemical and physical properties of porphyrins. To understand those properties, we will require a knowledge of porphyrin electronic structure. That electronic structure is based on a skeleton of 20 carbon atoms surrounding a central core of four nitrogen atoms. This atomic arrangement supports a highly stable configuration of single and double bonds, called an aromatic 1r-system. The simplest and, indeed, archetypal aromatic 1r-system is seen in benzene.
What happens when it all goes wrong?
Authors: Milgrom Lionel R
Published: November 2023

We have seen how porphyrins arc biosynthesised and, in the last chapter, how they are metabolised. In any normally functioning living system, these processes are usually held in balance, so that a steady-state concentration of any particular substance is obtained. But mistakes do occur and when they do, they lead to a variety of pathological conditions. In this chapter, we shall be examining some of these. We shall also look briefly at what happens when the protein (in particular globin) that surrounds a porphyrin, malfunctions due to genetic misprogramming and does not provide the correct working environment for the heme moiety.
Werner clathrates: guest-lattice intermolecular interactions
Authors: Lipkowski Janusz
Published: November 2023

The ‘clathratogenic’ ability of coordination complexes of the general formula M(Il)XzA4 was first reported by Schaeffer and coworkers [WD. Schaeffer et al., J. Am. Chem. Soc., 79(1957), 5870). During 1950-1970 the main reason for studying the subject was the possibility of practical use of clathration selectivity in separation of mixtures which are otherwise separable with difficulty, i.e. mixtures of isomeric compounds. Thus, the early literature contains extensive information on selectivity of clathration of a variety of mixtures of organic compounds (guests) by different Werner complexes (host) {Tobie 1}.
ISIS: a powerful new tool for organic crystal chemistry
Authors: Finney J L , Wilson C C
Published: November 2023

Crystallographic methods to solve crystal and molecular structures are central to organic crystal chemistry. X-rays havegenerally been the preferred probe for crystallographic work due to the wide availability and convenience of laboratory X-ray sources. Most of the structural work to date has been performed on single crystals, which have been capable of giving data of much higher quality than powder (polycrystalline) materials. Also important in this field are spectroscopic methods, which can be used to improve our understanding of the interactions between molecules. In spectroscopy, infrared and Raman, along with NMR, have been extensively exploited.
New developments on the Enraf-Nonius FAST detector
Authors: Schierbeek B
Published: November 2023

The Enraf-Nonius FAST system (Arndt & Gilmore, 1979) consists of a TV-camera based detector, combined with a four circle goniometer with kappa type geometry and interfaced to a microVAX computer and a TV monitor. The goniometer is the well known CAD4 kappa goniometer, which allows the user flexible control over orientation : no remounting of the crystal, easy alignment of the crystal and efficient covering of reciprocal space, which has high precision and furthermore an open design with minimum obscuration, allowing /-N2 cooling, shock freezing and the possibility to collect full absorption profiles.
Statistical descriptors
Authors: Schwarzenbach D
Published: November 2023

Many crystallographers are aware that estimated standard deviations (e.s.d.’s) of structural parameters routinely calculated by current least-squares refinement programs are unrealistic (a fitting acronym would be u.s.d.’s) and that the actual uncertainties are larger, and sometimes much larger (Taylor & Kennard, 1986). There are two types of reasons for this fact: The models used for calculating the observed quantities (in general diffraction data) are invariably deficient. The model includes all operations leading from the raw data to the final structural parameters: data reduction procedures used to calculate observed structure amplitudes are as much part of the model as is the structure factor expression used in the structure refinement. Even if some of the deficiencies of the standard structural model are well-known in principle (viz. aspherical charge density distributions, anharmonic vibrations, effects of disorder, angular dependence of anomalous dispersion, extinction, thermal diffuse scattering, scan truncation), their combined effect is difficult to assess. Model deficiencies are generally known as systematic errors.
Macromolecular crystallographic computing designed around the XTAL system
Authors: Watenpaugh K D , Holland D R , Collins, D M , Stewart J M
Published: November 2023

The XTAL System (Hall & Stewart, 1989) has been designed to be a highly portable, highly integrated system of programs that centers around a flexible data file concept allowing for efficient archiving of data. The master file contains all the crystallographic data, atomic coordinates, and auxiliary information necessary to carry most desired calculations with a minimum of user control input. On the other hand, the routines contain a large array of options to allow the experienced and expert crystallographer considerable flexibility in the calculations they may wish to perform or the paths by which they may wish to carry out structure determinations. Besides the archival data file, the XTAL System has a free formal control input based on the use of keywords requiring input information only when normally used defaults are to be altered. This overall philosophy has allowed for the successful implementation of an integrated system of programs not only for small molecule crystallography, but also for macromolecular crystallography. This integration provides not only for the use of routines commonly used by both groups of users (e.g. Fourier or structure factor calculating programs), but also, for those routines considered to be in one or the other domain (e.g. direct methods for small molecule studies). Finally the routines included in the system have been extensively documented both in the source codes and in the manuals, a practice that is too easily overlooked by many program developers. Detailed description of the system, users manuals, program development manuals and the distribution tape can be obtained from S. R. Hall at the Crystallography Centre, University of Western Australia, Nedlands. Questions regarding the XTAL system’s use in macromolecular calculations and problems should be addressed to K. D. Watenpaugh.