bluuebunny/crossref_metadata_2025 huggingface dataset:
Max Born
Authors: Cook A.
Published: April 2004

Max Born was one of the small group of theoretical physicists who established the mathematical structure of quantum mechanics in the 1920s. Born himself recognized that Heisenberg had the crucial idea that the variables in quantum mechanics should be observable quantities, not classical coordinates that were not observable. Heisenberg proposed to take instead quantities that were related to the transitions between states of an atom. The photograph shows Max Born (Copyright © Anne Meitner)
The publication of John Wilkins's
Essay
(1668): some contextual considerations
Authors: Lewis R.
Published: April 2004

John Wilkins's
Essay towards a Real Character and a Philosophical Language
was published in 1668. It was an attempt to institute an artificial language based on the order of things, and was expected to contribute to improved scientific practice, to facilitate inter–linguistic communication and to ameliorate religious controversy. Wilkins was a founding member of The Royal Society, and the
Essay
was published under its imprimatur. The printer to The Royal Society was John Martyn, and this article traces the occasionally damaging impact Martyn had upon the publishing practice of the early Royal Society, before considering the steps Wilkins took to ensure the best possible reception for his work. Prominent amongst these was the fact that although Martyn's name appeared on the title page of the
Essay
, Wilkins was principally dependent on Samuel Gellibrand—another, more creditable, printer with whom he had a long–standing relationship—for its publication. Wilkins's approach to the production of a book of the
Essay
's size and typographic complexity is also considered.
Sir George Cayley, the father of aeronautics. Part 1. The invention of the aeroplane
Authors: Ackroyd J. A. D.
Published: April 2004

This paper, in two parts, seeks to describe and assess Cayley's technical development of his invention, the fixed–wing aeroplane. Particular attention is paid to such scientific results as were known to Cayley at that time. Part 1 deals with the invention of the aeroplane itself, this being prefaced by a biographical sketch outlining his wide–ranging interests, both scientific and humanitarian; part 2 will show how Cayley was not only able to develop his invention but through this was also able to demonstrate many of the basic principles of fixed–wing flight. The paper is based on the author's Cayley Lecture to the Royal Aeronautical Society in April 2000.
Some final thoughts of Sir John Herschel, F.R.S.
Authors: Sharp R.
Published: April 2004

In a collection (MS350) in the Science Museum's Archive Collection, of some 325 letters to Thomas Andrews are four from Sir John Herschel written in the last months of his life. They, and a later memorandum by Andrews in the same collection, elucidate a particular case of priority with reference to an ‘ice calorimeter’, indicate Andrews's role in bringing it to light, and afford Herschel a last opportunity to muse upon aspects of priority invention in general.
James Ivory's last papers on the ‘Figure of the Earth’ (with biographical additions)
Authors: Craik A.D.D.
Published: April 2004

Sir James Ivory, F.R.S. (1765–1842), was best known for his work on the gravitational attraction of ellipsoids, and the ‘Figure of the Earth’; a problem that attracted great attention. The mixed reception of Ivory's late work on this topic is examined. Although refereed fairly and favourably by George Biddell Airy, it was attacked by Isaac Todhunter long after Ivory's death. Further biographical information about James Ivory is given. This includes evidence that reveals the identity of his mother and shows that he was not born illegitimately, as I had claimed previously.
Roland Trimen and the
Merope
harem
Authors: Cohen A.
Published: April 2004

Roland Trimen (1840–1916, F.R.S. 1883) began to publish his entomological research in 1863. Although his main interest was in the taxonomy of South African butterflies he made important discoveries that helped to lay the foundations of the study of mimicry in insects. Together with Charles Darwin, Henry W. Bates, Alfred R. Wallace, Fritz Müller and Raphael Meldola he was one of those natural historians who may be credited with creating the science of ecology.
The wide–ranging family history of Max Born
Authors: Born G. V. R.
Published: April 2004

This article gives an account of the life of Max Born, one of the founders of quantum mechanics and the author's father, in the context of his forebears, family and descendants. It traces the family's history from Martin Luther to the present day, ranging as far afield as Ben Elton and Olivia Newton–John.
Charles Babbage and his world
Authors: Wilkes M. V.
Published: April 2004

Most people have heard something about Charles Babbage, F.R.S., whose work on computers in the nineteenth century was much ahead of its time. Babbage worked on two computing devices, neither of which he completed: the Difference Engine and the Analytical Engine. It is the Analytical Engine that gives him a claim to major fame. Unfortunately, most of the details remained buried in his manuscript notebooks and were not unearthed until the modern computer age had begun. For that reason, it is rather overstating the case to describe him, as is often done, as the father of the computer. I shall not here be concerned with Babbage's technical achievements, but rather with the age in which he lived. It was an age in which rapid scientific and industrial progress was being made and in that respect it resembles our own. Babbage was born in 1791 and went up to Cambridge University in 1810. Steam engines were then rare, and railways and electric telegraphs lay in the future. The word ‘electricity’ denoted static electricity generated by friction, and there was no hint of the marvels that electric currents would bring.
Le Sage's
Essai de chymie méchanique
Authors: Rowlinson J. S.
Published: April 2004

Le Sage's
Essay
was an ingenious eighteenth–century attempt to explain both the cohesive forces between particles of matter and gravitational forces, without recourse to Newtonian attraction at a distance. His explanation of cohesive forces never gained acceptance but the application to gravity drew some attention in the nineteenth century, and some recent physical work has a curious similarity to his ideas on cohesion.
Book reviews
Authors: Heap B.
Published: April 2004

Four book reviews in the January 2003 issue of
Notes and Records
. Henry Harris,
Things come to life: spontaneous generation revisited,
. John Ziman,
Real science: what it is, and what it means
. Richard Yeo,
Encyclopaedic visions. Scientific dictionaries and Enlightenment culture
. Eric G. Forbes, Lesley Murdin and Frances Willmoth,
The correspondence of John Flamsteed, the first Astronomer Royal, volume 3 (1703-1719)
.
Address of the President, Lord May of Oxford OM AC KT FRS, given at the Anniversary Meeting on 29 November 2002
Authors: May R. M.
Published: April 2004

Down through the years, Anniversary Addresses have again and again echoed the motto given to The Royal Society by its founders: ‘
Nullius in verba
’. The Latin words are taken from a passage in Horace in which the poet likens himself to a gladiator who, having earned retirement, need no longer bow to authority (
Nullius addictus iurarae in verba magistri
): ‘I say no master has the right to swear me to obedience blind’. Such classical arcana raises some eyebrows today, and we might often do better with the motto's equivalent in contemporary demotic—from the American TV series Dragnet—'just the facts, Ma‘am’. Independent of the details of the translation, our motto sets out the core values of The Royal Society: pursuit of secure, experimentally verifiable knowledge of how the world works, unfettered by the received wisdom of past belief or the constraints of past authority. It is no less a radical agenda in 2002 than it was in 1660.
Two anniversaries
Authors: Cook A.
Published: April 2004

Introduction to the May 2003 issue of
Notes and Records
The Tonkin tides revisited
Authors: Cartwright D.E
Published: April 2004

A description of the once-daily tides of the Gulf of Tonkin in 1678 came at an awkward time for natural philosophers, before Newton's
Principia
had been published. Halley (in 1684) noticed the strong dependence on lunar declination (not phase), but was over-hasty in trying to reduce the varying amplitudes to a simple rule. Newton proposed a mechanism for the absence of the half-daily tide, but admitted that further observations were required to confirm it. Another explanation was made by Euler in 1740. The exact site of the original observations is obscure but is here identified through Dampier's
Voyages
. The subsequent history of prediction practice is briefly summarized, and attention is drawn to a recent computer model of the South China Sea that belatedly solves all the outstanding problems.
George Pearson MD, FRS (1751-1828): ‘The greatest chemist in England’?
Authors: Coley N.G
Published: April 2004

George Pearson, the son of an apothecary, studied medicine at Edinburgh under Joseph Black. He entered medical practice at Doncaster in 1777, but moved to London and became a physician at St George's Hospital in 1787. He lectured on chemistry and was the first English chemist to adopt the oxygen theory; he was elected FRS in 1791. One of the first to advocate Jenner's cowpox vaccination, he thought himself superior to Jenner in promoting it. He expected recognition and when this was given exclusively to Jenner, became embittered. His reputation was damaged and he has largely been forgotten.
Essay review: The ultimate commentary: a consideration of I. Bernard Cohen's
Guide to Newton's
Principia
Authors: Zinsser J.P
Published: April 2004

An Essay Review of ‘Isaac Newton,
The Principia: mathematical principles of natural philosophy
’, translated by I. Bernard Cohen and Anne Whitman, assisted by Julia Budenz; preceded by ‘A guide to Newton's
Principia
’ by I. Bernard Cohen.
The ancestry of Robert Hooke: John Hooke of Wroxhall
Authors: Breeze P.
Published: April 2004

New evidence suggests that Robert Hooke is descended from a nonconformist minister, John Hooke of Wroxhall, his grandfather. This identification makes it possible that Robert Hooke had a cousin, John Hooke, who was his contemporary at Oxford and was later rector at Blechingdon in Oxfordshire between 1662 and 1672.
Robert Fitzroy and the myth of the ‘Marsden Square’: Transatlantic rivalries in early marine meteorology
Authors: Agnew D. C.
Published: April 2004

Marine data (especially in meteorology) are often grouped geographically using a set of numbered 10° latitude–longitude squares known as Marsden squares, which are usually attributed to William Marsden, Secretary of the Admiralty (and Vice–President of The Royal Society), who supposedly invented them early in the nineteenth century. Available records suggest that this system was in fact probably invented by Robert FitzRoy soon after his appointment as head of the British Meteorological Office in 1854. FitzRoy felt that early English work in marine meteorology was being ignored, notably by the American Matthew Fontaine Maury, who had pioneered the collecting of marine meteorological data from ship's logs. A desire to undo this wrong led FitzRoy to emphasize earlier (though abortive) British projects by A.B. Becher (in 1831) and by Marsden (probably in the 1780s), both of which involved grouping marine data geographically, though only over limited areas. FitzRoy's treatment of this earlier work seems to have created, much later, the belief that Marsden had invented the system of 10° squares. Given both Maury's and FitzRoy's desire to demonstrate priority in this field, it is ironic that the first clear proposal to collect and group data from ship's logs was made by the American (and British) natural philosopher Isaac Greenwood in 1728.
Viruses and the development of quantitative biological electron microscopy
Authors: Crowther R. A.
Published: April 2004

The electron microscope has become an important tool for determining the structure of biological materials of all kinds. Many technical advances in specimen preparation and in sophisticated methods of image analysis, initially based on optical systems but latterly on computer processing, have contributed to the development of the subject. Viruses of various kinds have often provided a convenient and appropriate test specimen. This paper describes the major technical advances and shows how viruses have had an important role in most of the developments.
REPORT. Newton on the Net: first and prospective fruits of a Royal Society grant
Authors: Iliffe R. , Young J.
Published: April 2004

Report of The Newton Project
REPORT. Robert Hooke revivified
Authors: Hunter M.
Published: April 2004

An international conference held from 6 to 9 July 2003 under the auspices of Gresham College and The Royal Society, and with the support of the Royal Academy of Engineering.
REPORT. Robert Hooke at Christ Church, Oxford
Authors: Cook A.
Published: April 2004

This year is not only the 300th since the death of Robert Hooke, it is also 350 years since he was admitted to Christ Church, Oxford. Hence on 2 October a symposium in honour of their distinguished son was held under the auspices of Christ Church, at which some of the recent studies of his life and achievements were noted. Many of the speakers held posts that Hooke had held, such as the Gresham Professor of Geometry and Secretary of The Royal Society.
REPORT. OxDNB welcomes new old Fellows
Authors: McConnell A.
Published: April 2004

The Oxford dictionary of national biography (OxDNB), due to be published in 2004, replaces and extends the original Dictionary of national biography (DNB), comprising 50,000 articles and 10,000 likenesses, covering all aspects of the British past from the earliest times to the end of 2000.
Book reviews
Authors: authors Various
Published: April 2004

The greate invention of algebra: Thomas Harriot's treatise on equations
, by Jacqueline A. Stedall,
reviewed by
J. Gray.
Collected works on Benjamin Roberts and Charles Hutton
, by W. Johnson,
reviewed by
A. McConnell.
The man who changed everything—the life of James Clerk Maxwell
, by Basil Mahon,
reviewed by
B. Pippard.
'The common purposes of life': science and society at the Royal Institution of Great Britain
, ed. Frank A. J. L. James,
reviewed by
J. S. Rowlinson.
The 2003 Wilkins Lecture: Dr Wilkins's boy wonders
Authors: Jardine L.
Published: April 2004

In the second half of the seventeenth century in England, a procession of great figures emerged to become the founding figures of modern science (what was then called natural philosophy). Today it is the originality of these ‘men of genius‘ that we are inclined to celebrate. Yet the most innovative aspect of the period's scientific activities was a whole series of collaborative intellectual enterprises, which were unlike any that came before them in their capacity to mobilize and organize original ideas and their technical application.
The wartime work of Hinshelwood and his colleagues
Authors: Rowlinson J. S.
Published: April 2004

C. N. Hinshelwood and his physical and inorganic chemical colleagues in Oxford worked throughout World War II on the improvement of charcoal for use in respirators and on other physicochemical problems. The surviving reports and correspondence give a detailed picture of what they accomplished and on the way in which extramural research contracts were then handled.
The role of
Notes and Records
and some future anniversaries
Authors: Quinn T.
Published: April 2004

Introduction to the January 2004 issue of
Notes and Records
with a picture of Sir George Airy who, as Astronomer Royal, was a member of the International Commission on the Metre (1870) which established the Metric Sytem and led to the Convention du Mètre (1875) and the International Bureau of Weights and Measures.
Mechanisms involved in regulating DNA replication origins during the cell cycle and in response to DNA damage
Authors: Early Anne , Drury Lucy S. , Diffley John F. X.
Published: April 2004

Replication origins in eukaryotic cells never fire more than once in a given S phase. Here, we summarize the role of cyclin–dependent kinases in limiting DNA replication origin usage to once per cell cycle in the budding yeastSaccharomyces cerevisiae. We have examined the role of different cyclins in the phosphorylation and regulation of several replication/regulatory factors including Cdc6, Sic1, ORC and DNA polymerase α–primase. In addition to being regulated by the cell cycle machinery, replication origins are also regulated by the genome integrity checkpoint kinases, Mec1 and Rad53. In response to DNA damage or drugs which interfere with the progression of replication forks, the activation of late–firing replication origins is inhibited. There is evidence indicating that the temporal programme of origin firing depends upon the local histone acetylation state. We have attempted to test the possibility that checkpoint regulation of late–origin firing operates through the regulation of the acetylation state. We found that overexpression of the essential histone acetylase, Esa1, cannot override checkpoint regulation of origin firing. We have also constructed a temperature–sensitiveesa1mutant. This mutant is unable to resume cell cycle progression after α–factor arrest. This can be overcome by overexpression of the G1 cyclin, Cln2, revealing a novel role for Esa1 in regulating Start.
Interplay between DNA replication, recombination and repair based on the structure of RecG helicase
Authors: Briggs Geoffrey S. , Mahdi Akeel A. , Weller Geoffrey R. , Wen Qin , Lloyd Robert G.
Published: April 2004

Recent studies inEscherichia coliindicate that the interconversion of DNA replication fork and Holliday junction structures underpins chromosome duplication and helps secure faithful transmission of the genome from one generation to the next. It facilitates interplay between DNA replication, recombination and repair, and provides means to rescue replication forks stalled by lesions in or on the template DNA. Insight into how this interconversion may be catalysed has emerged from genetic, biochemical and structural studies of RecG protein, a member of superfamily 2 of DNA and RNA helicases. We describe how a single molecule of RecG might target a branched DNA structure and translocate a single duplex arm to drive branch migration of a Holliday junction, interconvert replication fork and Holliday junction structures and displace the invading strand from a D loop formed during recombination at a DNA end. We present genetic evidence suggesting how the latter activity may provide an efficient pathway for the repair of DNA double–strand breaks that avoids crossing over, thus facilitating chromosome segregation at cell division.
How good is our genome?
Authors: Weill Jean-Claude , Radman Miroslav
Published: April 2004

Our genome has evolved to perpetuate itself through the maintenance of the species via an uninterrupted chain of reproductive somas. Accordingly, evolution is not concerned with diseases occurring after the soma's reproductive stage. Following Richard Dawkins, we would like to reassert that we indeed live as disposable somas, slaves of our germline genome, but could soon start rebelling against such slavery. Cancer and its relation to the
TP53
gene may offer a paradigmatic example. The observation that the latency period in cancer can be prolonged in mice by increasing the number of
TP53
genes in their genome, suggests that sooner or later we will have to address the question of heritable disease avoidance via the manipulation of the human germline.
Telomeres and telomerase
Authors: Chan Simon R. W. L. , Blackburn Elizabeth H.
Published: April 2004

Telomeres are the protective DNA–protein complexes found at the ends of eukaryotic chromosomes. Telomeric DNA consists of tandem repeats of a simple, often G–rich, sequence specified by the action of telomerase, and complete replication of telomeric DNA requires telomerase. Telomerase is a specialized cellular ribonucleoprotein reverse transcriptase. By copying a short template sequence within its intrinsic RNA moiety, telomerase synthesizes the telomeric DNA strand running 5' to 3' towards the distal end of the chromosome, thus extending it. Fusion of a telomere, either with another telomere or with a broken DNA end, generally constitutes a catastrophic event for genomic stability. Telomerase acts to prevent such fusions. The molecular consequences of telomere failure, and the molecular contributors to telomere function, with an emphasis on telomerase, are discussed here.
Association of BRCA1 with the inactive X chromosome and XIST RNA
Authors: Ganesan Shridar , Silver Daniel P. , Drapkin Ronny , Greenberg Roger , Feunteun Jean , Livingston David M.
Published: April 2004

Breast cancer, early onset 1 (BRCA1) encodes a nuclear protein that participates in breast and ovarian cancer suppression. The molecular basis for the gender and tissue specificity of the BRCA1 cancer syndrome is unknown. Recently, we observed that a fraction of BRCA1 in female cells is localized on the inactive X chromosome (Xi). Chromatin immunoprecipitation (ChIP) experiments have demonstrated that BRCA1 physically associates with Xi–specific transcript (XIST) RNA, a non–coding RNA known to coat Xi and to participate in the initiation of its inactivation during early embryogenesis. Cells lacking wild–type BRCA1 show abnormalities in Xi, including lack of proper XIST RNA localization. Reintroduction of wild–type, but not mutant, BRCA1 can correct this defect in XIST localization in these cells. Depletion of BRCA1 in female diploid cells led to a defect in proper XIST localization on Xi and in the development of normal Xi heterchromatic superstructure. Moreover, depletion of BRCA1 led to an increased likelihood of re–expression of a green fluorescent protein (GFP) reporter gene embedded on Xi. Taken together, these findings are consistent with a model in which BRCA1 function contributes to the maintenance of proper Xi heterochromatin superstructure. Although the data imply a novel gender–specific consequence of BRCA1 loss, the relevance of the BRCA1/Xi function to the tumour suppressor activity of BRCA1 remains unclear and needs to be tested.
Plant perceptions of plant growth-promoting
Pseudomonas
Authors: Preston Gail M.
Published: April 2004

Plant–associated
Pseudomonas
live as saprophytes and parasites on plant surfaces and inside plant tissues. Many plant–associated
Pseudomonas
promote plant growth by suppressing pathogenic micro–organisms, synthesizing growth–stimulating plant hormones and promoting increased plant disease resistance. Others inhibit plant growth and cause disease symptoms ranging from rot and necrosis through to developmental dystrophies such as galls. It is not easy to draw a clear distinction between pathogenic and plant growth–promoting
Pseudomonas
. They colonize the same ecological niches and possess similar mechanisms for plant colonization. Pathogenic, saprophytic and plant growth–promoting strains are often found within the same species, and the incidence and severity of
Pseudomonas
diseases are affected by environmental factors and host–specific interactions. Plants are faced with the challenge of how to recognize and exclude pathogens that pose a genuine threat, while tolerating more benign organisms. This review examines
Pseudomonas
from a plant perspective, focusing in particular on the question of how plants perceive and are affected by saprophytic and plant growth–promoting
Pseudomonas
(PGPP), in contrast to their interactions with plant pathogenic
Pseudomonas
. A better understanding of the molecular basis of plant–PGPP interactions and of the key differences between pathogens and PGPP will enable researchers to make more informed decisions in designing integrated disease–control strategies and in selecting, modifying and using PGPP for plant growth promotion, bioremediation and biocontrol.
Quaternary diversification in European alpine plants: pattern and process
Authors: Kadereit Joachim W. , Griebeler Eva Maria , Comes Hans Peter
Published: April 2004

Molecular clock approaches applied previously to European alpine plants suggest thatPrimulasect.Auricula,Gentianasect.CiminalisandSoldanelladiversified at the beginning of the Quaternary or well within this period, whereasGlobulariahad already started diversifying in the (Late–)Tertiary. In the first part of this paper we present evidence that, in contrast toGlobulariaandSoldanella, the branching patterns of the molecular internal transcribed spacer phylogenies of bothPrimulaandGentianaare incompatible with a constant–rates birth–death model. In both of these last two taxa, speciation probably decreased through Quaternary times, perhaps because of some niche–filling process and/or a decrease in specific range size. In the second part, we apply nonlinear regression analyses to the lineage–through–time plots ofP.sect.Auriculato test a range of capacity–dependent models of diversification, and the effect of Quaternary climatic oscillations on diversification and extinction. At least for one major clade of sect.Auriculathere is firm evidence that both diversification and extinction are a function of temperature. Intriguingly, temperature appears to be correlated positively with extinction, but negatively with diversification. This suggests that diversification did not take place, as previously assumed, in geographical isolation in high–altitude interglacial refugia, but rather at low altitudes in geographically isolated glacial refugia.
The tempo of avian diversification during the Quaternary
Authors: Zink Robert M. , Klicka John , Barber Brian R.
Published: April 2004

It is generally assumed that the Quaternary was a period of heightened diversification in temperate vertebrate organisms. Previous molecular systematics studies have challenged this assertion. We re–examined this issue in north temperate birds using log–lineage plots and distributions of sister–taxon distances. Log–lineage plots support earlier conclusions that avian diversification slowed during the Quaternary. To test plots of empirical sister–taxon distances we simulated three sets of phylogenies: constant speciation and extinction, a pulse of recent speciation, and a pulse of recent extinction. Previous opinions favour the model of recent speciation although our empirical dataset on 74 avian comparisons failed to reject a distribution derived from the constant and extinction models. Hence, it does not appear that the Quaternary was a period of exceptional rates of diversification, relative to the background rate.
Climate change and evolving human diversity in Europe during the last glacial
Authors: Gamble Clive , Davies William , Pettitt Paul , Richards Martin
Published: April 2004

A link between climate change and human evolution during the Pleistocene has often been assumed but rarely tested. At the macro–evolutionary level Foley showed for hominids that extinction, rather than speciation, correlates with environmental change as recorded in the deep sea record. Our aim is to examine this finding at a smaller scale and with high–resolution environmental and archaeological archives. Our interest is in changing patterns of human dispersal under shifting Pleistocene climates during the last glacial period in Europe. Selecting this time frame and region allows us to observe how two hominid taxa, Neanderthals and Crô–Magnons, adapted to climatic conditions during oxygen isotope stage 3. These taxa are representative of two hominid adaptive radiations, termedterrestrialandaquatic, which exhibited different habitat preferences but similar tolerances to climatic factors. Their response to changing ecological conditions was predicated upon their ability to extend their societies in space and time. We examine this difference further using a database of all available radiocarbon determinations from western Europe in the late glacial. These data act as proxies for population history, and in particular the expansion and contraction of regional populations as climate changed rapidly. Independent assessment of these processes is obtained from the genetic history of Europeans. The results indicate that climate affects population contraction rather than expansion. We discuss the consequences for genetic and cultural diversity which led to the legacy of the Ice Age: a single hominid species, globally distributed.
Do species populations really start small? New perspectives from the Late Neogene fossil record of African mammals
Authors: Vrba E. S. , DeGusta D.
Published: April 2004

This analysis of all known African larger mammals of the past 10 Myr offers new perspectives on the geographical circumstances of speciation. Our central question is: does the fossil evidence support the idea that most new species start as small populations and, if true, how long is the average growth interval until species are established at their mean later size? This simple question is important to unravelling the competing claims of rival models of speciation. We approached it by direct use of fossil data, which, to our knowledge, has not been done previously. We compared the numbers of fossil site records, as a proxy for magnitude of geographical spread, between survivorship intervals across all species. The results show that the average mammal species has indeed started its life in a relatively small population, and thereafter increased rapidly in geographical spread to reach its long–term equilibrium abundance by about 1 million years after origin. Some theoretical implications of these results are discussed.
TheN–methyl D–aspartate receptor glycine site and D–serine metabolism: an evolutionary perspective
Authors: Schell Michael J.
Published: April 2004

TheN–methyl D–aspartate (NMDA) type of glutamate receptor requires two distinct agonists to operate. Glycine is assumed to be the endogenous ligand for the NMDA receptor glycine site, but this notion has been challenged by the discovery of high levels of endogenous D–serine in the mammalian forebrain. I have outlined an evolutionary framework for the appearance of a glycine site in animals and the metabolic events leading to high levels of D–serine in brain. Sequence alignments of the glycine–binding regions, along with the scant experimental data available, suggest that the properties of invertebrate NMDA receptor glycine sites are probably different from those in vertebrates. The synthesis of D–serine in brain is due to a pyridoxal–5'–phosphate (B6)–requiring serine racemase in glia. Although it remains unknown when serine racemase first evolved, data concerning the evolution of B6enzymes, along with the known occurrences of serine racemases in animals, point to D–serine synthesis arising around the divergence time of arthropods. D–Serine catabolism occurs via the ancient peroxisomal enzyme D–amino acid oxidase (DAO), whose ontogenetic expression in the hindbrain of mammals is delayed until the postnatal period and absent from the forebrain. The phylogeny of D–serine metabolism has relevance to our understanding of brain ontogeny, schizophrenia and neurotransmitter dynamics.
Metabolic profiles to define the genome: can we hear the phenotypes?
Authors: Griffin Julian L.
Published: April 2004

There is an increased reliance on genetically modified organisms as a functional genomic tool to elucidate the role of genes and their protein products. Despite this, many models do not express the expected phenotype thought to be associated with the gene or protein. There is thus an increased need to further define the phenotype resultant from a genetic modification to understand how the transcriptional or proteomic network may conspire to alter the expected phenotype. This is best typified by the description of the silent phenotype in genetic manipulations of yeast. High–resolution proton nuclear magnetic resonance (
1
H NMR) spectroscopy provides an ideal mechanism for the profiling of metabolites within biofluids, tissue extracts or, with recent advances, intact tissues. These metabolic datasets can be readily mined using a range of pattern recognition techniques, including hierarchical cluster analysis, principal components analysis, partial least squares and neural networks, with the combined approach being termed metabolomics. This review describes the application of NMR–based metabolomics or metabonomics to genetic and chemical interventions in a number of different species, demonstrating the versatility of such an approach, as well as suggesting how it may be integrated with other ‘omic’ technologies.
Virulence in malaria: an evolutionary viewpoint
Authors: Mackinnon Margaret J. , Read Andrew F.
Published: April 2004

Malaria parasites cause much morbidity and mortality to their human hosts. From our evolutionary perspective, this is because virulence is positively associated with parasite transmission rate. Natural selection therefore drives virulence upwards, but only to the point where the cost to transmission caused by host death begins to outweigh the transmission benefits. In this review, we summarize data from the laboratory rodent malaria model,Plasmodium chabaudi, and field data on the human malaria parasite,P. falciparum, in relation to this virulence trade–off hypothesis.The data from both species show strong positive correlations between asexual multiplication, transmission rate, infection length, morbidity and mortality, and therefore support the underlying assumptions of the hypothesis. Moreover, theP. falciparumdata show that expected total lifetime transmission of the parasite is maximized in young children in whom the fitness cost of host mortality balances the fitness benefits of higher transmission rates and slower clearance rates, thus exhibiting the hypothesized virulence trade–off. This evolutionary explanation of virulence appears to accord well with the clinical and molecular explanations of pathogenesis that involve cytoadherence, red cell invasion and immune evasion, although direct evidence of the fitness advantages of these mechanisms is scarce. One implication of this evolutionary view of virulence is that parasite populations are expected to evolve new levels of virulence in response to medical interventions such as vaccines and drugs.
Quaternary Ice-Age dynamics in the Colombian Andes: developing an understanding of our legacy
Authors: Hooghiemstra Henry , Van der Hammen Thomas
Published: April 2004

Pollen records from lacustrine sediments of deep basins in the Colombian Andes provide records of vegetation history, the development of the floristic composition of biomes, and climate variation with increasing temporal resolution. Local differences in the altitudinal distribution of present–day vegetation belts in four Colombian Cordilleras are presented. Operating mechanisms during Quaternary Ice–Age cycles that stimulated speciation are discussed by considering endemism in the asteraceous genera
Espeletia
,
Espeletiopsis
and
Coespeletia
. The floristically diverse lower montane forest belt (1000–2300 m) was compressed by
ca
. 55% during the last glacial maximum (LGM) (20 ka), and occupied the slopes between 800 m and 1400 m during that period. Under low LGM atmospheric
p
CO
2
values, C
4
–dominated vegetation, now occurring below 2200 m, expanded up to ca. 3500 m. Present–day C
3
–dominated paramo vegetation is therefore not an analogue for past C
4
–dominated vegetation (with abundant
Sporobolus lasiophyllus
).
Quercus
immigrated into Colombia 478 ka and formed an extensive zonal forest from 330 ka when former
Podocarpus
–dominated forest was replaced by zonal forest with
Quercus
and
Weinmannia
. During the last glacial cycle the ecological tolerance of
Quercus
may have increased. In the ecotone forests
Quercus
was rapidly and massively replaced by
Polylepis
between 45 and 30 ka illustrating complex forest dynamics in the tropical Andes.
Some aspects of ecophysiological and biogeochemical responses of tropical forests to atmospheric change
Authors: Chambers Jeffrey Q. , Silver Whendee L.
Published: April 2004

Atmospheric changes that may affect physiological and biogeochemical processes in old–growth tropical forests include: (i) rising atmospheric CO2concentration; (ii) an increase in land surface temperature; (iii) changes in precipitation and ecosystem moisture status; and (iv) altered disturbance regimes. Elevated CO2is likely to directly influence numerous leaf–level physiological processes, but whether these changes are ultimately reflected in altered ecosystem carbon storage is unclear. The net primary productivity (NPP) response of old–growth tropical forests to elevated CO2is unknown, but unlikely to exceed the maximum experimentally measured 25% increase in NPP with a doubling of atmospheric CO2from pre–industrial levels. In addition, evolutionary constraints exhibited by tropical plants adapted to low CO2levels during most of the Late Pleistocene, may result in little response to increased carbon availability. To set a maximum potential response for a Central Amazon forest, using an individual–tree–based carbon cycling model, a modelling experiment was performed constituting a 25% increase in tree growth rate, linked to the known and expected increase in atmospheric CO2. Results demonstrated a maximum carbon sequestration rate ofca. 0.2 Mg C per hectare per year (ha−1yr−1, where 1 ha = 104m2), and a sequestration rate of only 0.05 Mg C ha−1yr−1for an interval centred on calendar years 1980–2020. This low rate results from slow growing trees and the long residence time of carbon in woody tissues. By contrast, changes in disturbance frequency, precipitation patterns and other environmental factors can cause marked and relatively rapid shifts in ecosystem carbon storage. It is our view that observed changes in tropical forest inventory plots over the past few decades is more probably being driven by changes in disturbance or other environmental factors, than by a response to elevated CO2. Whether these observed changes in tropical forests are the beginning of long–term permanent shifts or a transient response is uncertain and remains an important research priority.
Through enhanced tree dynamics carbon dioxide enrichment may cause tropical forests to lose carbon
Authors: Körner Christian
Published: April 2004

The fixation and storage of C by tropical forests, which contain close to half of the globe's biomass C, may be affected by elevated atmospheric CO
2
concentration. Classical theoretical approaches assume a uniform stimulation of photosynthesis and growth across taxa. Direct assessments of the C balance either by flux studies or by repeated forest inventories also suggest a current net uptake, although magnitudes sometimes exceed those missing required to balance the global C cycle. Reasons for such discrepancies may lie in the nature of forest dynamics and in differential responses of taxa or plant functional types. In this contribution I argue that CO
2
enrichment may cause forests to become more dynamic and that faster tree turnover may in fact convert a stimulatory effect of elevated CO
2
on photosynthesis and growth into a long–term net biomass C loss by favouring shorter–lived trees of lower wood density. At the least, this is a scenario that deserves inclusion into long–term projections of the C relations of tropical forests. Species and plant functional type specific responses (‘biodiversity effects’) and forest dynamics need to be accounted for in projections of future C storage and cycling in tropical forests.
Forest-climate interactions in fragmented tropical landscapes
Authors: Laurance William F.
Published: April 2004

In the tropics, habitat fragmentation alters forest–climate interactions in diverse ways. On a local scale (less than 1 km), elevated desiccation and wind disturbance near fragment margins lead to sharply increased tree mortality, thus altering canopy–gap dynamics, plant community composition, biomass dynamics and carbon storage. Fragmented forests are also highly vulnerable to edge–related fires, especially in regions with periodic droughts or strong dry seasons. At landscape to regional scales (10–1000 km), habitat fragmentation may have complex effects on forest–climate interactions, with important consequences for atmospheric circulation, water cycling and precipitation. Positive feedbacks among deforestation, regional climate change and fire could pose a serious threat for some tropical forests, but the details of such interactions are poorly understood.
Fingerprinting the impacts of global change on tropical forests
Authors: Lewis Simon L. , Malhi Yadvinder , Phillips Oliver L.
Published: April 2004

Recent observations of widespread changes in mature tropical forests such as increasing tree growth, recruitment and mortality rates and increasing above–ground biomass suggest that ‘global change’ agents may be causing predictable changes in tropical forests. However, consensus over both the robustness of these changes and the environmental drivers that may be causing them is yet to emerge. This paper focuses on the second part of this debate. We review (i) the evidence that the physical, chemical and biological environment that tropical trees grow in has been altered over recent decades across large areas of the tropics, and (ii) the theoretical, experimental and observational evidence regarding the most likely effects of each of these changes on tropical forests. Ten potential widespread drivers of environmental change were identified: temperature, precipitation, solar radiation, climatic extremes (including El Niño Southern Oscillation events), atmospheric CO
2
concentrations, nutrient deposition, O
3
/acid depositions, hunting, land–use change and increasing liana numbers. We note that each of these environmental changes is expected to leave a unique ‘fingerprint’ in tropical forests, as drivers directly force different processes, have different distributions in space and time and may affect some forests more than others (e.g. depending on soil fertility). Thus, in the third part of the paper we present testable
a priori
predictions of forest responses to assist ecologists in attributing particular changes in forests to particular causes across multiple datasets. Finally, we discuss how these drivers may change in the future and the possible consequences for tropical forests.
Spatial patterns and recent trends in the climate of tropical rainforest regions
Authors: Malhi Yadvinder , Wright James
Published: April 2004

We present an analysis of the mean climate and climatic trends of tropical rainforest regions over the period 1960–1998, with the aid of explicit maps of forest cover and climatological databases. Until the mid–1970s most regions showed little trend in temperature, and the western Amazon experienced a net cooling probably associated with an interdecadal oscillation. Since the mid–1970s, all tropical rainforest regions have experienced a strong warming at a mean rate of 0.26 ± 0.05 °C per decade, in synchrony with a global rise in temperature that has been attributed to the anthropogenic greenhouse effect. Over the study period, precipitation appears to have declined in tropical rainforest regions at a rate of 1.0 ± 0.8% per decade (
p
< 5%), declining sharply in northern tropical Africa (at 3–4% per decade), declining marginally in tropical Asia and showing no significant trend in Amazonia. There is no evidence so far of a decline in precipitation in eastern Amazonia, a region thought vulnerable to climate–change–induced drying. The strong drying trend in Africa suggests that this should be a priority study region for understanding the impact of drought on tropical rainforests. We develop and use a dry–season index to study variations in the length and intensity of the dry season. Only African and Indian tropical rainforests appear to have seen a significant increase in dry–season intensity. In terms of interannual variability, the El Niño–Southern Oscillation (ENSO) is the primary driver of temperature variations across the tropics and of precipitation fluctuations for large areas of the Americas and southeast Asia. The relation between ENSO and tropical African precipitation appears less direct.
Estimating genetic parameters in natural populations using the ‘animal model’
Authors: Kruuk Loeske E. B.
Published: April 2004

Estimating the genetic basis of quantitative traits can be tricky for wild populations in natural environments, as environmental variation frequently obscures the underlying evolutionary patterns. I review the recent application of restricted maximum–likelihood ‘animal models’ to multigenerational data from natural populations, and show how the estimation of variance components and prediction of breeding values using these methods offer a powerful means of tackling the potentially confounding effects of environmental variation, as well as generating a wealth of new areas of investigation.
Pattern and process in Amazon tree turnover, 1976–2001
Authors: Phillips O. L. , Baker T. R. , Arroyo L. , Higuchi N. , Killeen T. J. , Laurance W. F. , Lewis S. L. , Lloyd J. , Malhi Y. , Monteagudo A. , Neill D. A. , Núñez Vargas P. , Silva J. N. M. , Terborgh J. , Vásquez Martínez R. , Alexiades M. , Almeida S. , Brown S. , Chave J. , Comiskey J. A. , Czimczik C. I. , Di Fiore A. , Erwin T. , Kuebler C. , Laurance S. G. , Nascimento H. E. M. , Olivier J. , Palacios W. , Patiño S. , Pitman N. C. A. , Quesada C. A. , Saldias M. , Torres Lezama A. , Vinceti B.
Published: April 2004

Previous work has shown that tree turnover, tree biomass and large liana densities have increased in mature tropical forest plots in the late twentieth century. These results point to a concerted shift in forest ecological processes that may already be having significant impacts on terrestrial carbon stocks, fluxes and biodiversity. However, the findings have proved controversial, partly because a rather limited number of permanent plots have been monitored for rather short periods. The aim of this paper is to characterize regional–scale patterns of ‘tree turnover’ (the rate with which trees die and recruit into a population) by using improved datasets now available for Amazonia that span the past 25 years. Specifically, we assess whether concerted changes in turnover are occurring, and if so whether they are general throughout the Amazon or restricted to one region or environmental zone. In addition, we ask whether they are driven by changes in recruitment, mortality or both. We find that: (i) trees 10 cm or more in diameter recruit and die twice as fast on the richer soils of southern and western Amazonia than on the poorer soils of eastern and central Amazonia; (ii) turnover rates have increased throughout Amazonia over the past two decades; (iii) mortality and recruitment rates have both increased significantly in every region and environmental zone, with the exception of mortality in eastern Amazonia; (iv) recruitment rates have consistently exceeded mortality rates; (v) absolute increases in recruitment and mortality rates are greatest in western Amazonian sites; and (vi) mortality appears to be lagging recruitment at regional scales. These spatial patterns and temporal trends are not caused by obvious artefacts in the data or the analyses. The trends cannot be directly driven by a mortality driver (such as increased drought or fragmentation–related death) because the biomass in these forests has simultaneously increased. Our findings therefore indicate that long–acting and widespread environmental changes are stimulating the growth and productivity of Amazon forests.
Taxonomy as a fundamental discipline
Authors: Wilson Edward O.
Published: April 2004

There are at present, at rough estimate, ca. 6000 taxonomists at work worldwide on all organisms combined. That is a tiny slice of the biological community as a whole, and their discipline remains one of the weakest and most underfunded (Wilson 2002). From my own museum experience, I believe that twice this number, with several technical assistants each and the aforementioned new technologies, could move the global biodiversity survey to near completion within a single human generation.