Title:
International Tables for Crystallography Volume G:
Editors:
Sydney Hall, University of Western Australia and
Brian McMahon IUCr
Publisher: Springer Verlag for the International Union of Crystallography 2005
Price: Price: £135, Euro205,
$220 (institutions/libraries) - half-price for personal use.
ISBN 1-4020-3138-6, 594 + xii pages + CD
This latest Volume of International Tables for Crystallography deals with the definition and exchange of crystallographic data. The intended audience comprises working crystallographers, programmers who write crystallographic software and data managers. The volume describes the standard CIF format for exchanging and archiving crystal data. It is divided into five Parts covering the historical context; concepts and specifications; the definition and classification of CIF data; the core and supplementary CIF dictionary and finally CIF applications.
The first Part details how electronic handling of crystallographic data has undergone just as much change over the past 15 years as have X-ray sources, detectors or software. In 1990 there were only limited facilities for electronic data exchange, and a lack of standardisation seriously limited the ability of one application to read and understand the output from another. However, the impact of the introduction of the CIF format was such that by 1996 Section C of Acta Crystallographica was able to require that all standard material for a paper except Figures and Schemes be submitted in that format. The widespread acceptance of CIF has also transformed the deposition of supplementary data: to those who can remember them, the days of having to submit multiple hard copies of structure factor tables now seem to belong to prehistory.
The second Part describes the challenge of developing a language which can convey precisely and reliably the complexity and variety of scientific results. This language also has to be flexible and capable of being extended to cope with new developments. The CIF is therefore a subset of the Self-defining Text Archive and Retrieval (STAR) format. Standardisation of data items is clearly of vital importance to the successful application of the CIF format, and this is the responsibility of an IUCr committee. The STAR format has been extended to cover related areas, including molecular information, macromolecular crystallography, powder diffraction and modulated structures. CIF fits well into the broader area of scientific data and is easily transferred to and from XML (extensible markup language). However these links develop, CIF is already firmly established in its central role within crystallography. The specification of a STAR syntax lies at the heart of the CIF format: it must be free-format and contain sequential lines of ASCII characters comprising text strings. Paired data names and data values comprise data items which convey the information, with a loop facility to allow the specification of multiple data values for a single data name.
The third Part deals with the definition and classification of CIF data. After a general overview, it describes the core CIF dictionary containing the data items common to most CIFs, for example those relevant to a standard laboratory X-ray structure determination of a small molecule. Subsequent sections cover powder diffraction, modulated and composite structures, image data and symmetry information.
Part 4 defines all the data names for the core and other dictionaries. These
names include not only experimental information but also other data such as
the author details for a paper. The data items are arranged alphabetically
by category (such as atom_site) within which data
items are also listed alphabetically
(e.g., from _atom_site_adp_type to _atom_site_Wyckoff_symbol).
Part 5 deals with the creation of new "CIF-aware" applications, as well as
the adaptation of existing applications to render them capable of dealing
with CIFs. A program which has to be able to read CIFs, perhaps from a
variety of sources, is much more of a challenge to write than one which has
simply to output data in CIF format. A number of types of application are
then outlined, including STAR file utilities which are capable of handling
any data in the format: such programs might include ones which extract
selected data from the CIF; allow editing of the contents of the CIF;
transform the STAR format to HTML, etc. Syntactic utilities for CIF include
syntax checkers, interactive editors, visualisers and validators. For
programmers, a Fortran function library (CIFtbx) covers the common
operations likely to be needed in order to deal with a CIF.
A separate
section of Part 5 deals with the application of the macromolecular CIF
architectures to the management of Protein Data Bank information, while
another describes an ANSI C library allowing the manipulation of binary
files and image CIF files. Finally, there is a case study of the publication
of small molecule crystal structures using CIF, as practiced by Section
C of Acta Crystallographica since 1991 and by Section E
since its inception. This study outlines the advantages to authors, editors,
referees and the journals of the highly automated procedures for submission,
validation and publication which are possible because of the adoption of the
CIF standard.
The accompanying CD is a important resource which contains machine-readable versions of STAR and CIF specifications, the various CIF dictionaries, along with a collection of software libraries and applications. It also provides extensive supplementary information for each Part.
Although this is primarily a work of reference, with Part 4 requiring over 260 pages to describe the data dictionaries, it also contains substantial narrative and explanatory sections which are very effective, for example in describing the evolution of the handling of crystallographic data and the concepts which underpin the operation of the STAR and CIF formats. The volume will clearly be indispensable for any programmers writing applications which need to read or write information in CIF format, but the pervasive nature of CIF in everyday crystallographic work means it will be a useful addition to any crystallographic laboratory.
Sandy Blake
Title:
Michael Polanyi - Scientist and Philosopher
Authors:
William Taussig Scott, and
Martin X. Moleski, S.J.
Publisher: Oxford University Press 2005
Price: Price: £ 26.99 (hardback)
ISBN 13 978-0-19-517433-5 364 + xvi pages
Biography of Michael Polyani |
The first full biography of Polanyi describes well the early life and subsequent career of one of the pioneers in Berlin of metal structure and deformation and of X-ray fibre analysis. It relates how Polanyi, moving as a refugee to a chair in Manchester, enhanced his scientific reputation developing the transition-state theory of reaction kinetics but later gained even wider celebrity as a social scientist and philosopher of science. |
Michael Polanyi (1891-1976) qualified first in medicine in Budapest (although publishing in thermodynamics on the way). He then spent nearly thirty years in Berlin and Manchester in front-rank research in physics and physical chemistry (but concurrently wrote, lectured and campaigned on social sciences), and in his later years became an international figure in philosophy and the humanities. During World War I, Polanyi was a medical officer in the Austro-Hungarian army and in the latter part of World War II he was able in Manchester to investigate catalytic polymerization to form synthetic rubber, while his son George served in the British forces. Following consecutive full-time chairs at Manchester in Physical Chemistry (1933-1948) and in Social Studies (1948-1959), one of Polanyi's later Professorships was in the Department of Religion at Duke University! By then, in what he regarded as his chief contribution to intellectual life, Polanyi had become a philosopher of science, writing and lecturing across the world and embracing economics, aesthetics, political theory and theology. His close friends included Arthur Koestler and the economist John Jewkes.
It has taken an American physicist and philosopher, W.T. Scott, and a Professor of Religion, M.X. Moleski, many years and the resource of 150 interviews across several disciplines, but including some distinguished British chemists, to compose a fine comprehensive biography of this remarkable man. Scott, the senior author, knew Polanyi for the last seventeen years of Polanyi's life. The chronological list of books and papers (with titles translated into English where necessary), compiled by Polanyi's son John, a Nobel prize winner in Chemistry in 1986, in itself provides a measure of the contributions to diverse fields. Eleven chapters cover phases of family, scientific and philosophical life successively in Hungary, Germany, Manchester and, though based mainly in Oxford, effectively in the world at large. Polanyi' s scientific period, which, with his education, takes up two-thirds of the book, is covered well (thanks partly to detailed advice from an eminent physical chemist) and at a level that should be intelligible to the non-specialist. Strictly chronological biographers have their opponents but, for a life that was influenced by political attitudes and always carried parallel intellectual threads, I felt that it was appropriate to interleave the account with family events, generally happy, but occasionally tragic.
For crystallographers and solid-state scientists, the crucial period of Polanyi' s scientific creativity began in 1920 when he moved from the Karlsruhe Technische Hochschule (where he had gone to escape persecution in Hungary) to Berlin. Despite having experience of neither X-rays nor fibre chemistry, Polanyi was assigned the problem of interpreting the X-ray pattern of cellulose fibres at the new Institute of Fibre Chemistry. Thus he became the first to suggest that the unit cell of cellulose could be interpreted in terms of a long-chain molecule. With this success, he was able to engage Brill, von Gomperz, Mark, Schmid and Weissenberg as assistants, and the rotating-crystal method was established. Polanyi commended Mark, who was to devote his career to high polymers, for manipulative skill and Weissenberg, whose name is linked with X-ray and rheological instruments, for mathematical ability.
Scott and Moleski describe how the emphasis of Polanyi' s group then shifted from fibre structures to the strength and plastic flow of solids through stretching of zinc and then crystals and microcrystalline wires. Experiments with Ewald on cold working of a rock-salt prism led to notions of dislocation in "Versetzung". Among several references to Polanyi in The Crystalline State, WL Bragg credits him as the pioneer in single-crystal deformation and the theory of metal crystals. Although he transferred in 1923 to the Institute of Physical Chemistry and Electrochemistry in Berlin to concentrate on reaction kinetics, Polanyi continued to publish on the solid state, especially with Bogdandy, Sachs and Schmid on plasticity and annealing of metal crystals and the deformation of ductile materials through the 1920s.
Publications on rates of chain reactions and sodium-flame reactions steadily increased as the concepts of activation energy and transition state emerged and were developed at Manchester after 1933. However, many of the papers from groups that he had set up and directed, such as those led by Bawn and Fairbrother did not carry Polanyi's name. His FRS came in 1944 for a broad catalogue of achievement that specifically included rotating-crystal analysis and the strength of metal crystals.
Students in the 1940s attending Polanyi's first-year lectures on X-ray diffraction and the equipartition of energy were barely aware of his early contribution to both topics, still less that much of his thinking time was now spent on social sciences rather than physical chemistry. On economics, his views on Employment and Money, on which he produced two films as well as books and many papers, were close to these of Keynes. In social science, Polanyi made one of the most spirited responses, opposing central planning of science, to the influential 1939 book The Social Function of Science by the crystallographer J.D.Bemal (who, in the 1920s, had been one of the first to take up Polanyi's rotating-crystal X-ray method).
From 1948, having transferred to a chair of social studies at Manchester, Polanyi was able to devote all his attention to economics, social studies and philosophy. In science he raised doubts about absolute objectivity and recognized the importance of "tacit knowledge" in interpretation. After formal retirement in 1958, Polanyi became a celebrated world scholar with many visits to the USA. Emphasising freedom and responsibility in science, Polanyi's published lectures revealed a mind groping towards a relation between scientific knowledge and religious knowledge and faith.
We also learn from the biography that in the 1930s and 1940s, professors at Manchester, such as Polanyi and his contemporary WL Bragg, enjoyed large houses staffed by several servants, were enveloped in a vigorous social-cum-intellectual life, and had considerable freedom for leave. In his new chair, Polanyi "gave over 1949 to writing" (for prestigious lectures at another University), spending lengthy periods at a country inn in Wales!
The reproduction of old photographs is mediocre and the captions are inadequate, while the absence of a brief date-summary of Polanyi's career is regrettable. However, the book is well annotated and indexed and has a clear biography of Polanyi' s scientific and other publications. Overall, this bibliography gives a fascinating account of a polymath who established his scientific credentials in X-ray analysis, went on to be a major contributor to the transition-state theory of reaction rates and then emerged as an acclaimed philosopher of science.
Derry W. Jones