Writing and speaking: communication for biologists

A workshop for university biology teachers examined the teaching to undergraduates of writing and speaking. There was agreement that the communication of results and ideas was an integral part of scientific method. Proposals for the teaching of different aspects of communication during the undergraduate course are given and an Appendix lists some material which has been used with, and found suitable for biology students.     

A computational image analysis glossary for biologists

Recent advances in biological imaging have resulted in an explosion in the quality and quantity of images obtained in a digital format. Developmental biologists are increasingly acquiring beautiful and complex images, thus creating vast image datasets. In the past, patterns in image data have been detected by the human eye. Larger datasets, however, necessitate high-throughput objective analysis tools to computationally extract quantitative information from the images. These tools have been developed in collaborations between biologists, computer scientists, mathematicians and physicists. In this Primer we present a glossary of image analysis terms to aid biologists and briefly discuss the importance of robust image analysis in developmental studies.     

A communication channel model for information transmission in the blowfly photoreceptor

Biological photoreceptors transduce and communicate information about visual stimuli to other neurons through a series of signal transformations among physical states such as concentration of a chemical species, current, or the number of open ion channels. We present a communication channel model to quantify the transmission and degradation of visual information in the blowfly photoreceptor cell. The model is a cascade of linear transfer functions and noise sources that are derived from fundamental principles whenever possible, and whose parameters are estimated from physiological data. We employ the model to calculate the information capacity of blowfly phototransduction; our results compare favorably with estimates of the capacity derived from experimental measurements by de Ruyter van Steveninck and Laughlin (Nature 379 (1996) 642-645) and Juusola (J. Gen. Physiol. 104 (1994) 593-621). The model predicts that photon shot noise and ion channel noise are the dominant noise sources that limits information transmission in the blowfly photoreceptor.     

A microcomputer based program for the storage and retrieval of experimental animal information

A microcomputer based program for the storage and selective retrieval of experimental animal information has been developed for use on any system which runs under CP/M system software. The program has been designed to be completely conversational, to communicate with the user in French, English, or Spanish, and to allow the user to define the data format and the alphanumeric coding scheme.     

Structures and technology for biologists

Structural genomics efforts are already producing a quarter of all 'new' macromolecular structures (<30% sequence identity to previously solved structures) and are stimulating development of systematic and automated approaches to structure determination. The thousands of new structures likely to be determined and the technologies and infrastructure likely to be developed over the next decade will benefit all biologists.     

Storage and retrieval of information in systematic zoology

Progress in systematic zoology is dependent upon a means of communication that transcends the boundaries of immediate space and time. Systematics has a very wide scope and provides a framework within which meaningful biological work can be done. Its development can be traced from Aristotle; the advent of printing in 1450 encouraged progress in systematics, with the works of Conrad Gesner (1516-65) and Ulissis Aldrovandi (c. 1522–1605) deserving special mention. Then came Carl Linnaeus (1707-78) and the writing of the Systerna Naturae, along with the fashion of natural history cabinets and private museums. In 1768 Captain Cook made his first voyage round the world, inspiring organized collecting by amateur and professional naturalists attached to expeditions. This was followed by a period of enlargement and elaboration, with the founding of the great national collections, which were soon to become recognized places for systematic work. They also published detailed catalogues of their collections. With this increase in knowledge came an increase in the amount of zoological literature, much of which now disappears into scientific limbo. The average, although conscientious, worker at one of the large institutions may feel fortunate if he retrieves about 80% of the existing information on the particular subject he is working upon at the present time. In identifying material, the systematist has a constant need to retrieve information –a long laborious task for numerous reasons–and a quick retrieval system is required for both specimens and literature. Index Biological Abstracts, Zoological Record, Sherborn's Index Animalium (1902-) and Neave's Nomenclator Zoologicus (1939-) are attempts to facilitate this retrieval with regard to literature. As far as the specimens are concerned, preservation is an important factor; dried specimens conceal much of their information, storage in alcohol and formalin produces problems and some of the new preserving liquids and techniques, e.g. freeze-drying, have yet to stand the test of time. Only a computer can keep systematic information up-to-date and easily retrievable. Before us lies the era of the non-printed word.     

Dilemmas in conservation for applied biologists

Prevention of the use of DDT has been made the target of a powerful propaganda drive in certain prosperous countries because, it is stated, DDT is a danger to man and harms wild life. On the other hand, DDT is by far the most economical, effective and safe insecticide for many uses, particularly for protecting men from certain insect-borne diseases and for enabling cotton to be grown in poor countries. Some risks can be reduced by eliminating those uses of DDT for which adequately safe, economical and effective substitutes exist, whether chemical or not; other risks can be reduced in other ways. The known risks to men are trivial, except when DDT concentrate is deliberately drunk, and the scare is made up of unknown risks -which could equally exist with any object or material, new or old. Risks to wild life have been greatly exaggerated and scares depending on falsehoods have become current. The postulated threat of progressive accumulation of DDT along a long food chain is not adequately supported by evidence, much of which has been misinterpreted. Thus the main dilemma is how to balance the great and undoubted benefits of DDT to millions of men, women and children against harm to wild life, sometimes genuine and remediable and sometimes dubious. People who campaign for banning have possibly failed to recognize this dilemma. On the other hand, they may have made a deliberate choice in favour of wild life. In that case, to be logical, they should also oppose all other means of preventing premature death of other people, which they might justify as a means of postponing over-population. The use or abuse of DDT is a minor component in the rise of the worl's population.     

A microcomputer-based information storage and retrieval system for the maintenance of records for a culture collection

A microcomputer-based system for the storage and retrieval of information on strains in a culture collection is described. The system was designed around commercially available software packages written for microcomputers. Two additional programs were written using the BASIC language to allow a catalogue of the culture collection to be printed in a specific format. The details of each strain in the collection were stored on a floppy disc. Details of new strains were added to this database and information relating to existing cultures was modified or, where necessary, deleted from the collection. The database can be searched to supply details of a particular culture or to identify those cultures which possess certain attributes. The records for the whole collection were sorted alphabetically by species name, and numerically by accession number, and a word-processing package was used to print a catalogue of the culture collection.     

A microcomputer-based information storage and retrieval system for the maintenance of records for a culture collection

A microcomputer-based system for the storage and retrieval of information on strains in a culture collection is described. The system was designed around commercially available software packages written for microcomputers. Two additional programs were written using the BASIC language to allow a catalogue of the culture collection to be printed in a specific format. The details of each strain in the collection were stored on a floppy disc. Details of new strains were added to this database and information relating to existing cultures was modified or, where necessary, deleted from the collection. The database can be searched to supply details of a particular culture or to identify those cultures which possess certain attributes. The records for the whole collection were sorted alphabetically by species name, and numerically by accession number, and a word-processing package was used to print a catalogue of the culture collection.     

Geologists and biologists in palaeontology

Whereas zoopalaeontology is one-sidedly a geological science, palaeobotany is predominantly a science cultivated by biologists. Under the influence of increased application as a stratigraphical and palaeoenvironmentological tool in exploration geology as well as in pure geology, palaeopalynology is also becoming more and more a one-sidedly orientated field of science.