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The Journalist Corner©

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Contents


Presentation

Research is financed by public taxes or donations, and most of the time, by governments. It is therefore quite natural that the general public be informed about the outcome of the money used there, either as a voluntary contribution, or through taxes. The aim of this journalist corner is to help journalists, who have the most frequent contact with the general public, to be informed about topics of general interest in biology, and especially about diseases, genes and genomes. It is important that journalists understand their responsability in transmitting information. Exquisite care should be taken to control it. It is also important that what is reported on headlines is accurate. Remember that journalists are excellent accesories to the spread of epidemics... At some point, if this approach appears to be successful, we shall construct restricted connection pages, specifically for the media supporting us.

Summary of the work at the Centre

Three processes make life: metabolism (eating and digesting), compartmentalization (having an inside and an outside) and information transfer (controlling heredity: the genome is at the core of information processing). All three processes are imbedded in small entities named cells. Microbes are usually single cell organisms, while plants and animals are multicellular. Understanding, and hence controlling life means understanding the cell. While general functions such as assimilation, respiration, replication or digestion are common to all forms of life, the objects, and therefore the genes that make them work may be different. This tells everyone that in general knowing a gene is not enough to tell its function...

Understanding how microbes live and multiply has applications in the development of diagnostic tools and of new and powerful antibiotics for use in the treatment of illnesses caused by all pathogens, including bioweapons agents such as the deadly anthrax or plague agents. For this reason, the two model microbes initially chosen to develop genome studies at the HKU-Pasteur Centre were immediate parents of these terrible agents. In addition, foreseeing that mosquitoes would soon become terrible foes in the region, the Centre devoted some of its effort to a microbe which is a powerful insect killer (Photorhabdus luminescens).

Work at the Centre concentrates in particular on the first step of protein synthesis, which is deeply rooted in the assimilation of an atom essential to life, the sulfur atom. Many antibiotic drugs work by distorting the protein synthesizing machinery of disease-causing microorganisms to malfunction, killing the microorganism and curing the disease. Understanding the process will allow investigators to discover new tricks to lure microbe out of their deadly paths.

Our technique, which combines prediction using powerful computers and specialized database construction with experiments can be extended to the study of the functions of antibiotics acting on bacteria that can be used as potential biowarfare agents, such as anthrax, cholera, plague and shigella. They can also be the basis for investigating dangerous fungi, such as Penicillium marneffei, that is a frequent cause of death in AIDS patients.

The insight provided by the new database structure we are creating in collaboration with the Institut Pasteur and Genome Centres in Beijing and Shanghai is proof that unexpected functions of proteins can be predicted on a computer, which opens up the possibility for rapidly modeling metabolism organisation from a variety of organisms.

Organizing microbial sequence and annotation data is a significant challenge given the large number of genes present in the genome and development of both experimental protocols and software applications used for making the predicttions can be extended from the model organisms to other disease-causing microorganisms, also with the goal of giving antibiotic investigators valuable tools in the fight against microbial diseases, particularly diseases caused by bioweapons.

The recent outbreak of Severe Acute Respiratory Syndrome (SARS) prompted the direction of the Centre to focus its activity on viral diseases in the near future.

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Frequently Asked Questions

Some questions are frequently asked, and we endeavour to answer them when they seem to be of broad interest. If you wish to have an idea of the questions and of our answers, please click here.

We provide in this page not only explicit information, some of which is entirely original (and this is why this site and this page are free to use but Copyright-protected to guarantee this freedom), but also links which may help journalists to trace other relevant information, as well as further insight in the topics they are interested in. Note that not all important information is in English! It should be stressed againthat Chinese, mainly as Putonghua, is probably the language spoken by the most people in the world, followed by Latin languages (French, Italian, Portuguese, Romanian, Spanish...), and then by English (or perhaps languages from India). In addition, Greek provides most of the words and concepts used in science. Do not refrain from seeking information in other languages. Do not forget that most of Chinese scientific literature has not been translated into Western languages, and that it conveys information of its own. And note that English is not the sole tongue used at this site (see here, for example).

Of course, it is necessary for understanding biology to be able to write or speak about this science. Some reading may be useful. We shall provide useful links to the World-Wide Web, to help finding out relevant information. In addition, we shall refer to our own publications meant to be used as communicating media. A special page will be devoted to genomics, but broader information can be found in The Delphic Boat (Harvard University Press, Cambridge, USA) which is an updated and reorganized version of the French text, La Barque de Delphes, published by the Editions Odile Jacob in may 1998 (this can be used naturally, by French speaking journalists!).

The information presented here, naturally, does not try to compete with information provided by news agencies such as Agence France Presse or Reuters. It provides selected information (often not uncovered by standard media) related to the topics of interest for the HKU-Pasteur Research Centre. It also provides information in History of Science and in the creation of concepts used by modern biology. An important access to the very nature of Science is discussed in conference given at Zhong Shan University in Guangzhou. Finally, the importance of China is particularly emphasized: the Western world is so dominating in its control of media that this seems of necessity.

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For the latest data on emerging (and existing) diseases in Hong Kong and its region see the public Health and Disease Surveillance SAR HK site see also the dedicated site on Severe Acute Respiratory Syndrome by the HK government.

For the latest data on bioterrorism see Medline Plus.


Frequently asked questions about flu (in italian)

Facts about influenza, established by the World Healh Organization

The most deadly epidemics spread throughout the world at the end of World War I (1918-1919). The virulent agent was identified by Dujarric de la Rivière, at the Institut Pasteur, and, independently, by Charles Nicolle and Lebally in Tunisia; they demonstrated that it was not the common bacterium Haemophilus influenzae, as supposed earlier by Pfeiffer, but a virus. Recent work unravels significant properties or the virus, and extends information about the pandemic, to the Hong Kong H5N1 virus.

More about the history of influenza by CW. Potter.

Promed: The global electronic reporting system for outbreaks of emerging infectious diseases & toxins, open to all sources

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Hot topics about microbes, environment, infections and related subjects

Facts and hypotheses about SARS

En français: l'histoire de la double épidémie porcine en 1983-1985

Please note that the information provided here is purposedly uncorrected once placed at this site, for being later used for a historical analysis of important events linked to diseases. It is provided "as is" and reflects the perception of the daily events, using available information in real time (using Internet forums in China, in particular, and trying to escape rumors). This explains why there may be contradictions from one day to a later one. In some cases links disappear (and when this happens we unlink the sentence pointing to the obsolete link when we are made aware of that fact): for example, on april 23d an interesting link described in details that existing treatments of SARS were inefficient and probably dangerous. This link was cancelled out a few hours after it was created, for unknown reasons.... Remember that it is the structure of our societies which create our diseases and that epidemics are not separable from our way of life [pdf].

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  1. Strict personnel hygiene must be enforced: one should never see medical personnel in their work coats outside (in particular at cantines or such public places, as often unfortunately seen); spitting on the ground should be strictly forbidden; after visiting a patient one should wash one's hands carefully; as much as possible, direct contact with patients should be avoided (gloves can be used, and one should not forget, of course, to discard them properly immediately after use).
  2. Air conditioning should be monitored: temperature should not be kept too low (most microbes survive much longer at low temperatures), and ventilation should be efficient but indirect (remember that the nose and lungs act as air filters): filters should be cleaned up and as much as possible sterilized.
  3. Water quality should be controlled: filters should be cleaned up, and water circuits should be checked as much as possible.

At the present time several possible agents are considered (but none has been identified as a common cause): the influenza virus (which often causes pneumonia-like symptoms and is frequently lethal); Legionella pneumophila (a very dangerous bacterium often transmitted trough infection by amoeba that strive in water cooling systems or in the water circuit); Chlamydia pneumoniae (a very fragile bacterium, that may be dangerous in immunocompromized people); Rickettsia psittaci, the cause of psittacosis. Many other causes may exist among which viruses are usually the most difficult to identify readily unless well known previously. Sudden mutation of a rather innocuous virus such as syncytial respiratory virus may even be considered. The present observation that contagion seems highly confined to specific premises suggest either direct physical contact (this is the case with the Ebola virus) or some kind of transmission by water or air fluids.

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Previous Years

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A short description of relevant microbes


Microbes Nomenclature

Microbes have a name, which plays the role of an identifier. It is essential, to avoid duplication and erroneous assignments that the names are validated. The process, as in the case of other scientific activities is peer-reviewed.

Validation lists of bacterial species are lists published in the the International Journal of Systematic Bacteriology (IJSB) or in the IJSEM validating bacterial names effectively published elsewhere.
It is important to note that the publication of new names or new combinations in a validation list is the responsibility of the authors who propose the new nomenclatures. authors wishing to have new names and/or combinations included in a validation list should send the pertinent reprint or a photocopy thereof to the IJSEM Editorial Office (IJSEM Editorial Office, Society for General Microbiology, Marlborough House, Basingstoke Road, Spencers Wood, Reading RG7 1AE, UK. - e-mail: ijsem@sgm.ac.uk - Tel: + 44 118 988 1815 - Fax: + 44 118 988 1834).

A list of valid names and identifications is published at the site providing the List of Bacterial Names with Standing in Nomenclature.

Genes nomenclature

Genes nomenclature is not yet standardized, unfortunately. However many bacterial geneticists are endeavoring to implement Demerec's rules as the standard nomenclature. Because E. coli is the reference bacterium gene names will be usually derived from gene names given in E. coli. Some adjustment will be needed however, since many names in E. coli were just given more or less by chance, according to a phenotype that was observed by the first geneticists who came across mutants of this gene. The protein data library, SwissProt, is pioneering in this effort.

Demerec's rules are simple. A gene is written in italics. The name comprises three low case letters (usually a mnemonics of the gene function), followed by a capital. Then an arabic number, indicating a specific allele, follows. In case when there is no capital letter, a dash precedes the allele number. Examples:

argH1, cyaA610, leu-1

when genes are clustered in transcription units (operons) the gene full name is usually not repeated, but only the capital letters are noted, e.g.

hisABCDEFGH

For genes of unknown function the three letters of the gene (temporary) name start with a "y" (Why?), and the following letters are usually indicative of the position of the gene along the chromosome, e.g.

ywhE, ywhFG are located next to each other, and have not (yet) been functionally identified.

When sequences are inserted inside a gene, this is indicated in roman after two colons:

speA::Tn10 means that the speA gene is interrupted by transposon Tn10

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Microbes and cancer

Apart from viruses, many microbes are causing cancer. But the worse toll they take on patients is during cancer treatment. In fact, one of the reason why chemotherapy is often unsuccessful is that, during the treatment, patients become infected with a variety of pathogens, and die from infection. As a consequence, fight against cancer should involve a large effort in fight against microbes, in particular bacteria, and a fungus of the environment Aspergillus fumigatus.

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Controversies

The magazine Nature (10 jan 2002) writes an editorial on the use and abuse of citation statistics, pointing at major errors in the assessment of publication records of scientists by the only reference in the domain, the private Institute for Scientific Information.

The magazine Nature (8 sept 2001) writes an editorial on the future of electronic scientific literature, clearly favoring this new medium as the future of scientific exchange. Nature being a "paper" magazine, this triggered reactions at Publishing companies.

An interesting debate centers on the origin of the 1918-1919 influenza epidemic: while it was thought that the negative RNA segments of the virus could only reassort from one virus with another one, sequence data on that lethal strain suggest recombination. Mark Gibbs of the Australia National University at Canberra reported findings that support this hypothesis on April 25th at a Royal Society symposium.

The Human Genome Program began in the USA when Charles DeLisi managed to obtain 5.5 million US$ in 1987 to start a feasability study. This mandate derived from its predecessor agency (see A rattling good History) the Atomic Energy commission to study the effects of radiation and chemical by-products of energy production. The start point of this study was triggered by the interest of James Neel in physical anthropology, in particular in the becoming of irradiated persons from Hiroshima and Nagasaki and of their progeny.






Recently, the work of James Neel has been put into question in a bitter debate because of his keen interest for naive selection processes which might operate in Humans. This debate is strongly linked to ethical issues associated to the Human Genome Program. It is therefore interesting to have some flavour of its content. It is clearly developed in a recent issue of the New York Review of Books, where the role of Neel in the controversial study of a Venezuelian Indian tribe, the Yanomami, is vividly described. As stated by Clifford Geertz Neel's book: Physician to the Gene Pool: genetic Lessons and Other Stories (Wiley, 1994) "is a combination autobiography and homiletical treatise in "genetic medicine." Neel goes on to say; "One of the major disappointments of our fieldwork was that, despite much brainstorming, we could never devise a field test of Yanomama 'smarts' - and if we had devised one, the Yanomama would have no motivation to take it seriously." To Tierney he confessed in a 1997 phone interview, that his failure to isolate the alleles for his index of "Innate Ability", and thus pin down his big man/big smarts/big reproducer theory directly, "was the greatest disappointment of my life.'''' All the controversy is depicted in Patrick Tierney's book: Darkness in El Dorado: How Scientists and Journalists Devastated the Amazon" Norton, 2000. See the ongoing debate in the references provided here. This is an interesting background for the present and future debates about the ethical issues raised by the knowledge of the Human Genome.

Mid-january 2002 the controversy is not settled.



The campaign for free Internet access to full text material of published research papers is succeeding (april 2001). The number of publishers agreeing to give free access to the material in their journals six months after publication is steadily increasing. Only the largest commercial publishers (Reed Elsevier and the Nature group) have yet to declare their intentions and there is good reason to believe that even they are actively reconsidering their policies.

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The Origin of Life (preliminary information)

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Fads and Fallacies in the Name of Science

Tip: remember to be critical. This does not mean to ask nasty questions, but to always check the information you get from scientists and doctors! When somebody uses words such as "for the first time", "previouslyundescribed", "unexpected", "dramatic" etc please check. Often, this is indeed unexpected or the first time for the person who informs you (this can be a sheer lie...). This is relative, and has often already been observed elsewhere, or some time (often even a long time) ago. Many simple ways exist to control information. Here is a very fast and efficient one: use the words given by your informer, put them in the "search" field Entrez software at the NCBI, for example in the PubMed database, and read some of the abstracts of the papers you will get to. Often this will tell you about competitors or about related work. Most probably you will be surprised by their sheer number, and by their content. Remember that, at present, there are more than 2.5 million scientists involved in research in biology all over the world. Remember also that scientists of the past (and even of the remote past), were as intelligent, if not more intelligent than those of the present time. In particular, most were aware of the fact that, what they are building is constructed on previous knowledge. They were interested in History. This is an element that journalists should always consider as relevant (and, fortunately, this is deeply rooted in Chinese tradition). Beware of fashion! Fashion has, as a built-in principle, the property to be a non-lasting phenomenon. Fashion must create an ever-changing environment. And this is exactly at the opposite of the main goal of science, which is to provide long-lasting explanations of phenomena. Try to escape the "authority argument" where people who have got coveted honors are thought to know better, even in fields that are different from those where they are specialized, than people with good common sense. Prizes and Medals are deeply rooted in ideology, sociology and human psychology. You have the right to be informed, and not imposed by ready-to-use ideas, from people who think of themselves that they are the best. By construction, a scientist must be modest. And he should have as a motto, that of Montaigne "Que sais-je?" ("What do I know?") or the last sentence said by Jacques Monod when he was dying: "Je cherche à comprendre" ("I try to understand").

Caveat: It is important to note that crooks who construct attractive fallacies in the name of science, use practices (naturally, not all of them) which belong to science, so as to pretend to have a scientific approach. A common way is to use reproducibility as the only landmark of science. Naturally, these crooks ask you to reproduce their experiments. But, of course, systematic errors (are indicated in their name) are reproducible! The way to test for a crooked approach is simple: ask whether an appropriate control has been performed (correctly). For example, some assert that biological molecules can have an effect when they are diluted below Avogadro's number (which means that only their ghost could be active). Well, the control is obvious (but never performed): ask these people to measure the concentration of all components of their mixture, before proceeding further (this is the basic control which would have been asked to a student, and this is easy to do). Now, to correctly perform the required experiment you should monitor the concentration of the atoms and molecules present in the mixture (so that you know what you are doing). You can bet that they will never do it, but, rather, ask you to repeat their experiment! This is the trick... The fashionable magazine Nature thus published a work on the "memory of water" which did not propose or perform any appropriate control for the quality of water used! The study of this paper and related work is an excellent test to investigate ones gullibility.

Spring 2002: the magazine Science, publishes another account of "cold fusion", despite very negative advice of the community of physicists. This bad work will certainly increase the Impact Factor of the journal. See for example (the list is unfortunately ever growing, and this is just for the purpose of illustration):

retraction: Metal-insulator transition in chains with correlated disorder
PEDRO CARPENA, PEDRO BERNAOLA-GALVAN, PLAMEN CH. IVANOV & H. EUGENE STANLEY
retraction: A cytosolic catalase is needed to extend adult lifespan in C. elegans daf-C and clk-1 mutants
J. TAUB, J. F. LAU, C. MA, J. H. HAHN, R. HOQUE, J. ROTHBLATT & M. CHALFIE

Another retraction in microbiology (february 2002): the magazine Science had published an "interesting" study on the clonal nature of virulent Staphylococcus aureus isolates in the wild. This work is now retracted: Science (2002) 295: 971. Still another (involuntary) means to increase the Impact Factor of a Journal...

Still another case of (at best) sloppy work published in high profile journals. This time about a very sensitive issue (monitoring Genetically modified Organisms). This demonstrates the dangerous impact of fashion in scientific journals.

A German study on putative cancer vaccines has been invented by its authors (discussed in Nature vol. 412 p. 8: original paper Nature Medicine Kugler et al.). Unfortunately fraudulent articles are rarely retracted and retracted articles are still quoted for a long time....

Other fakes...


Hot topics about microbes, environment and infection

A short description of relevant microbes

Controversies

Some interesting dates

Fads and fallacies in the name of science

Your questions


Causeries

FAQ

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