Genomes, Infectious Diseases and Controversies

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).

Genes nomenclature is not yet standardized, unfortunately. However many bacterial geneticists are endeavoring to implement Demerec's rules as the standard nomenclature. Because Escherichia 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, UniProt (formerly, 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:

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.

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:

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.

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.

In 2001 , 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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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 data base, 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.

A remarkable work (again published by Nature, which should have known better 15 years ago than to publish the fantasies of a grossly irrational person) shows that there is ultrafast memory loss and energy redistribution in the hydrogen bond network of liquid H₂O. The loss of memory of a given state is of the order of 50 femtoseconds (50 thousandth of a billionth of a second)...

An amusing site where standard fads and fallacies in biology can be found as well as links to other sites with a variety of information. A simple control of the "high dilution" experiments (of course never made: note that silicate is soluble in water and present in all water samples that have at one time passed through glassware) can be found in Nature 334, 286 (28 Jul 1988).

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.