The comeback of whooping cough

October issue of Microbe, published by ASM.

I read a very interesting—and somewhat alarming—article in the October issue of the journal Microbe (formerly ASM News). In this article, Merry Buckley explains that whooping cough (aka pertussis), a childhood disease that has strongly declined since the introduction of a vaccine in the 1940s, is now on the rise again. We even see epidemics! says Buckley.

In 2012, in the USA, the number of pertussis cases is expected to be the highest in fifty years, approaching 40,000. Other countries such as Australia and the Netherlands also have high incidence of the disease—in the Netherlands, 6,000 cases were reported in 2009, against only 30 cases in 1980. The causes of this comeback are not fully understood, but scientists have gathered many clues.

Whooping cough is caused by Bordetella pertussis, a Gram negative bacterium belonging to the group beta Proteobacteria. It infects the respiratory system, causing a characteristic ‘whoop’ sound in sick children. Teens and adults can also be infected, although the symptoms are milder than in small children. In the prevaccine era, pertussis was a terrible threat, killing on average 5,000 children a year during the 1920s and 30s in the USA alone. At this period, the epidemics peaked following a cyclic pattern of a couple of years.

Naming Nature by Carol Kaesuk Yoon

Published by W. W. Norton & Company

For a book that aims at a large readership, Naming Nature (2009) dares to explore a topic that seems anything but sexy at first sight: taxonomy. But we know better and we won’t turn away from the book, since the act of naming and classifying organisms is of course a very exciting activity! (No, I’m not kidding.)

In her book, Carol Yoon recapitulates the history of the discipline and presents the main scientific actors who contributed to the advance of taxonomy. She thus tells us about important figures:  Linné (Carolus Linnaeus), who is considered the founder of modern taxonomy, and who notably popularized the use of the binomial nomenclature (Felis catus and Escherichia coli, to name two lovable examples); Charles Darwin, who needs no introduction, and who revolutionized taxonomy by showing that species were not immutable; Ernst Mayr,  one of the main architects of the modern synthesis of evolutionary theory; Linus Pauling, the Nobel laureate chemist who had the brilliant idea of classifying organisms by looking at the amino acid sequence of hemoglobin; and Carl Woese, microbiologists’ modern hero, who classified organisms by looking at their DNA sequence and turned the tree of life topsy-turvy. Nothing new to me here, but, after all, this book is not written for biologists.

On the other hand, I learned facts that I was ignorant of (and this seems to be an inexhaustible category of facts...). For instance, I learned that it was Julian Huxley (member of a family in which each member is either a literary or a scientific genius) who coined the term ‘systematics’ and proposed to use it in place of taxonomy.

Plant pathogen focus: black Sigatoka as a worldwide threat to banana

Banana trees affected by Sigatoka in Malawi. Photo courtesy of APS.

Since I work in the department of plant pathology at UCD—and even though I am not a plant pathologist myself!—I decided to start a series of posts on microbes that cause plant disease, focusing on stories that are of economic and societal importance.

A couple of weeks ago, one of my colleague—him a true plant pathologist—, managed to scare me by claiming during a talk that banana could disappear in the not-so-distant future! The culprit? The fungus Mycosphaerella fijiensis: This ascomycete causes a disease (black Sigatoka) that damages the leaves of banana trees and reduces photosynthesis. Moreover, the fungus triggers a premature ripening that spoils the fruit. Together these effects of black Sigatoka provoke the loss of 50% or more of the fruit production. 

[I learnt a lot about black Sigatoka in an online article by Randy Ploetz on the website of the American Phytopathological Society (APS). When no other source is explicit, the information in this post comes from the Ploetz article. In general, the APS website is a great starting point for everything related to plant pathology!]

The science and art of David Goodsell

Portion of an E. coli cell. Image courtesy of David Goodsell.

At the University of Lausanne, when I was a biology student, our great professor Jacques Dubochet tried to instil in us some sense of the physics at play in the biological world. He would ask us questions such as: “So, how thick is the plasmic membrane?” or “How fast will a protein diffuse in the cell?”.  And we would be like: “Huhhh….” So I’m convinced my former professor must be a great fan of the work of David S. Goodsell.

David Goodsell is associate professor of molecular biology at the Scripps Research Institute in La Jolla, California. He is an expert in the structure of biomolecules, and he uses computer simulations to illustrate molecular organizations and interactions.  But what makes his work truly unique is the use of classic watercolor painting to represent cells and their compartments: anything from a bacterium to the Golgi apparatus of a eukaryotic cell, nerve synapses or even viral particles. At odds with the oversimplistic representations of cellular organization that many biologists enjoy, David Goodsell’s drawings offer a real sense of what the biophysical world is. And did I mention they were beautiful too? His website—Molecular Art/Molecular Science—is a great resource to learn more about his work.

Has popular science writing become too wordy?

It’s probably a bit unfair to ask that question, but I can’t help it. These days, I feel like most of the recent science books I read dilute interesting information into too many pages. Well, it could be that the majority of readers prefer long books. It may be true, but it’s definitely not my case. [To be precise, what I mean by “recent” is what has been published in the past ten to fifteen years.] 

Thinking of what I read in the not-so-distant past, I find for instance: “The elegant universe” by Brian Greene (1999), 448 pages; “The stuff of thought” by Steven Pinker (2007), 499 pages; “A guinea pig’s history of biology” by Jim Endersby (2007), 499 pages. Don’t get me wrong, I’m not questioning here the quality of the books. Greene’s book is an informative introduction to string theory, Pinker’s is a clever journey into linguistics, and Endersby’s is a highly original work on the history of model organisms. I really enjoyed reading Endersby and Pinker; I didn’t enjoy Greene that much, but it might be the topic. But quality notwithstanding, could they have been shorter without losing of their substance? 

The tree of life versus the rhizome of life

Tree by Haeckel (1866). Source wikimedia commons

The metaphor of the tree of life—which illustrates the common descent of all life on Earth—was popularized by Darwin in its Origin of species and later by his contemporary Haeckel, but apparently its roots can be traced back as early as the 18^th century in the writings of various authors (Archibald,2009). On a different line, it also of course echoes the biblical tree of life mentioned in the Genesis.

However, about a decade ago, authors such as W. FordDoolittle (1999) have cast doubt on the tree as a valid representation of the history of living organisms. Since then, articles that question the tree of life have flourished¹. And the debate is far from being settled.

A tree or a rhizome?

Based on the recent development of comparative genomics, the microbiologist Didier Raoult suggested in the journal the Lancet that Darwin’s tree of life should be replaced by a rhizome of life (Raoult, 2010). Raoult sees the rhizome – a complex net of interconnected roots – as a more faithful representation of the history of living organisms.

The Logic of Chance by Eugene Koonin (continuation)

Published by FT Press

In the first part of this post, I insisted on living organisms (viruses, bacteria, eukaryotes) and their evolutionary history. 

Here I want to look at what Koonin writes about the mechanism of evolution.

What drives evolution?

One central idea in Koonin’s book, I think, is to propose an evolutionary outlook that is based on an analogy with the physical world. Central, for instance, is stochasticity, as a force shaping the genomic evolution. Equally important, in Koonin’s view, are the statistical principles that govern the interactions between all genes within a genome (he likens the collection of all genes in a genome to the ideal gas model in physics). Thus, genes are influenced by a number of statistical rules. On this line, even though it is apparently not possible to define “laws of genomics”, certain regularities can be identified, such as the proportion of different functional classes of genes within a given prokaryotic genome.

Koonin writes, p. 405:

“it is remarkable that the advances of genomics and systems biology, while revealing an extremely complex, multifaceted picture of evolution, at the same time allow us to derive powerful and simplifying generalizations. It is tempting to offer yet another version of the famous phrase: Nothing in evolution—and in population genetics—makes sense except in light of statistical physics.”