Science fiction meets microbiology: Vitals by Greg Bear

I can’t think of many sci fi books in which microbiology is the core element of the story—actually I can only think of one, the excellent Andromeda Strain of Michael Crichton, which deals with viral infection from outer space. As to Greg Bear, author of Vitals (2002), he had the brilliant idea of putting bacteria on center stage with, as we shall see, pretty good intuitions. 

Bear is an accomplished American science fiction writer. His short story Blood Music won both a Nebula and a Hugo Award, and his Darwin’s Radio won a Nebula Award for Best Novel in 2000. He’s considered a ‘hard SF’ writer, since science has a prominent place in his fictions (which is, by far, not a prerequisite in science fiction). 

Vitals tells the story of twin brothers, Hal and Rob Cousins, who happened to be microbiologists (the story is mainly told through the point of view of Hal, but we learn about Rob via another POV character). The Cousins brothers are in their late twenties and already very successful scientists. Hal had a tenure track position in Stanford, however, at the beginning of the book we learn that he has been fired due to a redistribution of resources at Stanford. So now he’s going rogue, that is, he’s looking for rich patrons to subsidize his research and he's renting lab space for his own use—a situation that I thought unrealistic, but I read something similar recently in Science, so... Good news for Hal, his trade is the prolongation of human life, a topic that has the ear of many rich old men. In the first pages of the book we thus meet Hal on a mission to seek the secret of eternal life in the deep ocean floor…

Adieu, François Jacob

François Jacob. Source: Nobelprize.org

François Jacob passed away on April 20, at the age of 92. He was one of the greatest biologists of the twentieth century and a very fine science writer. (Incidentally, my last post was about one of his latest books.) Excellent obituaries can be found online, including a nice piece written by Carl Zimmer.

Jacob's scientific merits are immense, but it is another aspect of his life that struck me when I discovered more about him in the days following his death. (I read the information below in the post by Zimmer and in an obituary by the French Ministry of Defense.)

In 1940, Jacob joined the French liberation army in England - he was only twenty. Since he was a medical student he served as a medic, participating to campaigns in African countries. Several times he brought back wounded soldiers under enemy fire, and was wounded himself.

In 1944 he participated to the assault at Utah Beach in Normandy, and a week later he was severely wounded (his arm and his leg) while helping the injured. He was then evacuated to Paris, and was demobilized in 1945.

Jacob finished his medical studies after the war; he wanted to become a surgeon. His wounds, however, prevented him to do so and he turned to biology and research. Needless to say, François Jacob made the best (and more!) of this forced career reconversion. 

Jacob was not only a brilliant scientist, he was also a brave man who fought to free his country. May he rest in peace.

Of Flies, Mice, and Men by François Jacob

Published by Harvard University Press

It is thanks to François Jacob that I began to understand what evolution meant at the molecular level, when I read his wonderful book Le jeu des possibles (The possible and the actual), more than ten years ago. And “Evolution is tinkering”, Jacob’s catchphrase, is with me ever since. 

Jacob, now 92 years old, began his scientific career after fighting in World War II, and studied lysogenic phages in bacteria at the Pasteur Institute in Paris. There he met Jacques Monod, starting one of the most fruitful collaboration of the 20^th century. Their work on genetic regulation in E. coli culminated in a Nobel Prize in 1965. In addition to their revolutionary contribution to molecular biology, Jacob and Monod also wrote books of great importance and large outreach, notably Chance and necessity (Monod) and The logic of life (Jacob).  

Of flies, mice, and men¹ (1998) is his last book to date, a personal journey across biology that spans several decades. The different chapters feel a little bit disconnected, because apparently they were first written as lectures for different occasions, but the book is very enjoyable. Jacob is one of these great scientific figures with a real literary culture, one who can invoke Dino Buzzatti and ancient greek myths, the poets Paul Valéry and John Keats, or Tolstoy. 

The Naked Ape by Desmond Morris

First American edition, 1967

"There are one hundred and ninety-three living species of monkeys and apes. One hundred and ninety-two of them are covered with hair. The exception is a naked ape self-named Homo sapiens. This unusual and highly successful species spends a great deal of time examining his higher motives and an equal amount of time studiously ignoring his fundamental ones. He is proud that he has the biggest brain of all primates, but attempts to conceal the fact that he also has the biggest penis, preferring to accord this honour falsely to the mighty gorilla. He is an intensely vocal, acutely exploratory, over-crowded ape, and it is high time we examined his basic behaviour."

Desmond Morris is a wonderful writer, and I think this shows in the first paragraph of his best-seller book "The Naked Ape" (1967), reproduced above. I hadn't read it for at least ten years, and this second reading (but first time in English) was as enjoyable as the first one.

The Naked Ape—subtitled A zoologist's study of the human animal—is Morris' attempt to teach us some anthropological and biological facts about ourselves, and this in a very clear and funny way. Morris is a British scientist who studied animal behavior at Oxford. He later worked at the London zoo  and he has participated to many radio and television programs. Last but not least, he's the author of many popular science books! (You can read his full biography and find his complete works on his personal website.)

Fluorescent bacteria under the microscope

Pantoea agglomerans and Pseudomonas syringae bacteria

Some time ago I made experiments growing two bacterial species on a gel surface, using fluorescence to distinguish between them. Since some of these pictures looked nice to me, I decided to share them here!

Here's some information about the bacteria and how the images were taken:

Pantoea agglomerans and Pseudomonas syringae are two bacterial species that live in association with plants: the former as a harmless inhabitant of plant leaves and the latter as a pathogen that can colonize the inside part of the plants. Because it is not easy to visualize these bacteria in their natural environment (the surface of plant leaves), it is common to use fluorescently-tagged strains. I discussed this type of research in a previous post.

Where have all the geniuses gone?

Nernst, Einstein, Planck, Millikan and Laue in 1931. From Wikimedia commons.

Is scientific genius gone for good? No more Darwin or Einstein on the horizon? That’s the intriguing and slightly provocative question recently raised by UC Davis psychologist Dean Keith Simonton in the comment section of the journal Nature. Simonton has extensively written on the topic of science creativity in books and articles, and here’s how he sums up the problematic:

“Geniuses have played a decisive part in science in two main ways. First, they have founded new scientific disciplines […]. Second, geniuses have revolutionized established disciplines. […] Yet, in my view, neither discipline creation nor revolution is available to contemporary scientists.”

Coliforms and operational definitions

Recently, I was talking about coliforms with my colleagues from the lab. ‘Coliforms’ is the name given to a group of bacteria that usually serve as indicators of fecal contamination in water and food samples, because most coliforms come from the intestinal flora of animals. For this reason, water and food that contain too high levels of coliforms are deemed unfit for human consumption (the US EPA recommends a limit of 10 or less per liter in drinking water). The most famous coliform, Escherichia coli, is a commensal in our intestine, although some pathogenic strains exist as well (for instance O157:H7, involved in deadly outbreaks in the US and Europe). Coliforms behave similarly as fecal pathogenic bacteria, notably regarding their survival in water. We can thus assume that a sample devoid of coliforms will also be free of fecal pathogens. Commercially-available tests for coliforms, such as the culture medium CHROMagar ECC, also permits us to differentiate between total coliforms and fecal coliforms (mostly E. coli), simply based on the coloration of the bacterial colonies on agar plates.