The Invisible Gorilla by Chabris and Simons

UK edition, published by Harper

The invisible gorilla and other ways ourintuition deceives us, by psychologists Christopher Chabris and Daniel Simons, is a wonderful book that contains a lot of food for thought for scientists – and actually for everybody. 

There is little chance that you missed this viral video, dating back from just before the turn of the millennium: two teams, dressed either in white or in black, play basketball, and you are supposed to count how many passes the white team manages to do. If you never saw that, watch it here before reading. OK, that was the one and only spoiler alert!

In the middle of the video, a student wearing a gorilla suit walks through the players, thumps her chest, and leaves. I didn’t see the gorilla, just as half of the people who watch the video, because I was too focused on counting the white team passes. With this video, Chabris and Simons showed us that we wrongly take certain things for granted, such as our ability to notice everything that enters our field of view. They write in their introduction (p. ix):

“We all believe that we are capable of seeing what’s in front of us, of accurately remembering important events from our past, of understanding the limits of our knowledge, of properly determining cause and effect. But these intuitive beliefs are often mistaken ones that mask critically important limitations on our cognitive abilities.”

Modelling the bacterial colonization of leaves

Photo courtesy of Jan Tech

Our world is a quite green world: a sea of trees, bushes, grasses, or, if you happen to live in the Midwest, corn fields… What is less obvious, though, is the fact that this green vastness harbors a huge community of microbes. Yeasts and filamentous fungi are often found on plant surfaces, but the most numerous inhabitants are first and foremost bacteria. Indeed, a centimeter square of leaf can contain as many as 10 millions of them! No worries, most of them are harmless to us or their plant hosts. On the contrary, many are required to maintain a healthy plant environment, by stimulating plant growth or by preventing the plant colonization by pathogens (they compete for the same space and the same resources). 

Because plants are so vital to us (think food, raw materials, landscapes, etc.), there is a real interest in understanding what the microbial contribution to the plant ecosystem is. One lingering question, for instance, is how bacteria colonize the surface of leaves (what we call the phyllosphere). What we do know is that bacteria on leaf surfaces appear as clusters of cells, rather than an even layer of bacteria covering the surface; the mechanisms that lead to this colonization pattern, however, is not well understood. I have already written about this question in a previous post that dealt with the use of bacterial bioreporters. Another way to explore these mechanisms of cluster formation is computer-based modelling, which enables us to test different scenarios and compare it with what has been observed on real plants. 

Physics meets Biology: Size!

Photo courtesy of Brendan Wood

One interesting thing about my new job is that my colleagues are not biologists, but physicists. To some extent, physics was quite absent from my biology curriculum; of course, as a freshman in biology I attended physics classes, but they were usually disconnected from the scope of biology (with some notable exceptions, such as mentioned in this post). If you think about it, there are reasons for this. Physics – and chemistry as well, for the matter – are fundamentally different from biology in the sense that each individual atom or molecule is undistinguishable from another one of the same kind, whereas in biology, in the words of Ernst Mayr, each individual is unique. The uniqueness of individuals stands at the core of evolution, since natural selection requires it to operate. 

Despite this observation, it is undeniable that biological organisms live and evolve in the physical world. In that respect, a lot of what organisms can or cannot do is under direct control of physical laws. If I want to jump, I’d better hope that my muscles can counteract the force of gravitation… Physics is thus intricately associated to biology, and when biologists forget this fact it can lead to absurd hypotheses or ideas that could be refuted by a wave of a hand.

With this in mind, I have decided to do some more reading about the influence of physics on biology. And one very savory topic is the one of size!

A new continent, a new city, a new job

City of Zürich, Switzerland

I did not expect such a long hiatus on this blog, but here we are: three months since the last post! Although I don’t plan to blog as frequently as in 2012, I certainly will resume posting every now and then. 

What happened to me during this three months period is that I left the University of California-Davis and I moved back to Europe. It was sad to leave California, truly. This is such a wonderful place, with wonderful people in it. But All things must pass, as George Harrison used to sing. I am now in the beautiful city of Zürich, Switzerland (my home country). So, I have mixed feelings right now: missing California but enjoying the discovery of a new city.

My new job is at the SwissFederal Institute of Technology in Zürich; this venerable institution, founded in 1855, is often ranked as Switzerland’s top university. Initially, the Eidgenössische Technische Hochschule Zürich (its official name – you can also say ETH Zürich, or simply ETH, that you should pronounce Hay-Tay-Ha if you want to be in) was a polytechnic institute, whose mission, given by the Swiss government, was to educate engineers and scientists. In 1909, however, ETHZ started to give PhDs and thus became a university. (Interestingly, Einstein, who is an ETH alumnus, was awarded a PhD by the University of Zürich. Because at that time, 1905, none were delivered at ETH!) 

Main Building of ETH Zürich

ETHZ has a sister institution in western Switzerland, the École Polytechnique Fédérale de Lausanne (EPFL), which became a federal institute in 1969. These two universities belong to what is called the ETH domain, together with four institutes of applied research: EAWAG (aquatic research), WSL(forest, snow and landscape), EMPA (Material Sciences) and the Paul ScherrerInstitute (Environment and Human Health). 

At ETH, I have joined the group of Soil and Terrestrial Environmental Physics, that is part of the Departmentof Environmental Systems Science. I am now part of a research project that aims at understanding the origins of bacterial diversity in soil. (I won’t give too many details here, since I plan to write more about it in a future post!)

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.