Sunday, December 22, 2013

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.”

Monday, November 04, 2013

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. 

Tuesday, October 08, 2013

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!

Wednesday, August 28, 2013

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!)

Sunday, June 09, 2013

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…

Monday, May 06, 2013

Adieu, François Jacob

François Jacob. Source:
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.

Sunday, April 07, 2013

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 20th 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. 

Sunday, March 17, 2013

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 Apesubtitled 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.)

Saturday, March 09, 2013

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.

Sunday, February 24, 2013

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.”

Sunday, February 17, 2013

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.

Tuesday, February 05, 2013

Bacteria in a wastewater treatment plant

Bacteria in activated sludge from a wastewater treatment plant

It is a remarkable fact that we fully depend on microbes to treat or sewage water. In every wastewater treatment plant, from the simplest to the most modern ones, the essential activity is biological and is mainly carried out by bacteria. In modern plants, sewage water is directed to large aerated tanks in which the pollution is consumed by a mixture of microbes and organic matter known as  activated sludge.

The video below shows how an aerated tank looks like. You don’t want to take a swim in there… 

For a microbiologist, a wastewater treatment plant is a delight: I’ve never seen another environment with as much diversity in the size and shapes of cells. It is a true microbial jungle containing countless bacteria and many protozoans that feed on them.

Sunday, January 27, 2013

Should science be apolitical?

Read the other day in the magazine the Atlantic: “The danger of making science political”, by Puneet Opal, medical doctor and professor of neurology at the Northwestern University Feinberg School of Medicine. Opal reflects on the relation between science and politics; he observes that, in the US, science is associated with the Democrat party, and he asks the question: why is it so?

Opal’s article is echoing another piece published recently in Nature, “Science must be seen to bridge the political divide”, by Daniel Sarewitz, from the Consortium for Science, Policy and Outcomes at Arizona State University. Sarewitz complains about a very US-centered situation, that is, the fact that most American scientists seem to side with the Democrats against the Republicans. He takes as an example the letter written by many Nobel laureates in support of Obama’s reelection in 2012. This bias, Sarewitz claims, is a bad thing for science. He writes:

“To prevent science from continuing its worrying slide towards politicization, here’s a New Year’s resolution for scientists, especially in the United States: gain the confidence of people and politicians across the political spectrum by demonstrating that science is bipartisan.”

Friday, January 18, 2013

Plant pathogen focus: Pierce's disease and the vineyards of California

Grapevine dying of Pierce's disease. Photo courtesy of PD-GWSS/CDFA.
Xylella fastidiosa  is not your ordinary kind of bug. It made it to the list of the most wanted plant pathogenic bacteria in 2012! (Mansfield, 2012.)

This is well deserved: X. fastidiosa can infect over a hundred species (grapevine, oleander, citrus, almonds,…), and it causes severe symptoms that can kill the infected plant. The Xylella bacteria colonize the xylem vessels, and by doing so they block the transport of water in the plant. The water-deprived leaves dry and scorch, until finally they drop to the ground. 

In 1892, Newton Pierce, California’s first professional plant pathologist, described the disease that now bears his name, although he failed to identify the causative agent of the disease (X. fastidiosa). Around the end of the 19th century, an epidemic of Pierce’s disease devastated thousands of hectares of vineyards in the Los Angeles Basin. Since then, southern California has considerably reduced its viticulture; this also explains why present-day Californian vineyards are mostly restricted to the north of the state. There is currently no other cure than getting rid of the infected plants!

Sunday, January 06, 2013

The new biology of Carl Woese

Carl Woese. Photo courtesy of Don Hamerman.

Carl Woese, one of the giants of contemporary biology, passed away a day before New Year’s Eve (see the NY Times obituary). Woese, an American microbiologist from the University of Illinois, revolutionized our understanding of life with the discovery of a new domain of living organisms, the Archaea, and the creation of a universal tree of life made of three main branches (Bacteria, Archaea and Eukarya) (Woese, 1990). This discovery is already more than thirty years old, but is not very well known to the general public, to say the least… And now with Woese’s death the possibility of a Nobel nomination vanishes.

Everything we do nowadays in microbiology labs is to some extent influenced by the work done by Woese in the seventies and eighties. This is one reason why I entitled this post “The new biology of Carl Woese”. The other reason is a 2004 article by Woese, “A new biology for anew century”, which offers a great perspective on our job and which contains some juicy controversial elements. But let’s begin with the landmark contribution of Woese to the field of biology.

Before the sixties and the advent of molecular phylogeny, the classification of bacteria seemed an insoluble problem, since morphology and metabolism were not good enough to allow us to order the bacterial life forms. Woese, a physicist by training, decided in 1966 that he could give it a try using the powerful tools of molecular biology. At that time many researchers had turned towards proteins in order to build phylogenetic trees, following the pioneer work of Linus Pauling on hemoglobin. Woese didn’t follow the consensus and decided to use ribosomal RNA as source material. Thanks to a tedious technique called oligonucleotide cataloging, he was able to reconstruct the rRNA sequence and did that for about sixty bacteria. It took ten years.