Oceans, bacteria, and the quest for new drugs

A marine sponge of the genus Theonella. Photo by Nick Hobgood.

We rely on natural products in medicine: the vast majority of pharmaceutical drugs are thus of plant or microbial origin. (The purely synthetic drugs, which have no counterparts in the environment, are the exception rather than the rule.) To name potent examples of natural products, take antibiotics (discovered in fungi and bacteria), the anti-malaria drug artemisinin (isolated from sweet wormwood) or simply aspirin (salicylic acid is present in willow bark). Many people, I think, forget about this, as they oppose a so-called ‘natural’ medicine to a ‘chemical’ medicine (the pills you get from your doctor). 

It is not easy to find new active compounds, however, and much more difficult to test them and turn them into a real medicine. The situation doesn’t look that good, notably because of the high increase of antibiotic-resistant strains of bacteria, and the paucity of new drugs available. A natural environment that has long been recognized as a promising source of new chemicals is the largest on Earth—oceans—, and many researchers are mining the sea in search of new organisms and their specific biochemical abilities. For instance, the research project PharmaSea, funded by the European Union, was launched in 2013 with the goal of discovering new microbial organisms that could be the source of useful chemicals for medicine or industry. This team of academics and industry researchers plan to explore the deep bottom of the sea, looking for environments that are poorly known and potentially harbor interesting organisms. Here’s an excerpt from the project website:

“Marine organisms that live more than 6,000 meters below the sea level are considered to be an interesting source of novel bioactive compounds as they survive under extreme conditions. "Trenches are separated from each other and represent islands of diversity. They are not connected to each other and life has evolved differently in each one", explains Marcel Jaspars [PharmaSea project leader]. “

PharmaSea is an ambitious project, and it may not be easy at all to get many new products out of it, but the goal has to be praised, as we surely are in need of new biochemicals, particularly new antibiotics.

Communicating science: TED talks

Is it even necessary to introduce TED talks?...  I guess everyone has seen at least one of these 18-minute-ish presentations on topics that deal with (broadly speaking) Technology, Entertainment or Design. These “ideas worth spreading” (as they are advertised), are presented during the TED Conference, an event occurring every year on the US West Coast since 1990. It is thanks to the development of the internet and video streaming, however, that TED talks have accessed global fame. The first talks were uploaded in 2006, and in 2012 the total views passed 1-billion! (According to TED.com, there are now more than 1,600 talks available!) With as famous speakers as Al Gore, Bill Gates or Bono, TED talks have become an unprecedented cultural phenomenon. 

Today TED conferences are organized not only in the US, but also in Canada, in South America, in Europe and in Asia. More than this, TED has become a label, since all over the world are organized so-called TEDx events, conferences that share the TED format but are organized by independent local committees. 

Given the format and the varied audience, TED talks are not meant to treat a topic exhaustively and should be accessible to the layman. This is not necessarily an easy job for scientists, still you can find almost four hundreds science talks on the TED website! It seems thus that science fares pretty well in the TED universe… 

Communicating science in 2014: Public Outreach

October 2013 issue of Science magazine

A few months ago, the magazine Science published a special issue on ‘communication in science’. Indeed, the way scientists exchange information has evolved considerably in the past decade, thanks notably to the internet and the rise of the open access movement. Conversely, older means of communication still fare pretty well; despite predictions of extinction, IRL meetings are still flourishing, and so are printed books… This year, I want thus to orientate this blog a little more towards questions related to science communication (internal and external) and how scientists deal with it. So I plan to write several posts about the way scientists communicate between themselves and with society. Here I want to start with how scientists communicate to the general public.

Science for the masses

Scientists today are constantly reminded of their duty to communicate their research to the public, and are encouraged to do what is called science outreach. I believe this to be fundamentally a good and a fair thing, if only because the vast majority of science funding is provided by the public society via taxes. In addition, and in my view more importantly, every citizen (as well as society as a whole) gain at a better understanding of science, this for pragmatic, aesthetic and philosophical reasons. 

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!)