The Logic of Chance by Eugene Koonin

Published by FT Press

About fifteen years ago, a revolution started in the biological sciences, which goes by the name whole genome sequencing. I don’t have memories of the announcement of the first bacterial genome in 1995 (I was in high school and not really following biology news…), but at the time of the human genome project I was a biology student at the University and I remember very well when the paper describing the human genome came out in 2001 (we had to read it in class!).

Until recently, my feeling about whole genome sequencing was that it was a technical revolution, not a conceptual one. After all, I thought, the sequence information revolution already took place in the seventies, when Carl Woese pioneered the use of 16S ribosomal RNA to construct phylogeny. 

I revised this feeling, thanks in part to the excellent book of Eugene Koonin, The Logic of Chance (2011)—subtitled the nature and origin of biological evolution—and published by Financial Times Press (yes, they do have a science catalog!).

Something scientists should consider about nature

Here, for a change, I want to wander into philosophical territory. I should first admit that I am rather ignorant of it, since I never studied philosophy past the high school level. But my interest remained vivid and I read philosophical books regularly. More important, I believe that every scientist has to keep an eye – even if it is half-open – on philosophy. Isn’t science the daughter of philosophy? (After all, science used to be “natural philosophy”.) And ironically, aren’t I a doctor in philosophy (Ph.D.)?

One year ago I was talking about philosophy with a colleague in the lab (although I can’t remember how the discussion drifted to this topic!). At some point my colleague said that he couldn’t find any use in philosophy, and this baffled me. I mentioned the philosophy of science and Karl Popper as a counter example, but retrospectively I didn’t need to be so specific. Philosophy is important per se— if it has practical applications for scientists it is a good thing but not its final goal. 

Nonetheless, I started thinking about examples of philosophical inquiries that have repercussions in the day-to-day life of scientists, and I realized there’s plenty. Here I would like to share one which I think is essential: the reflection on nature and natural phenomena.

Back from ISME 14

I just left Copenhagen, where the 14th International Symposium on Microbial Ecology took place from August 19 to 24. This was a busy meeting, with 2,200 attendees (a new record), hundreds of presentations and countless posters. ISME is the biggest meeting of microbial ecologists – a wide crowd that covers everything from molecular biologists to bioengineers, ecologists and evolutionary biologists.

This diversity is part of what makes ISME an interesting meeting. Not only the diversity of the participants’ background, but also the variety of topics: within the same day you can follow talks about forest soil, deep-sea vents, biogas plants or the human body.

Francis Crick and Directed Panspermia

Francis Crick. Photo Marc Lieberman

Every biologist knows that Francis Crick is the co-discoverer of the structure of DNA. What is less known, probably, is the fact that Crick was a proponent of a theory that stands at the border of science, the theory of directed panspermia.

In 1973, Crick (together with chemist Leslie Orgel) published an article describing the theory, and in 1981 he dedicated a full book to directed panspermia, entitled Life itself. 

According to Crick, the idea of panspermia – which means “seeds everywhere” – was proposed by the physicist Arrhenius at the end of the 19^th century. Arrhenius suggested that life on Earth originated from space, that our world was seeded by spores of micro-organisms traveling between planets. 

But because the radiations in space were thought to be too intense for the spores to survive, Crick and Orgel postulated a variant of the theory in which spores were transported by an interplanetary spaceship sent by an alien civilization!

Indole teaches persistence to bacteria

Indole molecule (C8H7N). Source: wikimedia commons

When a bacterial infection is treated with antibiotics, bacteria that are in a so-called dormant, inactive state may escape death – this because antibiotics only kill growing bacteria. It becomes a serious problem when these sleeping beauties start to grow again, in particular when they do so after the period of antibiotic treatment has ended… Thus, an infection that was apparently cured could be followed by a secondary infection days or weeks later. This problematic phenomenon is called bacterial persistence, and it should not be confused with bacterial resistance, in which growing bacteria are immune to one or several antibiotics.

Now what about indole? (The molecule displayed on top of this post.) Actually indole is present in very common and important biomolecules, such as the amino acid tryptophan, the animal hormone serotonin and the plant growth hormone auxin. We have known for more than a century that E. coli produces indole in stationary phase (Lee, 2010), and it does so thanks to an enzyme called tryptophanase, which cleaves tryptophane into indole, pyruvate and ammonia. 

But E. coli is not the only bacterium capable of that: more than 85 species (both Gram-negative and Gram-positive) can synthesize indole (Lee, 2010).  For a long time the biological functions of indole were overlooked, but now we know that indole can act as an extracellular signal and can for instance increase antibiotic resistance and control biofilm formation in E. coli.

Are all our modern health issues linked to our microbiome?

June issue of Scientific American

The human microbiome is definitely the sensation of this Summer 2012. [Kind of a Carly Rae Jepsen for science!]

In June alone, our microbial inhabitants were featured on the cover of Scientific American (watch their beautiful infographics), Nature, Science and Microbe…

The Human Microbiome Project (HMP), a $170 million research consortium funded by the US National Institute of Health (NIH), just released two reports in Nature accompanied by fifteen publications in PLoS ONE. The consortium, strong of about 200 researchers, studied the diversity of microbes inhabiting the body (skin, mouth, nose, gut, urogenital tract) of 242 healthy people, using new sequencing technologies to catalog the microbes.

The bottom line? Microbial diversity is very high between healthy individuals. It is therefore impossible to define a typical ‘healthy’ microbiome. In a way, every individual develops his/her own personal set of microbes. The diversity, however, is not totally random and patterns are clearly present in various areas of the body.

Science publishes two reports that contradict the 'arsenic life' story

This is a short follow-up post about the bacteria from Mono lake (California) that allegedly incorporate arsenic instead of phosphorus in their DNA. 

The journal Science just published two papers on the topic. The first report is from Rosie Redfield's lab in Canada, the second from Julia Vorholt's lab in Switzerland. Together, they claim that the arsenic bacteria in fact must have some phosphate to grow, and that arsenic is not incorporated into DNA—thus refuting the main conclusions of the original arsenic bacteria paper.

I only read the abstracts so far, but at first sight it seems to bury the arsenic story for good... It's not that often that we see researchers repeating someone's experiment to challenge it, so Redfield and Vorholt should be praised for the effort.