Conference on quantitative principles in biology at EMBL

I just returned from a conference with the title ‘Quantitative Principles in Biology’ at EMBL in Heidelberg. There was quite a lot of ‘philosophical’ discussion there about the meaning attached by different people to the word ‘model’ and the roles of experiment and theory in making scientific progress, in particular in biology. The main emphasis of the conference was on specific scientific results and I will mention a few of them below. In general I noticed a rather strong influence of physics at this conference. In particular, ideas from statistical physics came up repeatedly. I also met several people who had moved their research area to biology from physics, for instance string theory. I was happy that the research field of immunology was very well represented at the conference and that Jeremy Gunawardena said to me that he believes that immunology is one area of biology where mathematics has a lot to contribute to biology.

In a talk of Susanna Manrubia I learned about a class of biological systems I had never heard of before. These are the so-called multipartite viruses. In this type of system a genome is distributed between two or more virus particles. To allow the production of new viruses in a cell it must be infected with all the components. The talk described experiments in which this type of system was made to evolve in the laboratory. They start with foot and mouth virus in a situation where infection takes place with very high frequency. This is followed through many generations. It was found that in this context a bipartite virus could evolve from a normal virus. This did not involve an intermediate situation where (as in influenza) a virus has several segments of genetic material in a single virus particles. When the bipartite virus was propagated in isolation under circumstances where the frequency of infection was much lower it evolved back to the ordinary virus state. There exists a large variety of multipartite viruses in nature. They seem to be most common in plants (where apparently multiple virus infections are very common) but are also found in other organisms, including animals.

I had a poster at the conference on my work on T cell activation with Eduardo Sontag. To my surprise Paul Francois, on whose results this work built, was at the conference and so I had the chance to discuss these things with him. In our work there is a strong focus on the T cell receptor and at the conference there were several other contributions related to the modelling of other receptors. Eugenia Lyaschenko talked about how receptors can sense relative levels of ligand concentration and how endocytosis plays a role in this. Nikolas Schnellbächer had a poster on the theme of how dimerization of receptors can lead to major qualitative changes in their response functions. There are also important differences between homo- and heterodimers. I learned something about the mechanisms which play a role there. Yaron Antebi talked about the dynamical significance of a situation where several related ligands can bind to several related receptors.

Turing instabilities came up repeatedly at the meeting and were getting positive comments. One ‘take-home message’ for me was that the usual story that a Turing instability requires different diffusion constants should be weakened. It is based on the analysis of a system with two components and as soon as there are more than two components no such clear statement can be made. In addition, taking into account cell growth can help to trigger Turing instabilities.

A talk by Pieter Rein ten Wolde deepened my understanding of circadian clocks in cyanobacteria. They have a clock on a post-translational level involving phosphorylations of the KaiABC proteins and also a clock which involves translation. In the talk it was explained how the bacterium needs both of these for its time-keeping. A key point is that the period of the oscillator defining the clock (around 24 hours) can be longer than the period of the cell cycle. Thus this is like a clock which can continue to tick while it is being disassembled into its constituent parts and put together again.

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