SystemsX.ch Newsletter #17
17
March 2009
-Letter
SySTEMSX.Ch MEETS EU how wE TAkE DECiSionS kEySTonE MEETinG
In Brussels, SystemsX.ch met «Neurochoice» wants to SystemsX.ch scientists at
Robert Jan-Smits, research discover how mice and men Keystone Symposium in
director of the EU. 02 make their decisions. 04 Breckenridge. 06
Charles Darwin and
Albert Einstein
Thomas Müller, head of
communication
Charles Darwin is known to be
one of the most important scien-
tist of all times. In 2009 we celeb-
rate the 200th anniversary of his
birth, and for this reason we will
present some of his citations in
the X-Letters throughout the
year. After Darwin, only Albert
Einstein reached similar promi-
nence. Below is a small compari-
son between the two geniuses.
Darwin assessed a huge
amount of data through which
19 Research, Technology and Development projects have been proposed. Photo Christian Flierl he concluded the variation
and selection principles al-
lowing evolution. He was con-
Second Call generates 57 Proposals for
scious that his discoveries
would displease mankind. This
SystemsX.ch Projects
was one reason he delayed
the publication of his theory.
Einstein, on the other hand,
Thomas Müller lion Swiss francs. This round of research pro- did not discover principles, but
Zurich. The Second Call for SystemsX.ch motion focuses on the development of new elaborated on them. The spe-
projects resulted in 57 proposals, 25 less technologies for Systems Biology and on proj- cial relativity theory is based
than last year. The deadline was midnight ects at the interfaces of biomedical research, on a single assumption and one
January 15, 2009. as well as genomics. measurement: physical laws are
19 Research, Technology and Development In addition, 22 proposals for Interdisciplin- valid everywhere, and: the speed
(RTD) Project proposals from eight different ary PhD Projects (IPhD) and 16 applications of light is finite. As a result, Ein-
hosting institutions were submitted. For this for Interdisciplinary Pilot Projects (IPP) were stein revolutionized the notion
Call, SystemsX.ch plans to fund about five to submitted. A variety of the SystemsX.ch part- of time and space. Furthermore,
six RTD projects with up to 28 Million Swiss ner institutions, as well as the Systems Biol- Einstein’s discoveries had a se-
francs. The institutions of the supported sci- ogy disciplines are represented. rious consequence. The atomic
entists will be required to contribute at least Proposals for RTDs and IPhDs are evalu- bomb was developed by applying
the same amount, summing up to a total re- ated by an international review panel of his special theory of relativity
source volume for research of about 60 mil- continued on page 2 and his famous formula E=mc2.
2 March 2009 SystemsX.ch Newsletter #17
continuation from page 1 SystemsX.ch introduced to the EU
Commission in Brussels
the Swiss National Science
Foundation, whereas IPPs
are subject to approval by
the SystemsX.ch’s Scientific
Executive Board.
Start in Summer
A preliminary decision
about the approval of proj-
ects will be made in the
beginning of May 2009. Sub-
sequently, the SystemsX.ch
Board of Directors will meet
to make final decisions on
the RTD-projects based on
the commitments about
each institution’s own con-
tributions. The final ap-
proval of all RTD-, IPhD-,
and IPP-projects will hence
be given by the end of June.
The approved projects are
expected to start in the sec- Ruedi Aebersold, Daniel Vonder Mühll and Robert-Jan Smits of the Commission in Brussels. Photo: SwissCore
ond half of 2009.
Thomas Marty* Board, Prof. Ruedi Aebersold and its Man-
Brussels. Robert-Jan Smits, director of aging Director, Dr. Daniel Vonder Mühll.
SystemsX.ch's the Research General Management of the Robert-Jan Smits presented the European
Scientists portrayed European Commission, coordination initiative for na-
recognizes similarities tional Systems Biology pro-
Zurich. The book and short between the set up of grams (ERA-net Erasysbio).
film «SCIENCEsuisse» take us research initiatives in In regards to the industry par-
into the fascinating World Switzerland and the EU. ticipation, the speakers see these
of Science. Twenty five re- Since both Switzerland kind of initiatives as a strategy
searchers from different and the EU function to attract contribution money
disciplines are portrayed, under federal systems, into those research areas hardly
offering us a broad view of one could compare the invested in by the industry due
the science platform in Swit- «Joint Programming» of to market volatility.
zerland. SystemsX.ch's mem- the EU with the Swiss Financing propelled by fed-
bers, Denis Duboule, Laurent Program structure. This eral programs could help to de-
Keller and ex-member Susan discussion took place in a briefing at Swiss- velop a market potential in specific fields.
Gasser are among the por- core, the Swiss office for Science in Brus- SystemsX.ch also strives for a closer involve-
trayed scientists. thm sels, where SystemsX.ch was introduced by ment with the industry.
www.sf.tv/sf1/sciencesuisse/index.php the Chairman of the Scientific Executive *Thomas Marty is the European consultant at SwissCore.
Systems Biology at the «Café Scientifique»
Basel. Recently, one of the sessions Institute in Basel, as well as Prof. engineering biology. The most striking
of the «Café Scientifique» in Basel was Markus Affolter from the Biozentrum definition comes from Prof. Affolter:
dedicated to Systems Biology. Speakers of the University of Basel. «Systems Biology is the sum of all pos-
of the event, as stated by Marcel Falk in «We want to simulate life inside the sibilities to understand life». What in-
the Science Journalism Blog «science- computer», this is how Prof. Hafen de- terests him is how a three dimensional
sofa», were some of the SystemsX.ch re- scribes the objective of systems biolo- form can emerge from a linear genome
searchers, including Prof. Ernst Hafen gists. In order to do that we must un- code. When asked by the public if living
from the Institute of Molecular Sys- derstand the operating system of life, creatures are machines, what remains
tems Biology from the ETH Zurich, which luckily is a more reliable oper- of the long explanations was: In reality
Prof. Susan Gasser, ex -member of the ating system than Windows. Accord- yes, only very complicated machines,
SystemsX.ch Scientific Executive Board ing to Prof. Gasser, it is about turning capable of reproducing themselves. thm
and Director of the Friedrich Miescher descriptive biology into some kind of See also: http://www.sciencesofa.info/
SystemsX.ch Newsletter #17 March 2009 3
PRAiSE AnD honoRS
Peter kunszt named Project Manager
Ernst Fehr
for IT-Backbone of SystemsX.ch Zurich. The economist Ernst
Fehr from the University of
that is able to integrate the CSCS, the Swiss National Zurich received the Benoist-
data gathered from the vari- Supercomputing Center Prize 2008 in the value of
ous SystemsX.ch projects. in Manno, Ticino. Kun- 100’000 Swiss francs. Ernst
Managing and leveraging szt’s background in physics, Fehr (SystemsX.ch Project
the data, and coordinating mathematics, and chemistry «Neurochoice«) has been
the specific needs across (from the University of Bern) awarded for bringing to evi-
the various projects and offers him the necessary ex- dence that the decision-mak-
SystemsX.ch institutions in posure to interdisciplinarity. ing behavior on economic
Switzerland constitutes the Additionally, the languag- matters in humans does not
biggest challenge in Peter es he masters (German, follow self-sufficient interests,
Kunszt’s new role. Hungarian, English, French, but rather ponders on justice
Kunszt has several years Italian, and Spanish) repre- and mutual benefit. thm
Peter Kunszt: the data guru. of experience in leading sent an asset in this func-
application and service de- tion, where interpersonal Michael hall
Zurich. Peter Kunszt will be velopment projects and in communication skills in di- Basel. Michael N. Hall, Pro-
the new Project Manager for providing support for op- verse linguistic and cultural fessor for Biochemistry at the
SyBIT, the SystemsX.ch IT- erations in complex distrib- geographies are as impor- Biozentrum of the University
Backbone. This challenging uted infrastructures. From tant as Information Tech- of Basel received the Louis-
position focuses on build- 2001 to 2006, he was a staff nology excellence. Peter Jeantet-Prize for Medicine
ing with adequate hardware member at CERN in Geneva. Kunszt will be based at the 2009. The Louis-Jeantet-Foun-
and software support a co- Since February 2006 Kun- SystemsX.ch Management dation honors Hall (Project
herent IT storage universe szt has been working at the Office in Zurich. NET «YeastX») for his research on
the fundamental mecha-
nisms in cell growth. thm
Mainly Positive new members of the SystemsX.ch
Survey Results Scientific Executive Board elected Philipp Gerber
Zurich. Philipp Gerber,
Zurich. The SystemsX.ch Swartz has been a professor postdoc in the groups of
communication team would at EPFL since 2003. She will Wilhelm Krek and Giatgen
like to thank those who re- replace Prof. Demetri Psaltis Spinas («LiverX»), received
sponded to the survey, and of EPF Lausanne in the SEB. the Servier Forschungspreis
offer you a summary of Mihaela Zavolan is Asso- (Servier Research Prize) 2008
the results. Overall the re- ciate Professor in the Com- from the Swiss Society for
sponse was positive, with putational and Systems Bi- Endocrinology and Diabetol-
the majority of responders Melody Swartz and Mihaela Zavolan ology Core Program of the ogy for his clinical research
satisfied with the Website Biozentrum, University of on islet transplantation. thm
and the X-Letter. Some read- Zurich. The Board of Direc- Basel, and she leads a group
ers criticized the French tors approved Prof. Mihaela at the Swiss Institute of Bio-
translation of the X-Letter. Zavolan and Prof. Melody informatics SIB-ISB. Through Thomas Müller stays
To tackle this problem we Swartz as new members a combination of compu- at SystemsX.ch
have changed translation of the Scientific Executive tational and experimental
office, and hope that our Board. approaches, her group aims Zurich. Until further notice,
French readers will find the Melody Swartz is Associ- to understand the impact of Thomas Müller will main-
new translation up to their ate Professor in the Insti- miRNAs and RNA-binding tain his 20 percent assign-
linguistic expectation. NET tutes of Bioengineering and proteins on the expression ment as the head of commu-
Chemistry & Chemical Engi- of target genes. These fac- nications of SystemsX.ch.
neering at the EPF Lausanne. tors have been shown to The Neue Zürcher Zeitung
Her research concentrates play important roles in cell decided to recall the posi-
on lymphatic bioengineer- division and differentiation, tion they had offered him as
ing, integrating physiology, development, metabolism, the head of the scientific sec-
transport functions, and bi- and immune responses. tion shortly before he could
ology of the lymphatic sys- She will replace Prof. Susan assume office on January
tem with interdisciplinary Gasser from the Friedrich 1st. The reason given for the
approaches. The two key foci Miescher Institute in Basel withdrawal was the massive
areas are cancer metastasis who served on the Scientific advertisement collapse since
and immune cell trafficking. Executive Board. AK October 2008. thm
4 March 2009 SystemsX.ch Newsletter #17
humans and Brains decide collectively.
The project «Neurochoice» searches for decision patterns
all the way from synapses to financial experts.
Project leader Fritjof Helmchen is building a laboratory with microscopes capable of showing decision-making processes in mice brains. Photo thm
Thomas Müller Helmchen heads «Neurochoice» and each other.», says Helmchen. Behind
Zurich. The current financial crisis – months before the financial crisis this idea lingers the hypothesis that,
was, and continues to be, the conse- erupted – joined forces with Professor although mice and men make very
quence of a collective shortcoming of Ernst Fehr, Director of the University’s different decisions, those decisions
brokers and managers positioned at Institute for Empirical Research in take place in the same or at least simi-
different stages in a commercializa- Economics. Fehr is a co-founder of the lar brain structures.
tion chain and who repeatedly took discipline neuroeconomics and has Typically, various brain areas work
the same decisions. Most likely, the been studying the neurobiological together to make a decision and take
financial crisis will continue to keep fundamentals of individual decision- an act of volition. A network of thou-
economists busy for years, if not de- making and social behavior for over sands of neurons clarifies each aspect
cades. However, they are not alone ten years. of the decision – for example, the risk
this time. In SystemsX.ch, biologists, calculation. Neurons are, to some ex-
economists, physicians and mathe- Are humans overtaxed? tend, network processors connected
maticians work together to find the It is known that humans use the with thousands of other neurons.
neuronal correlates responsible for same brain areas to assess expected These connection junctions, called
collective decision-making. «Neuro- reward as to rely on sensorial percep- synapses, represent the elementary
choice» is the title of the ambitious tion and to gauge potential risk. From layer of the brain structure and func-
research project launched last fall an evolutionary point of view, new fi- tion. What stands out on closer exam-
by nine research groups at five Uni- nancial risks differ gravely from the ination of the decision-making layers:
versities. traditional perception-risks, there- the work is always done collectively.
«Yes, one can expect to find evi- fore it is questionable if humans are
dence that the decision-making pat- well equipped to judge financial risks The origin of addiction
tern leading to a financial crisis is properly, or if they are fundamentally The synaptic clefts at a specific re-
represented in the brain.», says Profes- overtaxed. gion of the middle brain is the scope
sor Fritjof Helmchen from the Brain «To answer questions like this, we of an additional part of the socially
Research Institute of the University plan to do experiments with mice relevant project «Neurochoice». In or-
of Zurich. Physicist and physician and men, which we can compare to der to gain a short-term reward, drug
SystemsX.ch Newsletter #17 March 2009 5
addicts hazard the consequences of the University of Bern, will try to de- to find respective models. It would be
long-term damages. Christian Lüscher, scribe the biochemistry of substance interesting to know if such patterns
Professor at the Department of Basic abusing behavior through mathemati- also appear in decisions which are
Neurosciences of the University of Ge- cal models. Thus, addiction can ei- commonly not considered to be relat-
neva wants to discover how does «ad- ther be an exaggerated valuation of a ed to addiction – such as, for example,
diction» manifest itself in the brain. small, short-term kick, or a suppres- society's «indulgence» in fossil fuels
Among other things, he wants to ex- sion of a larger, long-term damage. consumption in the view of the global
amine the behavior of mice under the Which mechanism is at stake, from a climate problem.
effect of cocaine when weighing be- brain physiology point of view, is still This line of reasoning is, no doubt,
tween a small, short-term reward and controversial. Nevertheless, Senn’s a long stretch; nevertheless it is a
a large, long-term reward. The same mathematical models could deter- realistic stretch. The researches of
mechanism applies for various other mine which brain signals need to be «Neurochoice» are convinced that simi-
drugs, such as nicotine, alcohol, mari- observed during experiments to dif- lar decision-making principles exist in
huana, amphetamine and opium. ferentiate between the alternative de- the various layers – from the synapses
The group of Walter Senn, Professor cisions. As for the remaining decision- to the social groups. Helmchen: «We
for Computational Neuroscience at making layers, Senn’s group will try want to discover these principles.»
Filming the brain during decision making
Brain researchers use func- nique is applied to differ-
tional magnetic resonance entiate neurons from other
imaging (fMRI) to observe brain cells. In doing so, the
the brain during activity. group of Fritjof Helmchen
Depending on the task, a will succeed, for the first
specific brain area lights time worldwide, in depict-
up, allowing a map to be ing the activity of hun-
drawn of the activated dreds of neurons in a three
brain regions. dimensional and real-time
Through the use of fMRI, manner (10 images per sec-
the neuroeconomists of ond).
«Neurochoice» will exam- During the «Neurochoice»
ine the interaction between term, the amount of ob-
different brain areas during served neurons will in-
decision-making process- crease, and the image rate
es. However, the neuronal Cube: the network activity of some hundreds of brain cells is measured in will raise to 100 images per
networks located inside a the rate of 10 times per second with the help Square: Dyed neurons and second.
single brain area are more astrocytes Graphic art NET Furthermore, an endo-
difficult to observe. scopic miniature micro-
In this regard, optical methods, they will ing decision-making. scope, which allows ani-
«Neurochoice» will do pio- uncover the activity pat- A combination of a laser mals to move freely while
neering work. By using terns of networks in net- sampling procedure and a carrying it on their heads,
electrophysiological and works of mice and rats dur- sophisticated dyeing tech- will be adopted. thm
«neurochoice» – neuronal Correlates of Collective Decision Making» at a glance
Head Prof. Fritjof Helmchen, Brain Research Institute, University of Zurich
Involved research groups Institute for Empirical Research in Economics, University of Zurich; Institute
of Pharmacology and Toxicology, University of Zurich; Department of
Physiology, University of Bern; Swiss Finance Institute; Brain Mind Institute,
EPF Lausanne; Department Basic Neurosciences, University of Geneva.
Number of research groups 18
Researchers : Administration 30:2
Biologist : Non-biologists 3:1
Overall Budget (2008-2011) 14'778'900 Fr., from which SystemsX.ch 5'395'900 Fr.
6 March 2009 SystemsX.ch Newsletter #17
SystemsX.ch at keystone Symposium The Glossary of
SystemsX.ch
Breckenridge. Leading throughput methods profit fluxes in bakers yeast.
scientists of various disci- from recently established Prof. Ernst Hafen (ETHZ) Research, Technology and De-
plines came together at a high quality databases and nicely showed how large- velopment Project (RTD project):
Keystone Symposia end of reliable informatics work scale mutation screens of SystemsX.ch’s flagship project, multi-
January in Breckenridge flows. Furthermore, he drosophila flies with big year duration.
(USA) to discuss research pointed out that research is and small heads are used to
strategies and approaches moving towards structures find specific genes that are interdisciplinary Pilot Project (iPP):
using the -omics technolo- and functional analysis on involved in cell growth. The Research involving risks. One-year
gies available to Systems a whole network level. Prof. quality of the screen was duration.
Biology. Several members demonstrated by success- interdisciplinary Doctorate (iPhD):
of SystemsX.ch were among ful follow up studies on se- Duration of 3 to 4 years.
the approximately 200 in- lected targets. Finally, Prof.
ternational participants Pelkmans demonstrated the Board of Directors (BoD):
and presented their cur- potential of image based SystemsX.ch's highest steering body
rent research projects to RNAi screens to define cell composed of the presidents, rectors
the community. phenotypes and to obtain and directors of all participating
Prof. Ruedi Aebersold clues about virus infection institutions.
from ETH Zurich, scientific and endocytosis. Moreover,
co-organizer and speaker at Uwe Sauer (ETHZ) present- Prof. Christian von Mering Scientific Executive Board (SEB):
the conference, later sum- ed a project about condi- (University of Zurich) pre- Operative committee composed of
marized that many cell tion-specific networks of ac- sented the public available scientists from the participating
biology projects greatly tive metabolic regulation. «Sting» database that allows institutions.
benefit by including -omics It aims at unravelling the every researcher to learn
approaches. He also men- transcriptional regulation about protein-protein inter-
tioned that many emerging processes that control the actions and their functions.
new screening and high- distribution of metabolic Alexander Schmidt & Thomas Bock.
key to future medical breakthroughs is young Bioinformati-
Systems Biology, say European scientists cian Awards iMPRESSUM
Strasbourg. Crucial break- vide a detailed strategy for Lausanne. The Swiss In- Thomas Müller (thm)
throughs in the treatment the application of Systems stitute of Bioinformatics Head Communications
of many common diseases, Biology to medical research has launched the SIB 2009 Tel: +41 61 683 76 77
such as diabetes and Par- in the coming years. Young Bioinformatician Mobile: +41 79 614 06 77
kinson’s, could be achieved This could lead to signifi- Awards. The prizes, assigned Thomas.Mueller@SystemsX.ch
by harnessing a powerful cant advances in the treat- to young scientists in bioin-
scientific approach called ment of disease and help formatics, consist of two cat- Natalia Emery Trindade (NET)
Systems Biology, according with the shrinking pipeline egories: The SIB 2009 Young Assistant Communications
to leading scientists from of pharmaceutical com- Bioinformatician Award and Tel: +41 44 632 02 50
across Europe. In a science panies using traditional the SIB 2009 Best Graduate Fax: +41 44 632 15 64
policy briefing released by reductionist approaches to Paper. Closing date for en- Natalia.Emery@SystemsX.ch
the European Science Foun- drug discovery. thm tries is April 30, 2009. thm
dation, the scientists pro- For more information: www.esf.org For more information: www.isb-sib.ch. Dr. Daniel Vonder Mühll (VDM)
Managing Director
SystemsX.ch
Conferences und Events Tel: +41 44 632 78 88
Daniel.Vondermuehll@SystemsX.ch
March 23 - 25, 2009 Synthetic Biology, Systems Biology and Bioinformatics Cambridge, UK
April 16 - 19, 2009 The 3rd International Biocuration Conference Berlin Postal Adress:
April 19-20, 2009 Molecular Systems Biology of the Cell ISB, Seattle, USA SystemsX.ch
June 10-12, 2009 Computational Systems Biology, WCSB 2009 Århus, Denmark Clausiusstr. 45 - CLP D 7
June 18-19, 2009 Systems Biology of Human Disease 2009 Boston, MA, CH-8092 Zurich
Aug 09 - 12, 2009 Foundations of Systems Biology in Engineering Denver, USA Web: www.SystemsX.ch
Aug 30-Sep 4, 2009 10th International Conference on Systems Biology Stanford, USA
Sep 16-18, 2009 4th International Conf. on Computational Bioengineering Bertinoro, Italy To subscribe or unsubscribe to this
Nov 18, 2009 All-SystemsX.ch-Day 2009 Bern newsletter, please send an email to:
Dec 11-12, 2009 Latest Advances in Drug Discovery Modelling & Informatics Hyderabad Natalia.Emery@SystemsX.ch