Archive | June 2015

On correlation and causation

 

Guillaume Filion’s new post in “The grand locus” talks about Bayesian networks and how they can help distinguish correlation from causation, two concepts that are often mistakenly put into the same box.

You can read the whole post for some examples about how and when Bayesian networks can demonstrate causation – and when they can’t. Spoiler: Filion concludes that, as the great statistician George Box said, “all models are wrong, but some are useful”, and that, at the end of the day, experimentation is needed to prove causal relationships.

 

“Without 3D information it is very difficult to understand how the genome works”

Marc A. Marti-Renom is interested in three-dimensional structures. After eight years in the US dedicated to the world of proteins, the biophysicist returned to his native country, first Valencia and then Barcelona, to specialise in RNA and DNA folding. In 2006 he set up his own group, which today is divided between the CNAG, where there are ten people, and the CRG, where there are two. “We do the experimental part, the sample preparation, here in the CRG, and the sequencing and analysis happens in the CNAG”, he explains. For his research he requires a large sequencing and computing capacity, which he can get at the CNAG, the second-most important sequencing analysis centre in Europe. “We are fortunate to be in one of the best places in the world to do these studies,” he says proudly.

3, MARC MARTI RENOM_14_group

 

Proteins with clinical application

Proteins caught his attention while he was doing his PhD, and in 2004, when he was at the University of California (UCSF), he collaborated in the creation of the “Tropical Disease Initiative,” a drug-discovery initiative linking people from both academia and companies to try to reposition drugs in favour of neglected diseases such as malaria and tuberculosis. “The idea was to make it all open source so everything we found was published directly to the web and couldn’t be patented”, says Marti-Renom.

The Structural Genomics group was a major player in one of the first instances that genome sequencing was used at the clinical level. “There was a patient with tuberculosis and a high resistance to antibiotics. We sequenced samples from the patient and found out he was infected by two different strains, and one of them was mutated. When we made models of the protein structure resulting from this mutation we saw how it was affecting the function”, explains the scientist. According to Marti-Renom, in a few years not only will everyone have their genome sequenced, but it will happen several times. “When someone develops a disease like cancer we will sequence them again to see what has changed and why”, he predicts.

Beyond proteins: RNA and DNA

Proteins, the cell’s building blocks, are not the be-all and end-all of life. Since the 1960s we have known that RNA has essential functions other than converting the information in DNA into proteins. But of its three-dimensional structure very little is known, and in the end, the function occurs in 3D. For this reason the group is developing computational tools to incorporate experimental data and make structural predictions.

The most recent biological component to enter the ‘3D world’ was the genome. In this case, too, little is known about how it folds in space. The group of Marti-Renom, along with three other groups at the CRG (Miguel Beato, Guillaume Fillion and Thomas Graf) is carrying out the 4DGenome project, which has a budget of 12.2 million euros, in order to understand the structure of the genome and how it changes over time. “We know the genome sequence very well, thanks to molecular biology and the big genome projects. We also understand the chromosomal macrostructure, thanks to advances in microscopy; but we can’t see the middle ground, the step between the tangled skein and the well-defined chromosome”, says the head of the group. In 2006 they began using Chromosome Conformation Capture (3C) data to develop software that allows you to view the entire genome at high-resolution, a kind of ‘molecular microscope’. With this and other technologies, like Hi-C, and using computational algorithms they have been able to observe how different regions of the same chromosome tend to interact with each other. They have also seen that the 3D ‘photo’ of a moment when, for example, there is high gene expression may be very different to another where the expression is low. “Without this three-dimensional information it is much more difficult to characterise how the genome works”, concludes the researcher.

This article was published by Maruxa Martinez, Scientific Editor, at the El·lipse publication of the PRBB.

Why are we so few? About women in science

we-can-do-it_curie

 

Mar Albà, a PI at the IMIM, one of the centres at the PRBB, has just published in her group’s blog a reflection on the issue of the under-representation of women in permanent academic positions. A topic that has gained new impetus following the recent controversial comments by Tim Hunt.

A rare event which should not be that rare encouraged her to write it. We invite you to read her post entitled “Why are we so few?” and to reflect on this, sadly, still current topic.

 

You can read a related interview to Joan Steitz (Yale) published in the PRBB’s magainze El·lipse and in this blog here.

Interdisciplinary conference on neural engineering at the PRBB this September

Next 21-23 September 2015 an International Conference on System Level Approaches to Neural Engineering (ICSLANE) will take place at the PRBB. Organised by the Neural Engineering Transformative Technologies (NETT) Consortium, the conference presents an outstanding list of invited speakers.

Maciek Jedynak and Alessandro Barardi, both research fellows at the Jordi Garcia-Ojalvo group (CEXS-UPF), and local organisers of this exciting conference, tell us a bit more about it.

brain

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Neural Engineering is an inherently new discipline that brings together engineering, physics, neuroscience and mathematics to design and develop brain-computer interface systems, cognitive computers and neural prosthetics. Neural Engineering Transformative Technologies (NETT) is a Europe-wide consortium of 18 universities, research institutes and private companies. NETT consortium announces registration for this event is now open, and introduces a remarkable list of prominent Invited Speakers with Keynote Lecturers:

  • Eugene Izhikevich– a Co-Founder, Chairman and CEO of the cutting edge technology company Brain Corporation, located in San Diego, USA. The company’s mission is to design, produce and bring to everyday life intelligent machines equipped with the first-in-the-world operating system based on learning: BrainOS. He is also a former scientist well known for his rich contributions to the mathematical theory of dynamics of spiking neurons.
  • Nikos Logothetis– a pioneer in engaging fMRI measurements to neuronal activity studies, director of the department of Physiology of Cognitive Processes at the Max Planck Institute for Biological Cybernetics in Germany. His current research is focused on neural mechanisms of perception and object recognition. It involves a wide variety of brain imaging techniques, which allow to gather and consolidate data from different domains of neuronal activity.

The aim of this conference is to bring together theoretical and experimental neuroscientists and roboticists to discuss the state of the art in the field of Neural Engineering. This three-day long event will also provide young researchers with the opportunity to present their work.

The full list of confirmed speakers, divided into five different theme panels is:

Day 1

Brain-on-chip – engineering of neuronal circuits in-vitro with emphasis on microfluidics
Albert Folch – Department of Bioengineering, University of Washington, Seattle, WA, USA
Thibault Honegger – Laboratoire des Technologies de la Microelectronique, CNRS-CEA, Grenoble, France
Yoonkey Nam – Department for Bio and Brain Engineering, KAIST, South Korea

Optical neurotechnology Methodology – imaging and engineering techniques that allow recording of neuronal activity
Amanda Foust – Neural Coding Laboratory, Imperial College London, London, UK
Fritjof Helmchen – Brain Research Institute, University of Zürich, Zürich, Switzerland
Adam Packer – Department of Neuroscience, Physiology and Pharmacology, University College London, London, UK
Eftychios Pnevmatikakis – Department of Statistics and Center for Theoretical Neuroscience, Columbia University, New York, NY, USA

Day 2

Neural Dynamics – mathematical description of neuronal activity
Viktor Jirsa – Institut de Neurosciences des Systèmes, Marseille, France
David Liley – Swinburne University of Technology, Melbourne, Australia
Benjamin Lindner – Bernstein Center for Computational Neuroscience, Berlin, Germany
John Terry – College of Engineering, Mathematics and Physical Sciences, University of Exeter, UK

Neural learning and control – motion planning, controlling and learning neuro-inspired techniques for robotics
Dario Farina – Bernstein Center for Computational Neuroscience, Göttingen, Germany
Sami Haddadin – Institute of Automatic Control, Hannover, Germany
Alexandre Pouget – CMU, Geneva, Switzerland
Gregor Schöner – Institut für Neuroinformatik, Ruhr-Universität Bochum, Germany
Reza Shadmehr – John Hopkins University, Baltimore, MD, USA
Patrick van der Smagt – BRML labs, TUM, Germany

Day 3

Neural Coding – investigation of neuronal strategies for encoding information
Andre Bastos – The Picower Institute for Learning & Memory at MIT, Boston, MA, USA
Romain Brette – Institut de la Vision, Paris, France
Sophie Deneve – Laboratoire de Neurosciences Cognitives, LNC, Paris, France
Kenneth Harris – Institute of Neurology and the Department of Physiology, Pharmacology and Neuroscience, UCL, London, UK
Stefano Panzeri – Neural Computation Lab, IIT, Rovereto, Italy
Jan Schnupp – Auditory Neuroscience Group, Oxford, UK

 

REGISTRATION

We invite you to submit poster abstracts and apply for contributed talks. We introduced a one-day participation option: now you can attend one day of the conference for 80 Euros. The cost of participation in the whole event is 200 Euros (plus 50 Euros for optional conference dinner).

There is a 50% fee reduction for students who will present posters. Registration is available on the event’s on the registration form and all necessary information is on the event’s website. The registration deadline is on June 20th, so hurry up!!

 

“Being in the minority is part of the problem”, Joan Steitz (Yale University and HHMI)

6, Joan Steitz

Joan Steitz, professor of molecular biophysics and biochemistry at Yale University and the Howard Hughes Medical Institute, came to Barcelona in January 2015 to participate in the CRG faculty retreat. Considered one of the founders in the field of RNA biology and world-renowned for her many seminal contributions, she is also a prominent activist, promoting scientific careers for women. Mother to a son who followed in her footsteps and wife to a Nobel Prize winner, during her stay at the PRBB she gave a talk about her research into non-coding RNAs and participated in a round table about women in science.

Is science a particularly sexist field?

Not really. I would say it’s comparable to law, finances… all high-pressure and competitive professions seem to have the same problem! Actually, a recent issue of Science shows that the most sexist fields seem to be those which people think you need to be a genius to work in – like physics, and even philosophy! Within science, the biosciences are typically viewed as the most gender-balanced.

When you started, there were virtually no female role models in research… how did that affect you?

Well, as student and even a postdoc, it didn’t even enter my mind that I would become a group leader! I was shocked when I had a job offer. Molecular biology was a new field and there were hardly any US universities that had molecular biologists, so that helped. But I didn’t feel prepared for it at all! However, I always like to rise to challenges and I thought if someone can do it, why not me? But it was scary. There were only a couple of other women at Yale at the time.

Have you ever experienced discrimination due to your gender?

I have seen terrible things happen to others but I have only experienced minor issues. Probably like a lot of women in my generation, I feel I’ve been very lucky and escaped major discrimination.

How has the situation improved over the last 20 years?

Things haven’t changed enough, but they have changed incredibly! There used to be very overt discriminatory comments. Now everyone is more sensitised and these things are not said overtly – that doesn’t mean they are not said in private, at dinner tables, for example. And women still get paid less than men for the same job. So we’re still not there.

What can be done and who should do it?

All we have to do is increase the number of women in science, because being in the minority is definitely not helpful; it’s part of the problem! I don’t know how to do that, though. But changes should come from the top. I’ve seen things improving with a new director, only to go backwards again with another. Also, funding agencies and governments should collect information about the percentages of women applying for and getting grants, make it public, give it to people who are taking the decisions, use it to compare over time and see how things are changing. We need to keep an eye on this.

Some countries are better than others…

A good example is the “120% support grant” in Switzerland. A female researcher who has a small child can choose to work part-time and have a 20% reduction in her salary. She then receives 40% of her salary from the government, which she can use for hiring someone to help in her research, or for child care.

Any advice?

There are implicit bias tests which have uncovered really impressive things. You don’t realise how biased you yourself are and how subject to stereotypes until you do the tests. So, I would suggest all researchers do them and reflect on their own attitudes! Maybe part of the change can come from within.

 

This interview was published by Maruxa Martínez-Campos in the March 2015 edition of El·lipse, the monthly newspaper of the PRBB

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