Turning peer review upside down

We recently hosted Mark Patterson, Executive Director of eLife, as part of the Science & Society Program at EMBL Rome. In case you’re not familiar with eLife, it’s a journal supported by four major Life Science research funding bodies: the Howard Hughes Medical Institute, Wellcome, the Max-Planck Society, and the Wallenberg Foundation, with a mission to explore a more responsible selective peer review system. It’s been a surprising success. Although eLife follows DORA guidelines and formally asked not to be listed by Thompson Reuters, the ascribed Impact Factor is already 7.9. It is widely regarded as a top journal in the Life Sciences on par with the Nature specialty series.

Mark Patterson is Executive Director of eLife

As promised, eLife has been experimenting, and the highlight of Mark’s talk were the results of a recent trial in which they turned peer review upside down (see this paper from Bodo Stern and Erin O’Shea for the origins of the trial). For a limited time, manuscripts sent to eLife were accepted BEFORE being sent out for review. Sounds crazy – I know. No need to respond to the reviews if you don’t like them – your paper is already accepted! The hitch, however…

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EMBL Rome 20th Anniversary – Name that Beer Contest!

EMBL Rome is celebrating its first 20 years on 8 July 2019. As part of the celebration, I am brewing a large batch of beer in collaboration with Valentino at Pork’N’Roll, a Roman brewpub. We will be brewing this beer at the award winning Italian brewery, Mukkeller. The beer will be served at the anniversary party July 8 and hopefully you will be taking some home as well. It’s a Belgian Pale Ale featuring light spiciness and a twist of lemon for freshness on a hot summer day. How can you be part of this? You can help name the beer! The contest is open to current staff or anyone who previously worked at EMBL Rome. To participate send an email with your name, when you worked at EMBL Rome, and your suggested beer name. Keep in mind that the name needs to fit nicely on a bottle label.

—- Entries are due by 17:00 on May 10 —-

The following week all staff and participants will be asked to vote for their favorite entry. What’s in it for the winner? 1) Your name featured on the EMBL Rome 20th Anniversary Beer label (pretty cool!), 2) special prize to be determined (might be way more cool?). Get your entries in now!

Stunning science: Neurons that control defence

By Irene Ayuso Jimeno

This video shows neurons (in green) that control instinctive behaviours such as defence. They are located in the periaqueductal grey or PAG: an area in the midbrain with an important role in behavioural responses to stressors like threats or pain.

Credit: Irene Ayuso Jimeno (Gross group) / EMBL

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On big data in biology

by Nicolas Descostes

In recent years, big data is a term that invaded the media and that the public has been exposed to. From finance to social networks, data are collected to infer trends and sometimes to manipulate opinions as it has been observed during recent elections. However, the public is less aware of the big data revolution that is occurring in biology. In this post, I would like to begin by explaining how big data is used in biology, and more specifically in genomics, and end by sharing some thoughts on how big data is currently shaping research.

In the early 2000’s, a battle opposed J. Craig Venter and the International Human Genome Sequencing Consortium to publish the first sequencing data of the human genome. The race produced two articles published in Science and Nature but more importantly, opened an intellectual revolution giving new possibilities to explore the 3 billion base-pair DNA sequence of the human genome in its entirety. Even if sequencing was used a long time before, sequencing the human genome opened the door to sequencing the genome of many other species. Continue reading “On big data in biology”

Staying up to date and organised with scientific literature

By Santiago Rompani

Biological research has never been more vibrant and interesting, but the flipside is an ever-increasing number of studies to keep track of. Gone are the days when the ponderous intellectual could leaf through the latest journals while twirling a goblet of brandy or smouldering pipe. Therefore, I had to come up with other ways to keep up with the scientific literature.

The first is to spend a few minutes to learn how pubmed searches work, watch a tutorial here. Then register for “My NCBI”, which is free and allows you to setup automated pubmed searches and have the website output any new results every day via email. I have searches setup for specific scientists I wish follow, like “gross cornelius[Author]” (use without the quotation marks). I also have more complex searches for keywords in particular journals such as “(Lateral Geniculate) AND (“Nature”[Journal] OR “Science (New York, N.Y.)”[Journal] OR “elife”[Journal])” (the list of journals in my actual search is very long, again, don’t include the quotation marks, but keep the square brackets).

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Taste is King

Jim Sawitzke running Beer 101

We recently had out first Beer 101 course for staff members. International beer judge and Head of our Genetic and Viral Engineering Facility, Jim Sawitzke, first challenged us to a blind tasting and then a tour of major beer varieties. Take home messages were: “if you like it, it’s a good beer” and “if it doesn’t come in a brown bottle, it’s skunked!” – which left me wondering why I kind of like Heineken. Apparently Heineken tried to change their green bottle color at some point, but were forced to relent by popular demand. Find a scientific explanation for the skunk effect here. The tour ended with us sipping beers with names like ‘Arrogant Bastard Ale’ and ‘Rauchbier’ (trans. Smoke Beer) – both dreadful! Unless of course you’re at the higher levels of beer appreciation. Can’t wait for the advanced course.

Here’s why I became a neuroscientist

Brains come in all colours (Timm staining of mouse hippocampus with Warhol colouring; T. Ferreira, E. Audero, EMBL)

An intern in my lab recently asked me why I became a neuroscientist – he had read this piece about how it’s all just luck. I’m not so sure. I am convinced there are explicit and hidden environmental (and a few genetic) influences that restrict and channel our behaviours during our lifetime. It’s only the fiercely independent that escape these influences – and then that is usually itself a reaction to them.

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Why is Epigenetics so sexy? And other related questions.

Giuseppe Testa

By Sara Formichetti

When I was asked to write a post about the last Science & Society talk we had at our EMBL site in Rome I was particularly excited. Science & Society lectures are all about the impact of science on society and the speakers work in fields that are of utmost relevance to the public – but often misunderstood.

Most recently, Giuseppe Testa spoke at EMBL Rome. Testa works on epigenetic regulation, cell reprogramming and disease models. His talk dealt with the impact of epigenetics on society, which is a concern for all of us working at EMBL Rome, considering that we recently chose to rename our unit “Epigenetics and Neurobiology” to focus the interests of new group leaders in these two fields.

Continue reading “Why is Epigenetics so sexy? And other related questions.”

Lab Olympics anyone?

Here at EMBL Rome we aspire to scientific excellence. This means insightful ideas, hard work, state-of-the-art facilities and perhaps a touch of luck. Occasionally, we like to blow off steam too, and the recent ‘Lab Olympics’ was a light-hearted excuse for the EMBL Rome groups to test their labcraft against one another. Including such classics as the Lab-bench race, Pasteur blow football, and of course the mind-boggling Chocolate-balls and a tape measure game, the evening fanfare was fun, a chance to interact, and fuelled by a freshly brewed batch of IPA from EMBL Rome brewmeister Jim Sawitzke.

The now annual Lab Olympics is spun out of an event organised last year by our lab to celebrate our arrival at EMBL Rome. Each lab enters a team of four people (preferably including a group leader) and then rotate around a series of loosely scientific-based games. Outstanding performances this year included the Asari lab in the Neuroepigenetics speed pictionary, the Hackett lab in the Lab-benchrelay, and finally a spectacular score by the Heppanstall lab/FACS facility in the Chocolate-balls and a tape measure game.

The Asari Lab with the 2018 Lab Olympics Trophy

Naturally, the evening had a theme, this year being the World Cup, with EMBL Rome bedecked in flags and international football colours. Of course, any respectable EMBL social has a best dressed and the Lab Olympics was no exception, with costumes reflecting an international culture/figure. There were some remarkable efforts including a full Mexican mariachi band, full Viking, and Napoleon complete with inflatable horse. The winning effort however was King Louis XIV (well done Violetta!). Which leads to the final question, who took the Lab Olympics crown this year. Well, once the scores were totted up and the dust had settled, and after an impressive performance, the victors were… the Asari Lab. Congratulations!

Fortunately, on hand was Sean Sawitzke, who made a great film about the evening, which you can find below.

 

Bitter about Brexit?

 

The author about to do the hard work of taste testing his latest creation – “Still bitter about Brexit”.

As the “official” beer producer for EMBL Rome, I have a demanding job, one that I take nearly as seriously as my real job as Head of Genetic and Viral Engineering. I started producing homemade beer over 25 years ago. I have won many competitions and brewed my recipes in multiple brewpubs to be sold. Along the way, I have become an international beer judge and educator and am always happy to discuss beer with anyone. In fact, it is one of my favorite things to do! Hopefully, in the near future, I will hold some of my beer appreciation courses here at EMBL Rome. Believe it or not, you are all beer judges and I can prove it to you in my course! Continue reading “Bitter about Brexit?”