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Journal club on the Node

SpotOn London

Posted by on November 20th, 2012

audienceLast week I attended SpotOn London – a conference focused entirely on the role of the Internet on research, science outreach, science policy, tools, and related topics. There were talks about using alternative metrics to asses the value of research papers, discussions about doing outreach while working in the lab, issues related to women in science, workshops about new tools or tips on how to talk to politicians about science. The attendees were all interested in science, but not all of them were researchers. There were people working at tech companies, and writers, and even politicians. It was also a great opportunity to meet people in other fields, and be reminded that everything is different for physicists, for example.

Juggling jobs panelCompared to scientific conferences, SpotOn is much more inclusive. The discussion sessions and workshops were all selected from submitted proposals, but it didn’t matter whether you were a student or a professor, or anyone else – any interesting proposals were assessed at face value. For example, the discussion session about juggling science communication and a research career was proposed and organized by two PhD students (Heather Doran and Jonathan Lawson) and included postdoc and PI panelists who all combine their research life with science communication activities. If you’re interested in this topic, you can watch the entire session here:



Yes, all the talks and discussions were recorded. I also ran one of the discussion sessions, which is somewhat related to the one above. It was on “Stories behind the research” and the panel gave three different perspectives on the role of storytelling in science: Vibhuti Patel works for the Royal Society of Chemistry, a publisher and learned society; Ben Lillie runs The Story Collider, an event/podcast/magazine where people tell stories about science; Anne Osterrieder is half researcher, half science communicator. Between the three of them they covered issues related to finding out what makes a good story, when and where to share what, and why people – researchers as well as others – care about this.

In my intro to the discussion I also showed an example from the Node – this post by Tohru – to show how there can be interesting stories behind a paper that don’t make it into the paper itself, and how you can use blogs (such as the Node) to record those stories where relevant, and even link them to the paper in question. The discussion with the audience was really entertaining (with lots of laughs!), but also informative. There were professional science writers in the audience who said that they had a hard time getting scientists to share more than just the plain basics of the work, and researchers who were reluctant about connecting their work to the human experience of being a researcher. A full report from the “stories behind the research” session can be found on the SpotOn blog and the video is on their media page.

You can find links to all individual session pages (all with video!) here. My summary above is heavily focused on the science communication track and on talks aimed at researchers, because I think that’s what most of you are interested in, but there was a lot more: publishing, crowd-funding research, discovering new tools to manage your lab work, social media at conferences, publishing data, research fraud etc. If any of that sounds interesting, check it out, and come to the conference next year!
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Celebrating stem cells

Posted by on November 1st, 2012

Last month was an exciting one for stem cell research. I’m sure you all saw how stem cells hit international headlines with the announcement of a Nobel Prize for John B. Gurdon and Shinya Yamanaka. I thought you might be interested to read reactions from several leading scientists and check out a film clip about the prize-winning work in our blog on eurostemcell.org

We’ve got a new short film all about reprogramming and iPS cells coming very soon too. Watch out for it going live on our website www.eurostemcell.org at the end of November or early December, in time for the formal Nobel Prize awards ceremony of 10th December.

We were also celebrating in October because it was Stem Cell Awareness day on the 3rd of the month. Researcher Christèle Gonneau helped us celebrate the day by giving us a great window into life as a stem cell biologist on twitter. You can check out a summary of her day’s tweets and pictures in our blog too.

You can keep up to speed on stem cell news and our activities by following @eurostemcell on Twitter or, if Twitter’s not your thing, say hello to us on Facebook or our website.
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Stem Cell Revolutions: A Review

Posted by on July 2nd, 2012

Stem cells are often in the media and are promoted as wonder cells that can solve the problems of most diseases. The stories told throughout this film give the story of stem cells behind the hype and describes the  real state of stem cell research and therapies today as well as what we are aiming for in the future! My first thought after watching Stem Cell Revolutions was: wow, is education supposed to be this entertaining? Although I have been working in the stem cell field for a few years now, I learnt a lot from watching this film so a big personal thank you to the makers of the film- Amy Hardie and Clare Blackburn for producing a documentary that provides such amazing and enthralling insights into the stem cell research field.



Stem Cell Revolutions takes us on a journey that begins with how stem cells were discovered around 50 years ago following  the study of patients in Hiroshima who were suffering from radiation damage. Following research examining the “factory where blood cells are made” , the bone marrow, Canadian scientists Till and McCulloch discovered blood stem cells: the first discovery of stem cells!! The story moves on to the discovery of other adult stem cell populations and the development of therapies for example Howard Green’s work on skin grafts and then onto restoring vision in India using stem cells. This then brings us to possibly the most controversial stem cell category, embryonic stem cells, whose discovery is discussed by Sir Martin Evans, who won the Nobel Prize for medicine in 2007 for his discoveries involving embryonic stem cells.

We then change gears and move on to the fascinating story of  how Professor Shinya Yamanaka’s work in which adult cells e.g. skin cells can be turned into an embryonic stem cell-like state, which as Connie Eaves says “turned our understanding of human development on its head” . The field of iPSC research is a relatively new stem cell field and I think what is great in this section is that we learn that this work had its basis in the cloning work completed in frogs by Sir John Gurdon and the creation of Dolly the Sheep by Sir Ian Wilmut. The ending of the film is led by the interesting question ‘Where Could It Lead?’. I for one am excited by finding out where stem cell research leads us in the next decade. Furthermore, the challenges that the stem cell field faces in terms of restrictions by legislation, ethical issues and current limitations of stem cell technology are all dealt with in a manner that gives the truth behind sensationalism reported in the media.

The stem cell story is told via interviews with many of the key players who work at the cutting edge of stem cell research field from Connie Eaves to Sir Martin Evans and Austin Smith to Shinya Yamanaka, many of whom I have been lucky enough to learn from directly, and whose expertise and inside knowledge provide great strength to this film. Additionally, the documentary really shows of the global nature of stem cell research and how communications across the globe are leading to progression.  However, I believe the real genius in this documentary was the inclusion of acclaimed author Margaret Atwood, who provides a perspective from a non-scientist. I particularly enjoyed the challenging interactions between Margaret Atwood and Professor Austin Smith- director of the Cambridge Stem Cell Institute. Another great highlight is the animations and illustrations along the journey- stem cell biology really comes to life via these means. I have to admit I am not sure of the significance of the dancing man, or why we need to see Austin cycling to/from the institute, though the latter really did make me smile.

Stem Cell Revolutions gives us the current status of stem cell research in a captivating yet easy to digest manner and leads us into what is possible in the future! It is a must see for anyone who wants to learn about stem cell biology. It is amazing to think that many discoveries that lie in wait may be uncovered by a very simple question as posed by Margaret Atwood to describe the origins of both art and science:-“What if?”.
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Biotechnique’s Lab Grammys 2012

Posted by on March 8th, 2012

The Grammy Awards are held every year to celebrate the best of the music industry, however, they seem to miss one crucial catergory - the Science Parody. The Biotechnique’s website has remedied that by having it’s own Lab Grammys for the past two years.

This year’s Grammy was won by Mark Grabiner and his colleagues from the department of Molecular and Cell Biology at Berkeley for a brilliant parody of LCD Soundsystem called “Grad School, I Love You (But You’re Bringing Me Down)”.



Last year’s Science Parody Grammy was won by the Zheng Lab for Bad Project.

The full list of nominees for the 2012 Lab Grammys can be found here.
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Under the microscope

Posted by on February 15th, 2012

Cambridge University Research has recently launched a series of videos called “Under The Microscope”, that showcase some of the microscopic research carried out at the university. Two of the eight videos they’ve published so far have featured developmental biology:



PhD student Matt Benton talking about beetle development.



Research fellow Erica Watson describes mouse development.

The “Under the Microscope” videos are meant for a wider audience, and it’s interesting to read some of the comments the videos get on YouTube, from people who are sometimes only thinking about development for the first time. But I thought even the seasoned developmental biologist might enjoy having a look at them.

Find all the videos on their video and audio page.
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Bio Web Conferences – Critical discussions with developmental biologists for deep learning.

Posted by on February 10th, 2012

Dear Developmental biology community,

I would like to bring to your attention a potentially valuable resource for your teaching and research endeavors.  I am a neurodevelopmental biologist at Smith College.  I started teaching a course in Developmental Biology back in 2005, and since then have been utilizing web conferencing technology to bring the research behind concepts alive in the classroom.  My students have been interacting with leading scientists in the field of developmental biology holding organized Q&A video conferences focused on current and seminal research articles.  I am posting this to the Node as since I started using this pedagogical approach I have been recording these discussions, and with full consent provided, I have established an online repository of these recordings via my lab website.  I have each conference (40 now and growing) organized by topic for ease of searching, and each individual session is further broken down by specific question to facilitate quick access to your greatest interest.

Because these sessions are based on key research papers they are extremely applicable for any teacher or student to use in their own courses as supplemental resources to what is probably the very same topics being covered.  For instance, I often assign my students select conferences to watch to supplement their readings or coverage of the material.  Moreover, in class I will poise certain questions about a topic to my student and after some discussion, click on say, Dr. Cliff Tabin’s response to the similar question.  It provides a new and real perspective to the information that students truly appreciate and fosters long-term retention of the material.

There are also many other positive outcomes to both conducting and watching these conferences.  Namely students gain a very different and revealing perspective of not only where a particular field of Dev Bio is moving, but more personal understandings of who the scientists are and how they got to where they are today.  Listening to these remarkable scientists articulate their thinking process to address the research question is extremely illuminating to the developing scientist in your classroom.

So I invite and encourage you to check out these discussions as I am disseminating them for your benefit and use.  I hope you find them helpful.  Feel free to let me know what you think and, if you like them, how you might use them in your teaching.

“Bio Web Conferences” http://sophia.smith.edu/~mbarresi/lab/biowebconferences.html

Best regards,

Michael J.F. Barresi

P.S. additional post on stem cell documentaries coming….

 
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SDB Collaborative Resources (CoRe) Launched

Posted by on January 27th, 2012

The Society for Developmental Biology (SDB) has launched SDB Collaborative Resources (CoRe), an online collection of images, movies, and diagrams for learning and teaching developmental biology.  SDB CoRe is a free and open website developed to help increase understanding of developmental biology at all levels.




SDB CoRe is easily-searchable and can be browsed by topic, organism, or featured objects.  All objects have short descriptions aimed at helping users learn something about development with glossary words highlighted in green.  Object pages contain references as well as  links to related CoRe objects, links to reviews in the soon-to-be-launched WIREs Developmental Biology, and when relevant, to original research papers in SDB’s official journal Developmental Biology.  All users can create a My CoRe account in order to comment on an object or save it in their favorites.


SDB needs your help in building this community resource!  We are looking for visuals that help explain basic concepts in developmental biology across numerous plant and animal species.  Here are the guidelines for submitting to CoRe.  If you are an SDB member you can login to CoRe with your email address to submit.  Non-members that would like to submit to CoRe please contact me at info@sdbcore.org.  If you have any questions or suggestions for the site please email me as well.  Enjoy SDB CoRe!
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PHD Comics on the big screen

Posted by on November 17th, 2011

The web comic Piled Higher and Deeper (PHD) has been commiserating with graduate students since 1997. And now you can watch the comics come to live on the big screen, as universities and institutes across the world (including Antarctica!) are screening the PHD movie.

Fans of the comic will recognize most of the jokes, but now the individual 3-panel strips have been turned into a full-length movie with a plot that summarizes the main story of the long-running comic. The film was shot in its entirety at the Caltech campus last spring, and all actors are students and staff from Caltech. As they’re by and large professional scientists rather than professional actors, the acting isn’t always very sharp, but they did a great job at bringing the comics to life. The trailer below gives a good indication of the film.

PHD Movie Trailer from PHD Comics on Vimeo.



Most screenings are only open to students from the hosting institution, but I was lucky to hear about an open screening at University College London. Even though the screening was open to absolutely everyone, the lecture theatre was not entirely full. Perhaps it really does appeal specifically to grad students? Nevertheless, the people who did attend seemed to enjoy the film, and laughed at every joke. Even the ones that you could see coming from a mile away if you were familiar with the comics.



But this was not just any screening: it was one of the few that PHD Comics creator Jorge Cham was attending. After the film, science-loving comedian Robin Ince hosted a Q&A with Jorge and with Alex Lockwood - the actress (and graduate student!) who plays the character of Cecilia in the film. Alex initially kept her role in the film a secret from her advisor. “I didn’t tell him I was doing it for a while, but his wife is really nosy on Facebook…” Once he found out, he was a lot more excited about the film than she was – as long as she still got her work done, of course.

Despite being based largely on the existing comic strips, the end of the film breaks a longstanding tradition. In the fourteen years that Piled Higher and Deeper has been running, the main character was never named. In the film, he finally introduces himself. When this came up during the Q&A, Jorge explained why the student didn’t have a name to begin with: “First I was just kind of lazy, but then it became a funny thing. It took my own professor about four years until he learned my name.” But now, wanting to give the film a more interesting resolution, the student gets a name. “I figured it was about time. And I can always deny that it’s not comic-canon, that it’s just movie-canon…”

After the Q&A, we caught up with Jorge and asked him how the film translates to international audiences. It’s set in the US, where PhD degrees can regularly take 5-7 years, and many jokes are based on the fact that graduate school takes forever. My own favourite joke involves Cecilia’s encounter with a high school classmate:



But in the UK, where several universities have now screened the film, PhD degrees are much shorter than in North America. Do the jokes hold up?

“Well I heard that the guitarist from Queen took 35 years to finish his PhD, so I think he pulls up the average,” jokes Jorge, “But I think what translates the most is that feeling of uncertainty, feeling stuck and not being quite sure what you’re going to do next. That’s international.”

Regular readers of the Node may recall that we’ve interviewed Jorge before, and that he mentioned a “biologist character” that would appear in the comic very soon. What is happening with that, we wanted to know. “That’s still coming, but probably not for another year, at least.” Aww. But of course, this is the man who has turned procrastination into a career: Jorge left research several years ago to pursue the comic full time, and to give talks about procrastination to graduate students. To tie in with the various posts we’ve had on the Node about alternative careers, we asked him what he learned in his PhD degree that he still uses today.

“Many things. I think part of what I do as an artist is trying to discover where the truth is - or at least ask the question “where is the truth?” - and being able to think analytically in a big picture sense but also being able to drill down, and work on the minutiae of the details. I think the PhD gives you that kind of macro/micro vision at the same time. But mostly it just gives me the ability to avoid questions…”

If you’d like to see the movie yourself, here is a list of places that are showing it. And if you’re a bit more patient (now there’s something you learn in grad school!) you can wait for the DVD release, tentatively planned for Pi Day (March 14) next year.
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PhD Movie

Posted by on September 26th, 2011

Whether you’re familiar with the web comic or not, most of you will probably recognize your own current or past career as a graduate student in the new PHD Comics movie.

PHD Movie Trailer from PHD Comics on Vimeo.



It’s playing at university campuses across the world. If your city is not on the list, don’t fret: the website contains information on how to organise a screening at your own institute. Now if someone in Cambridge would like to host a screening, I’ll be there!

(See last year’s interview with Jorge Cham on the Node.)
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The Cell – Finalist in the Labby awards – Please vote to help us win.

Posted by on June 16th, 2011

The Cell: An Image Library is honored to be named a finalist in the website Labby Awards. Please help us win this award and vote for us at the site below. Please be patient if the site does not load right away and apologies for cross posting. Please tell your friends to vote for us as well.

http://the-scientist.com/2011/06/15/2011-labby-website-finalists/
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