This week, Cold Spring Harbor Laboratory Press launched bioRxiv, a preprint server for the biological sciences. This is very exciting for those of us who have moved into biology from physics (as well as other quantitative disciplines, such as mathematics and computer science). Scholarly publishing in physics has changed dramatically as a consequence of a service introduced by Paul Ginsparg at Cornell in 1991 that users call the arXiv (see also http://en.wikipedia.org/wiki/ArXiv). Many of us are hoping that bioRxiv will motivate similar changes in biology.
What is a “preprint server” and why are people like me so excited about it? The original arXiv is a website where researchers can post manuscripts for free and without any peer review. Physicists typically post newly written papers directly to the arXiv even before submitting to a journal. The authors benefit from being able to immediately claim priority on their discoveries. The physics community as a whole benefits by being able to read new research without the lengthy delay often caused by the peer review process. And a much larger community of interdisciplinary scholars across the globe benefits from having free access to everything that is posted.
One might worry about the effect such a preprint server would have on the peer-review process. But in the physics community, the arXiv is widely believed to have strengthened the peer-review process. When physicists read an article that makes questionable claims, or is hard to understand, they often just email the authors and (politely) say so. And after the authors have received feedback, either from such emails or from the formal review process at some journal, they will post a revised manuscript.
What about the bad research or pseudoscience that remains on the arXiv? Frankly, people just ignore it. For instance, every weekday morning I get an email from the arXiv listing the abstracts of all the papers that were posted to the q-bio (quantitative biology) section the previous day. Most are not of any interest to me, and not infrequently I see a manuscript that is obviously pseudoscience, but so what? It doesn’t take that long to read the email, and whenever I do see something that might be interesting — either from some author whose research I like, or on a topic I’m interested in — I add it to my reading list.
There has been a lot of hand wringing lately about how to improve scholarly publishing in the biological sciences — how to improve the quality of papers, how to prevent lengthy delays in publishing, how to avoid the unnecessary experiments often asked by reviewers, how to reduce delays in the publication process, how to guarantee free access to research that, after all, was likely paid for by taxpayer dollars. I would argue that physics has already solved this problem: freely accessible preprint servers. This is why I believe the bioRxiv is such an exciting development.
On Monday October 28th, the Cold Spring Harbor Laboratory community filled Grace auditorium to hear noted biologist and author Sean Carroll discuss the role of chance and circumstance in the life of the French scientist Jacques Monod. While many in attendance were familiar with Monod’s Nobel Prize-winning research about how organisms tune their gene expression to respond to the environment, few knew about his prominent and dangerous role as a member of the French resistance in Nazi-occupied France.
In his introduction, James Watson described Monod as biology’s “only true movie star.” Indeed, as Carroll chronicled Monod’s life during WWII, events unfolded like a historical thriller. In early 1940, Monod was an ordinary doctoral student who directed choral groups in his free time. Everything changed with the shocking Nazi occupation, which threatened his family. Monod (a Christian by birth) sent his Jewish wife and children to the countryside and joined one of France’s most militant Resistance groups. As an officer, he carried out covert cross-border missions into neutral Switzerland and orchestrated a network of anti-Nazi saboteurs who operated in the streets of Paris – all the while carrying out biological experiments that laid the groundwork for his 1965 Nobel Prize.
Through firsthand accounts and newly uncovered documents, Carroll discovered just how close Monod came to capture during the war. In his book Brave Genius, Carroll explores how the chance encounters and lucky breaks that carried Monod safely through WWII instilled in him a sense of urgency and purpose that ignited his scientific genius. Monod believed that the most important science could change the way people viewed themselves in relation to the world. The transformative truth he found in Darwin’s theory of evolution and the early discoveries of molecular biology was that humankind is the product of an incalculable number of fortuitous events.
As Carroll’s remarkable story suggests, the same could be said of Monod himself.
The lecture was part of an annual series held in memory of Gavin Borden, the late publisher of the influential Molecular Biology of the Cell textbook. The series is intended to enhance the educational experience of graduate students at Cold Spring Harbor Laboratory and annually includes a roundtable discussion with the visiting Gavin Borden fellow. Carroll, whose research has focused on how genes control animal development as well as the evolution of animal forms, is vice president of science education at the Howard Hughes Medical Institute. He directs initiatives to increase the public’s understanding of science by educating and inspiring its youngest members. You can read more about Brave Genius at here.
Check out this SCIENCE SHORT – “The Social Brain and Autism” – in which postdoctoral researcher Yongsoo Kim, Ph.D., of Associate Professor Pavel Osten’s laboratory helps us understand more about how we are using mice to study behaviors associated with autism. Statistics from the U.S. Centers for Disease Control and Prevention (CDC) identify around 1 in 88 American children as on the autism spectrum –a ten-fold increase in reported cases over the last 40 years.
In the Osten lab, researchers focus on the analysis of brain regions and how brain cells connect and communicate with each other to drive behaviors. This communication between neurons may be disrupted in disorders like autism and schizophrenia. The lab uses the latest technologies to image entire mouse brains and to map brain-wide neuronal activation evoked by various behaviors, including social behavior. Dr. Kim and his CSHL colleagues try to identify the specific cell types in the brain regions involved, and test the role of different cell types and brain regions in mediating specific aspects of the behaviors. The goal is to identify targets for therapeutic development.
Congratulations to Yongsoo, recent winner of a coveted NARSAD Young Investigator Award, which he will use to pursue research on the hormone oxytocin in a mouse model of autism. Because oxytocin has been associated with certain behaviors including social recognition, bonding, anxiety and maternal behaviors, it is sometimes referred to as the “bonding hormone.” Yongsoo is looking at which brain regions respond to doses of intranasal oxytocin, and how administration of this hormone alters brain activity in response to social stimulation. Read more about the award here.
About SCIENCE SHORTS: Each short talk of approximately 5 minutes explores a topic or area of research at CSHL. They were designed for non-scientific audience and given by a CSHL Ph.D. student or postdoc. So far we have covered the question “Why haven’t we cured cancer yet?“; the beautiful imagery generated by the important scientific technique of florescence microscopy; and, how protein structures are determined using “molecular photography.”
A 3-D Diagram of a new microscopic technique which shows every brain cell within a mouse's brain. Image taken from video.
Instructors and participants of the single cell analysis course at CSHL, June 2013.
In June I had the chance to sit down and talk with Professors Jim Eberwine (University of Pennsylvania) and Cynthia McMurray (University of California, Berkeley/Lawrence Berkeley National Laboratory) about the Single Cell Analysis course they co-direct, held here at Cold Spring Harbor Laboratory (CSHL).The course, currently in only its second year, was a natural branch from a meeting and concurrent workshop on Single Cell Analyses. I wanted to know what made this nascent course so special. Jim and Cynthia enthusiastically recounted how the course got started, where it is going, and just what makes this area of science and the course they have put together so unique. Continue reading →
Following on from our last SCIENCE SHORT about fluorescence microscopy imaging, postdoc Jonathan Ipsaro, Ph.D., of Professor and HHMI Investigator Leemor Joshua-Tor’s laboratory, takes us even deeper into the molecular world as he talks about what he calls “molecular photography.”
This 5 minute SCIENCE SHORT delves into how scientists determine the structure of proteins and build pictures of them in order to design therapeutic drugs for malaria for example, amongst other important questions. The malaria protein shown decorates the surface of the malaria parasite and enables it to bind red blood cells. Jonathan presents the 3D structure of this protein in order to show just how much information they can get from “molecular photography.”
About SCIENCE SHORTS: Each short talk of approximately 5 minutes, explores a topic or area of research at CSHL. They were designed for non-scientific audience and given by a CSHL Ph.D. student or postdoc. So far we have covered the question “Why haven’t we cured cancer yet?“, the beautiful imagery generated by the important scientific technique of florescence microscopy, and, in this current installment, determining protein structures using “molecular photography.” Coming soon, the final one in this year’s series.
Malaria surface protein 3D structure; determined in the laboratory of Professor and HHMI investigator Leemor Joshua-Tor
This past April 25th was the 60th anniversary of the publication of Watson and Crick’s famous paper describing the double helix structure of DNA. Many events were held around the world to celebrate the historic day, including a contest organized by James Taylor of Emory University and myself, and sponsored by the journal GenomeBiology.
The contest consisted of a series of 5 DNA-related analysis problems released over 4 days, organized so that the solution to one stage was needed to unlock the clues to the next. Continue reading →
The next in our series of 5 minute SCIENCE SHORTS we are posting is All about fluorescence microscopy by Arun Narasimhan, Ph.D., a postdoc in Associate Professor Pavel Osten’s laboratory.
Fluorescence microscopy not only creates beautiful, glowing images of cellular structures, but is an important scientific technique in itself. Arun takes us through the basics and science of this important type of imaging.
About SCIENCE SHORTS: Each short talk of approximately 5 minutes, explores a topic or area of research at CSHL. They were designed for non-scientific audience and given by a CSHL Ph.D. student or postdoc. So far we have covered the question “Why haven’t we cured cancer yet?“, and, in this current installment, explored the beautiful imagery generated by the important scientific technique of florescence microscopy. Look out for the next in our series.
Fluorescence microscopy image of a cell, still image taken from the above video.
Team CSHL: l-r - Shane McCarthy (Research Investigator, half marathon), Leah Sabin (Postdoctoral Researcher, half marathon), Tim O’Neill (CSHLA Director, half marathon), Josh Dubnau (CSHL Associate Professor, 10K), Jessa Giordano (Public Affairs, 10K), Miriam Fein (Graduate Student, full marathon)
I run. Not terribly far, and not every day, but enough so that I can say that I run. Every now and then I’ve gotten to run to raise money for various worthy causes, which has made the motivation to get out and run that much easier. So when the opportunity came up this year to raise money for this great place where I work, challenge myself a bit and do it all here on Long Island, I jumped at the chance. Continue reading →
After the success of the 5 minute science talks at the recent open house we decided they could be helpful for a wider audience. So we reconvened the speakers and re-did the talks with that in mind, thus creating our new CSHL SCIENCE SHORTS series.
About SCIENCE SHORTS: Each short talk of approximately 5 minutes, explores a topic or area of research at CSHL. They were designed for non-scientific audience and given by a CSHL Ph.D. student or postdoc.
CSHL Professor David Tuveson and Skyler Palatinick
The following interview was conducted and written by Skyler Palatnick
Of all the things kids and teens think about when the topic of scientists comes up, the last thing you would expect to hear is that they are normal–but from my experience at Cold Spring Harbor Laboratory, I can tell you they are. Thirty minutes with one of the most renowned cancer researchers in the world, Dr. David Tuveson, and my view on everything in the science department was changed. Not only did he have a warm and friendly personality, but he had devotion to his cause that could be compared to that of any of the greatest athletes and politicians. Continue reading →