Data Sharing

If you ask scientists “Why do science?”many of the answers will be along the lines of “In order to advance human knowledge.”  But if the goal of science is to contribute to the sum of human knowledge, why don’t scientists place more emphasis on sharing data? Wouldn’t the most efficient path to advancing knowledge be to pool our information and work together?  Scientist may have idealistic intentions and magnanimous motivations, but the fact remains, they do not share well.
So why don’t scientist share data well? Nature recently addressed this question in a special issue dedicated to data sharing  that  is available free of charge online.
Data sharing is an incredibly important issue and I am very happy to see it being addressed by such a respected and widely-read publication.  With modern, high-throughput techniques bringing us into an age of data-driven science it may be more important now than ever before.  But sharing data has always been central to science, it takes many minds and many perspectives to extract the full value of knowledge from data.  As Cambridge professor and Rufus Pollock says : “The best thing to do with your data will be thought of by someone else.” (Voices from the future of science: Rufus Pollock of the Open Knowledge Foundation)
Nature’s special data sharing issue contains:
An editorial  titled Data’s shameful neglect
A feature by Bryn Nelson called Data sharing: Empty archives
Two collaboratively written opinion pieces
Prepublication data sharing
Post-publication sharing of data and tools
Any one of them provides a thought-provoking read. Taken together they make a thorough statement on where we are now and where we need to get to in order to take full advantage of the massive amount of experimental data being generated.

If you ask scientists “Why do science?”many of the answers will be along the lines of “In order to advance human knowledge.”  But if the goal of science is to contribute to the sum of human knowledge, why don’t scientists place more emphasis on sharing data? Wouldn’t the most efficient path to advancing knowledge be to pool our information and work together?  Scientist may have idealistic intentions and magnanimous motivations, but the fact remains, they do not share well.

So why don’t scientist share data well? Nature recently addressed this question in a special issue dedicated to data sharing that  is available free of charge online.

Data sharing is an incredibly important issue and I am very happy to see it being addressed by such a respected and widely-read publication.  With modern, high-throughput techniques bringing us into an age of data-driven science it may be more important now than ever before.  With that said, sharing data has always been central to science, it takes many minds and many perspectives to extract the full value of knowledge from data.  As Cambridge economist Rufus Pollock says : “The best thing to do with your data will be thought of by someone else.” (Voices from the future of science: Rufus Pollock of the Open Knowledge Foundation)

Nature’s special data sharing issue contains:

Any one of them provides a thought-provoking read. Taken together they make a thorough statement on where we are now and where we need to get to in order to take full advantage of the massive amount of experimental data being generated.

Book Review : Internet Cool Tools for Physicians


Hope Leman

Guest Blogger Hope Leman: Hope Leman is a Research Information Technologist at the Samaritan Health Services Center for Health Research and Quality, co-founder of Next Generation Science, a staff writer at AltSearchEngines and the Web administrator of ScanGrants. You can find her on NextBio, FriendFeed and Twitter.

Review of Internet Cool Tools for Physicians by Melissa L. Rethlefsen, David L. Rothman and Daniel S. Mojon

Okay, this is going to one of those book reviews full of praise and every conceivable adjective connoting the concept of “must-read.” And don’t be put of by the cutesy use of “cool” in the title—this is a book of substance and not just for physicians, either. Anyone interested in the provision of health information on the Internet should buy a copy of this book and certainly all public libraries should have it on their shelves. Even experienced medical librarians should at least page through it. I can think offhand of quite a number of professionals and students who would benefit from reading it: nurse researchers, pharmacists, physical therapists, dentists, medical students, nursing students, anyone who does any sort of health sciences research. And given the rise of increasingly sophisticated laypeople as typified by the term e-patient there is a need for well-written, authoritative books such as this one that discuss how to find health information beyond Google, MedlinePlus and Wikipedia.

Before I launch into my paean for nearly every aspect of this book, I do have a few grumbles to get out of the way.

First of all, given the time lag these days between when a book is written and when it is published this book is already dated in that neither Twitter nor FriendFeed nor Facebook appear to be mentioned. That is a major flaw in this otherwise superb book. I say “appear” because the book lacks an index, so I could not simply look for the words “Twitter,” “FaceBook,” and “FriendFeed” in the index. The lack of an index is really dismaying and unfortunate in a book whose subject matter is the acquisition of information. Maybe we can blame the lack of an index on the publisher and not the authors. If so, shame on you Springer. We expect better of such a prestigious publisher. Cutting back on book basics such as indexes is penny wise and pound foolish and a no no for publishers who are reputation conscious.

Also, the incredibly rich research tool of ScienceDirect is given all of one paragraph. This is another case in which Internet Cool Tools for Physicians has been overtaken by the march of time. The host of this blog, NextBio, has rendered ScienceDirect immensely more useful and searchable to users. Here is an edifying screencast (that is itself a model of that genre and one that search engine start-ups hoping to build up usership would do well to emulate):ScienceDirect and NextBio

Click here to see what Elsevier itself says.

As someone who revels in the richness of Elsevier’s riches but who has been frustrated over the years by the clunkiness of ScienceDirect I can only say, “Go, NextBio, go!”

These are the kinds of things that can be addressed in the next edition of Internet Cool Tools for Physicians. I am hoping that there will be one, as this is an outstanding book.

Now that I have gotten the grumbles out of the way, I will proceed to the gushing praise part of this review.

One of the wonderful things about this book is that it is a book. Why is that important? Because so much of what physicians and other medical professionals and medical librarians need to know about medical literature searching and current awareness is known by one group by not necessarily by another. As a non-physician, I can’t mosey around the social network for physicians Sermo.

And I may have to learn important developments like that by attending conferences such as Health 2.0 or hoping to learn about them by happening across blog postings and tweets. Far better to invest in a book such as Internet Cool Tools for Physicians and thereby gain a grasp on key technologies, such as the basics of RSS and have a ready reference to suggest to doctors and others in the health sciences who need a comprehensive guide to such important topics.

The book has very concise, busy professional-friendly sections on how to use Google, Google Health and Google Scholar, PubMed and Medline effectively and efficiently. It covers such useful topics as personalized start pages, third-party PubMed tools (that alone is worth price of the book), reference managers (that section is somewhat dated, but all the more reason for this book to be continuously updated and to become a standard text), email alerts, social bookmarking tools, wikis, collaboration tools. Indeed, the book in all of those respects could be read profitably even for those whose primary interest is not medicine.

The authors do such a fine job of discussing leveraging the power of the Web that I wished that they had included a section on searching for grants, scholarships and other types of funding. They could have included the site I help on, ScanGrants, had they done so. (See how I sneaked in a mention of ScanGrants—that is a given in almost everything I write). But seriously, more and more physicians who are not primarily researchers are engaging in clinical research or community/public health projects and info on how to gain funding for such projects would be a useful feature of the next edition of Internet Cool Tools for Physicians.

The next edition should also contain discussion of search engines such as DeepDyve, NextBio, Mednar, Novoseek given that it does discuss their rival, GoPubMed. Also, we need discussion of the rise of the impact of the Smart Phone and the iPhone specifically. There may be applications that may be optimized for or available only on the latter and those will need to be addressed, as will the rise of new services for connecting frontline physicians, researchers and patients via such services as Private Access and services such as Trial-X, which I read about today in the invaluable blog of one of the authors of this book, David Rothman.

Physicians will need to acquaint themselves with the increasing numbers of trial finders because patients are soon going to ask their personal physicians about such things—or bypass them entirely if the physicians don’t seem open to some pretty assertive instances of patient empowerment.

I mention everything I hope to see in the next edition of this book because this book is a contribution to the betterment of health information acquisition and organization. Kudos for the authors for compiling so much information and presenting it in such a clear, straightforward fashion. The title suggests that the book is gee-whiz sophomoric. It is not. It a work of substance and from a purely aesthetic standpoint, it is a pleasure to handle. What a sad commentary on our times that I was actually surprised to handle a book that was a model of copy editing and production.

I wish that this book had been available when I first entered the field of medical librarianship in 2004 and I hope it will be assigned to all library science students. I have just finished my master’s in library and information science, for instance, and can see that reading it would have greatly enhanced the education my classmates and I have just completed.

In short, buy this book.

Winners of the Summer 2009 NextBio Travel Grant

After a long and difficult deliberation, we have selected the recipients for the Summer 2009 NextBio Travel Grant!

We were impressed with the quality of essays and very happy to hear about the different ways in which NextBio has been useful to graduate students in the pursuit of their research. The three students who were selected for this quarter’s travel grant are:

    Abhishek Tiwari
    Sayan Mondal
    Yunyun Jiang

Abhishek is a second year PhD student in bioengineering at the University of Auckland who using modeling to study hormone dynamics. In his essay, Abhishek relates how a discovery in NextBio helped direct his research.

In order to develop a mathematical model of the steroid synthesis I was searching for functional mechanism of the steroidogenic acute regulatory protein or StAR. A simple keyword search using StAR returned a well categorized results page and further exploration and filtering of results landed me on a data correlation between StAR and congenital adrenal hyperplasia. Inspired from this small but crucial finding I devoted one section of my model to simulate the mechanistic basis of the congenital adrenal hyperplasia, and based on model sensitivity analysis we found new insights into the underlying process and emerging trends in diseased system. This was possible only because of the NextBio which provided an abstracted data correlation derived from several high-throughput data sources.

He goes on to discuss the collaboration features and the NextBio recommendation service and then wraps up the essay with a wonderful final paragraph on his vision for the future of science. I highly recommend you read the full text of Abhishek’s essay.

Sayan is a graduate student in the Physiology, Biophysics and Systems Biology department at Weill Medical College of Cornell University. His essay describes how NextBio has been helpful to his systems biology research.

My chemical kinetics-based computational model has identified and elucidated a key role of the phosphodiesterase (PDE) -mediated degradation of cyclic adenosine monophosphate (cAMP) to adenosine monophosphate (AMP) in maintaining the acidic pH in the lumen of the male reproductive tract. Now, as the pH homeostasis is necessary for sperm maturation (spermatogenesis), I wanted to find out if phosphodiesterase has previously been related to spermatogenic dysfunction. I used NextBio to look up this information, and it was quick and easy to do so. Interestingly, NextBio’s data correlations utility referenced microarray data showing downregulation of two phosphodiesterase genes (PDE1A and PDE4A) in the diseased condition of infertility due to incomplete spermatogenic arrest. We are greatly encouraged by finding this result, and my experimental collaborators are now moving ahead with biochemical experiments to test my model predictions.

I should add that the aforementioned microarray study performed a global gene expression profiling of testicular biopsies, and mentioned only a few selected genes in the text of the article. In particular, the text makes no mention of phosphodiesterase genes, so it would have been difficult to find this result using a typical Pubmed or Google Scholar search. In general, most papers reporting such high-throughput studies can reasonably focus on only a few genes in the text, so I find it useful that NextBio’s data correlations utility can search across publicly available high-throughput datasets from these papers and connect proteins of my interest to specific diseases.

The essay also discusses other NextBio features Sayan finds useful. It really illustrates the power of NextBio, in fact the next time someone asks me what NextBio can do for a researcher, I might just give them Sayan’s essay.

Yunyun is a biochemistry graduate student at Rice University who works on the cohesion complex. In her essay, Yunyun discusses her appreciation of NextBio’s filtering functions and “high specificity”. (The pun lover in me really appreciates that a biochemist chose to compare NextBio to PubMed in terms of “specificity”) The community features of NextBio are also very appealing to Yunyun.

Studying the published literature is one way to learn about the latest progress, communicating with scientists from related fields provides another great way to keep up with the newest findings. NextBio provides a platform for us to find people or groups with same research interest. It has been a pleasure to meet people with same or similar interest through NextBio and share opinions about our research.

All of the essays submitted to the travel grant were well-written and the judges had a very difficult time choosing just three essays. On behalf of the entire NextBio team, please allow me to offer our sincere thanks to all those who applied and to everyone who helped us to spread the word about the grant.

The NextBio Travel Grant program is ongoing. We give out travel grants four times a year, so if you missed the chance to apply for this one, you can submit to for Fall 2009. The deadline is September 30th 2009 and you can find details here.

Enhanced ScienceDirect Goes Live

Remember my blog post NextBio Elsevier Partnership telling you that Elsevier was going to use NextBio technology to enhance ScienceDirect? Well, the updated version of ScienceDirect went live yesterday and now you can see the enhancements for yourself!

ScienceDirect users who are logged into their account will now see a box titled “Relevant Terms extracted from this Article” beneath the familiar “Article Toolbox” box.
ScienceDirect Screen Shot 1
The relevant terms are extracted from the text of the article using NextBio’s ontological tools and each is linked to a custom page with a wealth of information on experimental data, literature, clinical trials, news and key researchers.
Science Direct Screen Shot 2
I am very happy that ScienceDirect has chosen to integrate all these different types of content on a single platform. It will be a powerful tool for researchers. Hopefully, this enhancement of ScienceDirect will help illustrate the power of integrating information and data rather than isolating them in silos. Many people believe that future of life science research lies in making data more open, accessible and integrated. I am among those people and therefore very glad to see Elsevier take this step towards data accessibility and integration.

Nature Takes A Look At Science Journalism

Today is the opening day of the 6th World Conference of Science Journalists (WCSJ2009) in London England. Nature, a publication that has been promoting scientific journalism for over 100 years, has produced a special edition on science journalism to accompany WCSJ2009.

The conference is sure to include a significant amount of reflection on how the profession has changed and speculation on what the future holds for scientific journalism. Nature’s special feature also addresses these issues.

Boyce Rensberger discusses the history of scientific journalism in his wonderful piece Science journalism: Too close for comfort. Rensberger portrays the role of early 20th century science journalists as passive translators of jargon who would never dream of questioning the word of a scientist.

science journalists at US newspapers in the 1930s and 1940s believed that it was their job to persuade the public to accept science as the salvation of society (B. V. Lewenstein Public Underst. Sci. 1, 45–68; 1992)

He goes on to describe how the mid-century saw a transformation as science journalists became more willing to be critical of scientists.

And so the next great age of science journalism began — the ‘Watchdog Age’ — as science reporters became much more like their colleagues in other parts of the newsroom.

Rensberger acknowledges that this century has seen yet another transformation with print journalism suffering and new media seeming to take over as we enter the Digital Age, but his article is primarily a retrospective and he does not venture into speculation on the future of science journalism.

Other articles included in Nature’s special feature do examine the digital age. Geoff Brumfiel ‘s article Science journalism: Breaking the convention? covers the new methods of reporting science. It looks at the issue of whether or not blogging is journalism. Should bloggers be held to the same rules as journalist when it comes to reporting? How do you draw the line between a scientist who blogs and a journalist who blogs? Brumiel also does an excellent job of reviewing the issues surrounding live-blogging or using services such as Twitter and FriendFeed at scientific conferences. Some scientists worry about being scooped and dislike having the information they are willing to share verbally with conference attendees taken down as notes and made available on blogs or social networks. Other scientists see these digital communication tools as the way of the future and praise the increased efficiency of information sharing.

Taken together, the six articles in Nature’s special issue present a full perspective on science journalism. The articles are free on Nature’s website for the next few weeks so be sure to check them out soon!

DNA Suduko

Researchers at Cold Spring Harbor Lab recently developed a sequence analysis strategy they call “DNA Sudoku”.

Cute name, right? I have to admit, it was the name that first caught my eye. But the Sudoko method is much more than just a cute name, it is a significant advance in multiplex sequencing.

Multiplex sequencing, or multiplexing, is a fairly recent development made possible by next-generation sequencers. Multiplexing relies on tagging DNA samples with short oligonucleotide “barcodes” which allow for the sequencing of many different samples at once. The advent of multiplexing was a substantial improvement over the previous techniques which could only sequence one DNA sample at a time. However, construction of a library of unique barcodes is expensive in terms of both time and money.

The authors of DNA Sudoku – harnessing high-throughput sequencing for multiplexed specimen analysis, report that they:

…have developed a novel multiplexing framework in which the identity of individual specimens is not encoded directly by an appended barcode sequence. Instead, specimen identities are encoded by positional information created by an optimized series of pooling schema. In this manner, more than 100,000 different samples can be analyzed using only a few hundred barcodes

Using the positional information of pooled samples was an ingenious innovation and because it decreases the number of barcodes required, it significantly decreases the costs of multiplex sequencing. The use of positional information is also where the method gets its name.

While each individual pooling pattern might yield multiple solutions to the link between sequence and specimen source, the combination of all pooling patterns would provide sufficient constraints that only a single, high-confidence solution would emerge for the vast majority of samples. Many elements of this approach were reminiscent of seeking the solution to a Sudoku puzzle, which led us to dub this strategy ‘‘DNA Sudoku.’’

The pooling strategy relies on number theory and is based on the Chinese Remainder Theorem. I didn’t delve too deeply into those ideas – I mostly took the authors’ word for it. But if you want to look into the details behind the background on the number theory, the authors’ suggest Du and Hwang 2006a for review. The important thing is that it works. And it does work. Their correct decoding rate was 98.2%, as good as or better than most current barcode methods.

The low cost and high accuracy of the Suduko method dramatically lowers the barriers to genotyping and may lead to major advances in human health research. I am very interested to see how quickly this new method is adopted and just how much impact it ultimately has.

The Four Musketeers

Guest Blogger Hope Leman

Hope Leman


Hope Leman is a Research Information Technologist at the Samaritan Health Services Center for Health Research and Quality, co-founder of Next Generation Science, a staff writer at AltSearchEngines and the Web administrator of ScanGrants. You can find her on NextBio, FriendFeed and Twitter.

As I try to grasp the revolution in scientific and medial research that Science 2.0 and Medicine 2.0 are effecting I often find that I am literally being rendered sleepless by trying to keep up on the writings of the leading thinkers on the subject such as Cameron Neylon, Jean-Claude Bradley, Michael Nielsen and the new kid on the block, Steve Koch.

It is quite daunting to try to keep up with the many fascinating things they have to say and the many links they provide to their colleagues in the field such as Bill Hooker and Rich Apodaca (How I wish that the latter two would add “Follow me on Twitter” buttons to their blogs. They have fascinating things to say and I find that the best way by far to keep up with thinkers and doers is via Twitter. RSS is so 2006.)

As I sat down to write this post about an hour ago (it is now 4:53 a.m.), I first decided to catch up with recent entries here on the NextBio blog.

I read through Steve Koch’s thoughtful discussion of Open Science and had the curious reaction of being both amused (by the use of the word “icky”) and moved by his statement, “I try to move away from all of the icky, unproductive, unhappy, and unnatural closed science behaviors that I have been taught.”

I remember well in the 1980s that a young biochemistry graduate student I knew at Oregon State University got into deep trouble simply for discussing with scientists at another institution his research. I was a liberal arts major and could not fathom why sharing his excitement and the joy of discovery with other scientists was a bad career move for him.

It really is hard for me to quite grasp the formidable obstacles that dedicated, pro-Open Science researcher/teachers like Koch and Bradley face in trying to bring science into the 21st century and their fortitude and perseverance in attempting to instill in their students the value of openness when so many scientific traditions militate against such openness. It is a hard slog and these men are truly heroes in the advancement of knowledge. They are tireless in their efforts to advance science and combine the ability to marshal eloquent, persuasive arguments with what seem endless reservoirs of energy and stamina. In the course of writing this essay, for instance, I had a plethora of tabs open in my browser linking to Koch’s essay and to fascinating posts elsewhere by Nielsen and Neylon.

One of those tabs was marking for me the same essay by Michael Nielsen that Koch refers to, Doing Science in the Open which is must reading for anyone interested in Open Science and indeed science, period.

Nielsen is a cogent explicator of matters that anyone interested in the future of science should follow. We all look forward to the book he is currently working on.

I thought of the dedication and leadership that Koch and Bradley show their students (Bradley even helps sponsor a prize, the Open Notebook Science Challenge, in an admirable attempt to generate interest in the sub-branch of Open Science, Open Notebook Science) and their exemplary role modeling and their engaging combination of infectious enthusiasm with unimpeached scientific credentials as I read Nielsen’s discussion of the major cultural barriers men like Bradley and Koch face in fostering the use of online collaboration and engendering in their students an ethos of sharing. They teach its value for both altruistic reasons and hard-headed scientific ones: transparency prevents wastage of time and resources and ambitious young scientists generally lack both.

And speaking of resources, Cameron Neylon is an absolute master at monitoring the flow of software tools that are discussed in such venues as the Life Scientists room of FriendFeed and providing both quick takes on them there and in thoughtful think pieces on his blog. I am still engaged in reading his series on the implications of Google Wave in science, for instance, and if I were a venture capitalist in the life sciences (would that I had that kind of bankroll), I would keep Neylon on retainer.

A single post of his, for example, “What Would You Say to Elsevier?” has several fascinating comments on ways that publishers could actually make money in the world of Open Access.

I spend many, many hours working on the health sciences grants listing service, ScanGrants. That entails visits to the Web sites of grantors in the health sciences (scientific societies, the professional associations of physicians, nurses, pharmacists, physical therapists and so on) and I am often struck by what a poor job they do in making the case of the value of the grants they have made. Often the material is quite dated and is presented in a perfunctory, lackluster fashion.

What a boon, then, it would be to such groups (and I admire very much the work they do—it is really moving to see how hard such organizations work to scrap money up for research and scholarships) as they try to persuade members to pony up to contribute to the foundations such organizations often back and need contributions from members for, if they could more easily aggregate data on previously funded projects and those currently in process. They could then present in a compelling way to their own members, to the general public and to potential applicants for grants: they want stellar applicants, after all, and looking like a galvanizing, dynamic force in science rather than a mediocre, inert one is the best way to do that. Simply acquiring facts on their own funding programs so that they can present them on their Web sites for PR purposes and so that they can be more effective funders is very much in tune with what Neylon says here:

“Tracking via aggregation. Funders and institutions want more and more to track the outputs of their research investment. Providing tools and functionality that will enable them to automatically aggregate and slice and dice these outputs is a big business opportunity. The data themselves will be free but providing it in the form that people need it rapidly and effectively will add value that they will be prepared to pay for.”

Clearly, there are firms that stand ready to provide such services—like ResearchScorecard and NextBio, which has very courteously allowed me to write this post which I had better wrap up so that I can read more of what the people discussed in it have been writing lately.

NextBio Elsevier Partnership

Last week the partnership between NextBio and Elsevier was officially announced!

Elsevier will be using our technology to enhance ScienceDirect. Elsevier is the biggest player in scientific publishing and ScienceDirect is used by millions of researchers. Their decision to incorporate our technology into their platform shows that they recognize the value of NextBio’s tools and we are very pleased to have the endorsement of such an influential company.

The new, enhanced ScienceDirect will utilize NextBio’s ontological framework so that users can search ScienceDirect’s literature along with publicly-available, experimental data, clinical trials, and news articles. There is a growing trend in the scientific community towards integrating multiple types of information. I believe that Elsevier’s decision to integrate literature, experimental data, clinical trials and news on the ScienceDirect platform is a big step in the right direction. Hopefully, we’ll soon see other vendors join the bandwagon.

The NextBio engineering team let me see a sneak peek of the enhanced ScienceDirect. Not to let the cat out of the bag, but there is a great interface that will let users easily navigate through the different types of content. You’ll be able to see the new ScienceDirect for yourself when it goes live later this summer!

Opening Science

Guest Blogger Steve Koch

Chef solo_square
Steve Koch is an experimental biophysicist. He is an assistant professor of physics at the University of New Mexico and the author of the blogs Steve Koch Science, Steve Koch Research, and Steve Koch Teaching. You can find him on NextBio, FriendFeed and Twitter.


Thank you, Lisa, for inviting me to post a blog here! In thinking about what to write, I noticed two previous entries on this blog: the first was one by Lisa discussing Francis Collins possibly being the next director of the NIH. Francis Collins was the leader of the wildly successful, amazingly collaborative human genome project—an awesome project that demonstrates the huge accomplishments that can come from scientists openly collaborating. Dr. Collins was the principle investigator of the first lab I joined at the very beginning of my academic research career. He is one of my science heroes, and I am really hoping that he becomes the next director of the NIH. With Collins at the helm, I have great confidence that the NIH will be a strong leader in funding and promoting Open Science and Science 2.0 innovations. The second post that caught my eye was by Jean-Claude Bradley discussing the possible necessity of science blogging. Jean-Claude is a huge proponent of Open Science and a leader in Open Notebook Science. Reading these posts made me wonder whether readers of the NextBio would like to know, “what is open science?”

I’m here to tell you that I can’t precisely answer the question. It’s actually a tough question that many well-known proponents of open science do not yet agree on (see, e.g., this summary from last year). To me, an exact definition of open science is not critical because there is usually (but not always) a bright line between open and closed scientific practice. Open is the opposite choice from closed. One way of directing a row boat is to find a landmark 180 degrees opposite from where you want to go, and then keep rowing directly away from that landmark. For me personally, there is a parallel device in the pursuit of open science: I try to move away from all of the icky, unproductive, unhappy, and unnatural closed science behaviors that I have been taught.

Many of these closed science practices are considered traditional, prudent, or even necessary. One example is the practice of keeping scientific ideas secret until making formal publication. The standard thinking is that if you share your unpublished ideas, someone will steal your ideas and become famous at the expense of your reputation, funding, and career promotion (this is called getting “scooped”). I have thought about these arguments and I am personally convinced that the risk of scooping pales in comparison to the rich rewards that are gained by completely open discussion of scientific ideas. But convincing myself is a much different story than proving I am right. There are in fact many examples of the devastating effects of scooping and given the realities of the science world today, it’s not a risk to be taken likely. For this reason, and many others, carrying out open science is quite challenging. You can get a flavor of these challenges from Michael Nielsen’s fascinating essay on the challenges of “achieving extreme openness in science.”

I have been lucky to obtain a position as principle investigator of a research lab. For the past three years, I and my lab members have been pointing our research in the direction of openness. We’ve been taking steps towards open notebook science, sharing data and protocols, open sharing of ideas, and participation in online science communities. Each step we take seems to have been rewarded by a stronger connection to the global scientific community as well as a healthy dose of feeling happy and productive. I reflect back to when I was that young, green undergraduate joining my first research lab. I believed that scientists were all on the same team, sharing discoveries, and working together to help humanity. I had to be taught otherwise during my graduate career. From my vantage point as leader of a research lab, I can see that that young scientist was not only naïve, he was right! Now my task is to help students in our lab trust their own gut instincts about openness in science and help them achieve it while successfully advancing in their own careers.

Will Francis Collins Be The Next Head Of The NIH?

Dr Francis Collins

Rumors have been flying about who President Obama will appoint to head the National Institute of Health (NIH). Since the beginning of the Obama administration, Francis Collins has been considered one of the frontrunners for the post, but in the last two weeks the rumor mill seems to think that Collins is as good as appointed.

On Saturday, the LA Times reported that “a source familiar with the selection process” said that Collins was in the final stages of screening. The general consensus of the scientific community is that Collins will pass the screening with flying colors.

Collins was the director of the National Human Genome Research Institute (NHGRI) for 15 years where he spearheaded the campaign to map the human genome. When he stepped down from that position a year ago the then-head of NIH, Elias Zerhouni, said “Francis has provided 15 years of outstanding leadership to NHGRI and has been a trailblazer in the scientific community at large. His contributions to the world of genomics and medicine have been enormous. He has been a tremendous colleague, friend, and brilliant visionary. I know that he will continue to make groundbreaking advances in biomedical research.”

In addition to an intimate understanding of both basic and clinical research, Collins also knows his way around Capitol Hill. When he led the human genome project, he created the ELSI program in order to research the ethical, legal and social implications of the human genome science. Collins’ concern about those issues led to him working closing with Congress on the Genetic Information Non-discrimination Act (GINA). Last summer the New England Journal of Medicine did a video interview with Collins as a supplemental to his paper Keeping pace with the times–the Genetic Information Nondiscrimination Act of 2008. Watching the interview you can see many characteristics that would make Francis Collins an excellent leader for the NIH.

Click here to watch the New England Journal of Medicine video – The Genetic Information Nondiscrimination Act of 2008:An Interview with Dr. Francis Collins