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 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

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.