Tag Archives: The Scientist

Perceptions of Promise, an art/science show at Glenbow Museum, Alberta

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The art/science show, Perceptions of Promise, at Alberta’s Glenbow Museum in Calgary features stem cell research, ethics, and art. It’s the outcome of a workshop that was held May 2010 in Alberta. Here’s an image from the show,

Derek Besant, Still from Metamorphosis Theory, 2010. Copy obtained from Glenbow Museum website.

An article by Jef Akst, Controversy on display; A Canadian art exhibit takes a different look at the ongoing debate surrounding human stem cell research,  in The Scientist provides an interview with one of the organizers of the show, Timothy Caulfield, a bioethicist at the Health Law Institute of the University of Alberta,

Over the last couple of years, Caulfield [Timothy] has worked with his brother Sean, a professor of art design also at the University of Alberta, to brainstorm ways to combine their interests in art, science, and society. The brothers’ first brainchild, a 2009 art show in Alberta called Imagining Science, explored legal and ethical issues surrounding biotechnological advances, such as cloning and genetic testing

While they were happy with the exhibition’s success, they felt there were plenty more issues left to cover. “Many of the people involved thought this conversation isn’t over,” Sean says. “It’s kind of just beginning.” So they decided to do it again, this time focusing on the contentious issues surrounding stem cell research.

Following the tradition of their first exhibition, they organized a workshop that brought together scientists, social commentators, and artists to present their work and represent diverse perspectives on stem cell research.

Here’s an excerpt from a posting by one of the participants, Matthew Nisbet, an associate professor in the School of Communication at American University. (At the time of writing, his blog was called Framing Science, Nisbet has since changed his blogging focus and has moved and renamed his blog, Age of Engagement; all the archival posts for Framing Science are included.) From Nisbet’s archived May 5, 2010 posting on Age of Engagement,

Last week I traveled to the Canadian Rockies to participate in a unique workshop organized by the University at Alberta that focused on the shared perspectives and collaborations among artists, scientists, ethicists, and social scientists. The workshop was the second in a series organized by brothers Sean Caulfield and Timothy Caulfield, professors of Art and Law respectively at the University of Alberta.

In 2009, the first workshop resulted in the “Imagining Science” exhibit at the Art Gallery of Alberta and a book by the same title. The critically acclaimed initiative highlighted the emerging genre of “bio art,” which Tim Caulfield in his contribution to the award-winning book describes as “a field of artistic inquiry that both utilizes the techniques of biotechnology and serves as a medium of reflection on the societal implications of the research.”

Here’s an example of a collaboration from the 2010 workshop which has resulted in the Perceptions of Promise show (from the article by Jef Akst),

Paul Cassar, a doctoral student at the University of Toronto who works with mouse embryonic stem cells, took an even more hands-on approach to his collaboration with artist Daniela Schlüter — he actually drew some scientific schematics from which Schlüter created her mixed media drawings.

“By no means am I a good drawer,” Cassar says. “Even my sketches could have been done better by a three year old,” he jokes. But when Schlüter overlaid her own drawings, she was able to “create this story to contrast some of these tensions [of] where we are now with this stem cell debate,” he says. “I think is a really neat example of how science can be inspiring to other creative minds.”

There’s also video of the show featuring the images,

Finally, the Perceptions of Promise website and the Glenbow Museum website.

Oil in the Gulf of Mexico, science, and not taking sides

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Linda Hooper-Bui is a professor in Louisiana who studies insects.She’s also one of the scientists who’s been denied access to freely available (usually) areas in the Gulf of Mexico wetlands. She and her students want to gather data for examination about the impact that the oil spill has had on the insect populations. BP Oil and the US federal government are going court over the oil spill and both sides want scientific evidence to buttress their respective cases. Scientists wanting access to areas controlled by either of the parties are required to sign nondisclosure agreements (NDAs) by either BP Oil or the Natural Resource Damage Assessment federal agency. The NDA’s extend not just to the publication of data but also to informal sharing.

From the article by Hooper-Bui in The Scientist,

The ants, crickets, flies, bees, dragon flies, and spiders I study are important components of the coastal food web. They function as soil aerators, seed dispersers, pollinators, and food sources in complex ecosystems of the Gulf.

Insects were not a primary concern when oil was gushing into the Gulf, but now they may be the best indicator of stressor effects on the coastal northern Gulf of Mexico. Those stressors include oil, dispersants, and cleanup activities. If insect populations survive, then frogs, fish, and birds will survive. If frogs, fish, and birds are there, the fishermen and the birdwatchers will be there. The Gulf’s coastal communities will survive. But if the bugs suffer, so too will the people of the Gulf Coast.

This is why my continued research is important: to give us an idea of just how badly the health of the Gulf Coast ecosystems has been damaged and what, if anything, we can do to stave off a full-blown ecological collapse. But I am having trouble conducting my research without signing confidentiality agreements or agreeing to other conditions that restrict my ability to tell a robust and truthful scientific story.

I want to collect data to answer scientific questions absent a corporate or governmental agenda. I won’t collect data specifically to support the government’s lawsuit against BP nor will I collect data only to be used in BP’s defense. Whereas I think damage assessment is important, it’s my job to be independent — to tell an accurate, unbiased story. But because I choose not to work for BP’s consultants or NRDA, my job is difficult and access to study sites is limited.

Hooper-Bui goes on to describe a situation where she and her students had to surrender samples to a US Fish and Wildlife officer because their project (on public lands therefore they should have been freely accessible) had not been approved. Do read the article before it disappears behind a paywall but if you prefer. you can listen to a panel discussion with her and colleagues Christopher D’Elia and Cary Nelson on the US National Public Radio (NPR) website, here. One of the people who calls in to the show is another professor, this one from Texas, who has the same problem collecting data. He too refused to sign any NDAs. One group of nonaligned scientists has been able to get access and that’s largely because they acted before the bureaucracy snapped into place. They got permission (without having to sign NDAs) while the federal bureaucracy was still organizing itself in the early days of the spill.

These practices are antithetical to the practice of science. Meanwhile, the contrast between this situation and the move to increase access and make peer review a more open process (in my August 20, 2010 posting) could not be more glaring. Very simply, the institutions want more control while the grassroots science practitioners want a more open environment in which to work.

Hooper-Bui comments on NPR that she views her work as public service. It’s all that and more; it’s global public service.

What happens in the Gulf over the next decades will have a global impact. For example, there’s a huge colony of birds that make their way from the Gulf of Mexico to the Gaspé Peninsula in Québec for the summer returning to the Gulf in the winter.  They should start making their way back in the next few months. Who knows what’s going to happen to that colony and the impact this will have on other ecosystems?

We need policies that protect scientists and ensure, as much as possible, that their work be conducted in the public interest.

Is peer review a good idea?

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I’ve been meaning to write a piece about science publishing and peer review in the light of a number of recent articles and postings on the subject. As there hasn’t been anything new for at least three or four days now this might be an opportune moment.

I did touch on a related topic in an April 22, 2010 posting where I focused amongst other issues on a paper about publication bias.  From my posting (quoting a news item on physorg.com)

Dr [Daniele] Fanelli [University of Edinburgh] analysed over 1300 papers that declared to have tested a hypothesis in all disciplines, from physics to sociology, the principal author of which was based in a U.S. state. Using data from the National Science Foundation, he then verified whether the papers’ conclusions were linked to the states’ productivity, measured by the number of papers published on average by each academic.

Findings show that papers whose authors were based in more “productive” states were more likely to support the tested hypothesis, independent of discipline and funding availability. This suggests that scientists working in more competitive and productive environments are more likely to make their results look “positive”. It remains to be established whether they do this by simply writing the papers differently or by tweaking and selecting their data.

These papers with their publication bias would have, for the most part if not all, been peer-reviewed which time-honoured system is currently being tested in a number of ways.

There’s the LiquidPublication project in Europe which offers scientists a faster and more dynamic way to publish. From the news item on Nanowerk,

Scientists spend too much of their time publishing papers and ploughing through the mountains of papers produced by their colleagues, and not enough time doing science.

That’s the observation – and frustration – that spurred Fabio Casati and his collaborators to launch LiquidPublication, an EU-financed [European Union] research project that seeks to revolutionise how scientists share their work and evaluate the contributions of their peers.

“The more papers you produce, the more brownie points you get,” says Casati. “So most of your time is spent writing papers instead of thinking or doing science.”

Besides wasting untold hours, Casati says, the current scientific publication paradigm produces other toxic fallout including an unduly heavy load for peer reviewers and too many papers that recycle already published research or dribble out results a bit at a time.

“The current system generates a tremendous amount of noise,” he says. “It’s hard to find interesting new knowledge because there’s so much to see.”

Casati and his colleagues are developing and promoting a radically new way to share scientific knowledge, which they call “liquid publication”. They want to tap the power of the Web – including its ability to speed communication, facilitate data storage, search and retrieval, and foster communities of interest – to replace traditional peer reviews and paper publications with a faster, fairer and more flexible process. [emphasis mine]

David Bruggeman at Pasco Phronesis commented on this project,

The project acknowledges the influence of arXiv.org, but would have some important differences. The plan includes having scientists and so-called ‘invisible colleges’ of researchers develop their own journals which would be created via the platform. There is also the thought that readers of these papers and journals could add value by linking related papers.

David goes on to give support for it while noting that LiquidScience should not be used in the place of peer review and that the more means of publishing research and critiquing it, the better.

The August 2010 issue of The Scientist features three articles on peer review. From the Breakthroughs from the Second Tier article by the staff,

Often the exalted scientific and medical journals sitting atop the impact factor pyramid are considered the only publications that offer legitimate breakthroughs in basic and clinical research. But some of the most important findings have been published in considerably less prestigious titles.

Take the paper describing BLAST—the software that revolutionized bioinformatics by making it easier to search for homologous sequences. This manuscript has, not surprisingly, accumulated nearly 30,000 citations since it was published in 1990. What may be surprising, however, was the fact that this paper was published in a journal with a current impact factor of 3.9 (J Mol Biol, 215:403–10, 1990). In contrast, Nature enjoys an impact factor more than 8 times higher (34.5), and Science (29.7) is not far behind.

One of the most commonly voiced criticisms of traditional peer review is that it discourages truly innovative ideas, rejecting field-changing papers while publishing ideas that fall into a status quo and the “hot” fields of the day—think RNAi, etc. [emphasis mine] Another is that it is nearly impossible to immediately spot the importance of a paper—to truly evaluate a paper, one needs months, if not years, to see the impact it has on its field.

Jef Akst offers a specific example in his article, I Hate Your Paper,

Twenty years ago, David Kaplan of the Case Western Reserve University had a manuscript rejected, and with it came what he calls a “ridiculous” comment. “The comment was essentially that I should do an x-ray crystallography of the molecule before my study could be published,” he recalls, but the study was not about structure. The x-ray crystallography results, therefore, “had nothing to do with that,” he says. To him, the reviewer was making a completely unreasonable request to find an excuse to reject the paper.

Kaplan says these sorts of manuscript criticisms are a major problem with the current peer review system, particularly as it’s employed by higher-impact journals. Theoretically, peer review should “help [authors] make their manuscript better,” he says, but in reality, the cutthroat attitude that pervades the system results in ludicrous rejections for personal reasons—if the reviewer feels that the paper threatens his or her own research or contradicts his or her beliefs, for example—or simply for convenience, since top journals get too many submissions and it’s easier to just reject a paper than spend the time to improve it. [emphasis mine] Regardless of the motivation, the result is the same, and it’s a “problem,” Kaplan says, “that can very quickly become censorship.”

In the third article, this one by Sarah Greene, there’s mention of a variation on the traditional peer review, post-publication peer review (PPPR),

In the basic formulation of PPPR, qualified specialists (peers) evaluate papers after they are published. Instead of hiding reviewers’ identities and comments, they become part of the published record and open to community review and response. Renowned educator Paolo Freire once said, “To impede communication is to reduce men to the status of things.” PPPR at its best facilitates ongoing dialogue among authors, peer reviewers, and readers.

Presumably, PPPR will be part of the LiquidPublication experience. Interestingly, in a recent article on Techdirt (a site focused on intellectual property issues), there was this mention of PPPR,

Apparently, people are realizing that a much more open post-publication peer review process, where anyone can take part, is a lot more effective:

We are starting to see examples of post-publication peer review and see it radically out-perform traditional pre-publication peer review. The rapid demolition […] of the JACS hydride oxidation paper last year (not least pointing out that the result wasn’t even novel) demonstrated the chemical blogosphere was more effective than peer review of one of the premiere chemistry journals. More recently 23andMe issued a detailed, and at least from an outside perspective devastating, peer review (with an attempt at replication!) of a widely reported Science paper describing the identification of genes associated with longevity. This followed detailed critiques from a number of online writers.

I’m not sure I’m ready to get quite as excited about PPPR as some of its supporters do. Traditional peer review is not the only process that can be manipulated as the recent events with Virology Journal point out. I first came across the incident in a Fast Company (which mostly focuses on business, marketing, design, and technology) in an article by Davdi Zax,

It must get tedious sometimes, running a scientific journal–all that dull data, all those pesky p-values. Wouldn’t it be cool if science journals had accounts of Biblical miracles, and speculation on events thousands of years in the past? That seems to be what the editors of Virology Journal were thinking, when they decided to publish a speculative analysis of a Biblical miracle by Ellis Hon et al., of Hong Kong.

Even from the very first sentence of the abstract, which mentions a woman with a fever cured “by our Lord Jesus Christ,” it ought to have been clear to the article’s reviewers that it was not written to the highest objective scientific standards. The authors go on to present evidence that the woman likely had the flu: “The brief duration, high fever, and abrupt cessation of fever makes influenza disease probable.”

…

The paper was swiftly eviscerated online, particularly on the blog Aetiology.

An apology was issued both the editor and the author fairly soon after, as per this news item on physorg.com,

Editor-in-Chief of the journal, Robert F. Garry, publicly apologized for publishing the article, saying it “clearly does not provide the type of robust supporting data required for a case report and does not meet the high standards expected of a peer-reviewed scientific journal.” He also apologized for any “confusion or concern” the article may have created among readers.

…

One of the blogs that brought the paper to notice was This Scientific Life, by Bob O’Hara. O’Hara said the lead author of the paper, Kam L.E. Hon from the Department of Paediatrics at the Chinese University of Hong Kong, had replied by email to his queries and confirmed he had agreed to the retraction and was “astonished” the article had produced such a negative response since it was only intended for thought provocation. He went on to apologize for the inconvenience caused to the Journal and anxiety caused to himself. He said he would never to write this kind of article again. [emphasis mine]

You might think it was a bad piece of science that was caught by the vigilant online community but according to an August 17, 2010 posting by Kent Anderson at the Scholarly Kitchen,

Recently, BioMed Central’s Virology Journal published a case report speculating that the woman in the Biblical story in which Jesus cures her of fever was suffering from the flu. The case report was obviously quite tongue-in-cheek, akin to many others in the literature, but also applied clinical reasoning to the scant evidence offered by the Bible.

In most case reports that seek to plumb historical facts, investigators review documentation, try to translate what they can into modern meaning, then attempt a diagnosis, usually for the sport of it.

…

I’ll wager that the authors and editors expected this little bit of fluff to pass quietly into oblivion, a harmless lark in an obscure journal. It’s not an unreasonable expectation. In the traditional journal world, reports like this were shielded from widespread evaluation due to relatively small circulations in tight-knit communities. Even in the last decade, the lack of robust commenting on journal articles has helped insulate scholars.

Today, things are different. Now, a science blogosphere bent on sensationalism and hungry for topics is perfectly willing to pick up on a silly article and beat the bejeezus out of it.

Sometimes people behave badly. No system is a perfect bulwark against this tendency. So while the Virology Journal article had been peer-reviewed (which has its own problems),  it was the set of post-publication reviews which resulted in an apology both from the editor and the author who has promised he’ll never write this type of article again. In essence, a kind of mob mentality seems to have ruled and I expect that mob mentality will be seen in the PPPR process as well. My conclusion is that the more ways we have of disseminating and publishing information the better.

Open Science Summit nears

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The July 29 -31, 2010 Open Science Summit is almost upon us (first mentioned here in a June 29, 3010 posting). The summit organizers pose this notion to set the themes for their conference (from the summit’s home page),

Renowned physicist Freeman Dyson identifies two kinds of scientific revolutions, those driven by new concepts (theoretical), and those driven by new tools (technological).

In the last 500 years we’ve witnessed paradigm shattering conceptual shifts associated with names such as Copernicus, Newton, Darwin, and, Einstein. Simultaneously, the evolution of technology drives progress in unpredictable ways—Galileo borrowed principles from the technology of eye-glasses to pioneer the use of the telescope in astronomy, while Watson and Crick relied on Rosalind Franklin’s skill with X-ray diffraction (a tool from physics) to probe the structure of life. (Undoubtedly, Franklin’s contribution would have been more fully recognized under a true Open Science Paradigm.)

To this classification of scientific revolutions, we can now add a third kind, an Organizational Revolution, the advent of a truly “Open Science,” which will profoundly affect the pace and character of subsequent theory and tool-driven paradigm shifts.

Looking at the speakers scheduled, the summit offers an interesting range including Christine Peterson of the Foresight Institute, Special Agent Edward You of the US Federal Bureau of Investigation (FBI)*, Michael Eisen, co-founder of the Public Library of Science (PLoS), David Koepsell, author of Who Owns You?, and more. It does seem to be largely oriented to genomics, bioinformatics, and other biological sciences.

If you can’t attend in person, there will be live streaming by fora.tv, go here.

* The FBI is quite interested in reaching out to scientists as per my posting of  May 25, 2010 about an article in The Scientist titled, SYNTHETIC BIO MEET “Fbio”; You may soon be visited by an FBI agent, or a scientist acting on behalf of one. Here’s why and written by Jill Frommer. The article is now behind a paywall.

The Scientist opens its archives for a limited period of time

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I received an email from The Scientist magazine website alerting me to their special open access at almost the same time I came across a posting by Dave Bruggeman at Pasco Phronesis about a recent synbio and the FBI article in the very same magazine.

The original article by Jill Frommer titled, SYNTHETIC BIO MEET “Fbio”; You may soon be visited by an FBI agent, or a scientist acting on behalf of one. Here’s why, provides an overview of the current situation with regard to law enforcement agencies and practitioners in the life sciences field (note: The Scientist is primarily a life sciences magazine).

From Dave’s posting,

The Scientist has a long, detailed article outlining the Federal Bureau of Investigation’s relationship with the biological sciences community. Unfortunately, recent cases such as those of Thomas Butler and Steve Kurtz have established a more adversarial relationship between the FBI and the biological sciences than would be beneficial – for both sides. …

I think some history could help understand why there are challenges in this area, where the nuclear science/weapons research areas didn’t quite have the combination of ambivalence and distrust that come through in the Scientist piece.

It’s well worth looking at both pieces, now especially if you are loathe to register at The Scientist for the privilege of reading an article. Note: I registered a while back and they send a monthly notice about the latest issue but have never bothered me otherwise.