"Science Policy and Perspectives" via Brandon in Google Reader

08/05/09 PHD comic: 'Nature vs. Science, pt. 4'

2009-08-07T18:49:25Z

Piled Higher & Deeper by Jorge Cham		www.phdcomics.com

title: "Nature vs. Science, pt. 4" - originally published 8/5/2009 For the latest news in PHD Comics, CLICK HERE!

Journal of FUBAR and Negative Results

2009-07-29T17:57:17Z

Last evening I attended a panel discussion entitled, “Making the Web work for Science” hosted by Science Commons. It was held at the Commonwealth Club in San Francisco and moderated by Tim O’Reilly. On the panel were Jimmy Wales, founder of Wikipedia; Stephen Friend, MD, PhD President, CEO and a Co-Founder of Sage; and John Wilbanks, VP of Science at Creative Commons.

While I was hoping more would be discussed on modeling the habits of researchers with web tools, the focus on Open Science was still a good conversation. At one point, Dr. Friend mentioned the need to publish negative results. With the ability to inexpensively self-publish and distribute data on the Web, why then, aren’t we seeing more of this?

Trying to answer from my own experience as a researcher, there are at least three reasons, or rather fears:

Negative results make either you look bad or your model look bad.
The competition will learn what not to do, iterate improvements faster than you, and could end up scooping you.
Negative results do not help you gain tenure or funding. So, why bother with the time involved in the write-up?

For the greater good of science, these points are superficial. As Dr. Friend pointed out, people need to read about negative results, so that the same wheel is not reinvented over and over again. While traditional journals do not have the capacity or resources to include negative results for peer-review and publication, the Web does.

While I was a doctoral candidate I faced this situation. My PI did not want to try to publish some results I had gotten from a project on mouse hematopoietic stem cells and gene therapy. The results were not even entirely negative, but were mild improvements over the existing science. In a thesis committee meeting, I was shocked to hear the response of one of my advisors, a Nobel Laureate, “Publish it. We need that information to build upon it.”

Sadly, those results never did make it into a proper journal, only my dissertation, yet because of the Web, that chapter is now freely available to everyone. I published it on my Mendeley profile. Download the awesomeness .

What about those three fears listed above though?

Negative results do not make you look bad. The key, of course, is that not all of your research is negative, but if you are actively self-archiving your negative results, that will get you recognized in a positive light. You will be considered a contributor to science.
Getting scooped. For one, I am not sure that has been proven (citation anyone?). And in fact, there is evidence to suggest that being open with your data will garner more citations. And in any event, if you are the first to publish the negative results that lead to an eventual positive, the credit and recognition, our incentives as researchers, will be given. The Internet and proper citation of previous (negative or positive) research demands it.
The Web is built such that long write-ups are not necessary. Publish the raw data and the materials and methods. How long does that really take? Then let the community come in to draw conclusions in a “living report.” The Wikipedia style. Small chunks of data are better than none, and perhaps better if it comes out faster. And getting back to fear #1, if you are considered the authority in publishing data on the Web in your field, that is going to get recognized by funding and tenure committees.

The Web is a wide-open frontier for the taking. There are very few experts in any field archiving their negative (or positive) data on the Web for others to annotate. Now would be the time to stake a claim on your piece of the frontier. While some are using Mendeley to do that, others are using PLoS ONE. Whichever outlet you choose, the world needs those FUBAR results.

To learn how Mendeley can help you publish and organize research, go here.

Follow Jason Hoyt, PhD on twitter here.

07/17/09 PHD comic: 'Nature vs. Science, pt. 2'

2009-07-19T19:27:44Z

Piled Higher & Deeper by Jorge Cham		www.phdcomics.com

title: "Nature vs. Science, pt. 2" - originally published 7/17/2009 For the latest news in PHD Comics, CLICK HERE!

07/15/09 PHD comic: 'Nature vs. Science, pt. 1'

2009-07-17T10:01:34Z

Piled Higher & Deeper by Jorge Cham		www.phdcomics.com

title: "Nature vs. Science, pt. 1" - originally published 7/15/2009 For the latest news in PHD Comics, CLICK HERE!

Are there too many PhDs?

2009-06-16T21:54:53Z

Ever hear of Douglas Prasher? Probably not. He just missed out on this past year’s Nobel in chemistry. That’s not unusual, as many scientists never even come close to a Nobel. What is unusual, is that Dr. Prasher works at a car dealership, not in a lab. Despite doing the critical research on discovering GFP that became the work for last year’s Nobel Prize, he was unable to find grant money and a job to continue his work.

Prasher’s story is what concerns me with science, engineering, math, and technology. In the U.S., we are constantly hearing about how the country is falling behind in science. We need more scientists to fill all of those jobs we want to create. And the cure to that is to fund more PhD programs! Yet, when you ask graduate students and postdoctoral scholars what their individual experiences are, a science career is a very tough road with low pay and few career prospects. It’s such a tough path that an entire PhD comic strip was born to alleviate the situation with laughter. Why then, is there such a disconnect?

As a friend of mine, who has worked for two decades in both academia and industry, recently put it, “it’s a Ponzi scheme” (name withheld to protect his job). Large corporations and universities need a lot of workers to meet their objectives. While conspiracy theories abound over biopharma lobbying the government for more PhDs with the secret ambition to lower wages, it doesn’t seem too far-fetched. Universities need grad students and postdocs to churn out the papers that bring in grant money for the professors. While that is a well-established tradition going on for more than a century, what is different now is how we are attracting students into science careers. With tuition paid-in-full PhD programs and benefits as a graduate student, many who would normally not enter science are lured in. Reality usually hits after the second year, in which qualification exams to continue in the programs are taken. Only then, do students realize the road that lies ahead is dotted with pit stops leading, not to Nobel glory, but a journeyman career with salaries well below that of their friends who went into business, law, or medicine. With a PhD, a postdoc can expect to start, at most, US $42K a year in academia and $52K in industry.

More over, 45% of all recent doctorates are now taking postdoc positions prior to a faculty appointment. This contrasts with only 31% following the same path 25 years ago (see NSF). And postdoc positions are increasing in length of time as well, and are often followed by a second or even third “tour of duty.” While the National Science Foundation’s (NSF) most recent data shows an average of two years per postdoc across all disciplines, my own anecdotal experience in the life sciences shows that number is closer to four years.

In reality, more PhDs are a good thing, but should something be done to help out recent graduates and what could be done? President Obama has included just a 1.5% increase in the National Institutes of Health (NIH) budget for 2010, which doesn’t even make up for the lost years of keeping up with inflation under the Bush era. Obama has promised to double NIH’s budget within 10 years. Great, but how will that money be spent? The NIH budget doubled from $7.5 billion in 1990 to $15.5 billion in 1999 and has doubled again to $30 billion in 2009, yet the career path to a tenured faculty position has become a tougher pill to swallow. While more money in science is a great thing and should be increased, the data suggests that money alone is not the answer to improving the engineer/scientist quality of life. Specific policy to increase salaries would do this, but the reality of that occurring is thin at best. And as data from the NIH shows in the figure below, despite an ever growing number of PhDs and increased national budgets, there are disproportionally fewer young faculty receiving NIH grants.

This is a fairly dark picture that has just been described. Being somewhat of an optimist, there are some changes beginning to occur that give me hope. As usual, it is a grassroots movement that is taking the lead. In the United States, The National Postdoctoral Association was established in 2003. It has made some major accomplishments in getting the NIH, NSF, and more than 160 universities to adopt new policies. The biotech industry was born in the late 1970s, and despite visions of grand careers in science, it has largely failed to deliver. One could argue that this failure is more related to the biotech industry being a failure itself, since it was billed as the “next computer industry.” Ironically though, biotech is slowly morphing with the computer industry in the form of genomics and computational biology. And the computer industry is starting to meet science in the middle with specific programs from Google, Microsoft, IBM, and others. And of course, Mendeley is a melding of academia with computers and online tools.

Despite calls for promoting alternative careers in graduate school, in the end it is going to be a slow organic movement toward cross-disciplinary careers, perhaps with in silico technology, that improves the life of a PhD. An actionable example of this would be the Singularity University hosted at NASA Ames, which is having its inaugural class this year. The “University” part is a bit of a misnomer, as it is really just a nine-week networking event with an intense lecture schedule. And it is far too early to measure its beneficial impact. However, this may serve as inspiration for real universities to establish more practical PhD programs alongside the critical basic research type of degrees.

Curiously, science has always been more of an art than a science, and artists are often exploited. With computers, one can remove artistry, at least somewhat. If there’s one piece of advice for graduate students and postdocs, it would be to inject a bit of computational work into your career. Don’t wait for policy changes to create greater salaries, benefits and more tenured positions. While treading the same arduous path that our predoctoral or postdoctoral advisors tread has become regarded as a rite of passage, it doesn’t need to remain such. The story of one Douglas Prasher losing a Nobel is one too many.

Update – A few others have also started a discussion over on Friendfeed

To learn how Mendeley can help you publish and organize research, go here.

Jason Hoyt, PhD is on Twitter and Mendeley

Brain Scanning May Be Used In EU Security Checks

2009-05-12T12:59:00Z

An anonymous reader writes with this excerpt from the Guardian: "Distinctive brain patterns could become the latest subject of biometric scanning after EU researchers successfully tested technology to verify identities for security checks. The experiments, which also examined the potential of heart rhythms to authenticate individuals, were conducted under an EU-funded inquiry into biometric systems that could be deployed at airports, borders and in sensitive locations to screen out terrorist suspects." The same article says that "The Home Office, meanwhile, has confirmed rapid expansion plans of automated facial recognition gates: 10 will be operating at major UK airports by August." I wonder what Bruce Schneier would have to say about such elaborate measures.

More Fake Journals From Elsevier

2009-05-09T16:16:00Z

daemonburrito writes "Last week, we learned about Elsevier publishing a bogus journal for Merck. Now, several librarians say that they have uncovered an entire imprint of 'advertorial' publications. Excerpta Medica, a 'strategic medical communications agency,' is an Elsevier division. Along with the now infamous Australasian Journal of Bone and Joint Medicine, it published a number of other 'journals.' Elsevier CEO Michael Hansen now admits that at least six fake journals were published for pharmaceutical companies."

Secret cabal of Bisphenol-A companies meets to sell the public endocrine disruptors

2009-06-01T08:57:12Z

Jimmy sez, "Someone leaked the minutes for a meeting of food-packaging executives and chemical industry lobbyists seeking to find ways to keep consumers buying goods laced with bisphenol-A. Attending companies included Coca-Cola, Del Monte, Alcoa and the Grocery Manufacturers Association (GMA)."

Attendees suggested using fear tactics (e.g. "Do you want to have access to baby food anymore?") as well as giving control back to consumers (e.g. you have a choice between the more expensive product that is frozen or fresh or foods packaged in cans) as ways to dissuade people from choosing BPA-free packaging. Attendees noted, in the past, the different associations have had a reactive strategy with the media, with very limited proactive outreach in reaching out to journalists. The committee agrees they need to promote new, relevant content to get the BPA perspective into the media mix. The committee believes industry studies are tainted from the public perspective.
The committee doubts social media outlets, such as Facebook or Twitter, will work for positive BPA outreach. The committee wants to focus on quality instead of quantity in disseminating messages (e.g. a young kid or pregnant mother providing a positive quote about BPA, a testimonial from an outside expert, providing positive video, advice from third party experts, and relevant messaging on the GMA website). Members noted traditional media outreach has become too expensive (they have already spent hundreds of thousands of dollars) and the media is starting to ignore their side. The committee doubts obtaining a scientific spokesperson is attainable. Their "holy grail" spokesperson would be a "pregnant young mother who would be willing to speak around the country about the benefits of BPA."

I don't know if these are real or not, though I am inclined to trust ScienceBlogs as a source overall, there's precious little provenance here (on the other hand, the industry association has confirmed that a document like this leaked).

BPA gets attention from industry spinmeisters (leaked minutes)

Merck paid Elsevier to publish fake journal, with no editor or board, filled with results favorable to Merck.

2009-05-01T17:55:54Z

submitted by londonzoo to science
[link] [75 comments]

Neuroethics Diavlog

2009-05-15T01:30:00Z

Brains and Gavels: Science writer Carl Zimmer discusses neuroethics with cognitive science pioneer Michael Gazzaniga.

Brain and behaviour video curating at PsychCentral, the web's most trusted source of mental health info.

data.gov is Live

2009-05-21T22:21:12Z

Twitter is currently echoing the excitement of open data advocates and data geeks alike, due the release of data.gov, an open and free web repository that aims to provide public access to US Federal Government datasets. Or, in official terms: "The purpose of Data.gov is to increase public access to high value, machine readable datasets generated by the Executive Branch of the Federal Government". However, while this means that the data has finally become freely available, it is certainly not yet accessible or even understandable for lay people. The huge homepage banner "Discover. Participate. Engage." therefore seems a bit hollow, as long as there are no interfaces and visualizations to really allow the general audience to explore the knowledge and insights hidden within. We are therefore all curious when and what online data visualizations will soon exploit this opportunity to bring data closer to people!

Hence Sunlight Labs has just launched, in partnership with Google, O'Reilly Media and TechWeb, a contest called "Apps for America", including $25,000 in awards." The contest submissions will also show the creativity of developers in designing compelling applications that provide easy access and understanding for the public, while also showing how open data can save the government tens of millions of dollars by engaging the development community in application development at far cheaper rates than traditional government contractors."

If you are interested in data.gov, you might also like USgoXML.com, another index of web services and XML data sources that have been provided by the US government.

You might also want to know that today was also the launch of the Open Government Initiative website.

More information and (mixed) reviews about the data.gov website can be found at Huffington Post, Wired and ReadWriteWeb, and probably at many more news outlets very soon.

European Union, what are you waiting for?

On the information alarmageddon

2009-05-23T08:00:00Z

New York Magazine has an article arguing that the concerns about digital technology drastically affecting our minds are just hype. I really wanted to like it but it's just another poorly researched piece on the psychology of digital technology.

Research has shown that distraction can improve exactly the sorts of skills that the digital doomsayers say will be broken by the high-tech world, but I've never seen it mentioned in any of the recent high-profile articles on the predicted digital meltdown.

In fact, there is a fairly sizeable scientific literature on how interruption affects the ability to complete a task, and instant messaging has been specifically studied.

But despite getting lots of opinions from everyone from attention researcher David Meyer to lifehacker Merlin Mann only one single 'study' on the distracting effect of technology is mentioned in the New York Magazine article: "people who frequently check their email has tested less intelligent than people who are actually high on marijuana".

This is quite amazing because not only was the 'study' in question not an actual scientific study, it was PR stunt for Hewlett Packard, this isn't even an accurate description of it (users were interrupted with email during an IQ test and scored worse, big surprise).

The issue actually breaks down into two parts, one is a scientific question: what is the psychological effect of distraction? and the other, a cultural one: have we become a society where high levels of distraction are more acceptable?

As I mentioned, the first question has been very well researched and the general conclusion is that distraction reduces our ability to complete tasks. Essentially, it's saying that distraction is distracting, which is hardly headline news.

But it also turns out that distraction is most disruptive to stimulus based search tasks, when we are flicking our attention around scanning for bits of information. Perhaps unsurprisingly, when we're on alert for new and different things, something salient like an instant message grabs our attention and knocks us off course.

More thoughtful tasks involving processing meaning are the least affected. This is interesting because most of the digital doomsayers suggest it is exactly this sort of deep thought that being affected by communication technology.

The other line of argument is that all this distraction makes us less creative because creativity needs focus to flourish.

Although not as well studied, it seems this is unlikely. While we assume that distraction reduces creativity, but lab studies tend to show the reverse.

Distraction has also been found to improve decision making, especially for complex fuzzy decisions - again exactly the sort that the doomsayers say will most be at peril.

These studies find that too much concentration reduces our creative thinking because we're stuck in one mind-set, deliberately filtering out what we've already decided is irrelevant, thereby already discarding counter-intuitive ideas (actually this is something the article does touch on). We can speculate that this may be why a preliminary study found that amphetamine-based concentration drug Adderall reduced creativity.

The cultural issue is perhaps more important, but on an individual level is more easily addressed.

You have control over the technology of distraction. If you can't concentrate, switch it off. It it is your job to be distracted and it is affecting other essential parts of your role, that is something to take up with your employers.

It's no different than if you're being distracted by the sound of traffic and can't do your job. Maybe you need an office away from the street? If you or your employers can't do anything about it, maybe that's just one of the downsides of the job.

What research hasn't yet shown is that digital technology is having a significant negative influence on our minds or brains. In some cases, it's showing the reverse.

History has taught us that we worry about widespread new technology and this is usually expressed in society in terms of its negative impact on our minds and social relationships.

If you're really concerned about cognitive abilities, look after your cardiovascular health (eat well and exercise), cherish your relationships, stay mentally active and experience diverse and interesting things. All of which have been shown to maintain mental function, especially as we age.

Technology has an impact on the mind but it's a drop in the ocean compared to the influence of your health and your relationships.

I'm constantly surprised that the impact of technology is clearly of such widespread interest to merit headline grabbing articles in international publications, but apparently not interesting enough that journalists will actually use the internet to find the research.

It's like writing a travel guide without ever visiting the country. I'm just guessing the editors have yet to catch on to the scam.

Link to NYMag article 'In Defense of Distraction'.

U.S. science policy. NSF is keeping it simple.

2009-05-17T20:36:33Z

Publication Date: 2009 Apr 17 PMID: 19372396
Authors: Mervis, J.
Journal: Science

MeSH Categories: Budgets, Financing, Government/*legislation & jurisprudence, Research Support as Topic/*legislation & jurisprudence, United States, United States Government Agencies/economics/*legislation &, jurisprudence/organization & administration

post to: CiteULike

U.S. science policy. NIH stimulus plan triggers flood of applications--and anxiety.

2009-05-17T20:36:28Z

Publication Date: 2009 Apr 17 PMID: 19372395
Authors: Kaiser, J.
Journal: Science

MeSH Categories: Biomedical Research/economics/*legislation & jurisprudence, Budgets, Financing, Government/*legislation & jurisprudence, National Institutes of Health (U.S.)/economics/*legislation &, jurisprudence, Research Support as Topic/economics/*legislation & jurisprudence, United States

post to: CiteULike

Newsmaker interview. John Holdren brings more than energy to his role as science adviser. Interview by Jeffrey Mervis.

2009-05-17T20:36:02Z

Publication Date: 2009 Apr 17 PMID: 19372403
Authors: Holdren, J.
Journal: Science

MeSH Categories: Conflict of Interest, Disclosure, Evolution, Financing, Government/legislation & jurisprudence, Nuclear Weapons, Research, *Science/education, Security Measures, Space Flight, United States

post to: CiteULike

How to keep science moving.

2009-05-14T19:13:52Z

Publication Date: 2009 Apr 24 PMID: 19390006
Authors: Cicerone, R. J.
Journal: Science

post to: CiteULike

Science in the White House.

2009-05-14T18:55:44Z

Publication Date: 2009 May 1 PMID: 19407163
Authors: Holdren, J. P.
Journal: Science

MeSH Categories: *Biomedical Research, *Public Policy, *Research, *Science, *Technology, United States

post to: CiteULike

Science and society. Hundreds gather for rally to defend animal research.

2009-05-14T18:55:28Z

Publication Date: 2009 May 1 PMID: 19407165
Authors: Miller, G.
Journal: Science

MeSH Categories: *Animal Experimentation/legislation & jurisprudence, *Animal Rights, Animal Welfare, Animals, California, Humans

post to: CiteULike

Brain imaging skewed.

2009-05-14T16:49:36Z

Publication Date: 2009 Apr 30 PMID: 19415822
Authors: Abbott, A.
Journal: Nature

post to: CiteULike

Can a computer discover scientific laws?

2009-05-12T18:24:02Z

In his first column for Seed magazine, my Institute for the Future colleague and pal Alex Pang looks at efforts to create software that doesn't just support scientific discovery, it actually does new science. From Seed:

Older AI projects in scientific discovery tried to model the way scientists think. This approach doesn’t try to imitate an individual scientist’s cognitive processes — you don’t need intuition when you have processor cycles to burn — but it bears an interesting similarity to the way scientific communities work. (Cornell professor Hod) Lipson says it figures out what to look at next “based on disagreement between models, just as a scientist will design an experiment that tests predictions made by competing theories.”

But that doesn’t mean it will replace scientists. (Cornell graduate student Michael) Schmidt views it as a tool to see what they can’t: “Something that is not obvious to a human might be obvious to a computer,” he speculates. A program, says Schmidt, may find things “that look really strange and foreign” to a scientist. More fundamentally, the Cornell program can analyze data, build models, and even guess which theories are more powerful, but it can’t explain what its theories mean — and new theories often force scientists to rethink and refine basic assumptions. “E=mc2 looks very simple, but it actually encapsulates a lot of knowledge,” Lipson says. “It overturned a lot of older preconceptions about energy and the speed of light.” Even as computers get better at formulating theories, “you need humans to give meaning to what the system finds.”

Why We're Not Obsolete: Alex Pang in Seed