Many of you know that I have my favorite blogs and I regularly check in with Derek Lowe over at "Corante: In the Pipeline." Derek once worked at "Wonder Drug Factory," which was not too far away from where I currently am working. Now, he is in Boston. He shares his posts regularly on this blog: http://pipeline.corante.com/

I wanted to share a recent posting with you, which covers some insights into understanding 'open-source science.' He points out that coming from industry with IP laws and such, the idea doesn't really make sense for him. However, upon closer inspection, Derek points out that science really has been 'open-source' from the beginning. Of course, since the very idea of having an idea is important for getting grants, putting thoughts into cyberspace is, at least for many of us, risky.

"August 22, 2008
Open Source Science?
Posted by Derek

The Boston Globe has a piece on the open-source science movement. Many readers here will have come across the idea before, but it’s interesting to see it make a large newspaper. (Admittedly, the Globe is more likely to cover this sort of thing than most metropolitan dailies, given the concentration of research jobs around here).

The idea, as in open-source software development, is that everything is out in a common area for everyone to see and work on. (Here's one of the biggest examples). Ideas can come from all over, and with progress coming more quickly as many different approaches get proposed, debated, and tried out. I like the idea, in theory. Of course, since I work in industry, it’s a nonstarter. I have absolutely no idea of how you’d reconcile that model with profitable intellectual property rights, and I haven’t seen any scheme yet that makes me want to abandon profit-making IP as the driver of commercial science. Of course, there's always the prize model, which is worth taking seriously. . .

Even for academic science, open source work runs right into the traditional ideas of priority and credit, and the article doesn’t resolve this dilemma. (As far as I can tell, the open-source science advocates haven’t completely resolved it, either). There’s always the lingering (or not-so-lingering) worry about someone scooping your results, and for academia there’s always that little question of grant applications. There have been enough accusations over the years in various fields of people lifting ideas during grant proposal reviews or journal refereeing to make you wonder how well a broader open-source system would work out, given the small but significant number of unscrupulous people out there.

On the other hand, maybe if things were more open in general, there would be less incentive to lift ideas, since the opportunities to do so wouldn’t be so rare. And if someone’s name is associated from the beginning with a given idea, on some open forum, it could make questions of priority easier to resolve. A subsidiary problem, though, is that there are people who are better at generating ideas than executing them – some of these folks, once unchained, could end up with their fingerprints on all sorts of things that they’ve never gotten around to enabling. Of course, that might be a feature rather than a bug: people who generate lots of ideas are, after all, worth having around. And over time, there might well be less of a stigma than there is now for someone else to follow up on these things.

The thing is, science has already been a form of open-source work for hundreds of years now. It’s just that the information has been shared at a later stage, though presentations and publications, rather than being put out there right after it’s been thought up or while it’s being generated. That’s why I always shiver a bit when I read about how long Isaac Newton waited before writing up any of his results – if Edmund Halley hadn’t pressed him to do it, he might never have gotten around to it at all, which would have been a terrible tragedy.

And it’s why stories like those told of physicist Lars Onsager strike me as somehow wrong. Onsager was famous for only publishing his absolute best work – which was pretty damned good – and putting the rest into his copious file cabinets (example here). (A related trait was that he was also apparently incapable of lecturing at any comprehensible level about his work). Supposedly, younger colleagues would come by once in a while and tell him about some interesting thing that they’d worked out, and ask him if he thought it was correct. Onsager would pause, dig through his files, pull out some old unpublished work that the new person had unknowing duplicated, and say “Yes, that’s correct”. It seems to me that you don’t want to do that, withholding potentially useful results for the sake of what is, in the end, a form of vanity.

And although I'm not exactly Lars Onsager, this is as good a time as any to mention that my summer student, who’s finishing up in the lab this week, has been able to generate a lot of interesting data, and that I’m going to be trying to write it up this fall for publication. Readers may be interested to know that this work is based on more ideas I’ve had in the vein of the “Vial Thirty-Three” project detailed here, so with any luck, people will eventually be able to see some of what I’ve been so excited about all this time. And that’s about as open-source as this industrial scientist can get!"

I noticed a very good article that should be read by all who believe that there is a scientific shortage in the United States. This blog, http://www.scienceprogress.org/2008/08/its-the-money-stupid/, indicates the fact that there is a very large margin between those students at the top of their game and those at the very bottom. The phrase "an enticing promise, an elusive goal" sums up the experience of many of the best and brightest pursuing science careers. All too often, the promise leads to an indefinite period of graduate school and postdoc training, which for many, is a difficult road that doesn't necessarily lead to any particular goal. Rather the inherent mobility that must take place for one's training in order to work at the "right institution" and for the "right person" can dissolve the familial roots. The author, a writer for ScienceCareers mentions that this option is not necessarily a good investment. A very good read for anyone considering a postdoc in the US and a reality check for all.

This quote pretty much sums it up:

"“I try to keep my best undergraduates away from my postdocs,” one professor confided, because meeting them would reveal what really lies ahead on the grad school track. But talented young Americans would flock to science study if it offered them the kind of career opportunities that previous generations enjoyed. Instead of a needless general overhaul of K -12 education, or an increase in graduate fellowships, which would only make things worse, the United States needs to overhaul what Brown University biochemistry chair Susan Gerbi calls the “pyramid paradigm.”"

WAYS has often talked about increasing accessibility to journals. As PLoS and other journals have allowed free-access, other journals/publishers are also beginning to increase accessibility. Publishers are now enabling access to biomedical journals through "Health InterNetwork Access to Research Initiative (HINARI). (See: http://www.who.int/hinari/en/)

Still, in many areas, the lack of physical infrastructure supersedes these initiatives. Hopefully, this may come online in a sustainable manner in the near future.

Young scientists, prepared with the skills of diplomacy, critical thinking, decision-making, and technical knowledge are in a position to stand at the forefront of economic growth. This link http://news.bbc.co.uk/2/hi/africa/7534315.stm describes a critical place where such input may be invaluable. Perhaps WAYS Africa can work together with policy makers and be empowered.

Before digital imaging, PIs could feel reasonably confident about the data that were being presented. In this day of age, however, with the advent of scanners and Photoshop, images can be readily manipulated. This article http://chronicle.com/weekly/v54/i39/39a00102.htm mentions the new trend for journals to be on the lookout for pictures that have been manipulated. Note, there are distinctions between changing the contrast of a whole image and changing the contrast of only on lane in your image. As research becomes more competitive, we must be vigilant about who works for us and the data being presented (before it goes to be reviewed).

Many of us are thinking about how to make the transition from "trainee" to "employee." As the types of jobs in the future are likely to be somewhat different from those already available, we may have the chance to 'trailblaze' and enable ourselves to offer skills in the emerging fields. This article (http://www.fraunhofer.de/EN/press/pi/2008/05/PressRelease03June2...) mentions potential future opportunities and gives hints about how we may be able to fully utilize our backgrounds.

Fraunhofer frontline themes: Tomorrow’s opportunities

People need an affordable healthcare system, security, energy, communications, mobility and a clean environment. The Fraunhofer-Gesellschaft has identified strategic research areas in which it is seeking answers to these challenges of the future. In focusing on twelve frontline themes, Fraunhofer is pointing out particularly effective courses of action. Its objective is to employ new technologies to devise solutions that will make our life healthier, safer and simpler, and will be kinder to the environment.

“The interests of ordinary people, their wishes and needs must always be a prime consideration in our research work,” says Fraunhofer President Professor Hans-Jörg Bullinger, explaining the approach taken by the research organization. “We have identified six research areas in which we believe that future technologies and products will be of the greatest benefit to mankind. People need health, an intact environment, security, communication, energy and mobility. These are the areas on which we will focus our research capacities in the years to come.”

Starting with these six focal areas, Fraunhofer has conducted an intensive discourse and identified fields of research that will be as fast and effective as possible in helping to meet present-day challenges such as global warming, dwindling resources and health problems. “In pursuing these twelve frontline themes, Fraunhofer is demonstrating its active role in securing the future of Germany as an industrial location. We not only show where tomorrow’s opportunities lie, but also systematically develop innovative solutions,” states Bullinger. “In order to do this, we invest our own funds in preliminary research and pool our distributed expertise in a manageable selection of frontline themes.”

Under the motto of “Fraunhofer frontline themes: Tomorrow’s opportunities”, interdisciplinary teams of scientists and engineers are working on new technologies and solutions that will help to make our life healthier, safer, simpler and more mobile. There are twelve different project:

Focus on health

Personal health assistant
The electronic guardian angel
Smart assistance systems can help even sick and elderly people to lead independent lives in their own homes. One such system is the digital health assistant. It monitors patients’ cardiovascular functions 24 hours a day, enabling them to contact medical specialists in the event of an emergency. Preventive healthcare, diagnostics, therapy and care are other areas of application for this technology.

Bio-functional surfaces
High tech with a sensitive skin
Medical implants are intended to uphold bodily functions, monitor individual risks or facilitate long-term treatment plans. In future this will be made possible by bio-functional surfaces: The “skin” of a material, instrument or device performs a specific function when in contact with biological environments. It picks out certain molecules, receives signals or stimulates a response.

Food chain management
Always fresh on the table
Kiwi fruits from New Zealand, mangos from Thailand, beef from Argentina – today’s shoppers can find an international selection of goods even in small supermarkets. However, globalization also poses challenges: Foodstuffs have to be produced in accordance with current food regulations, properly packaged and shipped, and finally arrive fresh on the customer’s table. Food chain management makes it possible to display and optimize the entire food production chain – from production and processing to the retailer and the end customer.

Focus on the environment

Decentralized integrated water management
Saving precious water
In Germany we consume a lot of water: over 130 liters per head dayly. If we are to continue providing high-quality drinking water at low prices in future, the water consumption must be cut. New technologies help to use drinking water economically and treat wastewater to make it suitable for domestic use. Intelligent sensors monitor the systems and report such failures as leaky water pipes.
Focus on energy

Energy-efficient modernization
More than just a facade
About one-third of the energy consumed in Germany goes into regulating the temperature in buildings. Old buildings, in particular, need a lot of energy: They eat up between three and five times as much heating energy as modern houses. Up to 80 percent of this energy could be saved by good insulation coupled with efficient heating and cooling systems. Researchers are testing multifunctional facade modules and new heat storage units for internal insulation. Planar heating and cooling systems for walls, ceilings and floors are taking shape in the laboratory.

Solid-state light sources
Bright and efficient illumination
A light bulb converts only 5–10 percent of the invested energy into light; most of it is diffused as heat. A team of seven Fraunhofer Institutes is developing alternatives: highly efficient cold light sources made of semiconductors. The researchers’ objective is to develop new light sources that produce an effect similar to daylight, and whose form and intensity can be adapted to any desired situation.

Energy storage in power grids
Solar and wind-generated electricity on demand
Renewable resources will play an increasingly significant role in the energy mixture of the future. But they are more difficult to calculate. The amount of current fed into the grid depends on the weather and the time of day. Fraunhofer scientists are working to make the supply of wind and solar energy as easy to plan as the production of energy at conventional power stations. For this to succeed, they need new and more efficient power storage units.

Green power train technologies
New impetus for eco-friendly cars
Very high demands are made on tomorrow’s cars: They must use up a minimum of natural resources during manufacture, have a low fuel consumption when driving, discharge as few pollutants as possible into the atmosphere, and require very little maintenance. Researchers from seven Fraunhofer Institutes are working to improve the power train, which comprises all the components involved in generating torque and transmitting it from the engine to the wheel. They are forging ahead with the development of the low-energy engine, the lightweight gear unit and the lightweight Cardan driveshaft.

Focus on security

Energy self-sufficient sensors and sensor networks
Vigilant clusters
The sensors of the future are tiny, robust, inexpensive and can be used anywhere. They draw their energy from motion, light or temperature differences. Because these sensors are interlinked, they not only acquire highly significant and conclusive data, but also improve a system’s responsiveness and reliability. Sensors like these can be used for purposes such as the monitoring of tunnels.

Focus on communication

Visual analytics
A clear overview in the data jungle
The Internet, company networks, sensors, simulations and electronic processes deliver a wealth of information. But how can you filter out just the precise information that really matters from this huge mass of data? “Visual analytics” provides a solution, making the best possible use of the different abilities of humans and computers. The computer processes large quantities of data and converts them into a visual display that people can understand. The user can concentrate on pattern recognition and the evaluation and analysis of the data studied.

Focus on mobility

Hybrid material structures
Combining the best of the best
The demands made on products and their properties are steadily becoming greater and more complex. Products are expected to offer a wealth of functions, weigh as little as possible, be easy to handle, and cost as little as possible to buy and maintain. This cannot always be achieved to the desired extent using conventional materials. One solution is to use composite materials, which combine different materials and their most useful properties. The researchers see the greatest market potential for hybrid materials in the vehicle and machine construction industry.

Integrated localization technology
On the move – quick and safe
Fraunhofer researchers are working on a unified technology for locating people and goods. Designed to benefit industry and commerce, transportation and mobility, it is based on global satellite navigation systems (GNSS) such as Galileo, which – unlike GPS – is not subject to military control. One of its objectives is to keep a constant watch on goods being unloaded in ports and transferred to rail or road vehicles. The new platform also offers numerous advantages for passenger transportation: Integrated navigation even for pedestrians, and parking without searching, are just two examples.

These twelve frontline themes will be systematically further developed by Fraunhofer researchers in the coming years and translated into practical day-to-day solutions. They will open up new opportunities for the German economy, which can only maintain its competitive edge through constant innovations.

If one is considering the prospects of coming to the (or living in the) US for any type of training mechanism, it is very important to be aware of the current trends in funding. Young scientists need to think strategically about their careers and how to better make sustainable arguments on funding practices to those whom are in charge of allocating funds. You can bet that I will be one of those people advocating for this type of activity and that I will utilize the skills of understanding pitfalls (garnered from my grant writing activities) in investing in human capital for the future. This article describes what is going on with those whom are at the top of their fields and how they are seeing their lives and careers. A must read...

See: http://www.brokenpipeline.org/materials.htm

On my recent reading of some blogs this week, I have been noticing a lot more people discussing plagiarism and what it means for research. Some people think ethics classes are the way to tackle the issue, but as papers are, for researchers, the currency that is paid to land a position, it likely becomes tempting... I came across this website, which apparently looks for similar text in published papers. Since 2000, the numbers of papers published containing material that has been "recycled" have reportedly increased. If any of you are involved in reading manuscripts/editing/reviewing proposals/grants/etc., you may appreciate this... See: http://invention.swmed.edu/etblast/etblast.shtml

Anyone reading Grist out there?
Recently, there was a major case involving a farmer and the seed company, Monsanto. While I am not a part of either party, the story is interesting.

Given the nature of breeding plants and the fact that pollen can travel pretty freely, it is frightening to think that Monsanto has, "according to a comprehensive 2005 study [PDF] by the Center For Food Safety, ' an annual budget of $10 million and a staff of 75 devoted solely to investigating and prosecuting farmers.' By the time of the study, the company had launched 90 lawsuits involving 147 farmers and 39 small businesses, CFS reports." I find this incredibly alarming and a disaster for farmers.

Enjoy the New Year. There is room to make a difference. Enjoy the following movie, which may be just as interesting as some of the TED movies we've been discussing lately.

http://www.storyofstuff.com/