Category Archives: Web 2.0

Open science 0.9 beta

sunrise by Wolfgang Staudt
The science exchange:
[Via Science in the open]

How do we actually create the service that will deliver on the promise of the internet to enable collaborations to form as and where needed, to increase the speed at which we do science by enabling us to make the right contacts at the right times, and critically; how do we create the critical mass needed to actually make it happen? In another example of blog based morphic resonance there has been a discussion a discussion over at Nature Networks on how to enable collaboration occurred almost at the same time as Pawel Szczeny was blogging on freelance science. I then hooked up with Pawel to solve a problem in my research; as far as we know the first example of a scientific collaboration that started on Friendfeed. And Shirley Wu has now wrapped all of this up in a blog post about how a service to enable collaborations to be identified might actually work which has provoked a further discussion.
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Open Science is really in the very early stages. It may very well evolve into an important adjunct for research. Collaborations are the prime driver of much of today’s science.

Collaboration is difficult in some organizations. Without it, they will not be able to effectively solve the difficult questions in science today. The organizations that can harness effective collaborations will survive and flourish.

Currently, collaborations are usually set up using well known social networking skills honed through years of experience. Who you know is important. What Open Science holds the potential for, when it comes to collaborations, deals with who you don’t know.

OS can leverage an online community so that connections can be made that would have been difficult or impossible if face time was required. However, it will take a little work, like porcupines mating, to make this really effective.

Part of the reason for this is trust. Science has some free loaders, people who take short cuts. Not many but they can degrade interactions until trust is established. which takes a little time. Reputation is an important part of this trust.

There are many examples of peer reviewers abusing the process and scooping someone on a paper that they held up in review, giving the reviewer time to replicate the work in his lab and submit a paper.

Grant proposals have been abused in a similar fashion. Researchers have altered data in order to fit a preconceived hypothesis. Collaborating with such people is a possible danger without more information.

So trust and reputation will have to be a part of OS, particularly since the participants may not meet face to face. But reputation and trust are a common problem with many Web 2.0 approaches.

One way Web 2.0 surmounts this is the very openness and transparency that gives it power. Ebay, for example, would not work if people did not trust the seller to have the item and the buyer to have the cash. Being able to see how each rates the other help establish trust.

Research has shown that what is important in human social networks is not that the network prevents cheats or freeloaders from existing. It is that the network has a method for identifying them and expelling them from the network if they fail to change.

Now OS will not be like Ebay, which is a site of commerce. But the power of many eyeballs watching the interactions will help apply social norms to the most egregious behavior. A reputation lost in the open like this will be very difficult to untarnish.

Another important aspect of scientific collaborations is power, a very human trait. Scientists with power (i.e. large, well funded labs) sometimes have a very different view of a collaboration than those with a small lab and a single grant. People often tend to confuse large and well-funded with innovative.

Remember well funded does not always mean cutting edge investigations of important questions. Sometimes it means doing what everyone knows will work, just more of it with greater efficiency. Risk is many times found in the smaller labs, not the larger, something also seen in corporations. The unwillingness to take a risk, found in many large organizations, often make collaboration with smaller, risk-taking groups problematic.

But on the Internet, this sort of power is defused somewhat. There is a leveling effect, allowing many more researchers to have an equal voice. On the Internet, no one knows you are a dog. They also may not know whether you have a lab of 40 researchers and $10 million in grants. What will be important are your ideas and how you treat others in the network.

So, watch as this discussion happens out in the open, as it should. Become part of it if you can.

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Paul’s Principles of Web 2.0

Spider by aussiegall
Web 2.0: Building the New Library
[Via Ariadne]

Paul Miller wrote this over 2 years ago but it amply describes the effects of new approaches will have on an area that lives by dispersing information. It is not the technology that will make a difference. It is an attitude, one that is almost as old as humankind.

Sharing helps the entire team, tribe or town. The collective intelligence of the group is only strong when the umber of information chokepoints is low.

Paul’s Principles of Web 2.0, as discussed here, still apply in almost any endeavor that must deal with information to succeed. Here they are:

  • Web 2.0 presages a freeing of data, allowing it to be exposed, discovered and manipulated in a variety of ways distinct from the purpose of the application originally used to gain access.
  • Web 2.0 permits the building of virtual applications, drawing data and functionality from a number of different sources as appropriate.
  • Web 2.0 is participative.
  • Web 2.0 applications work for the user.
  • Web 2.0 applications are modular, with developers and users able to pick and choose from a set of interoperating components in order to build something that meets their needs.
  • Web 2.0 is about sharing: code, content, ideas.
  • Web 2.0 is about communication and facilitating community.
  • Web 2.0 is about remix.
  • Web 2.0 is smart.
  • Web 2.0 opens up the Long Tail.
  • Web 2.0 is built upon Trust.

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Change 2.0

change by josef.stuefer
6 Drivers of Change:
[Via HarvardBusiness.org]
There were discussions at the ‘Innovation:Change Happens’ panel during the the Newspaper Association of America and American Society of News Editors Capital Conference 2008. Several elements were were found to be common in the change experience:

• The need for a crisis or some kind of “burning platform” to motivate transformational change
• A clear vision and strategy … that allows room for iteration
• A recognition that transformation is a multi-year journey
• A need to put the customer or consumer in the center of the transformation equation
• The critical importance of demonstrating to skeptics that different actions can lead to different results
• The need to over-communicate to employees, customers, stakeholders, and shareholders

While the first three have been mentioned in many programs involving change, the last three are particularly important for any project utilizing Web 2.0 technologies.

The end user needs to be front and center. They are the ones generating the content and effecting change.

Skeptics need to be approached. In fact, many times they can be the best allies. Their skepticism often comes from a healthy sense of reality, since in many cases, talk of change accomplishes little. But, demonstrating what can be done, and how they can have a direct hand in that change, often converts them.

Things usually do not change simply because they should. It has to be sold. People have to be told many times just what is going on and why. Moving change from Early Adopters to the bulk of the organization is what over-communication accomplishes.

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Openness helps everyone

Bursty science depends on openness:
[Via Science in the open]
An example of a social network diagram.Image via Wikipedia

There have been a number of interesting discussions going on in the blogosphere recently about radically different ways of practising science. Pawel Szczesny has blogged about his plans for freelancing science as a way of moving out of the rigid career structure that drives conventional academic science. Deepak Singh has blogged a number of times about ‘bursty science‘, the idea that projects can be rapidly executed by distributing them amongst a number of people, each with the capacity to undertake a small part of the project.
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There will be many of these little experiments – using online conversations for scientific endeavors. Even inside an organization, having an online area to ask for help can be useful. Trying to use email for this purpose has little effect.

There are several ways to  use Web 2.0 approaches to ask/answer questions. An online forum works well if it is substantially populated and active. A forum with a 3 month old unanswered question will not be very useful.

One approach that works is to have one person, or a small group, act as troubleshooters. They probably already exist in many organizations. They are the ones every one goes to when they have a problem in the lab.

They usually have a wide range of knowledge and often work to help people find a solutions to a research problem.

Have these people move online. A troubleshooting page on a wiki would allow questions to be asked. The troubleshooters have the opportunity to find answers. FAQs could be written to respond to the endless questions many troubleshooters receive.

Then when someone asks for some help, there is already a team with responsibility to find answers. And, because all this is open and transparent, the troubleshooters can finally get the well deserved credit they should.

Helping in the lab is generally invisible to others, particularly when evaluation time comes around. It is hard to document just what the help accomplished.

A troubleshooting wiki, on the other hand, would provide ample documentation on just what help was provided and the effect that help had on the organization. The ability to actually document who helps the organization move forward will be very valuable.

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Science in the open

University by jeffpearce
Progress toward Public Access to Science:
[Via PLoS Biology: New Articles]

PLoS Chairman of the Board Harold Varmus applauds the newly enacted NIH public access policy as a positive step toward ensuring greater access to and better use of the scientific literature.

This very nicely discusses some of the recent changes that are making Open Access to scientific information a going concern. Anyone receiving money from NIH has to deposit the accepted manuscripts into PubMed Central and allow freely available viewing within 12 months.

He also mentions the continuing problem of copyright. Many journals require the authors to turn over all rights to the journal in order to have the paper published. This is becoming a problem in the Web 2.0 world, since the concerns of the author do not often match those of the publisher.

As Varmus writes:

Finally, unless authors modify their copyright agreements with journals before publication—something they are urged to do—journals will continue to retain inappropriate control over the use of their articles, which is currently confined largely to reading online for most articles in PMC.

Harvard has recently addressed this. Faculty members must grant a non-exclusive license to the University for it to post on a website it maintains, one that is open and free. Faculty can opt out of this on a case by case basis if the journal will not permit this.
Varmus comments:

Moreover, the nuisance of writing to the Provost every time a desired journal refuses to conform to the Harvard policy may cause faculty members to rethink their choice of venue, thereby minimizing use of the “opt-out” option.

The journals make their reputation based on the reputations of its author scientists. If a journal has a restrictive copyright policy, these scientists may go elsewhere, putting pressure on the journal to adopt more open access.

This story is not over yet. But it has the potential to revolutionize scientific publishing. Stay tuned.

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Old versus New

sheet music by cesstrelle74
Web 2.0: In defense of editors:
[Via Bench Marks]

Ran into a few very interesting (and very different) articles last week, which I wanted to comment on (more posts to follow).
First up is a blog posting on Sciencebase that quotes chemist (and blogger) Joerg Kurt Wegner, with a proposal that the solution for information overload is to do away with editorial oversight and instead rely on social software. Now, obviously, I’m heavily biased here, and I admit that up front. I’m an editor, it’s what I do for a living, and if I didn’t think I made valuable contributions, I would do something else. That said, there are several problems with Wegner’s proposal.
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Web 2.0 encourages people to publish quickly, then work to make it better. This may not be the best route for many scientific endeavors, particularly biological ones.

Editors and peer reviewers perform a vital task – they make sure that the science is done right. It requires special training and a firm understanding of the topic to do this well. Even then there are some important mistakes, as recently happened in Proteomics, where a misleading and plagiarized article was published in February.

The editors/reviewers made a mistake in allowing publication. But the errors and plagiarism were discovered by well-educated people (mostly other scientists and interested individuals) on the web. And this information spread rapidly, forcing the journal to publish a retraction and pull the paper.

Science will need editors and peer reviewers from some time, since good science does require careful scrutiny by experts. But, of necessity, this will be a small group of people, who may not see the forest for the trees.

Perhaps some middle ground will be found between the old approaches and the Wikipedia’s of the world. I am sure that the editors of Proteomics, whose reputation was hurt by this, would have liked to have some way for a larger group to review before publication.

Preprints have been the standard way of sending a draft around to colleagues in order to get comments. Web 2.0 approaches using Open Science may hold similar appeal. Many hard science papers (physics, math, etc.) are online at very early points in the process.

The journal Nature is doing something similar with Precedings. These will be important adjuncts to the old way.

They will enhance but never replace. At least for scientists.

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Public collaboration

leafby Clearly Ambiguous
Work-in-Progress Culture:
[Via Transparent Office]
Michael Idinopulos makes a great observation – Web 2.0 is collaboration in public. Fewer closed doors and more open hallways.

The real paradigm shift in Web 2.0, I believe, is the blurring the line between publication and collaboration. In the old days, people collaborated in private. They talked to their friends and colleagues, wrote letters. Later they sent emails. All the real thinking happened in those private conversations. Eventually, once the key insights had been extracted, refined, and clarified, they published: books, articles, speeches, blast memos, etc.To me, the really exciting thing that’s happening in Web 2.0 and Enterprise 2.0 is that more and more of those private “pre-publication” interactions are happening in public (or at least semi-public). I think of this as the dawn of the “Work in Progress” culture. We no longer think that something has to be finished before we let strangers into the conversation.

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It will be a difficult transition for many people, since it may be harder for them to totally ‘own’ a work but the pathway that was taken will be available for others to follow; the nooks and crannies. It will be harder to end up in a dead-end when others are there to help you out. And, because of the Long Tail, there will be someone available to help.

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Discussing Science 2.0

toolsby geishaboy500
Web 2.0 for Biologists-Are any of the current tools worth using?:
[Via Bench Marks]

David Crotty has been leading a discussion regarding the acceptance of Science 2.0 by scientists. Or rather the non-acceptance.

It is ironic to use Web 2.0 approaches to examine why scientists do not use Web 2.0 approaches. But entirely appropriate. Because these technologies will help researchers.

But not because we tell them so. No Internet technology ever became used simply because people were told so. They used it because it made it easier to do what they wanted to do.

What scientists can be told is how Web 2.0 will make their life easier. Once they can see how these approaches deal with the glut of data being generated and will help create knowledge, they will be ready for some of the more emergent aspects of Science 2.0.

This is a presentation I gave last weekend at the Southwest Regional Society for Developmental Biology Meeting. It’s an updated version of an earlier talk posted here. It’s kind of a 180 degrees turn from the previous talk, in that the first one was delivered to publishers, and this one was delivered to scientists. Here I’ve tried to include the thoughtful comments and helpful suggestions that readers made on the first talk, and have also tried to point out currently useful tools and interesting future directions. I don’t come at this subject from the point of view of a programmer, that’s not my background. I’m approaching it as 1) a publisher, who wants to build these tools into our journals and online products to make them more useful, and 2) as a former research scientist, with a thought toward what tools would have made my life easier when I was at the bench. The same caveat applies as last time-I work for a biology publisher, and am a former biologist. My comments and analysis of the culture here refer to that culture specifically (and I’ll try to avoid using the generic word “scientist” where it’s inappropriate). Different cultures have different needs. Certain fields of science collect types of data that more obviously fit in with Web 2.0 approaches. These approaches may not apply directly to the world of wet-bench biology, but they do serve as valuable pointers and directions worth watching. I want to be clear that I’m not writing Web 2.0 off as useless. What I’m interested in doing is separating the wheat from the chaff. Much of what is currently being done under this umbrella is useless and doomed. But there are some gems already available and despite many likely failures, aspects of those failures are worth recognizing and incorporating into future efforts.

If you read the first talk, sorry for the redundancies, and sorry for re-using some of the same jokes. I’ll work on new ones for the next presentation.

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Justifying Social Software

galaxyby NASA /Hubble Heritage Team

Justifying Social Software:
[Via A Journey In Social Media]

It’s true that most organizations won’t move forward with significant investments without some sort of justification.

And it’s also true that the category of “productivity software” is perhaps the most difficult thing to justify.

So, I thought I’d spend this post on the flavors of business value we’re seeing from our internal environment.

How People Think Of Justification
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Chuck’s blog is getting to be one of my favorites. His metaphor about boulders vs. sand is absolutely right. It is a nice way to describe a power law curve with its Long Tail. The boulders are the big hits at the left of the curve, what everyone has been used to dealing with applying old style approaches to things like distribution costs. But, various web technologies, especially Web 2.0, have brought the Long Tail to innovation and social networks.

Now, instead of a few big boulders, companies can harness the huge amount of sand present in their organizations. This can be done in ways that not only help employees do their jobs but can also save the company money, enhance its IP portfolio and make the company a better place to work. As Chuck noted, employees really appreciate what the interactive web provides, viewing it as a major company benefit.

If done right, an intranet built on Web 2.0 technologies becomes a way to retain employees as well as attract new ones. Pretty good for something that can be built on OPen Source and could be launched in an afternoon.

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Going Live, Slowly

construction by m o d e

This site will be coming alive over the next week or so. We have a lot to cover and want it to be done without overwhelming anyone. SpreadingScience will make it easier for researchers to deal with the tremendous amount of information that threatens to overwhelm their efforts.

We do this through a teaching approach dealing with both Science 1.0 techniques to transmit information (papers, oral presentations and posters) as well as Science 2.0 ones.

What most scientists know about Science 1.0 comes from on the job training. We have developed some areas of good practice which permit much more effective use of their time for transferring information.

Science 2.0 approaches using online collaborative tools (wikis, blogs, podcasts) hold the promise of lowering many of the barriers to effective information transfer.

However, these tools must operate in a social network, even if it is online. Without an understanding of how the social networks of researchers are similar to those of other groups, and how they are different, the tools of Science 2.0 will not flourish.

This is where SpreadingScience has its greatest impact. Contact us to find out more about what we can do for your research organization.

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