Category Archives: Science

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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Working Transparently

lake louise by jurvetson
Working Transparently:
[Via Gurteen Knowledge-Log]
By David Gurteen

I am including almost all of the post bt David Gurteen for a reason. It brings together in one post the ideas espoused by several other people. So, I quote David, who quotes John who quotes Michael. Every step in the transfer of information is stated and linked, providing the very openness and transparency discussed in the post. David then brings in his personal experience and ands another wrapper with the article on Science 2.0.

All of this to weave his view on openness into the other views. I hope my small addition provides some more insight into the need for openness and transparency for Science 2.0 aproaches to be useful.

I wrote a Gurteen Perspectives article for Inside Knowledge Magazine recently titled Open and transparent? where I talked about the concept and need for openness and transparency in the way we work today. So I have been delighted to see others say similar things:

In this post KM 2.0 is about showing your workings out by John Tropea, John quotes from Michael Idinopulos:

“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.”

“…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.”

And then Gerry McKiernan in this post on Science 2.0.

A small but growing number of researchers–and not just the younger ones–have begun to carry out their work via the wide-open blogs, wikis and social networks of Web 2.0. And although their efforts are still too scattered to be called a movement–yet–their experiences to date suggest that this kind of Web-based “Science 2.0” is not only more collegial than the traditional variety, but considerably more productive.

Take a look. How might you work more transparently?

Transparency and openness are the lubrications that allow human social networks to create knowledge rapidly. If any one person prevents the flow by holding onto critical information, the power of the network can be degraded.

This can be a problem in hierarchies, where information flows through a few chokepoints. A well connected, diverse social network can deal with this problem.

In fact, small groups of humans have always been able to identify who these people are and often use social norms to either make them comply or to shun them, particularly if other sources of the information can be found. If these chokepoints no longer are getting any information, the power they hold is greatly reduced.

Now, this may not always happen because of someone’s unique position in a small group. But the huge scaling properties of the Internet, the Long Tail and its enormous potential, means that it becomes much less likely that a single point of failure will damage the network.

The Internet was designed to route around ‘damage’ and so can diverse, connected human social networks. The Web makes it much less likely that one person will hold unique information. Thus it weakens their advantages.

Power comes from weaving information into unique knowledge – knowledge to make decisions.

The positive effects of openness and transparency can very rapidly overcome any small advantage of an individual holding information close. They lose any advantage they might have because very little information is that unique.

If these information hoarders gain little advantage by being closed, and if the social network uses peer pressure to identify free riders and to deal with them, then it would appear that behavior would rapidly converge towards openness and transparency.

In fact, the groups that can more rapidly create knowledge using human social networks will be the first to solve many of the complex problems we face today. Groups with choke points will be much slower and, in the type of natural selection we see all around, will become extinct. At least where the need is to understand complex processes.

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Wikis in college

classroomby dcJohn
Using Wikipedia to Reenvision the Term Paper
[Via EDUCAUSE Learning Initiative]

At the just held online EDUCAUSE Online Spring focus conference, Andreas Brockhaus and Martha Groom, both at UW-Bothell, just around the corner so to speak, discussed unusual aspects to classes taught by Groom. She required the students to either create a new page on Wikipedia or to substantially add to a previous page. No term paper. It was going up on Wikipedia.

Befitting a discussion about using new technologies in the classroom, you can see the Powerpoint presentation and hear the talk online. Almost like being there.

While there were some barriers to break through, the effect on the students and their writing was almost electric. Normally, only the teacher and a few other students might see what was written.

In this example, the entire Web could see what they wrote. To ameliorate this somewhat, she had the students work in groups.

Martha Groom has been using this approach for the last few years. There are still a few things to work on. Writing for an encyclopedia is different than working on an essay.

She has added a recursive approach to the project, with proposals and peer review before it hits the Web. The community nature of Wikipedia required the students to really give up proprietary feelings about the essays. Sometimes the give and take of online discussions could be a little harsh.

But Martha has continued to tweak the approach. Generally, the students were very happy with the results. The quality of writing was very high also. With such transparency, the possibility of plagiarism is infinitesimal. It really highlights the need for proper sourcing of the work. All very good things.

And, if a really good job is done, the student can point out the page to others as evidence of their scholarship. All in all, much better than a one-off term paper.

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Social network analysis

by jurvetson
Six degrees of messaging : Nature News:
[Via Nature]

I’m not sure if anyone can see this or if you need a subscription. But, this being the Information Age, you can read the abstract of the paper itself and download a PDF of the paper. It discusses work done at Microsoft examining the connections used by its IM customers. The researchers examined the data from one month. this worked out to “255 billion messages sent in the course of 30 billion conversations among 240 million people during June 2006.” A lot of data.

After crunching the data they found some interesting numbers regarding this network – the average number of connections between people on the network, its width, was 6.6. This is very similar to what others have reported, even though the approaches were quite different.

Interestingly, these other reports used much smaller groups of people. One, in the 1960s, used only 64 people. Another in 2003 used 61,000. All three, using very different methodologies arrived a similar numbers for the width of the human social network. This is not too surprising since human social networks adopt a scale-free configuration. The hallmark of a scale-free network is that the average number of links connecting any two nodes, or people, does not increase substantially as the size of the network increases. Here the scale increases almost 4 million-fold, yet the average width of the network is still about 6.

Information in a well connected social network can percolate very rapidly. Using Web 2.0 approaches can harness the power of the Internet (another scale-free network) to disburse the information into an even larger social network much more rapidly than by utilizing face-to-face approaches.

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An Open Science Approach

waves by Airton kieling

[Via One Big Lab]

First draft of PSB proposal
PSB proposal up on Google Docs
PSB Open Science session proposal submitted!
PSB proposal up on Nature Precedings
PSB proposal accepted for a workshop

A very interesting progression from first draft to final approval. Exactly what one would expect for an Open Science advocate. While not all Science 2.0 approaches may be suitable for exposure on the open web, this was certainly a wonderful exercise to follow. And I learned something about the process they went though, just in case I ever want to do something similar.

I may have to find myself in Hawaii early next year, at the Pacific Symposium on Biocomputing. It’s the Big Island.

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Open Presenting

pythonby belgianchocolate

Publishing On OpenWetWare – Lessons Learned 4 – Presenting:Python
[Via Programmable Cells]

This is the fifth report of the ‘Publishing on OpenWetWare’ series. In brief, I am writing an article on OWW from start to finish: initial writing -> collecting comments -> publishing on -> presenting at a conference. For other articles, see one, two, three, four. In this report, I’ll share my experiences in presenting the work at Pycon 2008.

This is the most recent part in a continuing series by Julius Lucks about publishing on OpenWetWare, an example of Open Science. Initially, OpenWetWare was a great site to find protocols of all sorts. It has been expanding very rapidly to incorporate many facets of Science 2.0. This is one such. It led to a presentation dealing with his work and you can read the ‘paper’ dealing with his topic: Python All A Scientist Needs. Python is the programming language used here and it presents many advantages useful for scientists. It includes a special package, BioPython, just for biologists, which is supported by the Open Bioinformatics Foundation. So, we see an entire network of Open Source organizations that produce tools that not only make their work easier but also the work of others. By embracing these tools, one can engage the entire network and help use all the knowledge contained in it to help solve problems.

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TEDTalks are the best

TEDTalks: Jill Taylor (2008):
[Via TEDTalks (video)]

We are still working on the website to permit embedded Flash. Until we do, you will have to click the link above to see Jill Taylor’s presentation.

Neuroanatomist Jill Bolte Taylor had an opportunity few brain scientists would wish for: One morning, she realized she was having a massive stroke. As it happened — as she felt her brain functions slip away one by one, speech, movement, understanding — she studied and remembered every moment. This is a powerful story about how our brains define us and connect us to the world and to one another.

This is a great presentation. Some science. Some personal experience. The TEDTalks offer great examples of how to present difficult subjects. There are some with pretty standard approaches but they are often the best of their type. And, thanks to the Internet, we do not have to be attendees in order to see this.

But some of them display a unique method of presenting and are very useful for gaining a better understanding of HOW to present. Check out this one from Larry Lessig.

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Great photo resource

Galaxy Edge On by The Hubble Heritage Team (STScI/AURA)

Images help give a website a nice look. They break up the text and provide some visual interest. Flickr is a great spot to get images. There are a huge number that are covered by the Creative Commons license that can be used. But it is nice to find others.

The Hubble Heritage Image Gallery is another great site. Excellent images of objects in space. You can simply place these photos onto your web page and provide proper attribution. This is one of the great mashups on the Internet. Great photos taken by people can get spread around the Internet in ays that enhance both the user and the photographer.

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Scientists as cyborgs

Video @ the bench
[Vie Free Genes]

I saw the movie I Am Legend this weekend, and although it wasn’t exactly a ringing endorsement of synthetic biology (re-engineering measles is a bad idea, apparently) Will Smith’s character did have a slick lab in his basement. Good to see a little Garage Biotech in action.One component of the lab they made heavy use of was a video lab notebook. I assume this was done since Will Smith scribbling in a paper lab notebook wouldn’t have had quite the same cinematic effect. However, getting video into the lab will be important for democratizing biological engineering. A lot of the barriers to would be bio-hackers lay in the difficulty of learning biological protocols from texts. New graduate students benefit enormously from hands-on learning with a mentor in their early days in lab, and without this visual teaching getting booted up in the lab is extremely frustrating.

will.JPGNew science video sites like Jove and suffer because labs aren’t really equipped to capture video. So at best you’ll be able to disseminate talks, but video protocols are going to be very hard to pull off. I’ve been thinking about video lab notebooks / protocols since Tom Knight brought up some clever ways you might set your bench up to accommodate video capture (cameras in various spots, foot-petal control, and smart ways to handle the data). A more nerdy looking way to do this (no offense to Will Bosworth who used to work around the Endy Lab) is the head-mounted video camera described by Saul Griffith in Make magazine.

There are also some wireless web-cameras that might make your setup cheaper. If anyone is doing a good job of taking video at the bench, please let me know about your setup.

Video use in social media will be explosive when the tools get more mature. Will they be a major way that research is communicated? Maybe not always but I visited the Seattle Science Foundation last week and saw what medical theaters can do when hi-def video is built into the infrastructure. Almost everything can be transmitted/archived on video. How will things change when we really can archive everything?

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I missed the first 18!

by MuniMan

Bio::Blogs #18:

The 18th edition of Bio::Blogs can be read at Bioinformatics Zen. The main focus of this months’ edition is Open Science with many links to interesting new developments. In particular go have a look at this video that Michael Barton made about science and the web. Unless there are any other volunteers the 19th edition of Bio::Blogs will be hosted by me again at Public Rambling.

Bioinformatics and Open Science seem to be made for each other. There is a proposal to discuss Open Science at the Pacific Symposium of Biocomputing next year. I hope it gets accepted. I’d love a reason to go to Hawaii.

Additionally, the increasing use of these sorts of aggregations, also called Carnivals, is a very novel expansion of normal scientific tendencies. Each member of the community gets to host the Carnival, which is mostly made up of links to appropriate posts by other members. So, it is a great way for all the members of the community to get to know each other. It also allows new members to very quickly get up to speed with who does what in the community. Another example of how social media can speed up even internet time.


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