by SantaRosa OLD SKOOL
Three Thoughts on Interdisciplinary Research:
[Via Michael Jubb's blog]
Comments on Michael’s three thoughts following some meetings he has attended recently:

The first was a suggestion, perhaps a hypothesis, that interdisciplinary research will lead (has led?) to an increase in researchers’ interest in open access. The thought here is that researchers in some disciplines (notably some areas of the biosciences) are more inclined to adopt some form of open access in publishing their work; and that as researchers from other disciplines less inclined to open access join with, say, bioscientists in their research, they will be introduced to open access ways of thought. It seems a plausible hypothesis, and one that could fairly easily be tested. Does interdisciplinary research feature particularly prominently in OA journals, or in the contents of repositories?

I think part of this is that working in a interdisciplinary fashion fosters openness. That is, such researchers are often working in and relying on access to scientific disciplines other than the one that the researcher was trained in. If they can not access research from a discipline, they will not really be able to work in that discipline.

It would seem likely that collaborative efforts would most easily flow to those areas that foster open communication with collaborators. Hard to be multidisciplinary it there is not open collaboration with others.Thus open access becomes part of the culture of multidisciplinary research.

The second thought comes from a presentation by Carol Tenopir of the findings of the latest Tenopir and King reader surveys. One of the interesting findings is that interdisciplinary researchers are more likely than other researchers to follow citation links as their means of getting access to journal articles; and that the latest article they have read is more likely to be in digital, as distinct from print, format. Why that should be is perhaps worth some investigation.

Online is all about finding information quickly, incorporating it into the local community and then using it to create knowledge to make decisions. Rapid analysis followed by community synthesis. The collaborative cycle cranks much faster when online tools and Web 2.0 approaches are used. This allows multidisciplinary efforts to be launched that would be virtually impossible without these tools. This pace of collaboration can not be as rapidly sustained using paper means.

The third thought comes from a presentation by Mayur Amin of Elsevier about surveys of usage of journals in Science Direct. One of the interesting findings here is that while for researchers in physics and maths, 70% or more of usage is of journals within the discipline, for researchers in other disciplines, such including chemistry and environmental sciences, usage of journals within the discipline is at less than half that level. This may of course be an effect of the way in which Elsevier classify the journals. But it is at least open to the suggestion that researchers in some disciplines are more inclined to read beyond their own discipline. Is this evidence that some disciplines are more interdisciplinary than others? Is this something worth investigating?

One hypothesis is based on the hierarchy of science and the natural world. Math as a discipline is the most abstract; it can exist without any real need to be part of any other discipline but almost every other discipline needs math. Physics then comes next. It needs math to describe itself but little else other than physics.

Then comes chemistry and biology. Each level down involves lesser abstraction and closer dealings with the natural world. Each requires more and more simple experimentation and observation. Physics has gedanken experiments, which come close to the Greek ideal of not needing to do any experimentation. Math needs no experiments at all and can be done simply in one’s head.

Or maybe it is just sampling error.

Technorati Tags: Open Access, Web 2.0

by cowlet
Case study of the IR at Robert Gordon U:
[Via Open Access News]

Ian M. Johnson and Susan M. Copeland, OpenAIR: The Development of the Institutional Repository at the Robert Gordon University, Library Hi Tech News, 25, 4 (2008 ) pp. 1-4. Only this abstract is free online, at least so far:

Purpose -The purpose of this paper is to describe the development of OpenAIR, the institutional repository at the Robert Gordon University.

Design/methodology/approach - The paper outlines the principles that underpinned the development of the repository (visibility, sustainability, quality, and findability) and some of the technical and financial implications that were considered.

Findings - OpenAIR@RGU evolved from a desire to make available an electronic collection of PhD theses, but was developed to become a means of storing and providing access to a range of research output produced by staff and research students: book chapters, journal articles, reports, conference publications, theses, artworks, and datasets.

Originality/value -The paper describes the repository’s contribution to collection development.

Technorati Tags: Science, Web 2.0

I was discussing with one of our execs the progress we’d been making on social media proficiency internally.

And he asked a great question that made me think:

“So, has anyone fundamentally changed their work processes because of the platform?”

And I realized this is the next frontier on what’s turning out to be a large-scale social engineering project.

Getting Business Value Out Of Our Social Software

As we make progress in this journey, I’ve got my eye out for different catagories of business value we’re seeing.  I suppose, at the same time, I should also be keeping my eye out for business value we’re NOT seeing yet.

And, as I’ve mentioned before, we’re seeing business value — in many forms — across the board:

People with specific interests are finding other people with similar interests
Rather than searching big content repositories, people are asking other people for help and answers
A pan-organizational “social fabric” has been created that wasn’t really there before
Folks who spend time on the platform are better educated — and more engaged — in EMC’ business

And more And, just to be clear, there’s no shortage of business benefits — I still stand behind the broad assertion that this has been one of the most ROI-positive IT projects I’ve seen in my career.

Interesting “value nugget” of the week: 

EMC runs a healthy program to bring a large number of interns and co-op students into the company.  They started introducing themselves to each other on the platform.

What started with “name, rank, serial number” blossomed into a wonderfully diverse set of conversations about careers, favorite hangouts, what it means to work at EMC, what is everybody doing, and so on.

I would argue that — whatever millions that EMC spends on this intern/coop program — we’ve now made it 10-20% more valuable, simply because we connected people to each other, and connected them all to the broader company. 

At zero incremental cost.

But we want more. Much more.
[More]

If the data are plotted as the cumulative adoption of the innovation, it looked like this:

Both of these types of curves have been seen again and again when the diffusion of innovation is examined. They seem to be derived from basic forces present in human social networks.

Ryan and Gross made several key contributions besides the identification of the S-shaped curve. One was the process by which the innovation diffused. The other was the type of farmer who used the innovation.

They found that there were five stages in the adoption of an innovation by an individual: awareness, interest, evaluation, trial, and adoption. And there were at least 4 different types of farmers, of which the early adopters were the most important.

Early adopters heard about the corn from traveling salesmen and tried small plots to see how well it worked. Later adopters relied on the personal experience of other farmers, usually the early adopters. When there were enough positive reactions from the early adopters, when there were more stories of personal experience, the adoption rate took off.

It was the human social network that was critical for the rate at which the innovation was adopted. The more social connections an early adopter had, the more cosmopolitan they were, the more likely it would be that others would adopt use of the innovation.

Everett Rogers was instrumental in codifying many of the principles of innovation diffusion. Here is his famous rendition of the distribution:

Only 16% of a population is usually made up of the early adopters, the ones that are critical for spreading the innovation to the early majority. The key to the adoption of any innovation is the rate at which early adopters can transmit the knowledge of the benefits to the early majority. In the case of the farmers, it would often take 4 or more years for this to be converted form awareness to adoption.

In many areas of our world today, this is much too slow. Technology is disruptive, meaning that the people who adopt this technology actually deal with the world in entirely different ways than those who do not. It is similar to a paradigm shift, in that those on either side of the shift have a hard time communicating with each other. It is almost as if they inhabit separate worlds.

This can cause some problems because the early adopters are required to communicate with the early majority if an innovation is to diffuse throughout an organization. If they can not, it creates a chasm, which has been described by Geoffrey Moore in his book.

The organization has to take strong action to recognize that this chasm is present and to span it, either with training or, more effectively, with people who have been specially designated as chasm spanners. In many cases using Web 2.0 technologies, they are called online community managers.

Disruptive innovations seem to arrive almost yearly. Without a directed and defined process to increase the rate of diffusion in an organization, if just standard channels of communication are used, innovation will diffuse at too slow a rate for many organizations to remain competitive.

Because there is usually not just one innovation disrupting an organization at a time. Life is not that clean. There can be multiple innovations coursing through different departments, moving early adopters even further away from the rest of the group and expanding the chasm. This only makes communication harder.

It can no longer be possible to simply let the early adopters go through their 5 stages of adoption and then tell others about it at the water cooler. Designated online community managers, with the training needed to enhance communication channels, will be critical in getting this information dispersed throughout an organization.

Technorati Tags: General, Web 2.0

by dbking
Copy Number Variation Detection:
[Via Bench Marks]

With the sequencing of the human genome came the startling revelation that the number of copies of a given gene can vary widely between individuals. This Copy Number Variation (or CNV), contributes to our species’ genetic diversity but it has also been linked to genetic diseases. This month’s issue of Cold Spring Harbor Protocols features a new method for detecting copy number variation. Like all of our monthly featured protocols, it’s freely accessible for subscribers and non-subscribers alike.

Copy Number Variation Detection Via High-Density SNP Genotyping describes the use of PennCNV, a new computational tool for CNV detection in data from genomic arrays. Developed in the laboratory of Maja Bucan at the University of Pennsylvania, the software is freely available for download. Analysis with PennCNV will provide a more comprehensive understanding of genome variation and will aid in studies seeking the causes of genetic diseases. More information on PennCNV can be found in this Genome Research article, PennCNV: An integrated hidden Markov model designed for high-resolution copy number variation detection in whole-genome SNP genotyping data.

I took the liberty of showing the entire post from David’s blog because, in contrast to my story below, this demonstrates a very good approach for publishing scientific work online.

Protocols, particularly new ones are very useful to have. Making a small number available for free is a nice way to get people to check out the journal. I have it in my newsfeed. I like CSHP and enjoy David’s blog tremendously. Now I just need to find a way to become an adjunct professor at some research organization with an institutional license so I can read all the articles.

Technorati Tags: Open Access, Science, Web 2.0

I posted this at my personal blog but thought it might be of interest here since it demonstrates just how current online tools have changed the way scientific research is published, presented and read.

by Beige Alert
Why snakes don’t have legs:
[Via 2collab public bookmarks]

Tags: Hox gene, Homeobox gene, Limb
Authors: Cunliffe, Vincent
Source: Trends in Genetics; 15, 8, Page 306; 1 August 1999
Sharing: Public

I’m providing a detailed examination of an online journey I took this morning that demonstrates how the Internet has altered the landscape for publishing of articles in scientific journals. Online access certainly changes how we search for and how we read articles. It is also changing where we chose to publish.

So I see this interesting name for an article - Why snakes don’t have legs - in my newsfeed. I click on thru (why it is on 2collab I do not know?) and get this page. Great. ScienceDirect which usually charges for journal access. But this is an article from 1999. Surely it will be open by now?

I went to PubMed, the database of journal articles, and did a search for “snakes AND legs”. Got 48 articles. The critical one appears to be by Cohn and Tickle “Developmental basis of limblessness and axial patterning in snakes” in Nature from June 1999. Great. Now I have a subscription to Nature so this article is available to me but if you wanted to read it without a subscription it would cost $35! Wow! But at least now it has an abstract.

The evolution of snakes involved major changes in vertebrate body plan organization, but the developmental basis of those changes is unknown. The python axial skeleton consists of hundreds of similar vertebrae, forelimbs are absent and hindlimbs are severely reduced. Combined limb loss and trunk elongation is found in many vertebrate taxa1, suggesting that these changes may be linked by a common developmental mechanism. Here we show that Hox gene expression domains are expanded along the body axis in python embryos, and that this can account for both the absence of forelimbs and the expansion of thoracic identity in the axial skeleton. Hindlimb buds are initiated, but apical-ridge and polarizing-region signalling pathways that are normally required for limb development are not activated. Leg bud outgrowth and signalling by Sonic hedgehog in pythons can be rescued by application of fibroblast growth factor or by recombination with chick apical ridge. The failure to activate these signalling pathways during normal python development may also stem from changes in Hox gene expression that occurred early in snake evolution.

Sounds really interesting to me but still not sure it is worth $35. But right above that link from PubMed is another one - from Current Biology with pictures. “How the snake lost its legs”. It is a ScienceDirect link also but this one is available for free. And it has nice pictures while discussing the Cohn and Tickle article.

Except for this nifty one from the Journal of Experimental Biology - “Becoming airborne without legs: the kinematics of take-off in a flying snake, Chrysopelea paradisi” (The picture above is of a flying snake.) Open access and more recently published. Not exactly on topic but it comes with movies! These were just not possible to see without online access. And the movies are really cool and help explain what the author of the paper was describing. You can actually see the difference between a J-loop takeoff and other modes. Plus, flying snakes sound like something from a B-movie.

Back to the topic. I went to Google and searched “Cohn Tickle snake”. The top response is from a USA Today article about why snakes do not have legs. In the article there are links to Martin J. Cohn and Cheryll Tickle. Clicking the Cohn link takes me to his page at the University of Florida. Not a lot here but there is a link to his personal site.

Now we get the Cohn lab page. I could just email him and ask for a copy of the paper (a slightly updated approach to the old method of sending reprint requests by snail mail). But there is a link to Publications.

And here we find the PDF to the paper I was looking for. A quick runthrough reveals that it is a paper I will find interesting (I love Hox stuff). But I would not have paid over $30 for it.

So, for a few minutes of my time I got the article for free and also got to see some nice movies of snakes flying. Not a bad way to travel in an online world.

Technorati Tags: Open Access, Science, Web 2.0

by jayhem
How 300,000 IBM employees use Bluepedia wiki:
[Via Grow Your Wiki]

IBM gets wikis. In a 300,000+ person enterprise, a wiki enables emergent collaboration and expertise:

BluePedia is an encyclopedia of general knowledge about IBM, co-authored by IBMers for IBMers, which enables the collection of expertise and know-how of more than 300,000 IBMers around the world into a simple, searchable resource that is easily expanded, shared and used. The single, global co-authoring platform enables the development and implementation of a common worldwide vocabulary and easy recognition and identification of subject matter experts.

300,000 is a lot. Not many companies are going to have that many for a wiki. But from their press release, there is a lot more IBM is doing with Web 2.0 technologies. I am sure we will hear more in the next year.

I did like this from the release:

Web 2.0 technologies create open, collaborative spaces that eliminate the traditional hurdles created by time and distance that businesses worldwide have traditionally faced. The marriage of videos, blogs, and custom publishing enable working professionals to exchange ideas and perspectives using rich, multi-dimensional platforms that foster a two-way dialogue within an enterprise.

As a result, employees can leverage the technology available at their fingertips, regardless of time and place, to drive innovative ideas throughout their enterprises. By linking with several other development sites, guests experienced how IBM technologies drive efficiency, innovation, across the enterprise and tap into high-value skills from the company’s top talent, around the world, to solve the specific needs of its clients.

Companies whose basic products depend on the continuing creativity and innovation of its employees will have tremendous increases in productivity with these tools. The key will be that these tools have to be as flexible and open as possible, allowing new uses to be created by the user, not by the vendor.

The world will move too fast to wait for the vendor to provide the latest tools. IBM will fail here if they lock users into something bloated like Lotus . Lotus was useful for certain directed tasks but was unwieldy when required to adapt to changing or novel environments. It required a superior development staff to keep up. Web 2.0 tools will only succeed when the actual development is minimal and when the users can accomplish what they need themselves.

Technorati Tags: Web 2.0

Open science:
[Via Michael Nielsen]

The invention of the scientific journal in the 17th and 18th centuries helped create an institution that incentivizes scientists to share their knowledge with the entire world. But scientific journals were a child of the paper-and-ink media of their time. Scientific papers represent only a tiny fraction of the useful knowledge that scientists have to share with the world:

Enabled by a new media form, the internet, the last few years have seen a modest expansion in the range of knowledge that can be published and recognized by the scientific community:

The most obvious examples of this expansion are things like video and data.
However, there are many other types of useful knowledge that scientists have, and could potentially share with the world. Examples include questions, ideas, leads, folklore knowledge, notebooks, opinions of other work, workflows, simple explanations of basic concepts, and so on.
Each of these types of knowledge can be the basis for new online tools that further expand the range of what can be published by scientists:

It’s fun to think about what tools would best serve the needs associated with each type of knowledge. This is already starting to happen with tools and ideas like open notebook science, the science exchange, SciRate, and the Open Wetware wiki.

This is a very good point to make. Publishable information has increased tremendously. We are no longer limited by what the printing press is capable of displaying. We are no longer limited by the number of pages that can be printed a month.

This opens up the possibility of also making available not only the things that went right but those that went wrong. Preventing others from following a dead end would be useful.

Underlying this apparent problem is an opportunity to develop tools to assist scientists in finding relevant information, and to ensure that what they publish - their questions, ideas, and so on - is seen by those people who will most benefit. Ideally, the result will be not only a great expansion in the range of what is published, but also a great improvement in the quality of information that we encounter.

The reason new tools will be developed is that this approach will allow researchers to attack very complex problems in a much more efficient manner than those limiting themselves to the printing press. Success will breed success.

There are, of course, major cultural barriers to acceptance of these new tools. At present, there are few incentives to make use of new ideas like open notebook science. Why blog your ideas online, when someone else could be working on a paper on the same subject? This isn’t speculation, it’s already happening, and sometimes the blog posts are better - but try telling that to a tenure review committee.

Similar comments were made with regarding Open Source. What incentive would there be for creating software for free? It may well be that Open Science is not rewarded in the same fashion as science on paper. I think it is more likely that academia will change to provide proper rewards.

Certainly there are other places to pursue research than a university. In particular, I think there will be an even larger growth in non-profit research institutions over the next generation. They do not usually have the same arcane tenure problems universities do, and often rewarding people more like a corporation does than academia, that is for what they accomplish the meets the institution’s goals rather than where they published.

The successful institutions will find and use the tools that solve problems. They will also find ways to reward those that successfully use them

At the moment, many of these institutions are found in biotech and human health but as more money and focus moves towards using innovative tools to promulgate science, there will be ones for every discipline. And, as the brain drain from academia to these institutions increases, universities will either have to adapt or they will wither.

More flexibility, More collaborative environments. Less overhead. I believe that these research foundations will be the leaders in promulgating open science. It is to their advantage to do so.

Technorati Tags: Non-Profit, Science, Web 2.0

by Shereen M
Who needs coauthors?:
[Via Survival Blog for Scientists]

Young people, in tenure track positions, feel they to have to collect as many authorships as possible. Questions like “Will I be a coauthor?” and demands as “I have to be a coauthor” are part of daily conversations in science institutes.
But not only junior scientists are eager to boost their cv’s with authored papers.
[More]

Biology papers usually have large numbers of authors. It is rare to see a major paper in Nature or Science with two authors. Often modern papers are the results of collaborative research between multiple institutions. It makes it easier to get your name on a lot of papers but also makes proper assignation of credit difficult.

Credit for papers can be incredibly important and manipulation of the credit is not unheard of. Harvey Fletcher was a graduate student for Robert Millikan around 1910. Fletcher developed and designed the oil-drop experiments that measured the charge on an electron as well as investigations on Brownian motion that led to a better determination of Avogadro’s number.

Now, Fletcher could use a published paper in lieu of his Ph.D. thesis but only if he was sole author.

Millikin proposed that Fletcher be the sole author on the Brownian motion work and Millikan would be sole author on the electron charge work, even though Fletcher’s work was critical in both. Millikan knew which one would be the more important paper. As a graduate student, Fletcher really had no choice but to acquiesce to Millikan’s proposal.

Millikan published as sole author of the paper on the charge of the electron. Fletcher wrote on Avogadro’s constant. Millikan won the Nobel Prize in 1923. Although, Fletcher became the first physics student to graduate from The University of Chicago summa cum laude, he spent most of the next 38 years outside of academia, working at Bell Laboratories.

Although he did not win the Nobel Prize, he had a tremendous impact on many of the technologies that were developed in the 20th Century. At Bell Labs, he not only became ‘the father of stereophonic sound’ but was the director of the labs that developed the transistor.

What this shows is that while a true genius can not be stopped by who published what, in the scientific world, particularly in academia, the assignment of credit has huge ramifications. Almost anyone who takes physics knows about Millikan and the oil-drop experiment. Who knows about Fletcher?

These days, often the person who did the research is first author and the person who directed the research or whose lab supported the research is last. Everyone else involved in smaller amounts is in between.

But this can change. Often with 20 authors, no one ever gets to the last one when the article is referenced. The bibliography will just be ‘Smith, et al.’ So sometimes, the director of the lab will be placed as first author instead of last so everyone sees their name in the references.

So how does proper credit actually get assigned? In large measure, figuring out who designed the critical experiment, who simply provided reagents and who had critical intellectual input are all hidden from general view. This permits political pressures, such as what Millikan used on Fletcher, to determine placement, rather than actual worth.

Huge battles have been waged over where one’s name gets placed in a paper. Since this is what the world will see, it is worth it for many people to spend all their political capital to get a choice placement on a paper. A lot of scientific blood may have been spilt in order to get on a paper published in Nature.

Sometimes those in the know have an idea of proper credit but tenure committees, grant committees and other vetting bodies can have a difficult time telling just what contribution a scientist made on a paper with 40 authors.

There have been some attempts at better clarifying this, with authors making statements about who did what. Perhaps as we move away from the current model of publishing to one more digital in nature, there will be approaches to simplify this process.

In particular, there will have to be a way to assign credit for things other than just the number of publications. Scoring the impact people had on those publications, what work they actually performed and where they can be placed in the process that lead to novel scientific discoveries will become more likely, if the social media aspects of Science 2.0 comes to be appreciated.

Because every one of those aspects can be time-stamped and made accessible by using things like wikis and weblogs in ways that email will never accomplish. Openness and transparency, important aspects of successful Web 2.0 tools, will also make it possible to more accurately track the progress of creativity and innovation. Surely rewards will follow.

Will Science 2.0 make it less likely that political pressures can be used to claim credit that is not deserved? Being human, the pressures may never disappear. But Science 2.0 should make it a little more difficult to claim credit after the fact. Fletcher kept the secret of Millikan’s proposal until after he died. In those days, it was easier to control the flow of information, to hide political manipulations of the research.

Now, not as much.

Technorati Tags: Open Access, Science, Social media, Web 2.0

Video: Podcasting in Plain English | Common Craft - Explanations In Plain English:
[Via Common Craft]

These videos are always worth watching and do a wonderful job explaining how many Web 2.0 tools work. The videos can be downloaded and embedded into intranet pages for employees, allowing them to better understand the technologies.

The fact that these videos use such a low tech approach to teaching about high tech tools make them very original and eye-catching.

Technorati Tags: Social media, Web 2.0

by aussiegall
Social networking site aims to help fight malaria:
[Via News at Nature - Most Recent]

New website gives smaller African projects a bigger profile.
[More]

An interesting approach - using social networking tools to help increase awareness of anti-malaria projects and help fundraising effort. It is a novel way to use some of these tools but I wonder if these would be more successful as a stand alone project or under the wings of larger social media entities?

Technorati Tags: Non-Profit, Science, Web 2.0