Category Archives: Science

Science, Web 2.0

Confusing will not work

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key by ul_Marga

There is a possibly interesting paper in Genome Biology by Barend Mons et al: Calling on a million minds for community annotation in WikiProteins. I say possibly because the paper itself is quite confusing to me but the overall goal seems to be a cool concept. This group has created and is encouraging the use of “WikiProteins” a community annotation system for “community knowledge.” Sounds a bit fuzzy? Well, reading the paper does not completely help. For example here is the abstract

WikiProteins enables community annotation in a Wiki-based system. Extracts of major data sources have been fused into an editable environment that links out to the original sources. Data from community edits create automatic copies of the original data. Semantic technology captures concepts co-occurring in one sentence and thus potential factual statements. In addition, indirect associations between concepts have been calculated. We call on a ‘million minds’ to annotate a ‘million concepts’ and to collect facts from the literature with the reward of collaborative knowledge discovery. The system is available for beta testing at http://www.wikiprofessional.org webcite.

[More]

This is an interesting attempt but the community they are asking for is not in existence yet. The goal is extremely worthwhile, since the best way to create knowledge from the huge mountain of data being created is to incorporate large social networks. But the community must be created first.

However, at the moment in the science community there is a large activation energy (yes, human social interactions also require energy to be expended in creating the network before the information flow can become self-sustaining). First, there needs to be demonstrable proof that putting time into community annotation will be productive and rewarding. There is no proof of this yet.

Second, most scientists are creatures of habit; they have developed a workflow that is successful. In order to get them to change, it had better be easy. Again, time is important, especially in the early phases of community building.

I spent some time at the site trying to get an idea of what was involved. I still did not really figure it out. I do not believe many working scientists will either.

However, this is an important site and one that should be watched. Simply because the initial site is not there yet does not mean it will not quickly get a lot closer to perfection. It is a beta. It is easy to incorporate feedback and move rapidly to something more usable. Lowering the barrier to entry would help a lot.

These sorts of tools are too useful for them to remain unused. A million minds will someday be involved in this work. But it will not happen until a strong community is created.

Online communities will be how we solve the difficult problems facing us. The sooner they are functional, the sooner we can begin finding solutions.

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General, Non-Profits, Science, Web 2.0

Tending a garden

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garden independentman
Getting Conversation Ready:

[Via Beth’s Blog: How Nonprofits Can Use Social Media]

Holly Ross wrote a good reflection piece about public conversations on blogs and how to get your audience ready for that conversation. She makes the point:

What I am saying is that your audience may not be ready to have the conversation that social media enables. That’s because social media does not just enable conversations.It enables PUBLIC conversations.

I think we have to remember that it takes time build the community to have the conversation and that it doesn’t happen right away. You have to be ready as conversation facilitator. Alexandra Samuel did a workshop called “Bringing Your Community to Life” at Netsquared and offered some terrific practical advice about you get the conversation started.

Some key points:

Key points to encourage participation:

Focus on promoting conversation

Make it happen, don’t wait for it

Connect like-minded participants

Connect complimentary threads

Plan pro-actively, implement reactively

A community is not built rapidly and a conversation does not always easily begin. It requires nurturing and time, just like a garden. It has to be curated by active,enthusiastic members. They have to reach out to others, to begin the dialogs that will enhance the entire network.

Just as an outstanding garden does not spontaneously come into being, an online community requires active management. A lot of work, somettimes. But like a well-tended garden if given the right care, it can pay off handsomely.

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Open Access, Science

This is more like it

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Copy number 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.

It highlights a useful new protocol that can be downloaded for free. It also links to a Genome Research article that I can also download for free. Nice. I can quickly get up to speed on a novel protocol.

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.

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Open Access, Science

Some science journals are messed up

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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.

flying snake 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?

Nope. They want $31.50 for a nine year old article. With no abstract or any other way to determine whether this article is worth the price. $31.50! First off, few articles in science today that are nine years old are worth $5, much less $31.50. Secondly, with no abstract how am I to even figure out if it is worth the price?

This greatly limits access to the article and encourages other routes for getting the information than reading it. Why would a scientist want to publish an article that no one will read? We want as many people as possible to see our wonderful work. This is not like literature or art where older is better.

Seems to me that this is a losing business model. I can see paying a premium for up-to-date work. I understand someone has to get paid and can easily pay a reasonable price. But $31.50?! For an article that is almost a decade old!? That makes no sense in an online world.

Very few articles in biology that are ten years old retain much value. Just a few years ago, I would have been stuck but now I have other tools.

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.

So partial success. Now I have a better idea of the article’s content. All the other links from PubMed dealing with snakes and THEIR legs, as opposed to snakes and the legs they bite, have costs to access, up to $39.

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.

I certainly believe that downloading a paper from an open archive presented by the author of a paper is an ethical way to obtain the paper (It is just the online version of the reprint request, remember). So, it took me less than 10 minutes to find a copy of the article online. (And it turns out that if I had looked at my Google results just a little more, I would have found a direct link to the publications page, saving myself some time.)

I think that, except for the most highly paid of us, 10 minutes time would be less than $10. This seems about right. A paper for $5 I would buy immediately while much over $10 and I will go searching. I may not succeed but I can usually find an email link and request a copy from the author.

Online archives by the authors are becoming more common and are a basic aspect of many Open Access initiatives. Paying a small premium for access to a current article is a reasonable price, especially if it is convenient. But any business plan that wants to charge a huge premium for decade old work needs serious rethinking.

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.

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Science, Web 2.0

Use this tool for searching

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lemur by digitalART (artct45)
A search engine for open notebook science:
[Via Michael Nielsen]

There has been some great discussion in the comments on my post about “Open science”. One outcome is that Jean-Claude Bradley has created a search engine customized for open notebook science:

http://tinyurl.com/4multu

Fittingly, many people contributed to the discussion!

This demonstrates one of the nice abilities of Web 2.0 approaches. Google permits you to set up a custom search for a group of websites. This allows you to perform a directed search using specific terms against a designated group of websites.

This example examines a group of Open Science sites but it is easy to see how this might be useful for other sites. This way you do not have to work your way through a multitudeof irrelevant sites.

RSS is really good for bringing me content but what if I want to find an article from one of my newsfeeds from a few months ago? With this, I can simply add all the websites I track to the custom search. Then I am searching a much smaller but very directed subset of the web and am much likelier to find the old article I read.

A user-generated subset of Google web searches may be very useful for linking the content of several sites. This could be fun to play with. I’ll have to put one together for Science 2.0.

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Science, Web 2.0

New Science Tools

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Avogadro
Avogadro: Open Source Molecular Building:
[Via MacResearch – Online Community and Resource for Mac OS X in Science]

Avogadro is a new, open source molecular editor for Mac, Windows, and Linux. It is an advanced molecular editor designed for cross-platform use in computational chemistry, molecular modeling, bioinformatics, materials science, and related areas. It offers flexible rendering and a powerful plugin architecture.

While still in beta, the recent 0.8 release brings general usability to viewing and editing molecules on your Mac. You can quickly export graphics to PNG, JPEG, or even POV-Ray rendering, or copy from the editor and paste a transparent PNG into programs like OmniGraffle. Avogadro supports reading from over 80 chemical file formats, courtesy of the Open Babel library.

read more

These sorts of tools will become more and more common – Open Source, mashable, easy to use. The last paragraph says a lot about the goals.

Future plans for the Mac version of Avogadro include integration of Spotlight and QuickLook, as well as built-in scripting in Python. Work is also underway to allow copy/paste from ChemDraw and other 2D chemical drawing applications. Additional builders (e.g., for biomolecules, nanotubes, and nanoparticles) and interfaces to other computational chemistry packages are due for future versions as well.

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Open Access, Science

Publishable science

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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.

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Knowledge Creation, Science, Web 2.0

Virtual fun at work

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medusa by MrClean1982
Next generation of business software could get more fun :
[Via Washington Post]

Once upon a time, people bonded with their co-workers on office softball teams and traded gossip at the watercooler.

OK, so those days aren’t gone yet. But as big companies parcel Information Age work to people in widely dispersed locations, it’s getting harder for colleagues to develop the camaraderie that comes from being in the same place. Beyond making work less fun, feeling disconnected from comrades might be a drag on productivity.

Now technology researchers are trying to replicate old-fashioned office interactions by transforming everyday business software for the new era of work. The historically dry-as-sawdust products are borrowing elements from video games and social-networking Web sites.
[More]

People are social animals and usually need some unstructured time to blow off steam, relax and generally recharge their batteries. In many business environments there are a host of conventions to accomplish this, from birthday parties to golf tournaments to lounges.

Online work will also include similar processes. As this article discusses, there are many approaches to creating break time in a virtual world. Where these tools can be important in research is that many bright ideas come up from the random interaction of a couple of scientists, often in a bar or a party. Crick famously drew up the list of the twenty amino acids used in protein synthesis on a napkin while at a pub before any real evidence existed.

They will have to be careful that the areas are not TOO much fun. Disney is finding out how hard it can be to shutdown a virtual world years after it has served its purpose. But using aspects of Second Life in a business setting may be important for a truly creative research experience.

So online water coolers, ‘inward Bound’ sessions, and even golf tournaments (with trophies) will be important. Just as many research facilities are built today to foster the random interaction of researchers as they stroll between lab and office, online work areas will be designed to take advantage of the non-structured interactions all humans need.

There has always been a little bit of randomness in almost every great scientific endeavor.

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Science, Web 2.0

Science 0.5

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Science communication has changed as the tools have gotten better. But creativity has always found a way to effectively communicate even with crude tools.

Even without fancy computer graphics, very complex biological reactions could be visualized. It just took hundreds of people. From 1971. Narrated at the beginning in a tie by Paul Berg at Stanford. He won the Nobel Prize in 1980 “for his fundamental studies of the biochemistry of nucleic acids, with particular regard to recombinant-DNA.”

It is the followed by the best mashup of straight biological processes, Jabberwocky and people who look like they are from the road show of ‘Hair.’


No animation, just hundreds of people and a fire extinguisher. But you will probably never forget the mixture of Lewis Carroll, biology and large open spaces.

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Open Access, Science, Web 2.0

Credit where credit is due

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oil drop 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.

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