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 Randy Son Of Robert
8 Things We Hate About IT:
[Via HarvardBusiness.org]

You may think that hate is too strong of a word for feelings toward a corporate department. I don’t. Yesterday, I was interviewing an executive on his perceptions of IT and he couldn’t spit his frustration out fast enough. He said, “In the quest of getting things organized, they are introducing a bunch of bureaucracy and, in the process, they’re abdicating their responsibility for making sure the right things get done.” This is completely typical of management’s frustration – no, management’s hatred – of IT.

It’s hard to remember the time when criticizing IT was controversial. Now, it’s ceased to be even interesting. The now-classic HBR article “IT Doesn’t Matter” resonated so clearly because it underscored the pervasive belief that IT mediocrity is the norm. And how bad is an industry’s reputation when a major outsourcer, Keane, can get away with insulting its target market with the slogan, “We Do IT Right”?

It’s not personal – nobody hates the people in IT – it’s the system that’s broken. And here’s the rub: IT doesn’t like it either. One global Fortune 200 CIO describes leading IT as “a sucking vortex.”
[More]

Harvard Business is never shy about stoking controversy. Let’s take a look at some of these items.

• IT Limits Managers’ Authority
• They’re Missing Adult Supervision
• They’re Financial Extortionists
• Their Projects Never End
• The Help Desk is Helpless
• They Let Outsourcers Run Amok
• IT is Stocked with Out-of-Date Geeks
• IT Never Has Good News

The eight things almost all deal with an unwieldy section of a large company having to deal with rapidly changing circumstances. I believe that most of the eight things mentioned above derive from the two opposing aspects of IT in many companies.

So, many IT departments are driven by diametrically opposed needs. No wonder they do such a poor job of satisfying everyone. Stability necessitates limiting what the rest of the company can do. But innovation often needs large amounts of money to complete a project right now in order for the company to remain competitive.

I agree with F. Scott Fitzgerald. The people in IT usually possess first-rate intelligences but the requirements that are often put on them make it very hard to function effectively.

There will have to be changes in how IT is actually managed, how it is integrated into the corporation, in order for many of these problems to be attacked.

But maintaining these two opposing needs is the very definition of insanity.

Technorati Tags: Knowledge Creation, Web 2.0

by longhorndave
Adobe Adds Features to Boost Collaboration:
[Via Enterprise 2.0 Blog]

Adobe has introduced two new products, Acobat 9 and Acrobat.com. The goal is to transform the way people collaborate—Adobe’s new Acrobat 9 PDF tool now uses Flash to let you embed video, audio, animation and all manner of files, which is very cool. Another new capability lets you leverage web conferencing from Adobe to mark up documents on the fly, in real time, without launching a full-blown conference. Both people can take turns walking through the document, there’s no need to pass the baton, making it very ad hoc. If you decide you need to, you can launch a full-blown web conference (via Acrobat Connect) with a single click.
[More]

Adobe is now making a wide variety of collaborative tools available online with the launch of Acrobat.com. Buzzword allows people to create collaborative documents. It looks like it has version history, access control and real-time controls. Nice.

These tools offer some pretty compelling ideas. I will be examining them to determine just how useful they really are. There is more information at the Adobe site.

Technorati Tags: Social media, Web 2.0

by aussiegall
What’s Your Internal Social Networking Strategy?:
[Via Enterprise 2.0 Blog]

Nemertes recently noted that eighty-three percent of organizations are now “virtual” meaning that members of workgroups reside in physically separate locations. The emergence of the virtual workplace has radically changed not only how we communicate and collaborate, but how we build social bonds among employees.
[More]

Informal interactions are very important in any social network. They provide secondary routes for information to bypass chokepoints, they permit radically different viewpoints to influence the creation of knowledge and they are just plain fun.

It will be important for any defined internal online social network to provide this outlet. Because, frankly, if it is not provided, people will either ignore the network or find ways, perhaps inappropriately, to create such an outlet.

Technorati Tags: Knowledge Creation, Social media, Web 2.0

by b_d_solis
Appreciating A Seth Godin Post:
[Via chrisbrogan.com]

The other day, Seth Godin wrote about the new standard for meetings and conferences. I loved the article (but couldn’t comment that I did), and have been thinking about it ever since. I talked about it twice with two different people over the last few days, and part of the sentiment Seth put out there found its way into my jumping over a mountain post.

So, I’m presuming everyone reads Seth, but if not, check this out, or as Clarence would say, “marinate.”

Because Seth came by and commented reminded me to show that I am reading and paying attention to him. A side lesson to this: comment where you’re reading. It makes a difference.

Part of the way information flow is enhanced by Web 2.0 tools can be seen here. Someone comments on a post that was initiated by someone else’s thoughts. Each of us in the chain adds our own viewpoint, helping to not only transmit the information to a greater audience but also adding our own context.

He extends this to meetings of any sort. If we are going to take the time and expense to meet face-to-face rather than use social media to accomplish our goals, then we had better take advantage of the benefits those sorts of encounters provide than simply information transfer. Like using our hands to talk.

Seth says this:

If you’re a knowledge worker, your boss shouldn’t make you come to the (expensive) office every day unless there’s something there that makes it worth your trip. She needs to provide you with resources or interactions or energy you can’t find at home or at Starbucks. And if she does invite you in, don’t bother showing up if you’re just going to sit quietly.

What are some of the benefits of face-to-face encounters that can not be accomplished with Web 2.0 tools? I think engagement of real time thoughts and processes is one. Taking advantage of the simultaneous juxtaposition of time and place that can not happen online. Snacks and drinks are another.

Any other ideas?

Technorati Tags: Social media, Web 2.0

by flikr
We Do Different Things:
[Via chrisbrogan.com]
The roles many blogs take, not surprisingly, are very different. They fulfill many of the same functions seen in face-to-face social networks: connector, innovator, aggregator, gossip, etc.

We do different things.

There’s nothing more flattering than being lumped in blog posts alongside Robert or Jason Calacanis or all the other folks who also write a blog on the web. But you have to realize that we do different things. (people are welcome to disagree with my characterizations of them).

Robert Scoble writes about really exciting new things, and he shows videos, and he connects humans, and he scours this space for new amazing things.

Louis Gray seems to own the aggregator/repurposing space, with things like FriendFeed, SocialThing, etc.

Seth Godin is a marketer’s marketer, and points out the human experience with products and services.

Jason Calacanis has a strong history in the web space, and also talks from a media maker’s perspective.

Jeremiah Owyang writes more analysis-based posts on social marketing as an industry.

I could go on for a while, but I guess the point is this: we all keep blogs. We all type about things. But we’re different and offer a different set of take-aways from our writing and thought processes.

That is what is so important about newsfeeds and RSS. Using the right software, they bring together all these diverse thought processes. It is almost like have a virtual conference room filled with some extremely interesting and creative people.

What is often begun as a personal approach towards communication can become, when aggregated, a very rich and very deep conversation, particularly when you add your own perspective on your own blog.

Technorati Tags: Knowledge Creation, Social media, Web 2.0

by Felix Francis
Twitter’s growing pains:
[Via Buzzworthy]

It’s hardly news that Twitter is experiencing growing pains, but a couple of items have appeared in recent days that shed some new light on just how bad they’re getting.
[More]

As mentioned below, some of the problems Twitter is having while trying to scale are rooted in its basic communication paradigm. It is much more complex than a system based on the telephone company. It is almost as if every phone call was a 5 or 6 person conference call.

Difficult to do with the best experts. But it sounds like Twitter was somewhat surprised by the direction its technology took and was not prepared for the type of growth it sustained. It is still a very small company and one that may not have had onboard all the engineering help it needed.

Twitter is, fundamentally, a messaging system. Twitter was not architected as a messaging system, however. For expediency’s sake, Twitter was built with technologies and practices that are more appropriate to a content management system. Over the last year and a half we’ve tried to make our system behave like a messaging system as much as possible, but that’s introduced a great deal of complexity and unpredictability. When we’re in crisis mode, adding more instrumentation to help us navigate the web of interdependencies in our current architecture is often our primary recourse. This is, clearly, not optimal.

Twitter broke ground on a new manner of using Web 2.0 tools. Time will tell if it is able to maintain its initial success.There are some very difficult problems that have to be solved. But there will be somebody who solves the scaling problem because this tool is just too useful.

Google was not the first search engine., just the best one so far. Web 2.0 works by allowing rapid prototyping of new tools as one works towards perfection. Twitter was able to accomplish a lot with really very little. It has hit a barrier now. It will be interesting to see how this problem get solved. It is not too unlikely that a user who is really knowledgeable will propose a solution.

We have kept an eye on the public discussions about what our architecture should be. Our favorite post from the community is by someone who’s actually tried to build a service similar to Twitter. Many of the best practices in scalability are inapplicable to the peculiar problem space of social messaging. Many off-the-shelf technologies that seem like intuitive fits do not, on closer inspection, meet our needs. We appreciate the creativity that the technical community has offered up in thinking about our issues, but our issues won’t be resolved in an afternoon’s blogging.

We’d like people to know that we’re motivated by the community discussion around our architecture. We’re immersed in ideas about improving our system, and we have a clear direction forward that takes into account many of the bright suggestions that have emerged from the community.

To those taking the time to blog about our architecture, I encourage you to check out our jobs page. If you want to make Twitter better, there’s no more direct way than getting involved in our engineering efforts. We love kicking around ideas, but code speaks louder than words.

That would be the Web 2.0 way.

Technorati Tags: Knowledge Creation, Social media, Web 2.0

by kevindooley
Am I Done with Facebook? Twitter FTW!:
[Via Phil Windley's Technometria]

I got a message from Facebook today saying that someone had friended me. I realized I didn’t care. Not that I didn’t care about the person who’d friended me–I didn’t care about Facebook. It’s been weeks since I was there and my life is pretty much the same.
I think the reason is Twitter. Twitter is much more social, much more interesting, and the plethora of clients (including any mobile phone with SMS) means that I don’t have to remember to go check the site to see what’s happening. Twitterific displays a solid stream of the 140 character thoughts of my friends.

Because of Twitter, today I know:
There were tornados in Denver and Laramie
Twitter posted an article about their architecture on their blog
There’s a blogger dinner tonight in Salt Lake City
@tylerwhitaker and @bradbaldwin aren’t going to carpool to the blogger dinner

I like that.

Twitter has scaling problems even though their user base is reportedly quite small. As Nik Cubrilovic points out, Twitter isn’t like WordPress or Digg. Twitter is a group forming network (GFN). When a Metcalfeian network adds another user, the number of potential connections goes from N² to (N+1)². When a GFN adds one more user, the number of potential connections goes from 2^N to 2^(N+1). In case it’s been a while since you’d done that math–it’s a big difference.

There are three important ‘Laws’ dealing with networks, social or otherwise: Sarnoff’s, Metcalfe’s and Reed’s. Sarnoff’s Law states that the value of a network (David Sarnoff started NBC) is proportional to the number of nodes. Metcalfe’s Law states that the value of a network is proportional to the square of the number of nodes. Reed’s Law states that the value of a network increases exponentially with the number of nodes.

Metcalf’s assumes the nodes can communicate with each other, resulting in multiple connections. This is where network effects come into play. One phone is not useful. Two are a little better, but a network of 10 can be very useful. Metcalf first showed this using this figure:

The line corresponds to Sarnoff’s Law. Metcalf’s, which was derived from the first Ethernet networks, shows that the value for small numbers in a communication network is not great. But this increases rapidly with larger networks.

What this means is that in some social media settings, the number of groups can increase much faster than the number of connections. Here is a consequence of this:

To make this more real, consider TechCrunch’s twitter account. When TechCrunch, with almost 18000 followers, sends a message, that results in 18000 messages–one to each follower. This is like the phone system with infinite, always-on conference call capability. Sure, you can do things internally to collapse some messages, but you’re still dealing with exponential growth.

What is happening with Twitter, that is making it have problems scaling, is that the number of groups substantially increases the number of possible connections and messages it might have to maintain. With email, everyone on the list is sent a copy of the email, that sits on their computer and take up space. Twitter sends messages to phones, for example, possibly 18000 of them in this example.

That is a lot of wasted effort. Twitter may not be the best way to communicate with a large number of people in several different groups.

Technorati Tags: Social media, Web 2.0

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.

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.

Technorati Tags: Science, Web 2.0

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.

Technorati Tags: Social media, Web 2.0