by “T” altered art
Innovation, biotech, software, etc:
[Via business|bytes|genes|molecules]

There are a lot of synergistic effects of high tech on biotech. Much of the work done today requires high powered instruments running very complex algorithms.

But it still requires highly skilled people to do the work.

In a talk at E-Tech, Drew Endy apparently said that big money requirements of biotech are holding it back and one could make biotech innovation more like software and innovate much faster. Admittedly this is absent of context, but I responded to that tweet with one that said that while there is definitely a lot to learn, instruments and people cost money. My focus was actually on the latter. In the world of software, there is some specialization, but skills are more general, while in the life science world there is a lot of specialization of some very highly trained individuals (in fact one could argue that the amount these people get paid is a travesty compared to some other professions).

There are some things in biological research that can not be made easier by using computational approaches and processes. At least not yet. These systems are too complex and full of non-linear pathways.

There are a few things we can learn from the software world; DRY, iterative developments, organizational structure, etc, but biological systems are not perfect, they are not predictable, and most of all, our solutions have a lower margin of error. Whether it’s a drug, a diagnostic, or some kind of therapy, the process of development and associated regulations is always going to take time and it’s always going to throw nasty surprises at us. Biosimulation, protein structure prediction, robotics, improved collaborative tools, there are so many things to look into to make life science R&D faster and more efficient, and less prone to failure, but I find the idea that you can just use software development as a template a little insulting.

In fact, I think that in many ways biotech and high tech take very different approaches towards innovation. Computational techniques often take a procedural approach to solving a problem. Often, it is process driven and once the process has been found/optimized, you are pretty much done.

Process-driven sciences usually have well characterized components that act in defined manners. You start at point A and get to point C by going through point B.

Biological research at its base is not process driven. Not to say that there are not parts that can be encompassed in a process. But if a process is designed to provide a black and white answer (A to B to C), then the multitudes of gray that are biological results indicate its difference.

You start at point A and get to point C but you might go through points Q, R, and S before getting to point B. But only if the patient has a particular set of 20 different genes. For someone else, it could be a totally different game.

This is why it takes so long to develop any major drug. The model systems we use to develop them are not perfect. Then we have to hope that they will have greater beneficial effect in humans than deleterious.

We can, though, find ways to make some parts more efficient. Researchers are inundated with a surfeit of data these days. Disbursing these data throughout a social network helps alleviate this glut while making it more likely that the right data can get to the right person at the right time.

Human social networks are exquisitely formulated to tease out the underlying knowledge from a diverse set of information, and then pass this knowledge around quickly. Finding computational approaches to leverage these human social networks in order to solve these complex biological systems will have innovation as an emergent property.

It is a hardwired principle of humanity.

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

by FaceMePLS
Nonprofit Presenters: What are your best tips for preparing presentations?:
[Via Beth's Blog: How Nonprofits Can Use Social Media]

Humans often deal with a complex world by using simple stories, simple rules of thumb (or heuristics for the technobabblers). We use stories to teach us how to behave, how to react, etc. Almost any ad tells some sort of story.

The presentations that stick with people long after the talk are almost always based on a storytelling tradition. The same tools and tricks used by the teller of the Iliad still work, even in front of a small audience using a digital projector.

Beth Kanter gives a lot of presentations every year. Here are some of her thoughts:

Earlier this week, I was inspired by my good colleague, Alan Levine (aka Cogdog), I visited Save the Words. It’s an interactive flash site that lets users find and adopt words that are in danger of being removed from the dictionary.

I adopted the word archiloquy. It’s the first part of a speech or presentation. That’s the most important part of your presentation because you need to grab the audiences’ attention. I use a variety of techniques to do this, but one of my favorites is to create a story. I learned this from Andy Goodman — I’ve taken his workshops and read his books.

Andy is a master at storytelling. In his workshops, he offers the following formula for a storytelling based on Hollywood script writing:

• Introduce the central character
• Inciting moment: something bad happens to the character that will prevent them from achieving a goal related to the goal of your presentation
• Barrier to resolution #1: Character tries to solve the problem, but can’t
• Barrier to resolution #2: Character tries to solve the problem, but can’t
• Resolution: What you’re going to share in your presentation
• Widen the Lens: The bigger picture

I’ll have to help revive archiloquy. There are only 41 hits or so for the word on Google but it is a really useful term. The beginning of a presentation is the most critical to get people on board for the story you are about to tell.

Putting real thought into the start of a presentation, and to what sort of story you want to tell, are very important items to check off when preparing a talk.

As with any story, if you can make it personal, and make the audience connect with the narrative, you have engaged their attention. But remember PASS – Present A Simple Story.

You do not need to make the presentation a Shavian critique or a Swiftian satire. There is a nice legend (another way of saying story) that suggests there are only two types of narratives: a hero goes on a journey and a stranger comes to town.

Andy uses the former mode – the hero goes on a journey to achieve a goal that has been stymied. The latter also works quite well because the stranger coming to town almost always brings change. Here is one mode of this story:

• Introduce the town (perhaps in Iowa), which does not realize it yet but it is about to change forever
• The stranger arrives, bearing the tools of change (say 76 trombones, or perhaps only a novel way for communicating with others)
• Describe how the town reacts to these tools (perhaps by thinking the stranger is a fraud or by not understanding why they have to change)
• Show how a member of the village, perhaps a previously neglected member of the town with a lisp, finds the new tools open up avenues of success unseen before
• The town is changed forever by these new tools and the stranger moves on (or he can stay and marry the town’s librarian/piano teacher)

Which of these two stories you use really depends on whether you want the audience to adopt the viewpoint of the hero or of the town. But using just one of only two archiloquies helps you Present A Simple Story.

Technorati Tags: Social media, Web 2.0

by Boston Public Library
Nice guys can finish first and so can their teams!:
[Via Eureka! Science News - Popular science news]

Ever thought the other guy was a loser for giving his all for the team even if others weren’t pulling their weight? A new study, published in the Journal of Personality and Social Psychology, says that person can influence a group to become more efficient in achieving its goals by making cooperative, collective behaviour seem acceptable and appropriate, and thereby encouraging others to act similarly.

The study, authored by a professor at the Rotman School of Management at the University of Toronto and his collaborator at Northwestern University, calls such individuals “consistent contributors” – people who contribute all the time, regardless of others’ choices.

The findings challenge assumptions made by many game and rational choice theorists that people should cooperate very little in situations with a known end-point when there are short-term incentives to act selfishly.

[More]

This is a very interesting result. When people act selfishly in a group setting, they often change the behavior of others. There was a nice paper a few years ago that examined what a group did with cheats.

Now this study demonstrates that positive behavior can drive a groups approach simply by pushing forward no matter what. When people continue being consistently cooperative, they help everyone in the group.

“But our study found consistently cooperative actors even in places you might least expect them, and when they’re there they seem to set a tone and shape how their fellow group members understand situations,” says Prof. Weber. “Their clear, consistent behavior elicits cooperation, and once you get a few people cooperating with each other, they seem to enjoy cooperating. Groups become more productive, more economically efficient and, anecdotally, people enjoy being a part of them more as a result.”

In settings where there is an advantage to cooperating, groups with consistent cooperators were more successful than those who took a more ‘realistic’ approach. One can see why a social animal would evolve this way. Groups that cooperated would be more likely to survive than those where it was every man for themselves.

Given a level playing field, we want to cooperate with one another. The key is making the playing field level, insuring that the incentives do not push for behavior that is detrimental.

Technorati Tags: Social media, Web 2.0

For those interested, I’m hosting a open discussion group on science and sustainability called Idea Club here in Seattle on March 23. It is hosted by the Sustainable Path Foundation.

I have written about some of these at my other blogs, Path to Sustainable and A Man with a PhD. You can register for the free event there.

Hope to see some of you there.

Technorati Tags: Social media, Sustainability, Web 2.0

What happens when you set your content free with creative commons licensing?:
[Via Beth's Blog: How Nonprofits Can Use Social Media]

Winner of the Creative Commons 2006 Photo Schwag Contest

I believe in setting my content free. It provides a huge return on investment. Here’s why:

A way to crowd source ideas. People can add and embellish your content and if you have access to the remix, it can give you new ideas
It creates a gift economy and that help you build your network
It gets your work out there. My photos and blog posts have traveled around the world!

I use the “BY Attribution” creative commons license. I’ve used this license now for four years because it is simple, direct, and easy. “You are free to use the content, just me credit and/or a link.”

Creative Commons provides an easy way for individuals to control their IP without needing a huge array of lawyers. In fact, it permits one to easily make things available for others in ways that benefit everyone.

I’ve talked about using Flickr as a photo resource. It is easy to provide attribution and a link. Most people are honest and will do this to provide a benefit for those providing the photos. And for those who chose to be dishonest … well the Web has a billion eyes and it is very likely that someone will notice. Openness and transparency can sometimes help provide a reasonable governor on poor behavior.

All of this assumes that people really bother to look at the license, understand it, and respect the rules. I still sometimes see rather blank expressions when I ask about turning to CC licensed resources to find photos. It turns to surprise when they see what is there and it free for the using. Or, I get gasps of horror from some colleagues who more concerned about how to “lock up” their content with “all rights” reserved and hire IP lawyers to help them police and protect their work so no one “steals it.”

The possible benefits outweigh the possible detriments. But it may take a generation (probably only an Internet one, though) to change attitudes. But, as I mentioned in another post, even large pharmaceuticals are recognizing the benefits of opening up some of their IP.

Here’s a few (good) examples of how I have remixed other people’s work or other people have remixed my work.

1. Remix This Powerpoint. The powerpoint slides came from a webinar I did a couple years ago for University Extension professionals. The title was “Ten Steps to Extension 2.0.” The presentation itself is a remix of a remix. I remixed it from an earlier presentation called Associations 2.0 which was based on Marnie Webb’s Ten Ways To Use Web 2.0 to Change The World. It also incorporates cc licensed materials from others, including videos and flickr photos.

The cover is from a remix mashup that Mike Seyfang and I did a couple years back from a conversation about the least restrictive creative commons licensed. That photo is one of my most viewed flickr photos and resulted in a number of inquiries for work.

A difficulty with scientific presentations is that the copyrights of the graphs and figures are not even owned by the person who did the work. Scientists have historically turned over all copyrights to the publisher in order to get published in the first place. If you want to get published, you had to relinquish all rights.

You can check the policies of each journal. They are all different. If more papers were published under a Creative Commons license, which they should be since most were financed by public money, it would make it easier for all of us.

2. How Much Time Does It Take To Do Social Media? This was a blog post that I wrote remixing an earlier blog post with the same title from Nina Simon as part of thinking through some of the material for the WeAreMedia project, another open content project. The illustration is a powerpoint slide that I shared on slideshare. It’s been remixed with and without attribution. Many do not add more improvements on the idea itself, but rather just cut and paste. A number of folks have sent back thanks for saving them some time in prepping a presentation.

There was a brilliant example of remix from Morgan Sully who took the idea and remixed it for electronic musicians. Creating a remix that goes beyond cut and paste, takes some time, creativity and higher thinking skills!

Adding context or new information is a great reason for being able to remix. This is still problematic with a lot of scientific information since usually all rights are reserved. What is fair use then?

When I remix someone else’s work, I go to great lengths to give it proper attribution. But, I never know if people who have remixed my work have done so in return. Now there is an easy way to track it.

Attributor Corporation and Creative Commons have just launched FairShare which is now in public beta.

The press release describes it as:

A free service allowing bloggers and individual content creators to understand how their work is shared across the Web. FairShare allows anyone creating text content to submit an RSS feed of their work and choose a Creative Commons license to determine how it can be shared. Users then receive license-specific results via RSS with detailed insights into how and where their work is reused.

The FairShare service enters public beta supporting six Creative Commons licenses. Creative Commons is a not-for-profit organization, founded in 2001, that promotes the creative reuse of intellectual and artistic works, whether owned or in the public domain. The FairShare service will be integrated with the Creative Commons license selection process and available in each of the 12 languages that FairShare currently supports.

FairShare helps make the Creative Commons “Sharing Economy” vision a reality by enabling millions to reuse content in a way that provides a value back to the original content creator – value that each creator can define for themselves.

As you know, I do a fair amount of listening, so when I using monitoring tools I can see exactly who is using my content and in what context. That is if they mentioned my name or linked to me. My goal in using this tool is not to police my content. Rather, I want to see how it is being remixed so I reap the benefits of the Sharing Economy.

Update: Article in the LA Times

This is a great example of how mashups can use data in ways no one had anticipated. RSS was not designed to do this but FairShare can manipulate the data from RSS to make it not only easier for the creator of content to control their work but also to track ow others are using it. This only serves to foster information flow, helping increase the rate of diffusion of innovation in an organization.

Technorati Tags: Social media, Web 2.0

Genentech open sources Unison: [Via business|bytes|genes|molecules]

Image by Getty Images via Daylife While on the subject of open and pharma, a bioinform article (sub reqd) tells us about Unison, a protein sequence analysis platform from Genentech that has been released under the Academic Free License (why not the Apache License since they are very similar). What is Unison? Unison is a compendium of protein sequences and extensive precomputed predictions. Integration of these and other data within Unison enables holistic mining of sequences based on protein features, analysis of individual and sets of sequences, and refinement of hypotheses regarding the composition of protein families

Essentially Unison is a data warehouse, which includes a number of protein sequences, and a bunch of pre-computed data. They have also released the complete schema, API, and some of the predictions. The backend is PostgreSQL and the platform leverages the BioPerl API. So the web service serves as a reference implementation of the Unison platform. People can essentially replicate the system and contribute code within their own servers using.

I think that biotech/pharma companies may do this more and more. The advantages for a company do not really come from these particular tools but how they are used and interpreted. Making this available to a much larger group means it is more likely to yield useful results. Genentech can only do so much with these tools. If someone else uses them to find something novel, some thing that Genentech did not recognize at all, Genentech might be able to reap some rewards that they would not have if they had kept things to themselves. Even if they do not get rewards directly, the publicity is worth something. They see this as a way to extend their influence rather than something for competitors to use against them. By furthering collaboration and increasing the number of eyeballs using their tools, Genentech can accomplish some things that would be difficult to do with their cards held close.

Technorati Tags: Bioinformatics, Health, Science, Web 2.0

by Halima Ahkdar
Give Each Blog Post a Pretty Face With Flickr:
[Via chrisbrogan.com]

I was asked by a friend on Twitter where I got all the pictures that I use for my blog posts (like the one you see in the top left of this post). The answer is that I get them off Flickr. But there’s more to it than that. Here’s a quick run-through of how I use photos on this site, and some more about Flickr.

First, A Note About Creative Commons

The photos that I use on Flickr for this blog are licensed to be used under Creative Commons. That means there are some rules to using them, but if you abide by the rules, you can use them. (More on Creative Commons.). There are multiple rules for these photos. I use the least restrictive photos, found by searching using this link, which will give you any photos posted by people who simply want credit attributed to them for their work.

Attribution

First off, this post by Steve Garfield should be required reading. He’s right that Flickr’s system needs some tidying up. That said, I’ll write from the perspective of how I’ve been using photos and how I attribute them.

The word “attribution” in this case means giving credit to a person for their work. The photo above was taken (or at least posted) by someone who goes by the name M@rg. If you note above, I’ve made the photo clickable, such that it takes you directly to the person’s Flickr page. Further, skip down to the bottom of this post, and you’ll see an italicized area where I point out the photo credit.

The best way to give credit would be to have the text of “photo by” or something directly under the photo, but I’ve yet to figure out the proper html syntax to accomplish that neatly for my blog. (You’re welcome to recommend how, in comments). That aside, I’ve at least give two ways for you to realize who snapped the photo, and how to find more about him or her.

[More]

This is one of the great examples of how Web 2.0 tools can be repurposed to become even more valuable. I have been doing this for quite some time. It may take a little bit of searching to find a good, appropriate picture but it sure is easy.

And the results are sweet.

Technorati Tags: Web 2.0

What’s your social media elevator pitch for your nonprofit’s executive director or board?:
[Via Beth's Blog: How Nonprofits Can Use Social Media]

Photo by Marco Wessel

Yesterday, I had the pleasure of attending one of NTEN’s “Ask the Expert” calls and chats with Wendy Harman who is the professional listener for the Red Cross. She has a social media elevator pitch just in case she runs into one of the senior managers. It goes something like this: “I’m the social media lady who builds relationships with our stakeholders online.”

I bet she also extends that pitch to include the phrase “that results in increased goodwill, improves our reputation, and donations.”

You have to be able to explain social media, Web 2.0, etc. in terms that people can quickly understand. ‘Social media is about connecting online.’ ‘Web 2.0 is all about online conversations.’

As Jeremiah Owyang noted in a post the other day, measurement of social media is key because when marketing dollars are stretched, marketers are under pressure to prove their programs. With social media being largely experimental, it is imperative to measure quickly and make real time course corrections and to figure out what is working. This underscores the importance of listen, learn, and adapt.

But when you’re just starting out, organizational culture can get in the way of embracing social media. Wendy Harman shared some insights that Wendy shared parallel what has worked in the corporate sector. (See this IBM Social Media/Corporate Culture Case Study). What’s important is a social media policy

In order to measure something, you have to know what it is and why you do it. While the touch-feely stuff may make people feel good, measurables will be what makes it successful.

A couple of takeaways from Wendy:

• First thing every morning, she spends a couple of hours listening – reviewing hundreds of mentions that have been captured in their monitoring radar using a variety of free and professional tools, including Radian 6. Wendy estimates it’s about 1/4 of her time presently. I suspect it took more of time in the beginning as she developed her work flow and got over the learning curve – and of course was able to upgrade her tool set.
• Senior management is not turned off by the term listening. She often writes social media manifestos, filled with examples, pros/cons, and shows tangible, measurable results from their social media strategy.
• She has a social media elevator pitch in case she encounters one of the senior people at the organization in the elevator: “I’m the social media lady who builds relationships with our community online.” Perhaps she extends that to include “that results in increased goodwill, improves our reputation, and donations.”
• She and the others on staff are no longer afraid of negative comments or posts. “The opposite of hate is indifference, if someone bothers to post a negative comment it means they care.” She was also pleasantly surprised about how much was positive. Negative comments are an opportunity to educate and improve what they are doing. “It is about being polite and honest.”

Concerns of content and concerns of negative comments are big in most organizations with respect to Web 2.0 But, as Wendy says, hate can actually be more useful than indifference. Engagement and conversation can deal with hate, perhaps ameliorating it. Indifference will not respond to engagement.

People hate faceless organizations. They very seldom actually hate an individual who has a name and is trying to help. Listening is a very important aspect of Web 2.0 tools.

Technorati Tags: Web 2.0

by Joe Geranio
Social People and The Big Conversation:
[Via A Journey In Social Media]

Sometimes you get things right. Whether you’re smart, or lucky, or a bit of both — it should be a moment for rejoicing since it doesn’t happen as often as you’d like :-)

It’s struck me that when we put our overall corporate social media strategy together, there were two big themes: encouraging social media skills and applying them to ever-wider conversations.

Looks like that was the right thing to do …

The Germ Of An Idea

David Spencer offered up a telling comment to my last post that confirmed my thinking here.

“At EMC we didn’t tell people where to go, what to play with or what not to play with.

We have smart, social people who feel empowered to represent our brand and themselves at the same time all over the place, and the payoff is nearly automatic.

There are certainly other approaches to take, but I really enjoy the organic growth that our approach has led to.”

He’s absolutely spot-on. That’s exactly what we did.

[More]

Technorati Tags: Social media, Sustainability, Web 2.0

by Hey Paul
Why article tagging doesn’t work:
[Via Bench Marks]

Reading William Gunn’s recent blog posting, Could this be the Science Social Networking killer app? got me thinking more about the many online scientific reference list repositories like Connotea, CiteULike and 2Collab, and why they are failing to catch on. William is suggesting a Pandora-like system of expert reviewers tagging papers to set up a recommendation system. I’m not sure this would be really helpful–what you get from a scientific paper is very different from what you get from listening to a song, and their interconnectedness works in very different ways. And it brings to mind the failings of organizing your references by tags.

If you’ve ever dealt with any of these social bookmarking sites, you know how incredibly tedious they are to use. Even for journals like CSH Protocols, where we have buttons on every article to add it directly to these sites, you still end up jumping through hoops, filling out forms, writing summaries, adding tags. You’re on the spot at that moment to come up with a list of tags that will remind you about the content of that paper. As your worldview changes over time, and with it your research priorities, you’re probably going to want to revisit many papers and add additional tags. Even with all this time-consuming work, you still may not have added an appropriate tag to let you find what you want to find at a given moment. Did you add a tag for every method used in the paper? Every conclusion, every subject referenced? That band on the gel in figure 3 that you’re ignoring today might be very important to you tomorrow. How are you going to tag the paper in case you need to find it again?

[More]

I totally agree with David. There are two kinds of list-making people in the world – those that make lists and those that don’t. Applying tags to articles works well for the list-makers but many, many scientists are just too time-deprived to fill in boxes or check off squares.

Tagging research is not an easy problem to fix. We may all agree that it is worthwhile but we are a long way from any reasonable solution.