All posts by Richard Gayle

Web 2.0

Twitter and the election

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birds by Only Sequel
Using Twitter to Monitor US Voting on November 4:
[Via Portals and KM]

Here is a great use of Twitter and Web 2.0. The Twitter Vote Report will use Twitter.com and 1-866-Our-Vote Hotline, voters to provide a new way to share difficult voting experiences (e.g., long lines, broken machines, inaccurate voting rolls) with one another and ensure that the media and watchdog groups are aware of any problems.

 From questions like “where do I vote” or “how do I make sure that my rights are being upheld,” Twitter Voter Report will augments these efforts by providing a new way for voters to send text messages (aka tweets) via cellphones or computers. These messages will be aggregated and mapped so that everyone can see the Nation's voting problems in real-time.

A Nationwide web map will display pins identifying every zip code where Americans are waiting over 30 minutes to vote or indicating those election districts where the voting machines are not working. Collectively the project particpants will inform each other when the lines are too long and ensure that media and watchdog groups know when and where problems exist.

If you are a Twitter user be sure to tap into this network.

While Twitter may not have immediate uses for some businesses, this is a good example of the massive collaborative efforts that Web 2.0 can provide. It will be interesting to see just how this goes next Tuesday.

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Science, Web 2.0

Discussing Web 2.0

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boat by notsogoodphotography
Are scientists missing the boat?;.:
[Via Bench Marks]

….or has that boat already sailed?

I’ve read many a blog posting or magazine article declaring that scientists are behind the curve, and we biologists have been slow to pick up the new online tools that are available. I’ve repeatedly asked for examples of other professions that are ahead of the curve that we can use as models (are there social networks of bakers sharing recipes and discussing ovens?), but haven’t seen much offered in response. I tend to think that it’s not a question of scientists being slow, it’s that the tools being offered aren’t very appealing. Note how quickly scientists moved from paper journals to online versions, which only took as long as it did because of the slow progress on the part of journal publishers getting their articles up on the web. The advantages of online journals were obvious, and in comparison, the advantages of joining “Myspace for scientists” are less evident.

Are social networks )”Meet collaborators! Discuss papers!”) ever going to see heavy use from the biology community? Or are we starting to see that they’ve run their course in general, and scientists were prescient in not wasting their time?
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There are too many advantages that arise from using many of these Web 2.0 tools (i.e. the ability to leverage human social networks in order to examine large datasets). However, the race will not be to have 5000 friends, as often seen out in the wild.

In a closed environment, such as a corporation, there are some very good uses for wikis, blogs, etc. They can not only help workflow tremendously but also can allow new metrics to be used in order to track just who contributed what to a project.

Moving tacit information from insides someone’s head outside into an explicit database will have important consequences for many organizations.

I don’t think the next generation will shun these tools. They will just have a better idea of how to interact with them more usefully, with a focus that can really help their workflow.

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Open Access, Science

More discussion

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communication by dalbera
Is Science Being Distorted?:
[Via The Scholarly Kitchen]

A recent PLoS Medicine article claims that information economics distort science. But maybe it’s an obsession with journals distorting the views of the authors.
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As I said earlier, I thought there would be some interesting discussions. I guess one way of looking at it is that all the ‘good’ data gets published in the prestigious journals and there is nowhere for the ‘bad’ data to be published until after a clinical trial fails. Whether this is a real bias problem is difficult to assess.

I think any problem is due more to the complexity of human health studies than any bias but we have to keep moving forward as best as we can.

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Web 2.0

An opportunity

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180 406467113 B1776D05Aa by Erik Charlton

No surprise, it looks like we’re headed for a sustained period of tough economic times.

The hurricane has blown through, metaphorically speaking. Now it’s many long months of cleanup and getting back to normal, or maybe redefining what “normal” might be.

But there might be a silver lining to this economic storm.

A Quick Recap

If you’re a regular reader of this blog, you know we’re on a journey towards social media proficiency.

We’ve had our internal platform up for over a year, and we now have all sorts of external communities heading towards our external platform group.

But — challengingly — not enough people have been “thinking differently” about how to get things done.

Sure, we can revel in many successes. But against a vast backdrop of people, behaviors and legacy business processes, we’ve only just begun.

Forcing The Situation

It’s very likely that my company, like many, will be rethinking its budgets for 2009.

There probably won’t be a lot of budget for “expensive” stuff: in-person forums, face-to-face meetings, slick advertising and the like.

There’s been no official mandate in this regard yet. But smart business managers (mostly those in the marketing world) can sense the change of economic seasons, and are looking around for more cost-effective mechanisms for reaching and engaging with the outside world.

Besides, even if we can afford a nice event in a nice venue, who can afford to attend?

Randy (who runs our external community group) tells me his phone is ringing off the hook. All sorts of internal groups are coming out of the woodwork, interested in the idea of a near-zero-cost mechanism for achieving their marketing and engagement goals outside the company.

The good news? As a result, we’re accelerating change.

The challenges? None of these new groups are especially proficienct at what it takes to design, build and launch an external community. More problematic, they bring a host of pre-conceived notions about what they think they want, how they think they’re going about doing it.
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Finding ways to be more efficient, to be more productive, will be of prime interest as things go from bad to worse. So many Web 2.0 tools can accomplish this but too many people still do not know how to implement them best for their particular organization.

Some organizations are lucky and already have people who can help educate others. But many companies, especially small ones, do not have those sorts of ‘gardeners’. I expect this will be a useful niche, serving as a gardener-coach, as soon as the organizations actually realize they need something.

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Open Access, Web 2.0

Do it yourself

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building by tanakawho
Have a problem: Build a web resource:
[Via business|bytes|genes|molecules]

Via a post on Hacker News I ran into the Tulane School of Medicine Student Portal.

As one of the developers writes on Hacker News

Our goal is ‘making med school easier, one less click at a time’. We have no business model, just trying to make our own lives easier.

There is further description on the site

Hello, and welcome to the Tulane University School of Medicine’s Student Portal! This website came into existence over the course of the latter part of the 2007-2008 school year through the hard and volunteered work of a group of students concerned with making the lives of TUSOM medical students a bit easier. Our university community is a dynamic place with much do, and many resources to use on a daily basis. In an effort to reduce the amount of time and energy required to accomplish these activities, we developed this site. Our work has been led, and graciously supported by the Medical Student Government, the Office of Medical education, and the Deans.

This site was developed by students, and for students. As such, if there is a feature that you feel would benefit the community as a whole, please feel free to drop us a line at tmedweb@tulane.edu. We’ll take your suggestion into serious consideration, and see if it within our abilities to accomplish.

That’s the kind of initiative that one loves to see. With hosting cheap, good web frameworks and people increasingly looking to the web for information, not the last time you’ll see something like this either. The key is realizing that often, if you have a problem, you can solve it yourself, and relatively inexpensively. Sometimes you can build a business out of it, a la 37signals

They (or at least Niels Olson) have some pretty ambitious future plans as well.

Online tools are not only cheap, they are also mature enough that it no longer requires a CS degree and years of experience to put something together. Coupled with Open Source, an individual can create pretty complex sites.

A similar attitude is beginning to invade other areas, such as Biotech. So many of the support functions are now available from standalone companies (such as DNA synthesis, sequencing, etc.) that we are almost at the point of ‘garage biotech’, where a very substantial amount of work can be done through contract for much less cost that having to create the infrastructure yourself.

This will never be at the same level as IT sorts of processes but it can have a profound effect on the cost of doing the biotech business. Add in IT tools to facilitate rapid information dispersal and a small lab can accomplish things that required a much larger facility just 5 years ago.

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Web 2.0

Overturning pyramids

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pyramid by frankh
It’s Time to Invert the Management Pyramid
[Via HarvardBusiness.org]

As time passes by, people and things change. Now, what if time passes by and people change, but things that should change, don’t?

It is not a stationary relic I’m talking about. I’m talking about the brand new dinosaur on the block – the classical management pyramid. Time has come to dismantle it and adapt to a new evolutionary and unstructured model that leverages the team effect to ensure that companies can lead change rather play catch up or be left behind.

A little rewind might be in order here to make my point. The management pyramid, as we know it, began to take shape around the early 1900s. There were two important factors that influenced the classical (traditional) management school of thought: The Industrial Revolution and the World Wars.

The Industrial Revolution brought along with it the problem of management and the Wars brought with them the solution. In every war there was the General, the man who controlled and commanded. He had ‘managers’ who reported to him; these managers in turn had several ‘assistant managers’ who reported to them, and the whole configuration went on to make the traditional organizational structure, or the Management Pyramid.

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This is a very interesting article. It identifies the need to make organization less centralized. More bottom-up, less top-down. The organizations that can accomplish this with be more innovative. Those that fail will not be competitive.

This will not be easy. But, as with any selective system such as capitalism, the organizations that can more quickly harness innovation and creativity will more rapidly solve complex problems and become more successful.

The last part of the post is particularly important, regarding the task ahead.

Simple as it may sound, the truth is that this is a very tough task. The question we must ask ourselves is whether we have within ourselves the fortitude to deconstruct the traditional power centres so that more emphasis is placed on the troops instead of the General.

Business models have to change. In a football game, there are 22 players but only one has the ball at any particular time. The other 21 are forming a configuration. The open-ended structure we are in is not about the man with the ball, but about the configuration of the other 21 people.

Every forward-thinking organization has to carry out a reality check about its willingness and capacity to unstructure so that it can adapt to the new 22nd century business ecosystem.

So, do we have the vision to look upon our organizations as collaborative and evolutionary life forms that must keep changing along with the marketplace? Do we have the humility to step out of our egos and hand over the mike to our subordinates? Do we possess the courage to unstructure an existing, rigid regime that we have known to work in the past?

We often accept the verdict of the past and slumber into the cushioned inertia of best practices, until the need for change cries out loudly enough to stir us out of our comfort zones. It is time.

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Open Access, Science, Web 2.0

A new approach to publishing

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type by Marcin Wichary
An experiment in open access publishing:
[Via Bench Marks]

The new edition of Essentials of Glycobiology, ” the largest, most authoritative volume available on the structure, synthesis, and biology of glycans (sugar chains), molecules that coat cell surfaces and proteins and play important roles in many normal and disease processes” came out yesterday. What’s particularly interesting about this edition is that it is simultaneously being released online in a freely accessible version, which will hopefully allow the textbook to reach a wider audience.

The theory often espoused is that online release of books leads to higher sales of the print edition, and for us, this is a good test case. Quoting from the press release, John Inglis, Executive Director and Publisher of CSHL Press notes that,

“We will be tracking its usage and how readers of the site respond to the availability of a print version, for both research and teaching purposes.”

“This is an innovative development in the distribution of an established textbook that we hope will benefit readers, authors and editors, and the publisher,” says Ajit Varki, M.D., the book’s executive editor and a leader of the Consortium of Glycobiology Editors, which initiated the project. Varki is Professor at the University of California, San Diego. The Consortium also includes Professors Richard Cummings, Emory University; Jeffrey Esko, UC San Diego; Hudson Freeze, Burnham Institute for Medical Research; Pamela Stanley, Albert Einstein College of Medicine, New York; Carolyn Bertozzi, UC Berkeley; Gerald Hart, Johns Hopkins University School of Medicine; and Marilynn Etzler, UC Davis.

The online edition of Essentials of Glycobiology can be found here, and the print version can be ordered here.

This is a very interesting experiment. I knw that there are books I want to have to be able to access important data when I am not online, usually when I am writing. Being online can be distracting then.

But sometimes when I am online, I want a quick fact. Then finding them in an authoritative source is really important. I personally think that this sort of dual use could be very productive. It has been successful for some fiction works.

I too will be looking to see how well this works.

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Open Access, Web 2.0

Connected knowledge

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sydney by Corey Leopold
Knowledge wants to be connected:
[Via Science Commons]

That was the core message of a speech by Science Commons’ John Wilbanks at the Open Access and Research Conference 2008 a few weeks ago in Brisbane, Australia. The conference was an opportunity both to celebrate Australia’s burgeoning leadership in harnessing open approaches for advancing science and scholarship, and to talk about where the global open access (OA) movement is headed.

Thanks to the Web, we can gain knowledge about a meeting happening thousands of miles away. Then we can read what others thought of the meeting.

Here’s an excerpt from an article by the Australian Broadcasting Corporation’s Anna Sellah on the speech, which provides a succinct summary of the reasons why open approaches are vital for deriving value from the vast amounts of scientific data being produced:

“The value of any individual piece of knowledge is about the value of any individual piece of lego,” Wilbanks said in a keynote address to the Open Access and Research Conference held in Brisbane last week.

“It’s not that much until you put it together with other legos.”

He says the ability to connect knowledge brings scientific revolutions. For example Watson and Crick’s breakthrough on the structure of DNA involved them reading all the scientific papers on nucleotide bonding and encoding it in the form of a physical model, says Wilbanks.

But this kind of “human scale” analysis is no longer feasible in an age when automated laboratory processes generate vast amounts of information faster than the human mind can process it.

“For example, we have 45,000 papers about one protein or one gene,” says Wilbanks.

He says a scientist might once have analysed the impact of one drug on one gene, but now pipetting robots are capable of analysing 25,000 genes at a time.

“Most of the research says the smartest of us can handle five or six independent variables at once – not 25,000,” he says

You can read the full piece at the ABC website.

Those of you following news of the conference and developments in Australia may also be interested in Open Oz and Doing things with data, two posts by OA leader Dr. Alma Swan, who was also a keynote speaker at the event.

Social netowwrks evolved to deal wit large problems containing many variables (i.e. “what signs are present indicating that its save to plant?”) If we can have large groups examine the problem, many more variables can be looked at. A question would be “Does the number of variables increase linearly with network size or exponentially?”

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Open Access, Science

The Winner’s Curse

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trophies by Snap®
Current Biomedical Publication System: A Distorted View of the Reality of Scientific Data?:
[Via Scholarship 2.0: An Idea Whose Time Has Come]

Why Current Publication Practices May Distort Science

Young NS, Ioannidis JPA, Al-Ubaydli O

PLoS Medicine Vol. 5, No. 10, e201 / October 7 2008

[doi:10.1371/journal.pmed.0050201]

Summary

The current system of publication in biomedical research provides a distorted view of the reality of scientific data that are generated in the laboratory and clinic. This system can be studied by applying principles from the field of economics. The “winner’s curse,” a more general statement of publication bias, suggests that the small proportion of results chosen for publication are unrepresentative of scientists’ repeated samplings of the real world.

The self-correcting mechanism in science is retarded by the extreme imbalance between the abundance of supply (the output of basic science laboratories and clinical investigations) and the increasingly limited venues for publication (journals with sufficiently high impact). This system would be expected intrinsically to lead to the misallocation of resources. The scarcity of available outlets is artificial, based on the costs of printing in an electronic age and a belief that selectivity is equivalent to quality.

Science is subject to great uncertainty: we cannot be confident now which efforts will ultimately yield worthwhile achievements. However, the current system abdicates to a small number of intermediates an authoritative prescience to anticipate a highly unpredictable future. In considering society’s expectations and our own goals as scientists, we believe that there is a moral imperative to reconsider how scientific data are judged and disseminated.

Full Text Available At:

[http://medicine.plosjournals.org/perlserv/?request=get-document&doi=10.1371/journal.pmed.0050201]
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There are also several other article links at Scholarship 2.0 that are important to read. In particular, there is a discussion of the Winner’s Curse This is an observation that the winner of an auction in which all the bidders have similar information will usually overbid. The idea of the Winner’s Curse was first observed by oil companies bidding on offshore leases.

These authors make the point that publication in scientific journals may also suffer from a bias that resembles the Winner’s Curse. The Winner in an auction presents a price beyond the mean in order to succeed. The authors argue that in a similar way, papers often present data beyond the mean in order to get published.

It is an intriguing speculation and one that might deserve further examination. The data that do get published may be misleading and this may be a reason why early published clinical trials are often not replicated later.

And they make the point that the huge amount of data being generated has not seen a corresponding increase in the places to publish the data or conclusions based on the data. This introduces greater likelihood that what is actually published does not represent the ‘real value’ of the data.

I expect this work to produce some interesting discussions. I would be surprised if it is entirely true but it does propose some changes that might be worth implementing.

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