Data-intensive Scientific Discovery

May 23rd, 2010

It seems worth mentioning a book, The Fourth Paradigm: Data-intensive Scientific Discovery, found here.

The speed at which any given scientific discipline advances will depend on how well its researchers collaborate with one another, and with technologists, in areas of eScience such as databases, workflow management, visualization, and cloud computing technologies.

Most notably, the book can be purchased, and it can be downloaded in two PDF formats for free.

I suspect that events of history such as climategate and others lend force to ideas such as citizen science, multiple opinions, and transparency. My sense is that, given massive improvements in compute power, parallel processing, seti@home-like computing, we will see more opportunities for eScience to “take to the streets”.

On Sustainability

April 20th, 2010

A favorite quotation on sustainability is this from Tom Munnecke (personal communication):

My latest riff is to substitute “flourishing” for “sustainability.”  Aiming for sustainability is setting our sights too low, and inhibits flourishing.  Aiming for a flourishing civilization subsumes sustainability. Aiming for sustainable misery for all (“let’s all go live in yurts off the grid, using buckets for toilets”) is not the path to a flourishing civilization.

A further explanation is that this wasn’t implying that the free choice to live in a yurt was misery – it was the expectation that society in general would be forced to do so.

Looking at FriendFeed

January 10th, 2010

Björn Brembs wrote a blog entry Social filtering of scientific information – a view beyond Twitter in which he states that FriendFeed shares all of the features of Twitter but few of its limitations and provides many additional features valuable for scientists.

My interests in microblogging relate to backchannel communications, say, in the scenario in which you are engaged in an IBIS conversation and want to toss out ideas with others before committing to a response. But, the description of FriendFeed and signing on there as “gardens” (all my favorite login names were taken) suggests that it might serve other purposes. Certainly, the blog post’s links suggest that there is a lot of science going on there. Here are the salient points made:

Also in contrast to Twitter, comments to each contribution are archived in that context (and without a time limit), providing a solid base for fruitful, threaded discussions. In your user profile, you can choose to aggregate any number of individual RSS or Atom ‘feeds‘, including scientific publications you bookmark in your online reference manager (e.g. CiteULike or Connotea), your blog entries, social bookmarks (Google Reader, del.icio.us, etc.), and Tweets; and any other items you wish to post directly to your feed. You then look for other users whose profile is relevant to your work and subscribe to them. Every individual item posted in your subscriptions will then appear on your personalized FriendFeed homepage, plus optionally a configurable subset of the feeds you subscribed to. You can choose to bookmark (‘like‘) any of these items (Facebook copied this ‘like’ functionality just before it bought FriendFeed), comment on them, and share discussion threads in various ways.

At first, this aggregation of information and threaded discussions might seem daunting. However, the stream of information can be channeled by organizing it into separate sub-channels (‘lists’; similar to but more versatile than ‘folders’ in email), according to your personal preferences (e.g. one for search alerts). In addition to individual users, you can also subscribe to ‘rooms’ that revolve around particular topics. For example, the “The Life Scientists” room currently has 1,267 members and imports one feed.

Polylogues again

December 19th, 2009

I’ve noticed that there is sometime a bit of confusion, often detected when someone comments, in effect “oh, dialogues can be between more than two people”. Sure. I’ve been searching for some insight. Found some here (Arne Haselbach (Vienna) Polylogue – a paradigm for cultures
Based on a different notion of “polylogue”):

In my understanding there are two major differences between the words “dialogue” and “polylogue”. The first relates to the numbers involved, the second to the specificity of the participants.

As regards the numbers involved, “dialogue” refers to two or more, “polylogue” to many. Related to that is the second difference. The “two or more” that dialogue refers to are usually thought of as specific people – even if unknown -, while “the many” that the word “poly” refers to does not imply specific people.

The post goes on to explain those points, then gives the following summary:

Polylogues are, thus, the setting and the processes

  • in which people learn a language and acquire the stereotyped meanings and uses of language
  • in which people grow up into or enter a culture and acquire the stereotyped meanings and patterns of behaviour and its dominant rationality

and, at the same time, polylogues are the setting and the processes

  • in which languages and cultures develop and change over time.

Polylogues are central to all phenomena of living cultures.

Still chasing an intuition that the polylogues concept brings something to the table set by the knowledge gardening framework I have been outlining.

In Whose Conversation: Engaging the Public in Authentic Polylogue, (2004) Stephen Coleman suggests

that there is a radical cultural disconnection between the ways politicians think, act and express themselves and the norms of everyday sociability.

In a section on disconnection (and reconnection) between political entities and people, he tellingly states:

In reality, communication technologies can transmit signals, but cannot automatically or deterministically reconfigure relationships. The persistent question that must be addressed by the modernising proponents of reconnection is, Connection to what?

The paper then introduces conversation, suggesting many of the same points encountered in descriptions of Bohmian Dialogues:

Genuine polylogue, in the sense suggested by Buber, entails openness to conflicting
values as well as opinions. Within a deliberative context, openness involves the
abandonment of fixed preferences and values and a willingness to give reasoned
consideration to alternative preferences and values.

Then, the paper turns to deep listening:

In a collaborative dialogue, such as a conversation, listening comprises the
silent, reflective part of speaking. Buber refers to moments of communicative
interaction that are neither simply monologue nor reception as ‘the between.’ In this
sense, a genuine conversation between politicians and people should be based less on
speaking or being heard than those moments of common recognition where there is a
fusion between speaking and listening.

The paper finally envisions a space in which public polylogues are conducted, sketching six guiding principles:

Purpose: a reason for engaging the public

Design: appropriate use to technologies, known in my thesis work as boundary infrastructures and boundary objects

Recruitment: ensuring the right mix (as inclusive as possible) of participants

Moderation: needs to be fair, inclusive and transparent:

The traditional notion of the internet as a space of anarchy should be resisted

Summation: regular summaries of what’s going on

Response and outcome:

A link must be demonstrated between the initial purpose for engaging the public and
the outcome of their participation.

My own take on those six principles is that I have avoided the notion of moderation, though I am well aware of the wild west mentality and bad behavior that can crop up from time to time. I’ve been more inclined to seek ways to use a high-dimensional reputation and trust system to tame the wild frontiers of participatory behavior.

Polilogues revisited

December 3rd, 2009

Geert Drieghe articulates one of Leo Apostel’s goals in a quest for an integral philosophy thus (emphasis mine):

First, to unify different perspectives without maiming them. This is similar to Ken Wilber’s ’transcend and include’ where the different perspectives are included but transcended in a bigger whole. Wilber looks for the particular truths of each tradition or system and ties it in with other fields of knowledge while vigorously opposing the imperialist tendencies of any tradition who thinks it alone holds the whole truth.

Unify different perspectives without maiming them. That statement represents a view I maintain in relation to knowledge federation: bringing together world views (perspectives) without filters. Organize those information resources in a subject-centric way such that they are navigable, related, and available for social sensemaking processes.

Polilogues

December 2nd, 2009

Helen Titchen Beeth said this:

The bottom line, though, as Geert has said already, is that Polilogues is about worldviews. The world looks different from the perspective of each person who beholds it. But when we dig down into the invisible memetic mycelium that connects people in a culture, we start to find deeper, shared worldviews, based on assumptions about the nature of life and reality that people espouse unthinkingly and often never question from birth to death. Dig down deeper still and we creep into the miraculous gossamer dimensions where psychology is not other than biology is not other than astronomy and the individual and the collective arise, inseparably, together, as two aspects of the same mystery. Perspectives all the way down.

I am playing with an intuition that polilogues might be what you get when you federate many different IBIS conversations that are about the same issue.

Object-centric social networking?

October 5th, 2009

A 2005 post by Jyri Engeström is titled: “Why some social network services work and others don’t — Or: the case for object-centered sociality”. Among the points made:

The fallacy is to think that social networks are just made up of people. They’re not; social networks consist of people who are connected by a shared object.

The post cites as an example that Flickr turned pictures into objects of sociality. Point taken. Point questioned…

Is it the case that people go to Flickr to socialize around pictures, or is there something special about some pictures that attract social behaviors such as tagging and commenting?

I am inclined to spend time looking at pictures taken by friends, or pictures that are about things (read: subjects) of interest to me. I won’t go so far as to assert that behavior describes every visit to Flickr, but I will suggest that it seems far more likely that it is the subjects portrayed in the boundary objects that are pictures that bind and unite social interactions.

I am making a case for subject-centric social networking.

When we write a blog post about another blog post, we are not united by the blog (boundary object) itself; might have been an email, a journal article, whatever. It’s the subject of that blog post that counts, that provokes a response, a comment, a tag, a social gesture of one sort or another.

Subject-centric sociality, I believe, is an accurate way to think about social intercourse. There remains much more to say about that.

On further reflection on recent (2009) slides presented here, I’m not all that certain that Engeström’s object-centric assertion is necessarily missing the point I’m making, at least in some cases. Some of the point made in the slides could easily be interpreted as subject-centric.

Bohmian Dialogues with IBIS?

September 12th, 2009

I’ve been wondering how one goes about engaging in a Bohmian dialogue using the tools and craft of IBIS. To review, a Bohmian dialogue is one in which you check your agenda at the door; don’t bring your goals into the room. Instead, you learn who the other participants are, most importantly, where they are coming from while you share where you are coming from, all while bathed in the light of some stated context. Leave the contests for later.

Along the way, I am discovering a variety that exists in IBIS craft: the core notion seems to be that of mapping dialogues, hence, dialogue mapping.  I am learning that there is variety in the goals to which those dialogues must submit: finding consensus, solving problems, mapping issues, mapping decisions, and more. I just invented a new one: discovery. Sure, I’ll be the first to suspect that’s not a new or unique goal; the truth is most likely that someone else invented that, I read about it, then completely forgot I ever read it. So, I make no priority claims here. I just use it for what it brings to the table.

I will make this claim: discovery mapping is a form of Bohmian dialogue. This is the process, the IBIS craft during which participants lay out answers they have at hand–they express their individual world views–in the context of questions posed by the context of the dialogue.  “Questions posed” is loaded with this meaning: these are not “problems to be solved” since labeling some situation as a problem can sometimes cause a shift in lenses used to offer responses. Instead, if something in the dialogue becomes a “problem to solve”, that branch of the tree, in my view of discovery practice, should turn into a leaf node and stop. We are interested more in creating a thoughtful foundation of the core domain world views of the participants, and not their world views about the world views of others. That’s a Bohmian dialogue with IBIS.

One can easily imagine the argument that IBIS is about issues. I’ll not defend against that argument. So?

Contesting world views of other participants, in my view, shifts the goal to another discipline within the IBIS craft.

I’d love to label the IBIS craft a pattern language. That’s another story.

Collective Sensemaking in a Knowledge Federation

September 6th, 2009

The term I prefer for this is Knowledge Gardening.

Let me introduce the elements of knowledge gardening as I sketch them in my slides from the Knowledge Federation 2008 conference. The elements are these:

  • Tagging: leaving trails, markers, scents, reminders
  • Annotating: lifting key ideas, questions, and arguments out of much larger resources, creating addressable information resources in small chunks
  • Connecting: linking small and large chunks (ideas, etc) using semantic relations; Cohere calls the links coherence relations
  • Federating: bringing together all knowable information resources in a subject-centric fashion, without filtering; filtering is a social process left to those who participate in the federation and should not be performed when resources are merged into other resources according to the rules of subject-centric federation (topic maps merging processes)

Subject-centric federation aims to bring all beliefs, world views, facts, and so forth together without filters. It’s reasonable to expect that a lot of so-called noise will enter into the knowledge base; deciding what is noise and what is signal must be left to social processes. To deal with noise, we anticipate the application of tags as filters, reputation and trust and value metrics, and other devices will combine with user interface filters (sorts) to mitigate issues associated with noise and allow users to create experiences that provide the highest possible signal to noise ratio according to individual criteria.

Thinking about Open Notebook Science

September 6th, 2009

A lot of water under the bridge since my last post. For the most part, my thesis proposal is coming up for defense later this month, and a lot of thinking and experimentation has followed. Right now, I am looking at Jean-Claude Bradley’s comments to this blog post on Open Notebook Science; those comments provide an opportunity for me to explain my latest thinking. I’ll take his three points and comment on each.

Use a wiki as the actual notebook with one experiment per page.

I agree with that. In fact, one experiment per page relates closely to Wikipedia’s one topic per page, and appears to express the notion of subject-centric federation as I see it. In fact, I am now using MediaWiki as the platform of choice.

Use a blog to discuss milestones and key problems to a more general scientific audience and link back to the experiments in the wiki.

I agree with that. Use blog posts to advertise conference papers and so forth.

Use a mailing list for external collaborations.

Now, we depart the full agreement category, with all due respect to the long history of using the killer app, email. When it comes to using email for topic-centric discourse, the term killer app might not be so appropriate in its original sense. I believe that there are existing and emerging technologies that allow for the integration of structured conversations (which, in the long run, could be conducted with email clients after suitable features are added); here, I am thinking about the various dialects of argument or dialogue mapping. These platforms started out life as desktop applications and are now migrating to the web. Debategraph is among the pioneers; see Mark Klien’s blog for more about Deliberatorium, see the bCisive online platform for a new product, and see the Global Sensemaking wiki for more on such tools.

The recap of my view is this:

  1. Wikis satisfy the need to capture and organize knowledge resources, provide a platform for linking, as if behaving as a topic map, though a more general purpose topic map, a federation platform that unites many such wikis and other platforms, should be a web-services portlet window on each page
  2. Blogs satisfy the need for storytelling
  3. The many tools of hypermedia discourse, including IBIS platform such as Compendium, bCisive, Cohere, Debategraph, Deliberatorium and others, satisfy the dialogue needs in ways that, I believe, constitute improvement over traditional email clients, online forum platforms, and so forth.

My present projects include the fabrication of a prototype federation server, fabrication (through crowd-sourced “hackathons”) of a variety of AJAX-like adapters to allow communication between three platforms: Semantic MediaWiki, Drupal, and WordPress, to the federation server, and the construction of a MediaWiki instance that demonstrates these systems at work.