Category Archives: Thesis Research

Bohmian Dialogues with IBIS?

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

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

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.

More online notebooks

I just learned about this blog entry that points to iLeonardo among others. It would seem that online notebooks are gaining some momentum. In terms of my Knowledge Federation work, both in the up coming Knowledge Federation workshop, and my thesis, I’d like to think that online notebooks will provide a rich territory for a federation’s map.

Open Notebook Science–sensemaking

I’m collecting a bunch of links and notes here. Not too much else. While tracking Open Notebook Science, I’ve stumbled on a bunch of practitioners such as Michael Barton’s blog. I found that link by way of a discussion about Jon Udell blogging libraries and open notebook science. Somewhere in there, trust me things move quickly, I landed on a Nature Networks (cool stuff!) site where they are talking about collaboration.  Nature Networks is a provision of the Nature Magazine where you can pre-publish your work as a means of establishing dates and so forth.

From the Nature Networks site, there is a link talking about a pre-nup for collaborations, which leads to a Nature news item about a failed collaboration. More good stuff.

Then, there is the blog on Science in the Open, one of many blogs of the Open Wetware community. From what I can tell, the idea is to use a wiki with a lab notebook template for doing science in the open, and using a blog to advertise and discuss the research.

From this blog, we gather a couple of interesting quotes:

During the early stages of my project I found it quite useful to blog, as it helped me to clarify my results and ideas while the project was still taking shape. I tried to do this about once a week, on a Friday, and summarise my latest results. Having this record of results was also helpful to refer to when discussing my latest findings. When we were writing the manuscript I also found it useful to browse back through all the entries I had created and include any ideas I had forgotten about. However, as the project progressed blogging became less important, as I had already produced my main findings and was more focused on writing the manuscript.

As for sharing information I found that writing a summary blog my research takes rather a large amount of effort. Furthermore my  blog is the only gateway to my research, and results only become available when I make the time and effort write them up. This therefore doesn’t satisfy Jean Claude Bradley’s criteria of no insider knowledge, but rather could be described as being selectively open about my research. On the positive side a blog post is a concise summary that distills my most recent progress in a way I hope is easily accessible to a casual reader. Another interesting point is that posting all my results online meant they were indexed by Google, as you would expect, but this also lead to some strange occurrences when searching online for material. For example searching for “Akashi & Gojobori”, a paper I based my work on, brings up two links to my blog ahead of the original manuscript. I find this a bit embarrassing, and I wonder if the paper authors have also encountered this?

With less time to spend on blogging, I also tried to stream my research using Twitter, sending short messages automatically using a bash script every time I committed an SVN update. While this approach takes a lot less effort on my part, I think this is the opposite end of the spectrum to blogging, and spews out large amounts of obscure repository check in messages. Ultimately I think it is of little interest for even someone directly involved in the project.

In summary, open notebook science has not really had a large positive effect on my research. I think that this is mainly because using a blog alone is not an effective method of communicating scientific progress, because it requires substantial effort on my part to update, and second tracking the current state of the research can be difficult. However, I still believe that the principles of open notebook science can be beneficial to my research. In the next couple of months I’ll try some new methods to see what does work.

Mentioning two blogs of interest

I’m sitting here in beautiful baja Menlo Park (California) with my MacBook on my lap using the Carrot2 clustering  search engine to ponder topics of interest to my thesis. I landed on two blogs of note which I’ll share here. Each blog turns out to be of great surfing value for related topics. The most striking blog noted is that of Kia Pata, an Estonian researcher. The link given is to the first link from the search, and appears to be of great relevance to my work; Taming the Spaces even sounds like it’s talking about TopicSpaces, my project. The second blog is that of Ray Sims, a researcher orbiting planets (attractor basins) about which I, too, orbit.

My daughter, a psych major and also chapter author in the book XML Topic Maps together with her brother, is taking a new interest in topic maps as candidate platforms for the fabrication of immersive environments for epistemic communities of practice. Some of the links I am finding appear valuable to her work as well, particularly the work of Kia Pata.

It’s going to take me a few days to fully digest all the material I just found, but, it would seem, that’s the nature of research: feasts where one is inundated in a gold mine of information, and famine, where you go offline and digest everything (read: write your papers). If I don’t go offline soon, my head will hurt.

Final observation, Kia Pata appears to be making full use of the enormous power of the WordPress platform. If I had the time…

Metaphors. Lots of them.

I like metaphors. Consider the Periodic Table of the Elements. I like to think of that as a metaphor for discovery. It embodies everything I know about pattern recognition, extrapolation, prediction, and discovery. We’ve come a long way since Aristotle’s four main elements: air, fire, earth and water. Quoting from Wikipedia:

Earlier attempts to list the elements to show the relationships between them (for example by Newlands) had usually involved putting them in order of atomic mass. Mendeleev’s key insight in devising the periodic table was to lay out the elements to illustrate recurring (“periodic”) chemical properties (even if this meant some of them were not in mass order), and to leave gaps for “missing” elements. Mendeleev used his table to predict the properties of these “missing elements”, and many of them were indeed discovered and fit the predictions well.

I’d like to think that my work, when coupled with other research, will tease out of the aether recognizable patterns beyond those we now understand.

Then, there’s the Knowledge Gardening metaphor, in which we think of our collective sensemaking with the many tools and artifacts of hypermedia discourse as tending a garden, cultivating wisdom, planting the seeds of knowledge, weeding out bad information, and so on. Many moons back, a friend Richard Merrill wrote a book Radical Agriculture in which he introduced, to me, the term rhyzosphere, which is the matrix surrounding roots that supports nutrient and water uptake; it is essentially the ecosystem below ground that supports plant life. Thinking long and hard about that, where “thinking long and hard” is defined as using everybody’s favorite search engine, I ended up on a veritable romp through Wikipedia. For now, I’ll just toss up some links and maybe a few quotes to serve as H’ordourves…

THE RHYZOSPHERE, BIOLOGY AND THE REGOLITH talks about biological aspects of the rhyzosphere.

Rhizome_(philosophy) is the “philosophical” entry at Wikipedia about a rhizome, in this case, talking about that concept as a metaphor. This is the link that kicks open a rather stimulating tour.

Life has always seemed to me like a plant that lives on its rhizome. Its true life is invisible, hidden in the rhizome. The part that appears above the ground lasts only a single summer. Then it withers away an ephemeral apparition. When we think of the unending growth and decay of life and civilizations, we cannot escape the impression of absolute nullity. Yet I have never lost the sense of something that lives and endures beneath the eternal flux. What we see is blossom, which passes. The rhizome remains. (Carl Jung: Prologue from “Memories, Dreams, Reflections”)

And now the metaphor from that Wikipedia entry, one that opens a floodgate (to use another metaphor):

Gilles Deleuze and Félix Guattari used the term “rhizome” to describe theory and research that allows for multiple, non-hierarchical entry and exit points in data representation and interpretation. In A Thousand Plateaus, they opposed it to an arborescent conception of knowledge, which worked with dualist categories and binary choices. A rhizome works with horizontal and trans-species connections, while an arborescent model works with vertical and linear connections. Their use of the “orchid and the wasp” was taken from the biological concept of mutualism, in which two different species interact together to form a multiplicity (i.e. a unity that is multiple in itself). Horizontal gene transfer would also be a good illustration.

A_Thousand_Plateaus follows from the previous Wikipedia quote as another Wikipedia entry:

A Thousand Plateaus (French: Mille Plateaux) (1980) is a book by the French philosopher Gilles Deleuze and the psychoanalyst Félix Guattari. It forms the second part of their Capitalism and Schizophrenia duo (the first part being Anti-Oedipus). This book is written as a series of “plateaus”, a concept derived from Gregory Bateson, each identified by a particular date and title. Each refers to a peculiar age or date in which the state described in each plateau had a central role in the world. The book reflects Deleuze and Guattari’s rejection of hierarchical (arborescent) organization in favor of less structured, “rhizomatic” growth. The nomadic war machine is opposed to the state apparatus. In the last plateau the noosphere is invoked.

That the last sentence in this quote mentions the noosphere, about which I have read in other journeys, I am beginning to feel comfortable on this journey. Funny how seeing things one thinks to be familiar enhances the experience when thematic vagabonding new concepts. At the bottom of the Rhizome_(philosophy) entry is a link to rhizome-theory-directory. It’s a directory of blog entries made by Jeff Vail, each of which appears worth entry on my next journey.

Meanwhile, and to exhaust this journey, there is a concept mentioned along the way: Mutualism , yet another Wikipedia entry.

A Mutualism is an interaction between individuals of two different species, where both individuals derive a fitness benefit, for example increased survivorship. Similar interactions within a species are known as co-operation. Mutualism may be classified in terms of the closeness of association, the closest being symbiosis, which is often confused with mutualism. One or both species involved in the interaction may be obligate, meaning they cannot survive in the short or long term without the other species. Though mutualism has historically received less attention than other interactions such as predation,[1] it is very important subject in ecology. Examples include cleaner fish, pollination and seed dispersal, gut flora and nitrogen fixation by fungi.

Just playing, I wonder what happens when we mutate that definition by substituting “world views” for “species”, at least for the first instance of “species”. My work with subject maps is animated by the need to find or invent ways to merge different world views. Co-operation occurs when authors of two different subject maps find ways to enhance their respective representations such that they can merge their maps where merging is indicated. Merging is always indicated when two different representations are about the same subject. This process is called subject-centric merging. I call it federation. In fact, the umbrella concept that animates my work is called cultural federation. Hmmm…cultural mutualism. I suppose I should be careful here and not mention that in public yet…