Thursday, December 30, 2004

Free Speech

I have recently been informed that some of the comments on this Weblog are offensive. Some people, apparently, do not agree with my opinions. And that is supposed to be news? People have opinions and these pages reflect mine. They are not the opinions of any company for which I have ever worked.

It has also been suggested that some of my comments here are somehow unpatriotic. They are not. Get over it. I have opinions on the actions of every administration. I can also see interesting statistical corrolations without being unpatriotic. Those who think not should keep in mind that I am a medically retired naval officer who gave my health, and nearly my life, to my country. Unpatriotic? I think not.

To any of you who would criticize these pages I say this: Feel free. That is what free speech is all about. But don't expect me to change my mind in the face of anything other than a reasoned argument.

Wednesday, December 29, 2004

Changes at Tucana Technologies

Tucana Technologies is undergoing some major structural changes that will impact the way our technology is fielded and supported. Watch this space to get the announcements when they come.

The official board position that was posted here a while ago has been changed. In an effort to avoid confusion, I am not going to report their position until it is final.

Tuesday, December 07, 2004

Go Canadian?

CNN has a story on an American T-shirt company who "has a solution for their fellow citizens who want to vacation in Europe without having to answer questions about U.S. politics -- pose as Canadians." The kit offers Canadian patches, t-shirt and a phrase book, eh?

How did it come to this? Two generations of American chief executives hell-bent on protecting and expanding the power of the executive branch, that's how. Naturally, that undermines the careful checks-and-balance system laid down by the founding fathers. Sigh. I wonder if George Bush realizes that the Great Seal of the United States of America shows a bald eagle facing the olive branch of peace in its right talons, not the arrows of war in its left? No, perhaps he has been reading the Chinese Book of the Lord Shang: "If things are done that an enemy would be ashamed to do, there is an advantage".

Tuesday, November 30, 2004

Stickers and SUVs

You know those "Support Our Troops" stickers on the back of every SUV in America? I had, until recently, never seen them for sale. There was only one explanation: I don't shop where those people do. Since everyone seemed to have one, that could only be WalMart. It certainly isn't at the Apple store or Think Geek. I finally checked and, sure enough, WalMart has them by the metric tonne. Coming back from Thanksgiving I also saw some at a rest area on the New Jersey Turnpike. Is this intended to be an elitist comment on SUV drivers? You decide.

404 Self Storage

Choosing a name for a company can be hard. A good name should be short, pronouceable and memorable. A name should also not cause one to think of a double entendre. Newly emerging culture can have unexpected ramifications for names, as in the case with 404 Self Storage in eastern Maryland. I tried to find their Web site but, umm, couldn't get to the page :)

Thursday, November 04, 2004

Five Days in the West of England

I had the opportunity to spend a long weekend in Bristol, England preceeding a W3C Semantic Web Best Practices & Deployment Working Group face-to-face meeting (I suspect that words in organization titles are like keys; the greater the number you have, the less important you are).  The story is here and the photos are here.

Did only stupid people vote for Bush?

What happens if we compare the locations of the top institutions of higher learning with their host states' electoral results?

Tuesday, November 02, 2004

Driving on the umm, Right

I have recently noticed that in countries that drive on the left the
pedestrian traffic generally bares to the right. In countries that
drive on the right, the pedestrian traffic also tends to the right. I
found that counterintuitive until I realized that pedestrians will also
tend to the right when entering movie theatres, which is blamed to the
propensity toward right-handedness. If human society is of
predominantly right-handed people and right-handers tend to the right,
then I think Britain got it wrong; we should all drive on the right.

The seemingly natural movement of people to the direction of their
handedness is particularly complicated in left-driving cultures by the
placement of up pedestrian escalators on the left. Have you ever
watched the traffic jams at the bottom? Even when people are
experienced, they seem to happen more often than in right-driving

Sorry left handers!

Friday, October 29, 2004

Why Information Technology hasn't Transformed Life Sciences

Bob Robbins from Fred Hutchinson Cancer Research has a nice theory on
why information technology hasn't transformed life sciences research

UPS had an annual budget of US$20 billion (five year old numbers) and
spent about $1 billion per year on IT. That is about 5%. The National
Institutes of Health have a combined annual budget of $26 billion and
the National Cancer Institute part of NIH has an annual budget of $8
billion. However they are only spending $20 million in the first year
of caBIG. That is one quarter of a percent on IT for the largest life
sciences effort.

If the UPS model of a centralized, coordinated and efficient
distribution system is a reasonable basis for a cost model for a
distributed, uncoordinated and inefficient life sciences data sharing
environment, then information technology for life sciences research is
seriously underfunded. The reality is probably much worse.

So, Bob says, information technology has not transformed life sciences
research because IT spending by research organizations is underfunded
by one to two orders of magnitude.

Thursday, October 28, 2004

Day 2 at the SW/LS Workshop

Day two of the W3C Semantic Web in Life Sciences Workshop (agenda).

I watched the full lunar eclipse last night. We had a perfect view of it from Providence, Rhode Island where my sister-in-law lives. One can just imagine how scary that kind of event must have been to primitive agricultural societies with celestially-oriented mythologies. The moon turned a beautiful blood red at passage. The goddess certainly appeared angry, but I doubt the harvest will fail this year.

The keynote this morning was given by Ken Buetow (Director, National Cancer Institute Center for Bioinformatics) on the Cancer Bioinformatics Grid (caBIG). This is a huge project funded by the National Cancer Institute (NCI) to the tune of US$20M for the first year and $30M for the second year. This is a pilot study and will attract further funding if successful. caBIG is probably the best-funded semantic project on the planet at the moment.

Sean Martin (IBM) said, "We haven't even begun using I.T. in the biology research community yet." Scary as it may sound, it collaborates the comments from Ted Slator about Excel and Powerpoint yesterday. IBM's paper on their Semantic Layered Research Platform is here. Their system purports to do a lot of things Tucana does currently, but it was described at a prototype, with no plans to release it for the moment. It will be interesting to keep an eye on it.

There has been a lot of discussion today on Life Science Identifiers (LSIDs). The community does not seem to grasp the difference between URIs and URNs. LSIDs are URNs (and therefore URIs), but some people seem to want them to be URLs (inclusive of location information).

Wednesday, October 27, 2004

Esoterica from the W3C Semantic Web in Life Sciences Workshop

Slides from my talk with Ben Lund from Nature Publishing on the integration of the Urchin RSS aggregator and Kowari are here. The full paper, with Taowei David Wang and Kendall Clark from the University of Maryland is here.

It was great to see that the University of Colorado at Denver Health Sciences Center (UCHC) Center for Computational Pharmacology is using Kowari, according to Ian Wilson. His paper was Exploring Semantic Web Infrastructure for Life Science Knowledge-bases.

Life Sciences Industry Perspectives on the Semantic Web

Still at the W3C Semantic Web in Life Sciences Workshop (agenda).

The most consistent message from the pharma industry has been that the data management and discovery problems they face are complex. Otto Rittter from Astrazeneca said, "Drug discovery is a complex, costly, risky, information-driven enterprise". Not a bad quote, but it doesn't make you feel the truth like Ted Slator's comments about Pfizer. Pfizer is the industry's largest R&D organization. They have 12,500 employees and plan to spend US$7.9 billion on R&D alone in 2004. They have hundreds of ongoing R&D efforts in 18 theapuetic areas. Now, take that money-to-person ratio and combine it with the fact that the current state of knowledge management is driven by M$ Excel and Powerpoint. That is, data is collected in Excel and shown to other reseachers solely (in most cases) via Powerpoint. Wow.

According to Eric Neumann (Global Head of Knowledge Management, Aventis Pharmaceutical), the primary concerns when developing drugs are safety, efficacy (will it do what it is supposed to do), cost effectiveness and timeliness. It strikes me that the same list could be applied to software engineering projects; they are simply statements of economics. However, software projects that violate the rules are often fielded, anyway.

A fundamental problem of the application of semantic techniques to the life sciences industry is that basic terms are not well defined. Even simple terms like "protein" and "gene" are the subject of much argument. This would definitely hamper the development of ontologies. Still, many people are doing it in the best spirit of just getting on with things.

Two subjects of discussion in the Semantic Web Best Practices Working Group have been highlighted here: Provenance and transitive relationships. Biology is complex, and the statement that a gene encodes a protein may only be true within a certain context (including species of the genome, the gene sequence used, version info, etc). That makes transitive relationships suspect, and infers (there's that word again) that they should be made only when context is very clear. Even simple in silico experiments suffer from a lack of software version capture, as well as operating environments. That situation gets worse when biological experiments fail to encode full provenance.

The industry currently has no information supply chain data exchange standards, nor are they likely to come soon. Trust issues and funding sources ensure that data is simply not shared. This could result in semantic techniques being applied solely within companies in the short and medium terms. I would love to see some of the pharmas get together to define common ontologies, though, even if the instance data is purely internal.

Overall, the industry is drowning in data and an inability to get their hands around it. Ted Slator (Pfizer) says, "Our domain is too big to fit in our heads", and yet data integration is generally being attempted that way. It is no wonder that this workshop attracted such a large attendence.

TBL Keynote at W3C Semantic Web in Life Sciences Workshop

Tim Berners-Lee presented the keynote at the W3C Semantic Web in Life Sciences Workshop, held in Cambridge, MA. The workshop agenda is here. Tim's slides are here.

True to form, Sir Tim ensured that everyone present understood that they should all use URIs for everything. I wonder what his sock drawer looks like. His example was to define a URI for a concept like "colour". He also railed against software patents (who doesn't??) and pushed SVG as a standards-based replacement for PDF.

The problem with using SVG is, of course, that Adobe Acrobat is free and works, while SVG still relies on (often poorly implemented) browser plug-ins. Similarly, the Semantic Web suffers from a lack of applications which absorb and produce RDF. Only time and effort can change that. At least we are seeing progress in academia, the open source community and the commercial market.

Tim was asked where to find a browser for the Semantic Web (again). The difference this year is that there is starting to be a good answer to that question. Have a look at (Longwell) and (Haystack. He also pointed to ( Ontaria, which is more of a directory than a browser. Haystack is slow, but quite cool. I haven't downloaded Longwell, yet. Ontaria needs input.

One of the life sciences guys (Bob Robbins from the Fred Hutchinson Cancer Center) asked Tim about using semantic techniques for both descriptive data ("What is this plant in my backyard?") versus active research ("What are the opinions in the community about how this plant may be used?"). I don't think his answer was great (summary: This is an exciting area of research), but there is a good answer. Jim Hendler likes to make the point that the difference between OWL and traditional AI data descriptions is that OWL allows (indeed, encourages) differences of opinion. The Web Ontology Working Group admitted this user requirement up front, which is anathema to traditional AI. Add Jen Golbeck's work on trust descriptions and I think we are getting there.

Friday, October 15, 2004

Endangered Species

More than one-third of the world's amphibians are threatened in a new round of mass extinctions, according to a new study. Amphibians, such as frogs and snakes, may reflect greater environmental damage than previously expected. Their porous skins make them vulnerable to environmental changes, including pollution. That makes them better than canaries at telling us something. Anyone listening?

At the same time, global trade is causing the spread of many super-species from their own hostile environments to the cosy corners of the world. Snakeheads have been found in the Great Lakes for the first time, indicating a failure to contain the Chinese fish to the Southeastern US. Fire ants are threatening my house in Australia. They came on a ship from South America.

I discovered today that I am an endangered species, too. This article in USA Today (I found it on /.), notes that US programmers are going the way of the dodo, err, amphibians. In the best quip from Slashdot, scientists will be forced to "set up reserves with massive attempts to create offspring". Heh. If only it were that simple. We're from the government and we're here to help you...

The failure of governments to address any of these problems comes down to one phenomenon: short-term thinking. They are reacting to events one at a time, failing to see long-term trends and putting the economy first. What do they think is going to happen to the economy when the environment has crashed?

The funny thing is, it is not their fault. Really. Memetics would expect governments and most individuals to fail to react to a long-term crisis. Human history is littered with examples, from the collapse of grain production in Libya to the Cuban Missile Crisis. Evolution has created species that are over-specialized and hence vulnerable, just as it rewards good short-term planning (until an extinction event).

The only way to create a governmental policy to effectively deal with long-term issues is to deal with these very human failings up front. Much as we institutionalize punishment for murder so that personal revenge and feuds are avoided, we must institutionalize the response to environmental degradation and job migration. Otherwise, short-term incentives will rule. Shell Oill will leave a mess in Africa, IBM will outsource to India and frogs will die.

Thursday, October 14, 2004

Selling Your Soul

When we shifted business models from software services to software products, we had to sell our soul to the venture capital community. It was always going to be different, but I didn't realize that we would refer to our investors as "the syndicate", our customers as "users" and periodically want to "shoot someone in the head". Every time we have a board meeting it is like spending the day in an episode of The Sopranos.

Wednesday, October 13, 2004

Apple Powerbooks and External Displays

I love my 17" Powerbook. When at home, I connect it to a 23" cinema display. Unfortunately, when connecting and unconnecting the external display from a suspended state, the Powerbook would occasionally appear to freeze. I believe that the state of the display hardware was confused. The machine was up, but simply had no active display. This problem can be solved by a change in usage pattern: I now ensure that the machine is awake before disconnecting the external display. One does not have to be logged in; simply pressing a key to show the login box is sufficient (if you require a password after suspension). Oddly, it appears that you may connect an external display without worrying about the suspended state.

The State of Health Care in the US

I, a medically retired veteran of the US Navy, am watching the US presidential debate and just heard President Bush say that veterans have excellent health care. I am counting to ten. One, two, three, ARRRRGGGGHHHHHH! What an asshole. That man should spend some time in VA hospitals.

Thursday, September 30, 2004

Fixing US Foreign Policy

Well, the first presidential debate of 2004 is over and I think Kerry beat Bush. Still, neither candidate adequately identified what I beleive is the key issue of this race: How US foreign policy should be fixed. Kerry expects you to read his plan online, so you can read mine, too.

My opinion is that "America the Meme" is the US's largest export. It is not McDonald's or the Mouse but the very idea of checks and balances, individual choice and the belief that anyone can grow up to be president. Thomas Jefferson pusued the ideas and ideals of Locke, Bacon and Newton and turned them into a system of governance that many yet aspire to. It is these ideas, not the Mouse and the Big Mac, that make America great and an envy of the world.

Thus, America the Meme is the issue worth defending, growing and nuturing in US foriegn policy. The current administration involved the US in the first unilateral war of aggression since the Spanish-American War of 1898 (in which the US wanted Cuba and was instead saddled with governing the Philippines for nearly 50 years). Wars of aggression are a trait of empires, not of free countries wishing peace and prosperity for all. We must be careful not to sully America the Meme with images of empire building.

My prescription is simple, if a tiny bit radical: America needs to lead morally before (and while) it leads militarily and economically. That may be accomplished by signing and actively pushing an international ban on landmines which kill more children than soldiers; by unilaterally reducing nuclear arms arsenals instead of pursuing new research into nuclear "bunker busters"; by leading the international community on the reduction of pollution (inclusive of signing and ratifying the Kyoto Protocols); by signing and ratifying participation in the International Criminal Court; by treating war as a last resort and by active and consistent engagement of rogue states on issues of peace. In short, we must do the right thing according to our own beliefs in order to morally lead the world back from the fear and partisonship caused by reactionist protectionism.

We are only just learning to what extent the US literally scared the USSR into the Cold War by use of the atomic bombs, constant bomber and surveillance overflights, and arms buildups on its borders. Similarly, Robert McNamara has only recently told us how badly Vietnam was managed, thinking it was about communist expansion - at the same time Vietnamese leaders have told us they initially wanted US support for their revolution from China and France. US foriegn policy, in an effort to protect US interests, has caused fear and uncertainty in friends, adversaries and non-aligned countries alike. We have caused our own worst problems and the fog of war has done the rest.

Moral leadership would seem to be the only answer other than the sort of constant low-intensity warfare which characterized the Roman, Ottoman and British empires. It won't happen that way, under an administration lead by either candidate, but how much better the world would be if the United States of America would lead the world from the moral high ground instead of a bunker of our own design.

Tuesday, September 21, 2004

The Good Old US of A

I have lived in the US (this time) for about two years. I can hardly believe it has been that long. So, I have started to reflect on the way of life here.

Every item of food here seems to come with sugar. Why is that? Why should bread have sugar? I opened a can of baked beans yesterday, only to discover that the can contained beans and brown sugar. In beans? It is really hard to find food that does not have sugar added. Orange juice, licorice, even hot dogs. At least there is a good use for the verbose labelling laws here. I can now spend an extra half hour per shopping run trying to find just food.

Toys used to be special, something to look forward to. They are now cheap, ubiquitous and made in China. Toys are disposable. That just can't be good for anyone. Except maybe the Chinese. For now.

I live in a nice neighborhood in a relatively distant suberb of Washington, DC. There is no public transportation here. No buses. I have waited hours for a taxi, only to finally give up. For the first time in ten years, we are a two-car family.

The people in my neighborhood come from all over the world. That is cool. People tend to tolerate cultural differences here in a way that much of the world could benefit from.

We tend to almost fill one trash bin per week. Our neighbors generally double that. We recycle here, as do about a quarter of our block. The recycling blows into the lake and it seems to be noboby's job to pick it up. We do it sometimes and a couple of others have started to do the same. There are few trees, because they all got mowed down when the houses were built. It will be a few years before they go back. Things grow slowly when they have to hibernate for half the year.

It seems like the economy is dominated by a few very large corporations. News broadcasting certainly is. There seem to be two book stores chains in any given area. Three supermarkets (the two old ones and a new one trying hard to kill the one not keeping up with the times). Some things you just can't buy unless you go to Wal-Mart, like kids sleds. Toys "R" Us told me that I had to go to a specially party store (or Wal-Mart) to buy certain items for my daughter's birthday party. The big companies have become bigger and they seem to be divding the market. Considering the source of innovation (small companies) and the historic drivers for the economy (small companies), this seems like a bad thing. I can't say that I am in any way better off by living in a society dominiated by large companies. How much farther will it go? My guess is that America's time in the economic sun is about over.

Overall, I like living here even though this has been quite a rant. I do wish that American society wasn't so wasteful and blind to the future.

Monday, September 13, 2004

Master Li and Number 10 Ox

I have been ill this weekend and have therefore been reading lighter
material than normal. I took the opportunity to re-read Barry
Hughart's excellent books Bridge of Birds and Eight Skilled Gentlemen. They are truly wonderful books and I am sorry that he does not plan to write more. He gave an interview where he blames his publishers for failing
to sell many copies, in spite of having won the World Fantasy Award.

He wrote another book in this series called The Story of the Stone, but
it is no longer being published. In spite of having read only a
handful of fantasy novels (these and some of Terry Pratchett's
Discworld series) I just ordered it from Amazon.

Saturday, September 11, 2004

Prototypo and TBL

Prototypo and TBL
Prototypo and TBL,
originally uploaded by prototypo.
Sir Tim and prototypo at WWW 2004 (NYC).

Making Links

I would be horribly remiss if I didn't link to Paul Gearon's Working Notes about everybody's favorite RDF database, Kowari and Andrew Newman's More News, which I have relied upon for years.

Making the Semantic Web Viral

The Semantic Web has not undergone the explosion of users that caused the early World Wide Web to be successful. Why? The answer appears to be that individual Web authors do not have simple tools for the creation of semantic linkages between existing content. The barrier to entry is currently substantially higher than it was in the early Web.

These tools cannot yet be built because two preconditions do not yet exist; a means to link Web resources while retaining meaning about the intended relationships between resources and a means of navigating (via URL) between all types of Semantic Web resources, both concrete (Web) and abstract (RDF).

I think there are ways to solve both problems with existing technology. Part of the answer, though, lies in the standardization process.

The way I see it, Web links with semantics need an attribute on a hyperlink that defines the relationship between the resources. The XHTML 2.0 Working Draft adds a 'rel' attribute to links to accomplish this. Thanks to Mark Birbeck for proposing this very necessary extension. The draft is in Last Call, so anyone who wants to comment should get on it.

Short of waiting for XHTML 2.0 browser support, one could always fake the intended behavior with Javascript and a little imagination. Pick up the 'rel' attribute contents and pass them along to a server that knows what to do about it. I hope to have some time to try this so I can flesh out a paper for WWW 2005. It would be cool to go to Japan, since I haven't been there in many moons.

Once you have links with semantics, you need to provide a means of navigating from the existing Web to the more abstract space of RDF and back again. You can already link a Web page to another Web page, but what do you do when you want to link to a person? Representing people as email addresses or even FOAF files is weak, silly and just plain insufficient. People exist only in Meat Space and so have to be represented in Semantic Web Space by some non-trivial means. RDF & OWL already provide a great answer for this: A person object can exist that link to email addresses, FOAF and all the rest. Now we only need a way to navigate it via the Web.

There is more than one way to do that. First, one could point to a node in an RDF datastore by URI and a transformation (e.g. an RDF query, some XSLT and a stylesheet) could present a view of RDF Space as a Web resource (an XHTML page, for example, but this could take many forms). The same technique (minus the RDF database) could be used if the RDF is serialized in an RDF/XML document or is extractable from a document (e.g. via GRDDL.

It would also be cool to return RDF information into a Web page without generating a new page, such as a layer box that lists several pieces of information about a link. Back to Javascrip to go get the data from RDF Space and present it. This would provide multiple destinations for a given link! I think that is pretty cool.