Dangers of blogging

So in a blog post from last October which was mostly devoted to mocking Stephen Wolfram, I casually insulted HistCite, a citation network navigation program developed by Eugene Garfield, who basically invented the very idea of citation networks. So half a year goes by and then I get mail from Dr. Garfield complaining about this slander. I was rather taken aback that someone of his prestige would take the trouble to respond to an offhand remark by a mostly-anonymous blogger, but I backpedalled fast and responded apologetically:

Please forgive my offhanded nasty remarks; I have the greatest respect for your work, and I'm honored that you'd take the time to respond.

Google and similar web services have spoiled us (or spoiled me at least) -- we expect everything to be free and instantaneous and very easy to use. I was just wishing out loud for something that would let me see citation networks without fuss, bother, or cost. I apologize for calling HistCite "ugly", what it really is (in my opinion) is a complex tool for a professional information analyst, rather than a simple tool for casual browsers, which is what I was idly wishing for. So much academic work is now available casually to non-specialists now (through Google and elsewhere); it would be nice if the citation relationships were equally available.

Since professionally I work in IT for life science and other areas where information and software costs money, I don't really believe everything can come for free.

Well, that's why I blog with a pseduonym, so I don't have to worry too much about saying nasty things and having it come back and bite me. What else is this for? Still waiting to hear from Stephen Wolfram.

The lesson that things on the internet stay around forever and can come back and bite you is of course not new. When Google Groups made usenet postings from the early 90s part of the permanent public record, it caused me some personal embarassment that persists today. For some reason my dumbest posts still seem to come out on top, I suppose because they produced the largest number of dumb responses.

Microsoft ignores semantic web?

The Semantic Web has been the fad of the moment for some years now, and if I was a major platform vendor I would at least make sure I had my toes in the water to support development of applications that wanted to interoperate with it. However, Microsoft seems to be mostly ignoring it, in terms of providing tools and libraries.

If you want to use the latest and greatest semantic web standards for representing ontologies (OWL and relatives), you need a package that can deal with the file formats and more importantly implement the reasoning and inference capabilities implied by this kind of representation. There are a few serious open-source packages that can do this, but they are all in Java or some other non-.NET language. If you want to work on Microsoft's platform, there is a nice package called SemWeb, but it operates only at the RDF-triple level, and is pretty much a one-man hack rather than a major research effort.

When I queried Microsoft about this, they basically said they don't care and I should try to use IKVM to run the Java packages on .NET. IKVM is a very cool hack but that doesn't sound very realistic given the bleeding-edginess of this technology and the need to debug across the API boundaries.

C'mon guys, aren't you about embrace-and-extend? Maybe the problem is they have their own splufty new language-integrated-data-access thingy (LINQ) and see the semantic web as something of a competitor/distraction. Maybe the whole flavor of Semantic Web is too cross-platform for Microsoft (but they took up the non-semantic Web, and XML, this is just the next phase).

So this entry isn't all kvetch, here's a useful compilation of semantic web toolkits for a variety of languages/platforms.

Doom, something we can all agree on

We expect this sort of thing from environmentalists and leftists, so we don't really take it all that seriously. But when prominent Republicans write doom-slinging books about immanent theocracy and economic collapse, I'd say it's time to kick up worry level a tad.

Math is hard!

I was complaining before about semantic web stuff being heavyweight? Here's a section from the SPARQL (RDF query language) specification:

2.5 Basic Graph Patterns

A basic graph patterns is a set of triple patterns and forms the basis of SPARQL query matching. Matching a basic graph pattern is defined in terms of generic entailment to allow for future extension of the language.

Definition: Basic Graph Pattern

A Basic Graph Pattern is a set of Triple Patterns.

Definition: E-entailment Regime

An E-entailment regime is a binary relation between subsets of RDF graphs.

A graph in the range of an E-entailment is called well-formed for the E-entailment.

This specification covers only simple entailment [RDF-MT] as E-entailment. Examples of other E-entailment regimes are RDF entailment [RDF-MT], RDFS entailment [RDF-MT], OWL entailment [OWL-Semantics].

Definition: Basic Graph Pattern equivalence

Two basic graph patterns are equivalent if there is a bijection M between the terms of the triple patterns that maps blank nodes to blank nodes and maps variables, literals and IRIs to themselves, such that a triple ( s, p, o ) is in the first pattern if and only if the triple ( M(s), M(p) M(o) ) is in the second.

This definition extends that for RDF graph-equivalence to basic graph patterns by preserving variables names across equivalent graphs

Now, this is not all that abstruse, but then I have a math degree and am used to it. Way back then I studied mathematical logic, thought it was fun but a lousy way to describe the world and a lousy model for computation. It seems to have triumphed, however, and now people are expected to speak that language (the RDF semantics spec is even worse). I have a hard time believing that working programmers (a set of which I myself am a member of, nowadays) are going to be gleefully soaking up all the model-theoretic semantic theory behind the semantic web.

Maybe I'm wrong, there are people willing to boil things down into understandability. This well-written article doesn't cover any sort of non-trivial queries however.

There seems to be a big gap between RDF-as-first-order-predicate-logic-with-model-theoretic-semantics and RDF-as-useful-flexible-emerging-data-standard. Looked at positively, it's a two-pronged thrust, from academia and hackerdom acting together.

Boring is worse than wrong

The real reason I find myself vaguely defending some religious ideas against village-atheism is the same reason I used to go around getting into arguments with libertarians. It's that overly simple belief systems really annoy me, even if (especially if) I mostly agree with them. Libertarians used to make me crazy, because I always knew exactly what they would say in any situation (the spur for this post is this column (TNR subscribtion required) which makes the same observation about the New York Times op-ed libertarian, John Tierney). Same for the atheists, like PZ Myers. I can pretty much predict his reaction to any piece of news involving religion, which makes his posts on those subjects information-free (they can be entertainingly nasty though).

I guess I don't like fundamentalisms of any sort. Libertarianism and atheism both tend to be all-explanatory and ignorant of nuance. Libertarianism in its fascination with the distributed market model ignores anything which doesn't fit its framework, such as public goods, distortion of the market by the overly powerful (who can manipulate it unfairly) and the poor (who may have no motivation to respect property rights). Atheism tends to ignore the nature of religious belief, treating as something like bad science, rather than trying to understand what it might really be about. Let's just say God is the referent of the word "God", and while it may not exist the way a chair exists, it has a real conceptual role in thought which it might be useful to understand.

Semantic Con

I don't really mean the pun in the title; the Semantic Technologies conference was actually pretty interesting, in a hypeish sort of way. It represnts the attempt to diffuse a set of academic technologies and standards into industry. Note that while the standards (RDF, OWL, etc) are promoted and developed under the rubric "Semantic Web", the web is notably absent from the conference title. That's because these technologies are not being taken up so much in by the web proper, but are being sold to huge organizations with massive and complex data integration needs. These include defense (aero), intelligence, finance, and biotech. At the grassroots, it is being pushed by working life scientists trying to solve the same sorts of problems. Here's a presentation by Carole Goble that summarizes the hype pretty nicely, and without much technical detail.

The Semantic Web standards are complex, verbose, and hard to understand. They are backed by Web programmers prefer simpler standards: REST over SOAP, folksonomies over ontologies. Web guys do mashups and go to ETech; semantic technologists propose complex architectures and require large funders to get them realized.

It surprises me but it looks like the pressure of hard problems with good funding will overcome the complexity barrier of the Semantic Web. It surprises me not even so much because the syntaxes are complex and verbose, but the results are fairly inexpressive and inflexible in certain ways (for instance, OWL, the ontology standard, is based on description logic which makes it hard to do something as simple as default reasoning, something any simple old-fashioned frame system could do). Having been out of industrial grade AI for awhile, I will reserve judgement.

Semantics in a San Jose Hotel

I'm not much of a conference-goer, but this week I'll be at Semantic Technologies. This amusing site of recommended meetings lists it as a "Chess Club Conference", ie, geeky, which is only partly right -- it's actually part geeky and part marketing, where architecture astronautics meets the hype machine. I should get my cyncial slogan printed up as a t-shirt.

There is actually some pretty interesting stuff going in this space, especially in life science, and an awful lot of coporate hype. I will be attempting to separate out the two.