12 February 2010

A question of perspective, and the deliciousness of cannibalism

Happy Darwin day!

Let me pose this obtuse question to you; how many generations removed from you do you think it is ok to mate with your relatives? And the follow-up; how many generations removed do you think it's ok to eat them?

Dear friends, and by that, I mean everyone in the world, past, present and future. Again I'm sitting here pondering the big questions in life (it is, after all, lunch time), and I've hit upon a sad but somber note that I wanted to say something about. And I know this is a slight deviation from my normal prose, but some times there are more important things that trickle through my system up to the surface of this blog.

There are some revelations of truth that most people can't bear to think about in daily life, and so we suppress them, hide them away, and make them into someone else's problem; Surgery and blood, butchering of animals for consumption, undertaking, biopsies, most dentistry, philosophy, sewage and drains, rectal operations, and the list goes on and on with jobs you'd rather let someone else deal with. But I want to pick up on one of these for my purposes here, the butchering of animals.

I mentioned in my review of Dawkins latest book the notion of geological time, but we can extend that a bit to include the big bang (which didn't bang) and the formation of stars as well, so we're going some 13.7 billion years back in time. To use Carl Sagans wonderful cosmic calendar metaphor, imagine that all that time from the beginning of our universe (well, from the time just after the singularity until now, as we can't measure nothingness) until now is evenly spaced out across a years calendar. We, the humans and our whole history from when we diverged from some other ape specie, about 5 million years in total, is nothing but a little footnote; the last 10 seconds of the last day of the last month.

Let's go one step further, let's take those 10 seconds, our past history, and slosh that one across another yearly calendar, where January 1 is the first upright (but not humanoid) apes and where every month is about 416 thousand years each (every day is about 14 thousand years). That would mean we meet us, the species Homo Sapiens, at around 21st of December, just in time for solstice. This also means that our recent history, the written one we know about from the first Sumerian tablets 6000 years ago and until today all happens just shy of 12 hours before midnight before New Years.

We humans, as aware Homo Sapiens, are but mere minutes in the great cosmological calendar, and a quick blink in the great scheme of things. You yourself is nothing but a fraction of a millisecond. A macrosecond! And this is the scale from which you observe the universe and try to find answers.

It's worth pointing out that we live in what Richard Dawkins (in another book of his) is a medium sized and macrosecond timed perspective; all that you know about the universe has to be compressed into this tiny perspective. Imagine your tiny perspective as a glass jar in front of you; in you pour cosmological time with all its components of matter and energy. The words you read right now is a structured pattern you recognize as words that your brain translates into meaning, so when we look at huge swaths of time we're looking for patterns, for things that we can find some meaning in. Unfortunately, all of our modern world of patterns you recognize, including our scale social patterns, our technologies, our modern cultures, all those things we have a nominal understanding of (if not at least a record of), all of it is nothing but a mere grain in a large soup of all that's ever been. You can try to find some meaning by looking for that grain, but even the chance of finding it would be hard in the extreme; your perspective of looking for words and sentences no less than 0.7 centimeters high, usually black on white background, is so not fit for the task of looking at microscopic grains all jumbled up, you're simply extremely out of your bounds.

That is cosmological and geological time for you; it's very hard to grasp.

Update: I've added this handy chart in order to try and draw the immense time. On this scale, we - the civilization of the human species, our last 6000 years of trying to understand who we are - are mere three-four pixels, fitted on a small line that you can hardly see to represent our entire human specie! We're so far removed from the scale of the universe to practically render us non-existent;

Now, let's move on to chemistry, how elemental particles are influenced by the various powers of nature such as gravity, viscosity, surface tension, and thermodynamics. If you take all particles around and stir them in a great pot adding heat, how long do you think it will take for certain atoms to form? Well, that's how our billions and billions of suns made matter, and when they exploded in supernovas scattered this material across the universe. So stabilize things a bit, but still you stir the pot. How long does it take for the atoms to form molecules? Remember that in each of these processes there are things that are naturally attracted to each other, and things that naturally repel. So, how long to make molecules. like, say, water? Next step, how long do you stir until you get strings or clumps of molecules? And how long until those clumps gets other clumps attached? We must realize that chemistry on this level is highly complex. Molecule A needs water to form, but water needs the fusion powers to merge two gases into a liquid. But what about molecule B? Well, it may need enough gravitational pull or surface tension of enough molecules A to be able to create a molecule B. And to get molecule C's, we need perhaps 5 other molecules, and it might all be perfectly natural as they all rely on the natural pull and push of attraction with other kinds of molecules. Molecule D might be attracted to molecules A and B, but repel molecule C. And we keep stirring the pop. A molecule F might only form if you have already formed molecules D and you freeze them next to molecules H. How long do we stir this semi-random pot until we get the first multi-molecular things? How long until a cell? How long until a replicating cell? How long until a one-celled replicator? Chemistry basically are interactions between things, so you can add one molecule to a pot of other molecules and use the energy from that chemical reaction to do other things, like moving, replicating, eating, sleeping, repairing damage, having sex, enjoy sunsets and writing long blog entries in the Internet.

It's really a question of perspective and of time more than asking silly questions about whether life can come from nothing or not. Of course it can as long as we define "nothing" as something that's hard for normal people to understand; it's just natural stuff, but because we can't reasonable imagine cosmological time we come to the wrong conclusions about the origin of life, that it can't just come out of "nothing." The answer is that it most certainly didn't come out of nothing; it came out of the amazing nature of the universe, and of chemistry. And a pinch of luck, probably.

Before I venture back to my original question, we need to define evolutionary time as defined through how long we think evolution of life on this planet has taken place; 3.7 billion years. So, from when roughly the time the earth came to be until life emerged, the semi-random chemical pot was stirred for about a billion years (that is a long, long time nothing much at all really happened) and then one day some multi-molecules did something astounding; it became alive. But what does that mean, alive?

In terms of chemistry, not much. Some define life as a cell able to replicate itself through DNA, but even that's a big stretch. These days lots of people are even talking about an RNA world void of DNA, and this went on for a very, very long time. Stirring the pot changed things around, perhaps made it better or different (even though we find traces of the RNA world still), but if you look at the details of chemistry slowly and carefully, there is no life, there is no one point we can say it starts Here! Because everything evolves sloooowly, so slow, in fact, that just like cosmological and geological time, we can't even phantom evolutionary time. If evolutionary time is mapped to our one year calendar, each day represents over 8 million years, bringing our human existence down to the last two minutes of the whole calendar. That's a long time to stir.

One thing few people grasp with all this is of course that most of the stirring and chance encounters and attraction and repelling yielded nothing, and that it was all this lack of results that made the tiny bit of result ever so interesting! It's again a matter of perspective, but did you know that 99.7% of all species that ever lived on this planet are all extinct? This is on par with; did you know that your body's cells have all be renewed, and that all your memories of a time older than about 13 years are transfered to you, that you are not the same being that was here when those memories formed? Well, it continues to blow me away, and it should blow you away, too;

We are complex molecular machines that somehow got this notion that we are important, if not to something external then at least unto ourselves. These are fine evolutionary traits that probably has saved our bacon from time to time, but think in terms of cosmological, geological and evolutionary time and you quickly forget about the importance of now and rather ponder the importance of all that time that has passed.

We are all connected. Through evolutionary time, life has shaped itself into countless forms, both on land, in the sea and in the air, on rocks, under rocks, everywhere, all shapes, sizes, it did it all in the name of just keep going, of replicating itself at all levels (molecular, cellular, as creatures, and now with Homo Sapiens we can add "ideas" to the mix). We came from chemistry between elements, from the same place. And all the atoms on this planet that was back then are still here, only reassembled a million times over through chemistry. Some times they assemble into water, other times into gases, but some times, under amazing circumstances, they come together and assemble you. You're here because of the continuous process of evolution created more and more complex things that use DNA to put a few trillion molecules together to shape the person that you are. And it only took cosmological time for the universe to become self-aware.

You have billions of cousins. We all do. All our ancestors, millions of generations of slowly changing and adapting to its environment, to a slight stirring of a chemical pot, you end up with the millions of species we know about today. And if we know this many living species, how many countless millions of extinct ones could there be? No one knows, of course. But the question still remains;

How many generations removed from you do you think it's ok to eat your relatives?

We're all connected, we're all descendants from the same primordial soup, and no matter if you eat a carrot or a juicy steak, you're eating a distant cousin. Now it's just a matter of deciding how many generations away you're willing to eat.

Bon appetit!

8 February 2010

Richard Dawkins "Greatest Show on Earth"

If I wasn't an indoctrinated corporate drone I would be a scientist, and indeed, back when I was a wee boy I dreamed of becoming a geologist. Boy, did I know my gray rocks from the slightly lighter gray rocks and so on. I took great delight in walks in nature finding moraines and tills and other long-gone remnants of geological implication (glaciers, mostly), and I could tell rombeporfyr from feltspat and point out the probable processes involved in creating the shapes and colors. It was a glorious time, and I've still got it I think (and I've passed it on to my kids who always make me carry tons of rocks back home ... there's poetic justice if I ever heard it), but nowadays mostly through the local geography (which is interesting in its own mind as the Kiama area are remnants of several epochs of volcanic activity on top of sandstone, with a strong iron presence. I'll probable make a post about all this in the future sometime).

Knowing something about geology makes you somewhat aware of what's known as geological time, a time frame that spans billions of years. And, as some might suspect, trying to get a grip on what 'billions of years' for a mere human is is a daunting and often failed task. But a rudimentary understanding of geological time and processes also rendered me immune to a lot of otherwise human misunderstanding and nonsense that our cultures have built up over time to explain all that which we didn't understand. So if you understand unstable (ie. radioactive) isotopes in rocks and their half-life, how they break down (as a figure of speech) from an unstable to a stable form, you have no problem understanding other processes that also runs across billions of years, and indeed, runs parallel to geological time and processes. And to someone who not only knows a few things about rocks but also those things which you find inside rocks, evolution is not hard to grasp, at least not the tenant that it is right there, in front of you, staring back at you after you chipped that piece of rock off from the rock wall. For me, it was the most natural thing, and indeed sparked my deep interest in all things biological as well.

So for me to read Dawkins book "Greatest show on earth" was more like a dumbed-down defense of something that I thought no one was stupid enough to refute. But, there it was, in the first chapter, a fleshing out that there were indeed idiots out there who just could grasp the most basic notions and evidence, people who actually thought everything we see now has been unchanging for all the time the earth and the universe have existed; about 10.000 years. Huh? *blink* Maybe the sub-title should have tipped me off; "The evidence for evolution", as if we needed more evidence than what was taught in school.

Then I realized that not all the kids I went to school with paid too much attention when such big issues came up. They probably passed the tests and all, but I did not see them engage with (or annoy with too many questions) the teacher the way I think I did, they didn't go out into the woods to climb rocks and find fossils themselves, they didn't deduce the layers of a side of a deep canyon with a river at the bottom who was responsible for the canyon, who dug it, how the shape came to be. I guess they ended up not knowing as much, at least not on these subjects.

And that was the greatest surprise for me; the world really needs to be convinced that evolution is real?

It was like someone pinched me; here I was thinking our human species were going places, and then I found out that the truth somehow is in question, that people were actively disagreeing with the fact that the earth was flat, young and static (and yes, that was satire). Looking at their argument against is nothing short of a laughing matter, all attributed to the fact that their faith is in disagreement with the science. Ouch. So who do we think is right? The people of faith and no facts, or thousands of scientists working together for hundreds of years on the greatest Utopian adventure humankind has ever ventured on? Oh, the irony.

A few observations I need to point out, though, is that when you read the book, try to read it in the voice of Richard Dawkins himself; it will make the book so much better, the arguments come alive and the longer hard words stand out with better diction. When I read some of the things it wasn't until I heard him read it himself that the words obtained a greater sense of beauty, and I'm pressed to say that I prefer him talking.

Another nitpick is how Dawkins repeatedly say that "he won't deal with that anymore" or at all, because he or someone else have written about it elsewhere. That is fine if the reader is an avid fanatic, frantically buying and reading everything the man or those others have ever written, but for the rest of us that stands out as a balloon of evidence just being deflated, making that horrible noise in the process. Don't do that; mention at least the main interesting tidbits that fit in your context, and then provide further references.

But still, for me, in short, is that the book is great; it's well-written, perhaps two notches too intelligent in places (c'mon, references to poetry? Who reads poetry anymore? And it uses a lot of big words, excluding huge parts of the intended audience), but a tad bit too apologetic as there is nothing excusable about being ignorant by choice (although I understand that this angle is mostly for the US market) and, I feel, just way too soft on the "opposition." These people are clearly not just history deniers, they are outright dishonest about their thirst for truth and knowledge, probably wouldn't know epistemology if it hit them over the head, cannot fathom that human traits and physiology only makes sense in evolutionary terms (have you checked your vestigial parts lately?), and since the discovery of genetics the huge amount of science that only works if evolution is true over geological time. I agree that thinking evolution is not true is crazy on a scale of, err, biblical proportions, and as much as I this book wasn't for me, I guess there is a strong need for it if there truly are this many nut cases out there who will deny anything if it doesn't sync with their faith or holy book. Weird and sad, but then that's what happens when you deny truth and, you know, that which sits right in front of you just waiting to be seen.

4 February 2010

Topic Maps, 10 years down the line

I'm told, by way of my own imagination based on loose rumors put out by flying pink fairies, that Topic Maps is a waning technology, poorly supported by the IT industry at large, hard to wrap your head around, and generally icky to deal with.

All of this is, unfortunately, true.

But, as in all stories told by only one side, there is an other side just waiting to come out into the light, just one day, real soon now. This day may never come, but here is my own little attempt to shed some light on a few of the issues with the Topic Maps world. It was about 10 years ago I first got a whiff of Topic Maps, so my first post in 2010 seems fitting to take some Topic Maps rumors, loose observations and vague statements, and make some comments along the way. Here we go ;

1. Topic Maps are hard

Why, yes, to a commoner or some person with a somewhat traditional approach to computing, Topic Maps can indeed seem like an alien concept at first. The first time I started reading up on it I was mesmerized and frightened at the same time, wondering where the magic would bring me and just how painful it would be for me when reality would kick in (and me) ; there were new notions and concept, new words, new paradigms everywhere! Reification, role types, associations, occurrences, occurrence type, typified information, subjects and topics, ontologies (upper, lower, specialized ones) the list goes on. It is terrifying indeed, and for many, many people they are so terrifying that SQL and C# and .Net and C and PHP seems like a comforting auntie lulling you back into things we know and know well, no hard thinking required (just lots of hair to pull out).

Until you realize a few things, that is. For example, the vocabulary is anchored in information science, and with a bit of research or learning it shouldn't take that long to get familiar with it. Even the complex issues of reification and ontologies after some time will be as normal and self-explainable as second-cousins and language. (And yes, there is a correlation between the examples given! See if you can find them!) And perhaps more importantly, the problems you can solve with Topic Maps can completely and utterly eradicate the major problems those traditional methods give us, one of the biggest bug-bears that I'd ever had! (Anyone wish to offer me a book deal on how to solve most of the main IT development problems in seriously interesting ways? :)

Can I just mention that having an small epiphany about Topic Maps have the effect of you never returning to the real world and look at it the same way, ever again? I have never met a person who got Topic Maps return to the old ways, at least not without making huge compromises. Getting it will change you in good ways, and is most definitely worth the effort despite the pain.

Tips to newbies: It's not really hard, even if it seems hard. But it requires you to change your mind on some key issues.

2. Topic Maps are poorly supported in the real-world

Oh yes, indeed. If you talk to anyone, any company in your immediate serenity (yes, a tautologically pun) and ask them about their use of Topic Maps, you'd most likely get a blank stare back and a careful "What would we need maps for?"

There's the odd technical-inclined person who might now a toddle about what these fabled Topic Maps are all about, but very, very few people understand what they are, and even less have implemented them into something useful. (The exception to this is, oddly enough, the country of Norway, and some scantily-clad areas of southern Germany) No mainstream software package comes with the stuff wrapped in, no word-processor touts its amazingness, no operating system comes with support for it, and no popular software of any kind use it.

But then, there's the odd system that use it. You'll find it also in the odd Norwegian government portal, which is bizarre in its own right, and perhaps deep down in some academic underfunded project or perhaps some commercial project where parts of the data-model masquerades as it. My old website use it. I have a framework or two. There's the odd other open-source project, a few API's, and a host of other well-meaning but obscure projects that perhaps has got it, albeit well hidden and kept away from children.

For a technology that stands out as something that can fix it all, I find it bizarre that it is found so seldom, but then bizarre is not the same as surprised. And when you look at the "competition", the well-funded, well-marketed, well-established world of the Semantic Web, championed by none other than the W3C and Tim Berners-Lee, well you have to concede that it shouldn't be much of a surprise at all, really. Topic Maps is a tiny group of enthusiasts (a few hundred, being liberal with statistics) who'll saw off their right leg if it meant we could get the specs done in time, while the Semantic World is littered with academia, organisations and companies (we're talking thousands upon thousands of people actively working on it), so no, you should not be surprised.

Tips to newbies: As the saying go, if a million flies eat it ... surely, it has some nutritional value or greater worth over, say, that green grass the cows are dumping it on?

3. Topic Maps is dying and obsolete; use RDF instead

There was a period about 10 years ago which I regard as the Topic Maps time of bloom ; the trees had beautiful flowers on, the pink and purple petals falling over the world of IT like a slow-motion rainfall of beauty. Everywhere you turned there was people talking about it and potential projects popping all the time.

But times went by. Topic Maps was too hard for most (see point 1 and 2), and not just the technical implications themselves and the language and terms used, but also the philosophy of it, the very idea of why we should be using it over, say, any relational database or traditional software stack. I mean, what's the point, really?

The point is easy to miss, admittedly. A technology that can be used for everything is hard to pin down and said to be good for something. And we have focused just too damn much on knowledge management systems, and not only that, but used our own special language in the process which often is quite remote from knowledge management speech in the enterprise arena (but you find it rife in academia). When the world looks to Topic Maps, all they see is a difficult way to do knowledge management. Ugh.

Myself, I'm using Topic Maps in highly non-traditional ways. I use maps for my application (definitions, actions and functionality), for functional topology (generic functionality in hyper-systems based on typification), for business logic (rules, conditions, interactions) and, perhaps just as important, for the actual development itself (modules and plugins, deployment, versioning, services) which makes for a highly (and this "highly" is quite higher than any normally used "highly") customizable and flexible framework for making great semantic applications. But more on the details at some later stage.

Tips for newbies: No, it's not dead nor dying, just not as popular as stuff that's easier or more accessible

4. Topic Maps is nothing new

Well, given its roughly 20 year history (and I'm counting from early days of HyTyme), in Internet years it's an old, old dog, so by that alone we can't say there's anything new, but most people would mean "new" here to mean something like "we've been doing X for years, so why do we need this?", where X usually points to some bit of the Topic Maps paradigm that indeed has been done before. Of course it has. There is nothing new in Topic Maps except, of course, putting it all together and standardize one cohesive and complete way of doing pretty damn most of what you would need for your complex data-model, identity management, semantic or otherwise relational, interoperable information and / or structural need, chucking in knowledge management, too, for good measure.

There are of course nothing new with Topic Maps, except that all that old stuff is bundled into a new thing, if you allow a 20 year old standard to be called "new." But then again, "the standard" is really a family of standards, all evolving and changing with the times. There's always a sub-standard (no pun intended ... well, not a lot of pun intended) in the woodworks, always some half-baked document to explain something or other, always something that is so damn specific and concise that the overall grooviness and funky bits are pushed to the side-lines.

Topic Maps is new and old at the same time, but it really is groovy and funky once you overcome the technical jargon and the concise nature of the standards.

Tips to newbies: The king is dead. Long live the king!

5. The Topic Maps community is, um, a bit tricky

Oh, yes indeed. And this one is the hardest to write about as I'm part of this community and know pretty much everyone, some more than others.

So let's say it this way; I'm a difficult person in certain ways, for example I talk a lot, I overflow with ideas rather than code, I don't care too much about political correctness, and I speak my mind and use language that could alienate people with too strong attachments to their ties or their social buckets.

And the core of the Topic Maps community is loaded with weirdos like me; highly opinionated, rough ideas, hard on woo, and soft on business. But the problem isn't the weirdos, but the low number of them. Any successful community with such a wide-ranging and all-encompassing area of what Topic Maps is all about (which is, uh, almost anything) going from epistemology to identity management to ontology work, well, you need a lot of personalities to match them all to make it seem like a lively place. We, on the other hand, have a handful of people, and the contrast between us all is sometimes just too great. And, I've noticed, we're not very good with newbies, either, so even if we answer their questions, quite often our answers are just too far out there for normal people to comprehend (and I've got a ton of circumstantial and anecdotal evidence to back it up).

I'm part of many different communities on the web, but there is only one champion of how fast an online discussion goes private (and it's not of the good kind; it's the kind where we need to express our frustrations in private [because, ultimately, we're nice people who don't want to offend anyone even when they deserve it, those bastards], lest we blow up and our eyes will bleed!), and that's the community which is located on a private server where you must write to the list owner in an email to be added. *sigh*

I tried my "question of the week" thing on the mailing-list for a while, and some of those went well, but too many of those question quickly descended into nothing or private arenas. So, I'm officially giving up on it for now. Maybe I'll come back stronger once my spine grows back, who knows?

Tips for newbies: Be strong, keep at it, ask for clarification! We don't know just how alien we are. And please join in as we need more weirdos.

6. What, exactly, is Topic Maps, anyways? I don't get it!

Yes, indeed, what exactly is this darn Topic Maps thing? The funny thing is that there is no correct answer to that question. First of all, it's a family of standards that we collectively call "Topic Maps", but it could also mean either the TMDM (Topic Maps Data Model) standard or the XTM (Topic Maps XML exchange format) XML standard, depending on your non-sexual preferences. Some might even go out on a limb (obviously not the limb cut off in point no. 2) and claim that it means the TMRM (Topic Maps Reference Model) which is a more abstract framework, or possibly even just the philosophical direction - or, dare I say it, zeitgeist? - of the thing, like a blueprint for how to build a key-value recursive property framework with identity- and knowledge management system. Your mileage may vary.

But then we have a problem as it is not a technology nor a format. It is more akin to a language, a model or a direction of sorts. No, not a language like SQL (even though the TMQL (Topic Maps Query Language) could be said to hold that place) that is to be parsed by a computer, nor a language like Norwegian or English. No, we're talking about a language that sits right in the middle between the computer and the human, a kind of mediator or translator, a model in which both machine and human can do things that each part understands equally well, a model which is defined through information science, math and human language.

So what is it? It's a language that both computers and humans can use without pulling too much in either direction, a language in the middle that, if spoken by many parties (computers and humans both), they can all join hands and sing beautiful knowledge management songs together, share and propagate with ease. But of course, Topic Maps isn't limited to just knowledge management, oh no. You can solve unsurmountable things with it as you can make it represent whatever you want it to, and I really, truly mean anything. If you want a topic to represent your thing, off you go. It's that flexible.

It can work as the basis for pretty much any system that has structures in it of any kind or shape, and that, by and large, is pretty much any system ever built. So it's actually quite hard to explain just what you can use it for, even though traditionally it's content management, portals and knowledge management.

Tips to newbies: It's only a model ...

So there you go, a quick summary of bits and bobs about Topic Maps. In my next installment, I'll summarize my naval fluff collection, next the train-table changes of Minnamurra station of the last 10 years, and finally I thought I'd summarize all the redundant technology that's gathering dust in my garage. Stay tuned for exciting times ahead!