No design, no purpose, no evil and no good

Great Saturday morning -- one of those rare moments when sunshine somehow manages to get into our livingroom (fortunately, this shadowy environment is going to change soon... in a couple of weeks we will be in our new home).

Stumbled upon a good old Richard Dawkins text that appears in River Out of Eden:

The total amount of suffering per year in the natural world is beyond all decent contemplation. During the minute it takes me to compose this sentence, thousands of animals are being eaten alive; others are running for their lives, whimpering with fear; others are being slowly devoured from within by rasping parasites; thousands of all kinds are dying of starvation, thirst and disease. It must be so. If there is ever a time of plenty, this very fact will automatically lead to an increase in population until the natural state of starvation and misery is restored.

Theologians worry away at the “problem of evil” and a related “problem of suffering”. On the day I originally wrote this paragraph, the British newspapers all carried a terrible story about a bus full of children from a Roman Catholic school that crashed for no obvious reason, with wholesale loss of life. Not for the first time, clerics were in paroxysms over the theological question that a writer on a London newspaper (The Sunday Telegraph) framed this way: “How can you believe in a loving, all-powerful God who allows such a tragedy?” The article went on to quote one priest’s reply: “The simple answer is that we do not know why there should be a God who lets these awful things happen. But the horror of the crash, to a Christian, confirms the fact that we live in a world of real values: positive and negative. If the universe was just electrons, there would be no problem of evil or suffering.”

On the contrary, if the universe were just electrons and selfish genes, meaningless tragedies like the crashing of this bus are exactly what we should expect, along with equally meaningless good fortune. Such a universe would be neither evil nor good in intention. It would manifest no intentions of any kind. In a universe of blind physical forces and genetic replication, some people are going to get hurt, other people are going to get lucky, and you won’t find any rhyme or reason in it, nor any justice. The universe we observe has precisely the properties we should expect if there is, at bottom, no design, no purpose, no evil and no good, nothing but blind, pitiless indifference.

Yes, it almost sounds like he is advocating that it is OK to behave with 'pitiless indifference', it is OK not to try to differentiate evil from good, and it is OK to live a life without a purpose. But, again and again, let's not fall in the trap of the naturalistic fallacy and let's follow Hume's guillotine: what is true is not necessarily ought to be true. From the statement that nature has 'nothing, but blind, pitiless indifference', it does not follow that this state of the world is awesome and we should be indifferent and selfish.

A legjobb hegymászófilm: A végtelen érintése

Megnéztük a tegnap este a "Touching the void" cimü filmet (magyarra úgy forditották a könyvnek a cimét, hogy "A végtelen érintése", ami persze elég erőltetett, mert a "void" semmiképp sem végtelent jelent). Két angol hegymászóról van szó, akik 1985-ben elhtározták, hogy megmásszák egy Peru-i hegycsúcsnak egy addig járatlan (mászatlan) falát. Ereszkedés közben az egyikük, Joe Simpson, eltöri a lábát, s a másik, Simon Yates, kötélhosszanként engedi le a szinte magatehetetlen Joe-t, egészen addig, amig egy áthajlás miatt az utóbbi nem tud kiszállni a kötélből. Több órás patthelyzet után Simon nem birja tovább, és elvágja a kötelet, nem tudva, hogy Joe két méterre van-e a földtől, vagy kétszázra. A valóság az utóbbihoz áll közelebb, és Joe bezuhan egy hatalmas jéghasadékba, de csodával határos módon túléli a zuhanást.

A lényeg az, hogy mindketten túlélik az akciót. A film olyan PBS-stilusu dokumentumfilmként meséli el az egészet. Egyértelmüen a legjobb hegymászó film, amit valaha is láttam: a szereplők őszintesége és minden miszticizmustól mentes, józan hangvétele, a túlzott drámaiság és a hatásvadászat teljes kerülése nagyon meggyőzően hat, és kiváló példa arra, hogy a valóság néha (gyakran?) túlszárnyalja a fikciót.

A couple of books

I went today to a Borders bookstore where Steven Johnson was talking about his new book, Mind Wide Open. I wrote here not long ago that popular science has become indeed popular in the US. However, this venue could not count as supporting evidence: in a city as large and as diverse as Houston only about a dozen people gathered to see a guy who is probably one of the best science writers around. He is certainly one of the best 'science speakers'. I haven't read yet any of his books, but bought now two of them (Emergence and Mind Wide Open), and hardly can wait to start going through them. Emergence must have some similarities to 'Linked', written by my fellow Transylvanian Albert-László Barabási.

For now, I still have to work on Jonathan Weiner's 'The beak of the finch'. It is a great book, with a somewhat different perspective from what I got used to in writings by Dawkins or Pinker. Apart from learning quite a bit about how evolution works (not in theory, but in practice, in the field), it also gives good insight into the research process. Reading about how the Grants and their graduate students were essentially tracking evolution on a small island, sometimes I think about how nice it would have been if I knew exactly what questions I wanted to answer when I started my PhD :) ...

Neural nets and arbitrary classification

I have been reading a bit about neural nets and - I must admit - most of the stuff that you find in books or on the web is not easy reading for me. Kevin Gurney's book (An Introduction to Neural Networks; its web version is available here) is an exception to a certain degree -- at least I could follow it pretty well until I got kind of tired and confused when he started discussing Hopfield nets. Kohonen maps or self-organizing maps were a bit easier to swallow, but I actually had to start playing with them myself before it started to make sense. And then I realized that thinking of Kohonen maps in terms of neural nets is much more difficult than their geometric interpretation -- that is, a two-dimenisional lattice with a certain number of nodes that moves and stretches in the data space until it fits or describes relatively well the data cloud. In other words, it is quite like nonlinear principal component analysis, which is still easier to grasp than input layers, winning neurons, etc.

I have stolen the animated gif above from a superb website on neural nets that has several java applets showing how these things work. I especially recommend the demo of the 3D Kohonen map.

It took me a while to realize that it is wrong to assume that a Kohonen map is picking out real clusters in the data. That could be true if, on one hand, there is good clustering in the data in a statistical sense, and, on the other hand, there are only a few nodes in the map - that is, about as many as in the data. However, often there are no real, well-defined clusters in the data, but Kohonen's classification method is still applied - and should be applied. What Kohonen's group recommend is a two-step classification: start out with a large number of nodes in the SOM (self-organizing map) and reduce the number of nodes or clusters in a second step, with k-means clustering (see details here) applied to the map itself.

I think however that the second step is not very useful if the data does not have clusters. It is still definitely worth applying the Kohonen classifier to reduce dimensionality and visualize multidimensional data, but applying the k-means clustering as well only results in an image with less resolution and more arbitrary boundaries. It is a little bit like posterizing a color photograph, that is, reducing the number colors to only a few, although there were a lot more information and no well-defined classes in the original image (I know this latter assumption is usually not valid, but put that aside for now). Why would one do that?

This type of classification (probably real nerds would say that 'quantization' is a better word), when there are no well-defined classes, is comparable in many ways to the classification systems used in the more descriptive natural sciences. For example, in sedimentary geology, sediments or rocks are often divided into facies A, B, C, and so on; and, in most cases, the boundaries between these facies are not very clear and it would be difficult to show any statistical siginificance for the existence of clustering. So, strictly speaking, this classification is incorrect, but it still can be useful (e.g., you can write long journal articles :) ).

Of course, once you leave these somewhat subjective territories of science and think about how 'clustering' is done in everyday life, you realize that this simple-minded 'quantization' is even more questionable. People like to and tend to think dichotomically: us vs. them, black vs. white, liberal vs. conservative, christian vs. muslim, and so on -- this is not news. The result is that, to use the Kohonen terminology, the quantization errors are huge, and the cluster boundaries are essentially arbitrary. The sad part is that sometimes - many times - people kill each other because of these errors.

In light of this, isn't it reassuring that two-dimensional Kohonen maps can use lots of nodes or clusters, thus describe reality better, and still be useful in making things more visible and intelligible?

Understanding evolution

I stumbled upon a new website on evolution, created as a teaching resource by the by the University of California Museum of Paleontology. Among its many authors are Eugenie C. Scott (director of the National Center for Science Education) and Carl Zimmer (who wrote Evolution: The Triumph of an Idea). Excellent website, there is material that could fill a book (or more), including subjects like the nature of science, evolution 101, history of evolutionary thought, etc. It is websites like these that increase exponentially the value of the internet and make it worthwile to pay the monthly fee for a high-speed connection...