Sunday, June 19, 2011

Spirals of the Abyss

In shales formed from deep-sea muds, all over the world, geologists keep stumbling upon the intriguing trace fossil Spirorhaphe. A perfect spiral, a foot or more in diameter, is imprinted upon the rock face like a bronze-age ornament. These spirals date back at least to the Ordovician period, some 460 million years ago, and continue through the geological record almost to the present day. But what are they? The organism responsible for these fantastic feeding traces was believed to be extinct, and its identity forever lost to science.

Then, in 1962, when a camera was lowered into the Kermadec Trench in the southwestern Pacific, beautiful, modern-day Spirorhaphe traces were finally revealed to scientists (Bourne and Heezen 1965). One of the pictures even seemed to capture the trace-maker in action. It looked like an acorn worm, a representative of one of those enigmatic groups that fit only uncomfortably into the System of Animals and require phyla of their own. And it was huge: with a diameter of 5 cm it was quite a monster compared with most of its shallower-water brethren.

As more pictures were taken from the deep sea, these spirals turned out to be relatively common. The famous photographic volume “The Face of the Deep” (Heezen and Hollister 1971) contains several examples. But it was not until 2005 that a good video recording of the actual trace making was announced, together with the spectacular capture of the organism. The story was sensational enough to make it to the pages of Nature, but without reference to the fossil record (Holland et al. 2005).

Almost since the conception of animal life, this slimy worm has been sitting in the eternally dark and cold depths of the sea, silently spinning its spirals at a speed of 5 millimeters per minute. Hundreds of thousands of millennia passed. Life ventured onto land. Dinosaurs came and went, mammals and birds conquered the dry world. For the deep-sea acorn worm, nothing of this mattered much. It sat down there where the sun never shines, surviving, hardly moving.

How appropriate that it builds a perfect spiral, the symbol of eternity.

Friday, April 29, 2011

Does a frog have a plan?

Darwin. We always come back to him. Archimedes, Leonardo or Gauss are too incredibly smart, superhuman, they must have come from another planet. The nice thing about Darwin is that we can relate to him, walking on his “thinking path”, studying his barnacles and earth worms, what a nice, nice man.

Charles and William Darwin

Darwin understood two fundamental things about animals and humans: 1) Humans are like animals, and 2) Animals are like humans. It is astonishing that the former has been accepted by science, the latter scorned and ridiculed. Come on: If A is like B, then B is like A. In Euclid’s Elements, the first “common notion” (a kind of axiom) is that “Things which equal the same thing also equal one another”. Combining this with reflexivity, that anything equals itself, it can be shown that equality is symmetric: If A equals B, then B equals A.

In Darwin’s “The Descent of Man”, he exposes a rather extreme anthropomorphism: “Even insects play together, as has been described by that excellent observer, P. Huber, who saw ants chasing and pretending to bite each other, like so many puppies”. Obviously, his intention is to place humans in their phylogenetic context, to illustrate that the difference between us and other animals is a matter of degree, also when it comes to cognitive abilities. Following in his footsteps, innumerable biologists have explained human behaviour in terms of mechanisms observed in other animals (Desmond Morris made this approach famous in his book “The Naked ape”, 1967). But the logical converse, to understand animals in terms of human behaviour, has been condemned as unscientific. It’s crazy.

No, it is the idea that animals are qualitatively different from us that is unscientific, based on an antiquated, pre-Darwinian concept that humans are something else, above the rest of the world, created in God’s image. So why has ethology become so warped, banning the merciless logic of anthropomorphism from science? I completely agree that we get nowhere using undefinable, unobservable, wishy-washy terms like “consciousness” when describing behaviour. But this goes for the study of humans as well as the study of animals – no difference there. It is perfectly possible to study animals in an objective way, using our unique knowledge of human reactions. This is called cognitive ethology.

Do not be ashamed to think that your cat is having fun when playing, that a moose feels horror and pain when hunted, that a duck can be in love. How could it be otherwise? We are like them, they are like us, we are all in this together, everything is connected. That was Darwin’s revolutionary insight.

I’ll have my hamburger now.

Finally: I never thought I would cite a philosophical paper, but this is a rather good one:

Monday, April 4, 2011

DNA and the information revolution

When I was a boy, Carl Sagan swept me and so many others away with the “Cosmos” TV series. And looking at it again, now thirty years later, I am reminded of his contagious enthusiasm and not least his cross-disciplinary cosmic vision where everything is connected, from his “billions upon billions of stars” and the mathematics of ancient Greece, to molecular biology.

In the second episode, titled (with characteristic baroque grandeur) “One voice in the cosmic fugue”, Sagan muses on the information content of DNA. I remember it vividly. Standing between shelves of books representing the human genome, he demonstrates how incredibly much information you can get into that little molecule.

That year, 1980, was also when I bought my first computer, a Sinclair ZX80. I was twelve. It was a marvellous toy – booted in a millisecond, never crashed, and so easy to program (in BASIC) that I felt like a master coder after a few hours.

The ZX80 had one kilobyte of random access memory. You read that correctly. 1024 bytes. This included the display buffer, meaning that as your program grew beyond a few lines, the image on the TV screen had to shrink. Admittedly, there were larger computers around at the time, and soon the IBM PC would be released with a whooping 128 Kb or something, but still, it gives an impression of the zeitgeist.

Your computer now has, I don’t know, maybe a gigabyte of RAM – one million times one kilobyte. The colour information contained in a 20x20 pixel square on your computer screen (the size of a single, largish letter) would not fit into the entire memory of the ZX80.

I believe this unbelievable explosion in the capacity of computer memory has radically changed humanity’s perception of information.

Sagan mentioned five billion bits in the human DNA. Not too far off: the current number is about 2.9 billion base pairs in the haploid human genome. Since it takes two bits to code for a C, A, G or T, that would be six billion bits, or 725 megabytes. Back then, people were awed. A third event of note in 1980 was the release of the IBM 3380, the first hard disk with gigabyte capacity. It cost $98,000 for 2.52 gigabytes, and was the size of a double wardrobe.  You could put three complete human genomes onto one of those:

IBM 3380 hard disk assembly (Nik Clayton, Creative Commons)

Today, you can store the entire genome on a memory stick. Taking this further, perhaps only about 3% of the genome consists of protein-coding regions (exons) and regulatory sequences. Although we don’t know yet, it is possible that the rest is “junk DNA” with no critical purpose. That leaves about 22 megabytes of useful information. In 1980, that would cost you perhaps $6,000 (four Seagate ST-506 drives, each holding 5 megabytes). Today, it corresponds to four good digital images on the memory card of your camera.

This technological revolution is perhaps why, in 1980, when Cosmos was shown, not many scientists asked the question: How on earth is it possible that you can code for a complete human being, with billions upon billions of cells, and a reasonable brain on top, with such a ridiculously small genome? As a boy, I thought: Is it not incredible that DNA contains so much information? Today, I think: Is it not incredible that DNA contains so little information?

The morale of the story: Always remember that we see nature from a subjective standpoint, liable to change. This applies not only to information content: Bacteria are only very small relative to us. The ice age was a long time ago only relative to our lifetimes. And, perhaps more profoundly, complexity is relative to the size of our brain. How is it possible that evolution produced so complex organisms? Well, to the Alpha Centaurian with brain the size of a house, a fruit fly is presumably not complex at all, and that it could evolve no surprise whatsoever.