Saturday, June 27, 2009

World of light?

If the uttermost particles are twists of energy, then matter is made of energy and energy is not made of anything else (though it must be, perhaps) then the world is made out of energy and if light is energy too, then you could say the world is made out of light. Then light doesn't just illuminate and reveal the world, it is the world. Which primitive Greek philosopher was that one? They took turns at saying the world was made out of different things: fire, water, air, butter, lemon drops...

Thursday, June 18, 2009

Life: an operating system?

It pains me to say it but DNA looks like an object class definition in object oriented programming (which is itself based partly on principles of heredity). The paucity of genes can be accounted for in a system where the DNA represents a program to be run by an operating system that is far more complex than the program itself.

In my analogy (below somewhere) I described DNA as like measurements and specifications such as colour and fabric for a suit, which is then made by a tailor. It is the tailor who knows how to make the suit, he or she initiates the processing and guides it by using techniques that are not described at all in the specifications for the suit. What I am saying is that you can take the material (a bolt of cloth, say) and the pattern and place them in the world and they will sit there forever and decay, fall to bits and no suit will appear. That is unless somebody or some thing - it could be a machine - takes the material, follows the pattern and after a time equivalent to gestation of a creature - outputs the finished garment.

So my question: What is it that takes the pattern of DNA and the material and not only makes it but like Pinocchio's carpenter brings it to life? And a possible answer, or rather another metaphor for it, is that Life is an operating system. In this view DNA is object class definition language, living things are object instances and Life is an operating system that implements our constructors, provides our operating environment and eventually disposes of us and recycles our material.

I foresee the objection that this is a tautology and that we have arrived at nothing more than the laws of nature, which are already described. However, the laws of nature may be described separately, as somewhat isolated phenomena, or phenomena whose interactions are investigated and catalogued as a series of fragments, whereas I suggest we are functions of a large system called Life which, in summary, drives us and all creatures, and without which we would just be piles of inanimate materials. Materials, as far as we know, do not get up and write A la Recherche du Temps Perdu or indeed anything at all, they rather tend to chaos (entropy) when left alone.

I am looking for something scientific, which will explain how DNA is translated into a finished product, to put it that way, and when the answer is known we will not be in any different position as regards "the meaning of life" - we still will not know, because behind every new mechanism lies another mechanism that must enable it. "All of our knowledge only brings us closer to our ignorance" (Eliot).

Saturday, June 13, 2009

Rocks and weaver birds

Can we agree that a stone is not alive? Let's not say "dead" because that implies once lived. It has no dynamic, does not interact or act with purpose of self-sustenance. Maybe it is the ability to reproduce that is definitive, although in theory something could be alive, having come to life and never died and never reproduced. A stone came to being but never reproduced itself and did not interact purposefully with anything, had no self-sustaining or any continuing process in which it was active. Then again, there are machines that are active and interact continually and purposefully, like those robots that go around and around vacuuming the floor, but are they alive? Intuitively no, so what are they lacking that for example a microbe inside a rock has? To make a self-reproducing robot is a major challenge, which as far as I know has never been achieved, but would we think that those robots were alive, if they were able to reproduce and perhaps even sustain themselves for a while? (not "indefinitely", or else the dinosaurs were never alive).

Maybe that's all there is to it: self-reproducing robots. There was a TV debate about religion (Christianity 2000 with Melvyn Bragg) where somebody in the audience argued against clerics on the panel that people were just like robots, to which the panellist replied well do you think that you are a robot and the speaker in the audience asserted that he (the speaker) was indeed a robot. It was very strange to hear somebody state in that way, "I am a robot" - almost as if it made that person into a robot by self proclamation, as if one could be or not be a robot by choice. There was a sense that that person had alienated himself from the entire audience and panel and got into a very weird situation.

But back to "What is life?" I think we can agree that a rock is not alive. If so, I guess we can also agree that a jar of acid is not alive. What if it's a jar of amino acid (some organic molecules)? We're told that DNA is made up of codes for a set of amino acids. When talking about robots and self-reproducing robots and acting purposefully for self-sustenance and continuation, what hasn't been discussed here yet is energy and motivation. We have material, sure, and we have "a scenario" (things act, reproduce, interact) but what is it that tells them how to behave, what to do and when: what starts them on a path and what guides their behaviour? (Turning straight to motivation and skipping the question of energy which is obviously just another mechanism, equivalent to the components of the robot.)

If we are agreeing that a jar of acid is not alive, is equivalent to a rock, and if we take it that DNA is code for a number of amino acids, then we are looking at a plan for items that are not in themselves inherently alive. We know that this pattern (DNA) is in living creatures ("duh") and we observe meiosis and all the events that cause half of one creature's DNA to combine with half of another creature's (for example - leaving cloning aside for the time being). We have, very obviously, the energy to power these processes. We have chemicals, patterns for chemicals and components, we can observe behaviour and formation of quasi-live spermatazoa (a form of life with a half-set of DNA, that looks and moves like plankton, say, but is humanoid?) but there is absolutely no explanation offered as to why these components proceed through very long processes (9 months in the human) of almost unimaginable complexity with clear purpose to create structures and creatures with inbuilt instincts, behaviours of their own and a big ETC.

What part of the weaver bird's DNA comprises the design of its nest and the talent and ability to create that nest from available materials in a timely way to provide a home for more little weaver birds? Hello, you've told us so far about amino acids.

Update 22/2/2016:
Darwin deals with some of this in his section on instinct, in the chapter on objections to his theory. He didn't know about DNA, so he just assumed there was some mechanism in which behaviour could be inherited and gradually modified. His paragon of instinctive behaviour was bees constructing a honeycomb, which comprises a mathematically complex structure of interconnected hexagonal (?) cells. He broke it down to each bee digging out some of the wax and neighbouring bees doing the same till a thin line remained between the holes being dug by each of the neighbouring bees. The evolutionary principle kicked in because the honeycomb structure is the form that can contain the most honey with the least wax, and so bees that tended to make that shape thrived more than ones that didn't. Plus there are different types of bees that have less perfect combs, sort of transitional ones in isolated places etc. But even knowing about DNA and epigenetics, it's still hard to see how behaviour could be encoded.

Saturday, June 06, 2009

The myth of DNA (continued)

(Notes) The contemporary belief that DNA encodes a human being is comparable to a belief in earlier times that the earth was flat and that it was carried on the back of a giant tortoise. To be able to cut and paste DNA and have an extra eye appear or something from one animal appear in another animal, is analogous with the early voyages of our ignorant ancestors, who sailed from place to place believing their absurd cosmology. Similarly, we operate and map DNA in a functional way but not realising what we are mediating. It's true that the earth seems flat, and that one can sail from Britain to Spain and back believing that the earth is flat, and that we can cut and paste bits of DNA and cause malformations or mutations. All of these activities can take place against a background of ignorance. In effect our genetic model is at the level of Keppler's mechanical model of earth, the sun and planets. It appears to correspond to what we observe and it is brilliant but it is profoundly simplistic and misconceived. What is missing is the dynamic principle, the gravity, the big bang, the extended cosmology. In DNA we are looking at our local planets and saying "This must be what's happening." Instead we need to relate life to time and space, growth to expansion of the universe, lifespan/duration/time's arrow to the expansion of the universe. I suggest (conjecture) that expansion of the universe = duration = time's arrow. The stretching of space gives us duration but also motion, an engine that can be connected to the passive cell with its DNA. We are told by physicists that time began with the Big Bang, since when the universe has been expanding. Surely expansion = duration: no duration without expansion, no expansion without duration, time's arrow is the sense of being stretched from where we begin to where we end. Could there not also be an "unpacking" effect, in which the kit of parts of DNA is inflated and extended, and which makes us move and act? (All rubbish, most likely.)