Modeling DNA and Cell Copying with 3-D Cubes
by Ted Huntington
June 5, 2003

Video example of 3D growing cubes

Copying appears to be popular on this tiny spherical planet called earth, and perhaps a billion other planets. DNA survived by being good at copying itself. Some bacteria can duplicate from 1 cell to 1 million cells in minutes. The building of robots in some way expresses a need for humans to duplicate themselves. Sexual reproduction is the intricate method that evolved for millions of species to copy themselves.

As humans uncover the simple 4 molecule DNA sequences of various living objects on this planet, people are trying to understand how these strands of DNA build the structures (cell walls, ribosomes, heart cells, ...) in each living body. What does the code mean? How does AGTCGTTAC = horse?

I think one of the most spectacular things to see would be a computer program that can draw a 3D model of a DNA molecule assembling a cell, an organ, and eventually a 3D model of any object living or imaginary. This is what I am trying to explore.

Some interesting experiments have been done in the past that many people may not be aware of. One of these inventions resulted in objects called "fractals". A "fractal" is an object that follows some mathematical rule in an iteration (or duplication). For example, if a line keeps dividing into 2 lines, a tree image may eventually be formed. This technique may result in complex objects and images from simple rules. I think that cells dividing with instructions coded in DNA may be similar to fractals. But what decisions are determined by the order of DNA? How is the physical structure of the DNA molecule used to build massive matter-filled trillion cell objects like elephants and dinosaurs?

If humans can understand how DNA physically builds various organs and why living objects age and die, perhaps we can change or build sequences of DNA that will stop aging in humans, allowing some future generation of humans to live for millions of years. Then nobody would want to get damaged, because even though you would not age, you could still be physically destroyed (although possibly put back together later). In addition to understanding aging, humans will probably solve more simple genetic problems. The code that exists now for a variety of species is probably highly evolved and shaped, but I would not doubt that much of the code is unnecessary and perhaps even dangerous to a living object. Perhaps people will remove code that evolved millions of years before, or will add code to improve the way a human can, for example, stop mutation, or help blood flow, or do away with a need for a digestion track altogether! Understanding how DNA physically builds cells and organs is clearly going to be important and exciting for humans living now and in the future.

In the empty space that exists between my understanding of DNA code and the final product of paramecia, pines, and chickens, I decided to investigate a number of possible ideas. Clearly when most cells copy the DNA is duplicated nucleotide for nucleotide, an exact match (certainly with some mistakes from time to time). So what explains the variety of cell growth? Perhaps only part of the DNA is used to build a certain cell, but then how is only part of the DNA code activated and the rest made to be inactive?

In 3D modelling the basic units are points, and polygons. Polygons (usually triangles) made of points can be put together to make very large 3D models like vehicles, buildings or living objects in arcade games, and simulations. The shape of a structure on a small scale may determine the shape of an object on a larger scale. I decided to make a cube, a very simple 3D object, represent a cell (a bacterium, skin cell, or any basic cell). Each cube contains a set of instructions that determine how the cube should copy it's own body. These instructions involve:

1) What axis (or side) to copy on (in the +/- x, y, or z dimension)

2) How many times to copy

There are parallels between cell duplication and molecule growth. The shape of the cell or molecule can effect the shape of the larger body, people should experiment with triangles that grow more triangles attached to 1 of the 3 sides, 4 sided, 5 sided, 6 sided, as many sides as possible to see how larger shapes look. For example if you copy octagons (8 sides) you can see there will be empty spaces or holes. Crystal growth may be similar to cell growth in that a new cell can only grow attaching to a side, or may be limited to the shape of the original molecule.

Some questions I have:
1) Are structures grown from DNA repeated by some high level group of DNA nucleotides, or is each molecule written in the DNA? In other words, does the DNA for a finger have a nucleotide for each atom, or a basic code that is repeated. Is the code optimized or does 1 nucleotide = 1 cell?
2) What decides what start point and end point in the DNA code to grow? Are all objects or segments grown by sequential nucleotides or do the instructions move around copying parts from different sections of DNA? How does the DNA indicate to stop growing one part (like a forearm) and start growing the next part (a wrist)?

By accumulating cubes, a larger 3D object can be made. This is probably not a popular method for people designing 3D models for computer games because nobody will ever see the cubes in the inside (much like the inside of a tree) and most people would never want to spend time drawing objects that are never seen. But this is the way most objects grow, the millions of cells inside a living body are rarely seen.

These properties can raise questions about the nature of real DNA. Is the number of times a cell can copy determined by DNA or by external objects? At some time does the DNA instruct a cell to stop copying, or does aging of the cell make copying impossible? Skin cells copy and die for the total life of a human, but the way skin cells grow is very controlled, they grow only when needed, and only in definite shapes.

This modelling is a very simple beginning to 3D modeling of DNA growing into recognizable cell structures. The physical shape of the DNA molecule is not modeled, photons colliding with the atoms of hydrogen in the DNA is not accounted for, however even this simple cube=cell modeling has produced some interesting results including objects that have the same shape as many objects found in this tiny part of the vast universe.

November 15, 2004

Perhaps when the protein that moves up the DNA ladder reaches the end, a cell stops copying and the organism is certain to die. Maybe this is why bacteria with a circle of DNA never stop copying. One experiment is to try and break the circle of DNA in bacteria and see if the bacteria stop copying. This may be one way to kill bacteria, or greatly reduce their life span, but maybe not. I am in favor of brain storming, even if the ideas prove to be of little or no value. Can you imagine that humans may find a way to loop the DNA of humans to allow people to live forever? I am sure that would be complex, the heart cell part needs to be looped, the skin cell reproducing code needs to be looped, etc...

Clearly DNA moves through stages, from zygote to oldest aged organism, there are many changes that happen in particular immediately after the first cell is created. I think that a protein may start on the first rung of the DNA chain and get to a certain point, for example nucleotide 104, and then divide into 2 cells. The second cell will also have a protein that is positioned at nucleotide 104, and the two cells continue to read the code, moving to nucleotide 105, continuing the instructions that control the development of the fetus.

One issue is this:
Perhaps the only mechanism DNA does is simply copying or not copying (not determining what side to copy on). In this way, huge objects, like hearts, lungs, livers, etc... can be formed simply by code that says, for some cells continue copying, while other cells have no copy instruction (although all are using the same DNA code, so as far as I understand only the place a protein starts processing in the code is different). Are the number of times to copy encoded in DNA? Is the side or location to copy encoded (I think that the process of copying must happen in the same dimension for all cells, and perhaps is not important in building objects like hands, heart, skin, etc...).