4. Simple Life Forms: an Oxymoron (3)

Building DNA - building a DNA molecule model

DNA (Deoxyribo-Nucleid Acid) contains the blueprint of a living organism. It is the set of detailed instructions that specifies and regulates what the organism is and will be. If the proteins are the building materials for a house, the DNA is the set of home building plans. Working together with RNA (RiboNucleid Acid), the DNA directs the correct sequencing of amino acids in proteins during the cell replication process. It is able to do this through biochemical instructions – information – that is encoded on the DNA.

The making of DNA and RNA would be an even greater problem than assembling proteins. These molecules are far more complex than our “simple” protein molecules. DNA is built like a string of pearls with the main chain consisting of sugars and phosphate groups. Each link in the chain has a base connected that actually spells a letter of the genetic code. There are four kind of bases that can spell the genetic letters G (Guanine), C (Cytosine), A(Adenine) and T(Thymine).  And just like our alphabet, combinations of these four DNA “letters” can spell any genetic instruction.

DNA makes is possible for a cell to build functional protein molecules from the available pool of amino acids. For this purpose, certain parts of the DNA specify the order of the amino acids in the protein. When the protein molecule is built, the DNA code is unraveled into RNA strands, which contains words – one word per amino acid. Each three letter word represents a specific amino acid.

DNA is combined with protein into structural units called chromosomes, which usually occur in identical pairs (23 pairs in a human cell). The chromosome is like a single, very long, highly coiled molecule of millions and millions (up to 250 million in human chromosomes) of DNA base letters. The DNA bases link the two chromosomes together (see figure).[6] 

Pair of Chromosomes

In every chromosome pair, a “T” base in one of the chromosomes links always to an “A” base in the other. Likewise, a “C” links to a “G.” This way each chromosome is the mirror image of the other one.  The links are called the DNA base pairs. On the chromosome, large groups of DNA base pairs form functional sub-units called genes. A gene occupies a certain place on the chromosome. It is basically a sequence of DNA base pairs (each base pair specifying a DNA letter) that work together as one unit of genetic information (an average gene in the human body is about 3,000 DNA base pairs long).  Each gene embodies the encoded instructions for the assembly of proteins and the inheritance of a particular characteristic or group of characteristics that are passed on from one generation to the next. Together the chromosomes contain all the information needed to build an identical functioning copy of the cell.

The information stored in human DNA is almost incomprehensible. Each of us starts at conception as a tiny little ball about the size of a period on a printed page. In that tiny ball, there is over six feet (!) of DNA. That DNA specifies our (future) characteristics (brown hair, blue eyes etc) in a manner that can be read like a book.  Every cell in the human body contains these same DNA strands. Therefore each cell has about three billion DNA base pairs comprising an estimated 20,000-25,000[7] genes. Compare that to an average page of text of 2,000 to 2,500 letters. Just the DNA letters in each individual cell of our body is equivalent to the information of a book with a whopping 1.5 million pages. That is equivalent to a pile of paper of about 625 feet high. And that is just for one cell. The average estimate for the number of cells in an average human body is in the range of 50 trillion (that is a 5 with fifteen zeroes, or 5 x 10¹⁵). So the total amount of information written into all the cells of an average person would be a stack of paper as high as 625 feet multiplied by 50 trillion = 520 trillion miles. To try to understand this humongous number, it helps to consider that the distance between us and the farthest planet in our solar system, Pluto is about five billion miles. Therefore the pile of paper written with the DNA letters of every cell in an average person would be about 100,000 times the distance between us and Pluto!

Building a human DNA molecule model was a huge undertaking. Completed in 2003, the Human Genome Project[8] – coordinated by the US Department of Energy and the National Institutes of Health – took 13 years to determine the sequences of the base pairs on the 26 chromosomes of the human DNA (referred to as the human genome) and store this information in a giant database. This gigantic effort only gave us a map of all the genes/DNA letters, for the most part we still do not know what controls what characteristics, nor how it works. Subsequent efforts are ongoing to use this information to complete the identification of all the genes in the human genome.

 

Figure 5-3: DNA is stored in chromosomes. Genes on the chromosome specify the assembly of proteins. Proteins work together to build new cell material or perform specific functions[9]

Could such an almost unimaginably complex chemical compound ever be formed by mere chance and time? We’ve seen how unlikely it is for a “simple” protein molecule to be formed just by chance. It is hard to make a calculation for the statistical chance of a DNA molecule to just “assemble” under the right conditions. Estimates for the probability of random assembly of DNA[10] present in a one-cell living organism (about 100 genes) range from 1 in 10^3,000 to 1 in 10^{100,000,000,000}. Whatever the exact number, these chances are all basically non-existent.

Molecular Machines

In home construction it is not enough to dump all required building materials (lumber, rafters, nails, concrete, sheetrock and so on) and a set of plans at the building site. Obviously nothing will happen until the workers arrive. Labor is required to read the plans, cut the materials, and put it all together.

So it is also in a living cell. If the amino acids and the proteins are the building materials and the DNA is the blueprint, then the so called molecular machines are the workers. They perform the labor needed to actually construct the different components of the living cell from the building materials according to the DNA blueprint.

These machines, made from proteins, use the information from the DNA/RNA to assemble and shape proteins, copy DNA, build new cells and also build other molecular machines. What is the job of a ribosome? Molecular machines operate in the cell and haul the amino acids to protein assembly lines. These assembly lines, which are also molecular machines, are called ribosomes. Other molecular machines turn cellular switches on and off, sometimes killing the cell or causing it to grow. Solar-powered molecular machines capture the energy of light and store it in chemicals. Electrical machines allow current to flow through nerves. Manufacturing machines build other molecular machines as well as themselves. Cells swim using machines, copy themselves with machinery, and ingest food with machinery. In short, mind-boggling, highly advanced molecular machines control every cellular process.

Needless to say these machines are extremely sophisticated and complex.  The molecular machines are the robots that – without any outside interference – build new cells and new robots.

We now have the technology at the cellular level to study and see these machines in action. Molecular biologists can analyze their composition, understand their function and marvel at their complexity. Evolutionary scientists have yet to offer any explanation for their existence.

“Can all of life be fit into Darwin’s theory of evolution?… If you search the scientific literature on evolution, and if you focus your search on the question of how molecular machines — the basis of life—developed, you find an eerie and complete silence. The complexity of life’s foundation has paralyzed science’s attempt to account for it.… I do not think [Darwin’s mechanism] explains molecular life.” [11]