DNA

Some days ago, I started reading the book "The Making of the Fittest" by Sean B. Carroll and I cannot put it down.  Finally, a book that explains how the study of DNA proves beyond any doubt that Darwin was right with his theory of evolution.  A clear and uncluttered explanation of how DNA works.  In fact, I like it so much that I will try to summarise it (!) here.

DNA consists of a double chain (or "strand") of compounds called "Nucleotides" (although, to be precise, not all compounds called nucleotides are to be found in DNA).  A nucleotide (also called "Base") is a simple molecule with one or two dozen atoms.  Four bases exist: Adenosine (A), Cytidine (C), Guanosine (G), and Thymidine (T).

Each base in a strand is linked via a Hydrogen bond to a base in the other strand: the As are linked with Ts and the Gs are linked with Cs.  That's how the two strands of DNA are kept together.  This means that for every A in one strand, there is a corresponding T in the other strand, for each C a G, for each G a C, and for each T an A.  Therefore, each strand contains the same information.  In other words, a DNA molecule contains the same information twice, once in each strand.  That's why you will find in the literature the description of DNA as consisting of "base pairs".  The Human DNA consists of about three billion base pairs.

A "gene" is a sequence of about 1200 base pairs that contain the information to build a protein, and humans have something between 20,000 and 25,000 genes.

A chromosome is only the name given to a portion of DNA.  That is, the fact that we have twenty-three chromosomes only tells you that our Genome (collective name for all our genes) is not contained in a single molecule of DNA but in a series of separate double-strands.  Chromosomes are important but, somehow, I don't find them very interesting, although, I might change my mind.  You can find a list of the number of genes and base pairs in each human chromosome here: http://en.wikipedia.org/wiki/Chromosome.

When a cell wants to generate a protein (don't ask me when and why that happens), it "transcribes" the sequence of one of the DNA strands of the corresponding gene into a single strand of what is called "messenger RNA", or mRNA.  mRNA is a sequence of nucleotides similar to a DNA strand, and repeats the DNA sequence of the gene but with an A for each T, a C for each G, a G for each C, and a U (Uracil, another nucleotide) for each A.

Proteins are chains of simpler compounds called "Amino Acids", which are quite simple molecules containing nitrogen.

The cell "translates" the strand of mRNA into the corresponding protein, one amino acid at a time.  To do so, it scans the nucleotide sequence of the mRNA in groups of three, and each triplet (which is called a "codon") of nucleotides identifies a particular amino acid.

Let's see: there are four different nucleotides in mRNA (A, C, G, and U).  Therefore, a group of three nucleotides can identify 4 x 4 x 4 = 64 amino acids.  In fact, there are only 20 amino acids (which is very convenient, because they can be identified by a single letter of the alphabet, as shown in http://en.wikipedia.org/wiki/Aminoacid).  This means that several triplets of nucleotides identify the same amino acid.  Note that pairs of nucleotides (instead of triplets) would have not been enough, because they could have only identified 4 x 4 = 16 amino acids.  In any case, there are also some codons that are used to "stop" a sequence.  When the molecule encounters a stop codon, it stops building up the protein.

Obviously, as each gene has on average some 1200 bases and three bases are needed to identify an amino acid, the average protein contains 1200 / 3 = 400 amino acids.

It turns out that about half of our DNA is "junk", left behind by genes that were no longer needed and have decayed due to natural mutation or resulting from the random duplications that often occur.

As you might have heard, evolution is due to variations (i.e., DNA mutations), selection, and time.  DNA frequently mutates for various reasons (for example, when a nucleotide is replaced by a different one), but it can also happen that entire sequences of base pairs are either duplicated or lost.  If the "new" gene is viable, the corresponding protein sometimes turn out to be advantageous for the carriers of the mutated gene.  In those cases, if the gene is passed on to enough new members of the species, even a little advantage can, after enough time, cause a complete replacement of the "old" gene.

Even minute advantages due to the presence (or absence) of a gene have, on the long run, significant effects.  Einstein (I believe) compared them to compound interest: even a small percentage, over many years, can result in substantial figures.  And evolutionary periods are measured in centuries and millennia, when not in millions of years.

If the mutation is damaging, the same mechanism of natural selection "purges" the DNA.  That's how some genes have remained unchanged for, literally, billions of years and can be found in almost all species.

It can also happen that, due to mutated environmental conditions, a particular gene ceases to be advantageous.  In those cases, natural selection no longer operates.  With time, as the gene mutates, there is no longer a mechanism to purge the DNA of those mutations that make the gene unviable.  As a result, eventually, all genes that cease to be advantageous decay and become irrelevant.  These fossil genes contribute to the junk base pairs in our DNA.

The fact that genes disappear is a big blow to the proponents of "Intelligent Design".  Isn't it?

There are genes that provide the material needed for our organs, and genes that regulate how those proteins are organised.  How these regulating genes do their job depends on a series of base-pair sequences in our DNA (called "Switches"), like a computer program depends on its parameters.  Changes in those switches can result in dramatic differences at the macroscopic level, because they also set things like the number of limbs.

Fascinating!