Biomedicine – Part 2: The Evolution of Computational Biology

By mapping the human genome in its entirety we are entering a new biomedical world using computational biology.  To understand the complexity associated with this new world we need to understand DNA.

DNA – Deoxyribonucleic Acid

Since the mid-19th century we have known that within our cells contained the building block of life. We didn’t know what that building block looked like until the mid-20th century when it was first described.

DNA is a molecule found in almost every cell of every animal and plant on this planet. There are a few exceptions – those cells that do not contain a nucleus such as red blood cells. DNA is also found in mitochondria and chloroplasts, organelles found within animal and plant cells that are energy factories.

In the diagram above we note 4 different colour-labelled segments attached to the double-helix structure of the DNA molecule. These are labelled A, T, C and G and represent four chemical bases. These nitrogen-based chemicals are organic molecules that when combined together turn chemical soup into living things.

A stands for adenine

T for thymine

C for cytosine

G for guanine

Note how these bases connect the double helix in a particular way, adenine always connects to thymine and cytosine always to guanine. These are called base pairs. The helical spiral material consists of sugar and phosphate molecules. In our diagram they appear as the blue and orange spiral staircase banister with the base pairs acting as the steps. The combination of  one of the nitrogen-based chemicals, a phosphate and sugar molecule together is called a nucleotide.

Human DNA consists of approximately 3 billion base pairs with accompanying sugar and phosphate molecules. It is both simple and complex. The quantity of base pairs within a DNA molecule determines whether we are human, or fruit flies. If the number of base pairs approximates 3 billion then it is the shuffling in  the order that determines whether we as humans have  brown or blue eyes. We call this shuffling in the order of base pairs, sequencing.

A sequence of DNA in the form of a number of nucleotide base pairs forms a gene. Genes can contain as few as 1,000 base pairs or as many as a million. Every human has approximately 20,000 genes. Our genes reside on 46 chromosomes in 23 pairs, all contained in the nucleus of our cells.

DNA – a Biological Programming Tool

Human DNA is an instruction manual containing the information necessary to make one of us. In every cell we have complexes of molecules called amino acids. Amino acids contain an amino group (NH2) and a carboxyl group (COOH). These are nitrogen and carbon-based molecules, the stuff of planets and stars. Amino acids are the  chemicals that  make up enzymes and proteins. DNA instructs both in a process described below:

1. There are all kinds of enzymes within a cell and each has a different task. Some read the information contained in the DNA molecule.
2. That information is then  transcribed to another complex molecule, RNA, Ribonucleic acid. The RNA acts as a messenger and hence is called Messenger RNA or mRNA for short. There are other forms of RNA but they are not part of this process.
3. The mRNA then delivers the original message from the DNA into a language that other enzymes read to create proteins.

DNA has one other remarkable characteristic. It can replicate by unlocking the bonds between nucleotides and joining up with other nucleotides. DNA does this with the help of another cell enzyme called DNA polymerase. This enzyme along with several other helper enzymes goes alongside the DNA strand and breaks the nucleotide bonds and replicates it into two DNA strands. The end product is two separate DNA molecules, virtually identical. The final act in this process leads to the cell dividing with each new cell containing its own DNA.

Genome Sequencing – a Prelude to Programming Ourselves

The full sequencing of the human genome is a very recent event. As of 2009 we now have the capability of describing ourselves completely. The cost of doing this has rapidly declined making it possible for almost anyone with $100 in their pocket to find out of what they are made.

What does this mean? For the first time medical professionals will have a tool that is predictive, personal and preventive in its use. How so?

Predictive – Because physicians will be able to study the genome doctors and detect all genetic variances that indicate a higher than normal likelihood of a patient getting a disease.

Personalized – Because individuals will receive treatment specific to what their genome indicates. For certain cancers where the genome indicates high certainty this means earlier intervention and better outcomes.

Preventive – Because doctors will be able to intervene before a disease starts making it possible to avoid its onset altogether.

Genome sequencing of every baby born will make it possible to develop a life plan heading off tendencies predicted in the reading of the child’s DNA.  The downside to this is obvious. Not all diseases are visible by reading DNA. Malaria, HIV, drug overdose, being hit by a car, dying in war, are not predictable in reading a person’s genome.

For parents who only want the best for their children, genome sequencing has the potential of offering a means to offset deficits visible in a child’s makeup. Can reading the genome predict OCD (Obsessive Compulsive Disorder), ADD (Attention Deficit Disorder), Autism, Asperger’s Syndrome, Schizophrenia and other psycho-behavioral disorders? Could preventive intervention before the symptoms show potentially do more harm than good?

Programming the Genome

Eugenics is the practice of improving humanity through selective breeding. As  practiced in the 20th century eugenic policies were enacted to cull “undesirables.” Probably the best examples were the racial practices of Nazi Germany in the euthanizing and murder of undesirables, gypsies, homosexuals, Jews, and lesser “races,” or the sterilization programs conducted in many Western countries against adults with Down’s Syndrome and mental disorders. War and saner, more humane leadership led to the end of these practices.

The new eugenics takes a very different approach. Instead of removing “undesirables” after birth, the idea is to engineer out the undesirable genetic factors before birth, even before conception. Enhancing existing in vitro fertilization techniques will make it entirely possible to introduce genetic improvements, the advent of designer babies.

Recently I read about a high-level programming language called Qath. Qath is software designed to build genomes. Like other programming languages, Qath generates source code to create new sequences. We are at the beginning of a new era, creating synthetic life.

The author of Qath is Zoltan Barczikay, a software developer with, as he describes it, “an avid interest in synthetic biology.” He has made Qath an open source tool available for free for anyone to download. The goal of Qath is to engineer human genomes “to create reprogrammed cells for therapeutic purposes” or perhaps to improve humanity.