SpongeBob SquarePants and the brave new world of comparative genomics

I wrote an article for On Line Opinion in 2008 describing the rapidly increasing detailed knowledge of the human genome. Developments in bioinformatics hand in hand with more powerful DNA sequencing technology had lead to the determination of the whole sequence of the 3 billion nucleotide base pairs that is in a human cell. The genome and its genes, composed of DNA and localised to the cell nucleus, is required for the finely tuned production and precise assembly of all the proteins that make up every multi cellular organism including us.

During my week on the beach in January I thought it might be interesting to revisit the area of genomic research to see what new exciting things that have been discovered on the interaction between the genome and the complex self assembling and self regulatory system that is life on earth.

The new book The Genome Generation by Dr Elizabeth Finkel published by Melbourne University Press seemed a tome that would keep my interest for a few days.

After reading the book it now seems that we know that there is a lot more to learn about how genes makes RNA and proteins which makes every organism different.

The emerging paradox is that the genome of most multi cellular organisms have roughly the same number of genes i.e. the fruitfly (Drosophila melanogaster) and the humble worm (Caenorhabditis elegans) have the same number of genes as a human.

Most interestingly a simple multi cellular organism like the Great Barrier Reef demosponge (Amphimedon queenslandica) that has existed essentially unchanged for 600 million years contains a similar number of genes (or 18 000 altogether) as the other genomes studied. The sponge is lacking a recognisable body plan and has no central nervous system compared to the fly, the worm and the human.

However the sponge genome also includes many analogues of genes that, in organisms with a neuromuscular system like us, code for muscle tissue and neurons. This seems counterintuitive and the author discusses this.

Why does a sponge have most of the genes it needs to make a brain? And why has it not developed a brain in 600 million years? Life in the balmy waters outside of the coast of Queensland can surely not be blamed for such turpitude.

It is here that the modular nature of genes and the LEGO block analogy and the intelligent design argument props up its head. A one-year-old human intelligent designer can stack the LEGO blocks in different colours in two dimensions while a six-year-old intelligent human designer can perform any permutation of the coloured blocks and create a multicoloured 3 D structure like a castle. I have seen a grown up man in Britain build a full size house including furniture of LEGO blocks on BBC1. And live in it. Enough said.

‘The operators’ that are responsible for the design the author discusses are located in the ‘junk’ DNA i.e. DNA without known function outside the genes. The human genome is full of such DNA of unknown function however the lower organisms are comparatively lacking in it

But how ‘the operators’ carry out their work and their exact nature is still a mystery. Some candidates are hinted at such as Interfering RNAs (RNAi) or micro RNAs which higher organisms are equipped with.

On the other hand the modular nature of genes gives a ‘molecular tinkerer’ or evolution a lot of tools to play with and put together in new and exciting ways.

Once the fundamental set of genes of animals had been established 600 million years ago the hypothesis is that gene duplication and modification of gene copies generated by such duplication could easily evolve new body parts with new functions. The different shaped bill of Darwin’s finches on the Galapagos Islands is a famous case in action. These finches show a huge variation in size and shape of their bills in adaptation to their environment and to competition by other finches for scarce food resources.

How did we evolve from a brain less sponge you might wonder?  This is the conundrum that the reading of the genomes of simpler and simpler multi cellular organisms has left us with.

When the car sales person in the television ad tells me that ‘the ‘zoom-zoom’ of the car is in it’s DNA’ it makes me think that our understanding of what really makes us tick has not come that far from SpongeBobs level of sophistication.