News | September '07 | The junk in the genome
Imagine you are an alien of immense size who has discovered the planet Earth and you are carrying out a scientific study on it.
After brief direct observation of the gross manifestation of the curious four-limbed creatures abounding there and a couple of simple experiments, you take samples back to your laboratory to find out more about them. You scoop up chunks, stabilise them in toxic chemicals to stop all the life-forms thrashing around, boil them in acid to free them of the multi-coloured debris which always seems to cling to them, and slice everything up into analysable sections.
You can make certain assumptions: due their small size and fragile physical structure, the life-forms must have limited intelligence, and will therefore be governed by largely mechanistic principles and innate involuntary responses to their environment.
Now, imagine what you would make of your scientifically recorded observation of football pitches?
Your report might might read something like ...
Characteristic rectangular patches tend to be present where the life-forms are concentrated. The tiny creatures surge in and out of them according to clear, but complex, circadian and seasonal rhythms. The conclusion is that the areas must be biologically important.
An outer, metal lattice surrounds the more mature forms of the rectangle. This provides an inert protective structure which traps excess levels of the life form by triggering a folding-mechanism in their bodies which then conform to the shape of the lattice.
The rectangle has white lines polarised to create a repulsive-force which the life-forms are unable to cross.
The few creatures which occasionally penetrate to the centre drift back and forwards driven by varying forces emanating from a pair of suspended grids at either end.
A spherical inclusion is often present in the rectangle. This is thought to be potentially pathogenic as it tends to obstruct free movement and may be an endemic virus, but is not biologically important.
An experiment on the relationship between the life-forms in the inner area and those attached to the outer structure was performed. Movement into the centre was able to proceed even when the very large numbers attached to the outside were stripped away. It was, therefore, concluded that the latter were unnecessary, and probably represented historical junk accumulating in an inefficient system.
Energy supplies in the rectangle were always low and when these became exhausted, the supporting structure became porous and all the life-form leaked out by a combination of osmosis and simple diffusion.
The final report you write on the Earth-creatures is peer reviewed and accepted for publication in a prestigious alien scientific journal. No one else has had a chance to study these creature, so your conclusions become the text-book standard facts of life-on-earth which require overwhelming scientific evidence to the contrary to overturn.
Now, stop imagining anything.
In 2005, the long-held theory that the 97% of human DNA suspected of being historical junk for which no purpose could be found was finally proven to be true. A team of scientists took some mouse cells and stripped out all the junk DNA leaving only the DNA known to consist of 'coding sequences' i.e. genes which can produce proteins. When the scientists generated new mice from the junk-free cells, no ill-effects were observed. The conclusion reached was that junk DNA had minimal, if any, function.
However, over the following years, closer analysis of the non-coding DNA began to reveal some interesting features. One was that the 'junk' in the genome seemed to be highly resistant to change. A second was that the structure of the junk DNA was highly characteristic of different species of organism. Such stability from generation to generation within a species suggested the 'junk' might well have some vital evolutionary role.
By 2007, the results of a 5-year study of the entire human genome, dubbed 'ENCODE' (ENCyclopaedia of DNA Elements), was published in the Journal, Nature. The project was the largest of its kind undertaken to date, involving 80 different scientific teams in 11 countries and costing $42 million.
The study revealed that, throughout both the coding and non-coding DNA of the genome, there are millions of identifiable repeated sequences of DNA, known as 'motifs'. Links began to emerge between certain motifs and the regulation of gene expression, and between certain motifs and the processes of inter-cellular communication. Further intensive study suggested that large swathes of junk DNA are highly active while other seem to be 'on standby'.
The picture emerging is that 'junk' DNA is vital to genetic stability, evolution and to the vital 'fine control' of gene expression.
Suddenly the genes which the biotech industry has been re-inventing and ramming into our food, are going to became a tiny, but disruptive, part of a much more complex, interconnected, interactive system. Beyond these chunks of artificial DNA lies a huge amount of no-longer-junk DNA which performs a multitude of important tasks and in which disruptions can also promote disease.
One author of this latest and largest study describes the genome thus:
“If you think of the letters that make up the human genome as the alphabet, then you can think of genes as the verbs. With this project we're identifying all of the other grammatical elements and the syntax of the language we need to read the genetic code completely.” He added “The findings highlighted how scientists had become so blinded by the importance of genes that the role of other parts of genome had largely gone unappreciated.”
State-of-the-art scientific research is abandoning the blinkered DNA-is-all approach. Much more exciting and revealing is the bigger picture of the proteins and RNA arising during gene expression and regulation, and the electro-magnetic nature of the molecules which make up the living matrix.
OUR COMMENT
If you're getting the impression that genes and DNA are old hat in science, that's because genes and DNA are old hat in science. Science has moved on, leaving the biotech industry simplistically forcing its man-made DNA into an ocean of controlling and interconnected DNA, RNA, proteins and associated molecules.
The biotech industry's assumptions of the mechanistic nature of life threaten the health and evolution of the organisms it has genetically transformed, the health and evolution of the environment on which the transgenic plants impinge, and the health of the animals which eat them.
The alien scientist you were role-playing a few moments ago may have seemed a bit limited in his powers of reasoning, destructive and lacking in sophistication in his analytical techniques, and arrogant in this assumptions. But his conclusions based on the study of 'unintelligent' life were as reasonable as the biotech industry's view of 'unintelligent' DNA.
If you are ever tempted to eat GM food, think about the deeper meaning of football pitches. Especially after they have been steeped in chemicals, cleaned up and sliced. And, just how wrong science can be.
SOURCES
- Metro 21.10.04
- Guardian 20.10.05 and 14.06.07
- BBC News 26.04.06
- Science in Society 33 Spring 2007