Saturday, 7 June 2014

ENCODE turns DNA junk into treasure (updated 7 June 2014)

 It is well known that the DNA which resides in a living cell houses a genetic code, stored in binary form. These genes store digital instructions needed to manufacture the proteins which are needed by the organism, anything from a fly to a blue whale, from a pea to a giant redwood. The architecture of these systems is so sophisticated and efficient that biochemists and bioengineers seek to copy and use it.

When the genetic coding scheme of the human being was first announced around AD 2000 the popular science media and the evolutionary biology establishment gave the impression that all manner of genetic diseases would now be curable and that all the useful DNA was concentrated in about 1.5% of the DNA in the nucleus of a cell.  This 1.5% was the part of the DNA which has protein- coding genes – i.e. instructions for the protein manufacturing process which occurs within the ribosome, a kind of factory, located in the cytoplasm which exists within the space between the nucleus and membrane of a cell.  The rest was believed by many evolutionary biologists to be junk and evidence of the inefficiency of nature in evolving life – evidence, many said, that evolution is a blind, mindless process, a story of self-replicating machines running amok and creating the illusion of order and purpose.

Within only a few years the initial hubris was found to be entirely unjustified. There was little progress in dealing with heredity disorders and diseases and it became obvious that processes were occurring which could not be explained by the extant models.

The naming of 98.5 % of the DNA as junk was bad science, i.e. a dogmatic adherence to a blind watchmaker view of evolution rather than a strong suspicion that this so-called junk may well have a function. Those who did suspect this were proved right.

Common digital signatures were detected in junk DNA from different specimens of different species, from different generations of the same species and from patients with the same genetic disorders. It rapidly became clear that meaningful processes of some kind were occurring in what many had  thought to be a functional desert; but nobody could have predicted just how breathtakingly complex and orchestrated were these processes.

The reality of this paradigm shift in perception of the sub-cellular, sub-genetic and  epigenetic  processes which go on inside a cell is now being assimilated as the findings of the ENCODE project attract the attention of biologists, science journalists and the public. My impression is that the findings are so worldview-shattering that many evolutionary biologists are stunned into a (hopefully temporary) state of denial.

ENCODE stands for the encyclopaedia of DNA elements, and this programme was devoted to studying just the human genome. It was started in 2003 and involved over 1600 research projects by 400 scientists in 32 labs in the USA, UK, Japan, Spain and Singapore and the bulk of the results were released early in 2012.

 It showed that 80% of the genome consists of 4 million genetic switches together with mechanisms for controlling where, when, in what dynamic configuration and how much of a particular protein will be produced. Over 300 years of computer time were used and there was deep cross referencing via the internet between the open access journals Nature, Science, Genome Research and Genome Biology. The fact that there is a highly structured set of data open to any researcher to use should lead to a cascade of new findings in quite a short time.

This project, together with others on non-human genomes, has shown that the microscopic processes in the cell nucleus and its surrounding plasma are similar in purposeful complexity to those of the natural world we see around us.  The rich variety of trees, plants, animals, fish and insects we witness forming an ecological network are the out workings of a hitherto unknown sub-microscopic universe inside each cell as well as data transfer between cells and some means of orchestrating  both the cells and their interiors to produce living organisms. Plants and animals are not made up of simple self-duplicating jelly-like blobs.

This still leaves about 20% of the human genome totally unexplored and no doubt scientists are already working on it. And when some of the present mysteries have been 'solved' another whole layer of mystery will unfold before us. Given the history of science I think that is a reasonable assumption.

How the theory of evolution will itself evolve is impossible to say but I suspect that ENCODE, and similar projects on DNA and the thousands of processes that go on in the cell,  will reveal that learning from the environment can be passed down the generations, i.e. that evolution is far from a blind, chance-driven mechanism. Evidence along these lines is already emerging in mainstream journals and falls within the province of epigenetics. In particular  each gene is not a single entity but comprises dozens of functional units.

On the medical front research is now able to move very fast because we now know that the genes themselves are only a small part of the overall picture. Treatments will be able to be tailored to individuals both for rare diseases involving single genes and for more widespread ailments associated with groups of genes.  

Stand by for some startling insights over the coming years.

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