Science Literature

Most students of genetics have learned that the important part of the human genome codes for genes, despite comprising only 2% of the available DNA. That's what the Human Genome Project focused on, and that's what has occupied the attention of most other researchers. The problem has been - what's the rationale for the other 98%? Why is it not eliminated by natural selection? Darwinians generally liked the idea that this DNA provided a pool of genetic material that experienced mutations - some of which could be expected to be favourable. This provided them with a conceptual model of genetics that appeared compatible with the Darwinian approach to evolutionary transformation. Two papers in the journal Nature (1980) provided a major boost for this way of thinking. These were: "Selfish Genes, the Phenotype Paradigm and Genome Evolution" by W. Ford Doolittle and Carmen Sapienza [pdf here] and "Selfish DNA: The Ultimate Parasite" by Leslie Orgel and Francis Crick.

Doolittle and Sapienza wrote: "When all attempts to assign to a given sequence or class of DNA functions of immediate phenotypic benefit to the organism fail, we resort to evolutionary explanations. The DNA is there because it facilitates genetic rearrangements which increase evolutionary versatility (and hence long-term phenotypic benefit), or because it is a repository from which new functional sequences can be recruited or, at worst, because it is the yet-to-be eliminated by-product of past chromosomal rearrangements of evolutionary significance." (p.601)
Orgel and Crick wrote: "In summary, then, there is a large amount of evidence which suggests, but does not prove, that much DNA in higher organisms is little better than junk. We shall assume, for the rest of this article, that this hypothesis is true. We therefore need to explain how such DNA arose in the first place and why it is not speedily eliminated, since, by definition, it contributes little or nothing to the fitness of the organism." (p.604-5)

Junk DNA is now revealed as a classic example of evolutionary story-telling. (Source here)

The impact of these papers was to amplify and reinforce "selfish gene" concepts popularised by Richard Dawkins who had written earlier in 1976:

"it appears that the amount of DNA in organisms is more than is strictly necessary for building them: a large fraction of the DNA is never translated into protein. [snip] Biologists are racking their brains trying to think what useful task this apparently surplus DNA is doing. But from the point of view of the selfish genes themselves, there is no paradox. The true 'purpose' of DNA is to survive, no more and no less. The simplest way to explain the surplus DNA is to suppose that it is a parasite, or at best a harmless but useless passenger, hitching a ride in the survival machines created by the other DNA." (Dawkins, R. The Selfish Gene, 2nd ed., pp. 44-5, Oxford University Press, 1989).

Dawkins draws attention to the significance of the 'selfish gene' interpretation in an endnote: "My suggestion that surplus, untranslated DNA might be a self-interested parasite has been taken up and developed by molecular biologists (see papers by Orgel and Crick, and Doolittle and Sapienza) under the catch-phrase 'Selfish DNA'." (op. cit. p.275) A similar analysis of the impact made by these two papers is made by Richard Sternberg here. An important suggestion made by Doolittle and Sapienza was that Junk DNA was not worth the time and effort of researchers. This point is one we return to later in this blog.

"When a given DNA, or class of DNAs, of unproven phenotypic function can be shown to have evolved a strategy (such as transposition) which ensures its genomic survival, then no other explanation for its existence is necessary. The search for other explanations may prove, if not intellectually sterile, ultimately futile." (p.603).

The influence of selfish genes/selfish DNA and the 'fit' between Junk DNA and neo-Darwinism has been extraordinarily strong. Dawkins wrote in the Preface to the 1989 edition that the message of The Selfish Gene "has become textbook orthodoxy" (p. viii). This is indeed the case, although reports of functionality in the so-called "surplus" DNA kept appearing. Consequently, there has been a growing awareness that non-coding DNA provides a regulative function for genes. The 2007 ENCODE papers provided a major boost for innovative ideas (see here), but it was not comprehensive enough to challenge the neo-Darwinian hegemony. Those with a vested interest in the Junk DNA concept have accepted the findings of functionality appearing in unexpected places of the genome, but have pointed out that the evidences for active regulation relate only to a small part of the non-coding DNA.

After much more intensive research, the position is far clearer. If there has been an impasse in the debate about Junk DNA, surely it is now broken. The newly published ENCODE research represents a milestone for education and the academic world. After nine years of coordinated research by many teams of scholars, the ENCODE consortium has published their major findings in 30 open-access papers, six of them in Nature (6 September issue). The editors of the Nature collection say: "Among the many important results there is one that stands out above them all: more than 80% of the human genome's components have now been assigned at least one biochemical function." The News Feature that accompanies the research papers reiterates the point: "The consortium has assigned some sort of function to roughly 80% of the genome, including more than 70,000 'promoter' regions - the sites, just upstream of genes, where proteins bind to control gene expression - and nearly 400,000 'enhancer' regions that regulate expression of distant genes." (p.46). The News & Views forum says the same thing: "One of the more remarkable findings described in the consortium's 'entree' paper is that 80% of the genome contains elements linked to biochemical functions, dispatching the widely held view that the human genome is mostly 'junk DNA'." And the consortium's 'entree' paper puts the figure of 80% in the abstract (reproduced below).

The finding that at least 80% of the genome has biochemical functions is a paradigm-shifter. It means that we should reject the concept of of Junk DNA as it was presented by Dawkins, Doolittle and Sapienza, Orgel and Crick. We can no longer think that 98% of the genome is uninteresting, nor that the DNA that codes for proteins should be the focus of attention. Genes do not provide a blueprint for life because the rest of the genome carries vital information for gene regulation. No longer can we 'bolt-on' functionality to the Junk DNA concept, because the regulation is pervasive and the concept of Junk DNA is now revealed as a deduction from ignorance. John Dupre reviews several lines of evidence that call for a "major, progressive reorganization of existing knowledge". Some relevant excerpts point to the importance of the ENCODE project findings.

"Further destabilizing evolutionary theory is the growing realization that many factors, not just the genome, determine an individual organism's development. Ironically, as the discovery of DNA's structure - initially lauded as the final act in the triumph of the new synthesis - led to a better understanding of genomes' functioning, it ended up weakening belief in their unique role in directing biological development. [snip] Recent developments in molecular biology have put the final nail in the coffin of traditional genetic determinism. For example, epigenetics - the study of heritable modifications of the genome that do not involve alterations to the genetic code - is on the rise. And the many kinds of small RNA molecules are increasingly recognized as forming a regulatory layer above the genome. Beyond undermining the gene-centered theories of evolution that have dominated public consciousness for several decades, these developments call for new philosophical frameworks. Traditional reductionist views of science, with their focus on "bottom-up" mechanisms, do not suffice in the quest to understand top-down and circular causality and a world of nested processes."

These discoveries are relevant to design thinking for two reasons. The first is that numerous design sceptics have used Junk DNA as an argument against design. For them, Junk DNA points to a pool of meaningless DNA out of which novel mutations can emerge by chance to provide benefits to organisms. This, it is claimed, demonstrates a complete lack of intelligent design. For further discussion of this argument, go here and here. Needless to say, the ENCODE findings undermine all such arguments against design.

Secondly, there can be no doubt that functionality of the majority of the genome has been a prediction of numerous ID scientists (not forgetting the same from creation-orientated scientists). Their typical response to those who have used Junk DNA as an argument against design has been to show that the argument is based on ignorance, not knowledge. It is an argument that runs counter to the norm in biology research: which is that design inferences are the default starting point. In biology, functionality is inferred and research is initiated to discover that functionality. Junk DNA was not the outcome of research - but was invented by scientists with an ideological agenda: deterministic genetic reductionism. The ENCODE research should help to make it clear that Junk DNA never was a finding of science, but only a deduction from a materialistic philosophy pretending to be science.

To conclude, it is worth reflecting on the words of Dr Ewan Birney, of the European Bioinformatics Institute near Cambridge, one of the principal investigators in the Encode project. These words are quoted in the Guardian's coverage of this story.

"In 2000, we published the draft human genome and, in 2003, we published the finished human genome and we always knew that was going to be a starting point. We always knew that protein-coding genes were not the whole story. For years, the vast stretches of DNA between our 20,000 or so protein-coding genes - more than 98% of the genetic sequence inside each of our cells - was written off as "junk" DNA. Already falling out of favour in recent years, this concept will now, with Encode's work, be consigned to the history books."

An integrated encyclopedia of DNA elements in the human genome

The ENCODE Project Consortium
Nature, 489, 57-74 (06 September 2012) | doi:10.1038/nature11247

Abstract: The human genome encodes the blueprint of life, but the function of the vast majority of its nearly three billion bases is unknown. The Encyclopedia of DNA Elements (ENCODE) project has systematically mapped regions of transcription, transcription factor association, chromatin structure and histone modification. These data enabled us to assign biochemical functions for 80% of the genome, in particular outside of the well-studied protein-coding regions. Many discovered candidate regulatory elements are physically associated with one another and with expressed genes, providing new insights into the mechanisms of gene regulation. The newly identified elements also show a statistical correspondence to sequence variants linked to human disease, and can thereby guide interpretation of this variation. Overall, the project provides new insights into the organization and regulation of our genes and genome, and is an expansive resource of functional annotations for biomedical research.

See aslo:

Tyler, D. Demolishing Junk DNA as an icon of evolution, ARN Literature blog (15th July 2011)

Jonathan M. Latest ENCODE Research Validates ID Predictions On Non-Coding Repertoire, Uncommon Descent (6th September 2012)

Luskin, C. Junk No More: ENCODE Project Nature Paper Finds "Biochemical Functions for 80% of the Genome", Evolution News & Views (5th September 2012)