ENCODE Project – Discarding ‘Junk DNA’ for Good!
You have to wonder how a big science project in biology, which involved 32 laboratories from 10 countries and 440 scientists, and which cost $130 million, could be controversial with many other mainstream biologists. The lead articles were published in the journal Nature on September 6, 2012. What could be controversial about that? Well it transpires that many scientists, who were not involved, did not like the initial thinking on which the project was based, how the research was carried out, and how the conclusions were drawn. What certain mainstream scientists particularly did not like was that so many intelligent design and creation scientists were so pleased.
It all began in the year 2003 when a smaller consortium set out to discover why so much human genetic information seemed to have no function. When scientists in the 1990s set out to document the entire 3 billion nucleotides (like alphabet letters) in human DNA, they expected to find about 100,000 protein coding genes (lengthy pieces of DNA that each determine the structure of one protein). But when the human genome was finally more or less fully described by 2003, scientists declared that the number of genes was much lower. Today the number is placed at about 20,000 genes which occupy only about 1% of the entire collection of 3 billion nucleotides. So what was the rest of the genome doing? Many scientists declared that the rest was ‘junk DNA’, discarded during the long process of trial and error in evolution. Others cautioned that at least some of the non-protein-coding DNA must have a purpose. Intelligent design and creation scientists, for their part, declared that these “gene deserts” must have a purpose and that we should try to find out what the purpose is.
Driven by curiosity about the nature of the genome, in 2003 an international consortium began a systematic survey of 1% of the human genome. This is like looking at everything in a small segment of the night sky. Such a study should give a representative indication of what occurs in the sky as a whole. So it was in 2007 that the ENCODE [Encyclopedia of DNA Elements] consortium released their results.
The initial ENCODE report was interesting enough to encourage the US based National Human Genome Research Institute to fund a study of the whole human genome. As a result, in 2012, a new larger ENCODE consortium published its results in 30 articles. In summary, they found that: “The vast desert regions have now been populated with hundreds of thousands of features that contribute to gene regulation. And every cell type uses different combinations and permutations of these features to generate its unique biology. This richness helps to explain how relatively few protein-coding genes can provide the biological complexity necessary to grow and run a human being.” (Nature September 6/12 p. 47).
What really annoyed many biologists was the repudiation of the concept of widespread “junk DNA” in the human genome. Commentary on behalf of the consortium had after all declared: “One of the more remarkable findings described in the consortium’s entrée paper (page 57) is that 80% of the genome contains elements linked to biochemical functions, despatching the widely held view that the human genome is mostly ‘junk DNA’” (Nature September 6/12 p. 52). So the good news was that the ‘deserts’ in the DNA were not junk after all. Another conclusion was that the regulatory system of gene expression in humans is vastly more complicated than we ever imagined!
A large number of other scientists in the field of DNA studies, now objected to every aspect of the ENCODE study. For a start, they did not like the systematic nature of the research. Systematic studies mean that the investigators approach the research without expectations as to what they will find. You might call their attitude neutral for purposes of the study. Thus every observation is equally welcome. Many scientists however prefer to see investigator initiated, hypothesis driven, more “creative” projects. In this case the investigator is asking a specific question and presumably hopes for a specific answer. Details not included in the scope of the question, will not necessarily be observed.
Closer examination reveals that in the present situation, many scientists object to the consortium’s unbiased approach to the data. One scientist (Sean Eddy) declared in his blog “ENCODE Says What?” that: “ENCODE is not actually trying to interpret their data in the light of current thinking about junk DNA, at least not in the actual paper.” (Cryptogenomicon September 8/12 p. 2) The current thinking, or course, is evolution based. He continued: “Personally, I don’t think we can understand genomes unless we try to recognize all the different, noisy, neutral evolutionary processes that work in them.” (p. 4) In a response to this blog, Glaudiu Bandea concurred: “Surprisingly, ENCODE theory is not explicitly immersed in one of the fundamental tenets of modern biology: Nothing in biology makes sense except in the light of evolution.” Yet another scientist (Phil Green) suggested that “We don’t exactly look competent when we confidently say first “junk” then “oops, no junk,” particularly when we were right the first time.”
It is evident that the consortium approached the study without expectations of what they would find, while the critics insist on an evolutionary interpretation. The latter are thus more closely wedded to the idea of “junk” DNA. The critics begin their discussion by noting that 50% of the genome consists of small pieces of DNA that occur in multiple repetitive sequences, some of which have presumably changed location in the genome multiple times. By definition, they declare that these sequences are junk DNA. Whether those sequences have a function now or not, they say, is irrelevant to the discussion. Any present function, they declare, came from “co-option” or drafting of something for a new function. For example, it is like drafting cardboard boxes to function as chairs and tables. The boxes did not start out with these functions and they were not produced for those functions. But this does not prevent an enterprising person from drafting them for that purpose.
It is true that a large proportion of non-coding DNA consists of pieces of DNA that can move about (transposons) and other fragments that are repeated almost endlessly. The initial reaction of scientists was that these phenomena must not have any function. Indeed evolutionary explanations were soon forthcoming for how these simple repeats appeared. Many speculate that moveable sequences are like parasitic viruses that somehow invaded the germ line (reproductive cells). Of course, the newcomer DNA would provide no benefit to the cell and probably would exert at least a minor negative influence.
The Nature article on ENCODE declared that “a large proportion of the transcripts in the human genome is thought to be initiated from repetitive elements” (September 6/12 p. 105). Obviously nobody really knows where these repeating sequences came from but, based on evolutionary explanations, they are typically judged to have originated outside the organism or its ancestors. Based on such assumptions, any observed functions would be after the fact, a case of the cell drafting a piece of code for a function. Such a suggestion ignores the difficulties of making something so random perform a function which is so precise. In any case, the evolutionists declare that, by definition, repeats and moveable pieces of DNA are junk whatever their role now is. Others, like the ENCODE consortium, declare that a phenomenon which exhibits a function, cannot be junk. Thus the consortium declares that human DNA appears to be at least 80% functional and could even approach 100%.
Publishing in 2005, James Shapiro of University of Chicago and Richard von Sternberg of National Institutes of Health, argued that instead of repetitive DNA functioning like parasites (as had been suggested by L. E. Orgel and Francis Crick in 1980 in Nature 284: 604-607), those repetitive sequences are “necessary organizers of genomic information” (Biol. Rev. 80 #2 p. 227). They further suggested that “we may come one day to regard erstwhile ‘junk DNA’ as an integral part of cellular control regimes that can only be called ‘expert.’” (p. 243)
Shapiro, in a blog posted by the Huffington Post September 12/12, declared about the 2005 article: “Our basic idea was that the genome is a highly sophisticated information storage organelle. Just like electronic data storage devices, the genome must be highly formatted by generic (i.e. repeated) signals that make it possible to access the stored information when and where it will be useful.” Now in retrospect, Shapiro declares that the mobile DNA is a “potent force for genome organization” and most emphatically not parasitic and not junk!
It is evident that the human genome is a highly coordinated information packaging and processing system. We owe the ENCODE consortium our gratitude for describing so many features of the cell, which testify to its wonderful design. These include several tiers of control, the fact that most “junk” DNA can now be defined as useful components (whatever the repetitive appearance it might assume), and that even the straightforward protein coding regions are compressed and highly complex. Who knew that the human genome project would prove to be so enlightening? It would be hard to find a clearer picture of wonderful design than the cells in our human bodies.
Subscribe to Dialogue