Junk DNA?

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Junk DNA Wheelie BinIn my review of Chap. 2, I highlighted Adrian’s citing of junk DNA as evidence in support of evolution. There I wrote:

Towards the end [of this chapter], Adrian makes a mistake common amongst those who seek to justify their faith in Darwin by science. His final argument against Biblical creation in this chapter starts, “Fourthly, if human beings were independently created by God, you might have expected the DNA that built our bodies to be elegant and flawless. What do you find? The majority of human DNA is ‘junk’ DNA. It doesn’t help build bodies. It just comes along for the ride (although it’s of great help to modern detectives solving crimes).” (p.19) That was the assumed wisdom of evolutionists when Adrian wrote his book, but things changed dramatically in September 2012. This was when a large group of scientists working together on the Encyclopedia of DNA Elements (ENCODE) project published coordinated papers announcing that the description “junk DNA” was a misnomer. The journal Scientific American put it this way, “The ENCODE project has revealed a landscape that is absolutely teeming with important genetic elements – a landscape that used to be dismissed as ‘junk DNA.’” Rather than add to this page, I provide more details of what is proving to be a contentious research project in an appendix.

Let me therefore explain what I alluded to above. Adrian’s argument has for a long time been used by evolutionists, but the ENCODE project set a cat amongst the pigeons in this respect. The ENCODE project began in 2003 with the objective of identifying all the functional elements within the human genome. Their findings were published in 30 linked open-access papers in three scientific journals. Based in 32 laboratories, a team of 442 researchers spread across the USA, Britain, Spain, Switzerland, Singapore and Japan put together a massive DNA database. This database enabled them to produce a map of the genetic switches that impact everything that happens in the human body. Junk DNA is technically known as non-coding DNA, because it does not encode protein sequences in cells. In humans, over 98% of genomes are non-coding DNA and were therefore thought to be mostly useless – hence the term “junk DNA”. Many, including Richard Dawkins, considered these “pseudogenes” to be evidence for evolution, in that they were left over from evolutionary paths which are no longer needed. In his 2009 book, The Greatest Show on Earth (pp. 332-333), Dawkins stated “It stretches even their creative ingenuity to make a convincing reason why an intelligent designer should have created a pseudogene – a gene that does absolutely nothing and gives every appearance of being a superannuated version of a gene that used to do something – unless he was deliberately setting out to fool us.” Perhaps it was this book which Adrian was taking his inspiration from. Of course Dawkins’ mistake was to assume that because we did not know the function of non-coding DNA it had no function at all.

Chief Rabbi Lord Jonathan Sacks and Richard Dawkins at RE:Think – BBC Website

A week after the ENCODE papers were published, Richard Dawkins discussed “Science versus Religion” with the Chief Rabbi, Jonathan Sacks, at the BBC’s RE:Think, Religion and Ethics Festival in Manchester. Sacks raised the news from the ENCODE project to make the point that he hoped “those people who think that ninety-eight percent of religion is junk, I hope that someday they might rethink that one as well.” Several minutes later, though not recalling why Sacks had raised it, Dawkins said of the ENCODE discovery, “I have noticed that there are some creationists who are jumping on it because they think that’s awkward for Darwinism. Quite the contrary it’s exactly what a Darwinist would hope for, is to find usefulness in the living world.” Did you spot Dawkins’ U-turn? In his book he argued that the presence of a gene that does absolutely nothing” was evidence against a Creator, but a week after the ENCODE announcement he said that the absence of such genes is “exactly what a Darwinist would hope for…”. Whilst this is not the first time that Dawkins has considered himself free to play fast and loose with truth, it does illustrate how unconcerned many evolutionists are with the facts!

There are however many who will not sing a different tune as quickly as Dawkins did. Seven of his fellow Darwinists published an article on 20 February 2013 in the journal Genome Biology and Evolution which attacked the ENCODE findings. The article had the lengthy and imaginative title of, “On the immortality of television sets: ‘function’ in the human genome according to the evolution-free gospel of ENCODE.” Notice the religious language of these dissenters! They go as far as accusing ENCODE of promoting a “gospel” which takes evolution out of biology. An article in The Guardian reported their complaint like this, “But this idea is now the subject of an astonishingly vitriolic attack from other scientists, who say that Encode’s ‘absurd’ ideas are the work of people who know nothing about evolutionary biology.” This group of authors insist “that ENCODE uses an evolution-free definition of ‘functionality.’”

In the past it has commonly been claimed that a belief in evolution is essential for a good understanding of biology. Now the argument is that biology can be studied only if research is confined to definitions which presuppose that evolution must be supported no matter where the evidence leads. The remarkable thing is of course that the ENCODE project is not a creationist initiative – would that we had the same funding available – it is, almost certainly, staffed by some very committed evolutionists. The argument over junk DNA is still continuing as I write, as many evolutionists are not prepared to follow Dawkins’ example of accepting the evidence and allowing the arguments in support of evolution to evolve even when they are undermined by the facts.

Here are links to three technical articles which have continued the debate. The first two are critical of ENCODE conclusions whilst the third is supportive of them:

Two further articles which have been published on the web are listed below. The first is critical of ENCODE, whilst the second agrees with their conclusions:

The following are articles written by those who reject Darwin’s naturalism. Not all are Biblical Creationists; the links are to sites run by Old Earth Creationists/Theistic evolutionists and Intelligent Design proponents as well as Evangelical Christians:

Drosophila Melanogaster – Wikipedia

Moving away from the controversy over “junk” / non-coding DNA, a very interesting piece of research was published recently. The research paper, which has the title, Origin and Spread of de Novo Genes in Drosophila melanogaster Populations, was published on the Science website on January 23, 2014. ScienceDaily published a summary, New genes spring, spread from non-coding DNA the same day, which is more accessible to those without technical knowledge. It provides this helpful summary, “‘Where do new genes come from?’ is a long-standing question in genetics and evolutionary biology. A new study shows that new genes can spring from non-coding DNA more rapidly than expected.” Drosophila melanogaster is a species of fruit fly and the researchers compared selected genes of wild strains of this species with what is known as the “standard reference sequence strain” (i.e. the strain which was studied at some time previously and has now become the standard against which other strains of the species are compared). It should also be noted that inevitably the researchers approached their work with a preformed evolutionary world-view through which they interpreted their findings. This is not therefore a case of Christians who are ignoring the evidence.

ScienceDaily reports David Begun, Professor of Evolution and Ecology at UC Davis and senior author on the paper as commenting, “This shows very clearly that genes are being born from ancestral sequences all the time.” “Ancestral sequences” are those pieces of genetic information which are stored in non-coding DNA. To the evolutionist this is assumed to be information which previous generations had acquired, but which their descendants have not been accessing for some reason. However, there is no evidence to show that this is how the information was obtained; it could have been placed there from the start. The important point is that it has been preserved in what has been nicknamed “junk DNA” and, if this fruit fly is typical of other organisms, it can be accessed by many living creatures. Whilst some storerooms contain a lot of junk, it does not make every one of them a junk room! Storing useful information rather than discarding it so that it can be retrieved at some point in the future is a sensible arrangement. Notice too that David Begun describes this retrieval of pre-existing information as occurring “all the time”.

This is not really a new discovery though. Explaining the popular reasoning behind the formation of new genes, mutations which occur when a gene duplicates, ScienceDaily adds, “Begun’s laboratory discovered a few years ago that new genes could also appear from previously non-coding stretches of DNA, and similar effects have since been discovered in other animals and plants.” This may well therefore have been discovered before ENCODE announced their findings. No matter when it was discovered, without a doubt it challenges the description of some DNA as junk. The research team also noted how effectively the new genes had spread through the population, assuming this was due to natural selection. Li Zhao, a post-doctoral researcher at UC Davis and first author on the paper, said that it is possible that these new genes form when a random mutation in the regulatory machinery causes a piece of non-coding DNA to be transcribed to RNA. She added, “If it has a beneficial effect, then it gets selected.” Notice that what she is describing is to her a possibility and not a discovery; this is the fruit of a Darwinian mind-set – other possible mechanisms for the retrieval of this stored information are not discussed, but failing to address them does not mean they are not possibilities. For example, they could be the actions of an in-built repair mechanism designed to correct degenerative mutations. Whatever the explanation, it should be noted that this research does not explain how genetic information is generated as it must be if evolution is truly a scientific understanding of life on earth. What it does show is that pre-existing genetic information is stored in what until recently was claimed to be useless DNA, and that, in a way which we do not understand, the cells of living creatures are able to access and make use of that information.

All this evidence undermines Adrian’s misplaced confidence quoted above that, “The majority of human DNA is ‘junk’ DNA. It doesn’t help build bodies. It just comes along for the ride.” But what of his assertion that our DNA should be “be elegant and flawless” if it was created by God? Well, it certainly is elegant and no doubt it contains many other hidden secrets which we have yet to discover, though perhaps we will never grasp its deepest ones. However, today we do see genetic information which has accumulated large numbers of flaws over the years. Adrian has dismissed the concept of creation being damaged by human sin [here] whilst claiming a role for mutations [here] in building the DNA of all organisms which has never been observed. The truth is that the majority of mutations are detrimental to the creatures they affect. It is nonsensical to insist that perfect DNA is essential evidence of a creator on one hand, whilst claiming that mutations build better organisms on the other. Non-coding DNA with its pre-existing store of ancestral genetic information which is able to restore what has been lost fits well into a world view where a benevolent Creator knew that an ungrateful mankind would ruin His good work, and consequently designed an in-built means of recovery. On the other hand, mutations which are regularly observed to damage successive generations really do not help the Darwinian theory of evolution in the least, for they cause a loss of information rather than the acquisition of it.

My aim in this appendix has been to provide readers with the means of testing one of Adrian’s claims for themselves. Of course I wonder whether Adrian, should he read this, will follow Richard Dawkins and do a U-turn over his “convictions” concerning “junk DNA” or whether he will join in the chorus of ENCODE sceptics. I cannot predict which he will choose, but I do hope it will be neither. I hope that both you and he will agree with me that the evidence for evolution is frail, and that the God of the Bible has not been discredited by the shallow claims of Darwin’s disciples who clutch at every straw in order to bolster their faith.