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Junk DNA

Les Sherlock

NOTES

The National Human Genome Research Institute (NHGRI) launched a public research consortium named ENCODE, the Encyclopedia Of DNA Elements, in September 2003, to carry out a project to identify all functional elements in the human genome sequence.*

At the beginning of September 2012 the results were published.

Long stretches of DNA previously dismissed as "junk" are in fact crucial to the way our genome works... In total, Encode scientists say, about 80% of the DNA sequence can be assigned some sort of biochemical function.*

It is still very early days, but one comment was that it is now very likely that there will prove to be no DNA that is totally without purpose.



* Quote from here.



* Quote from here.

According to ENCODE’s analysis, 80 percent of the genome has a “biochemical function”. More on exactly what this means later, but the key point is: It’s not “junk”.... “Almost every nucleotide is associated with a function of some sort or another, and we now know where they are, what binds to them, what their associations are, and more,” says Tom Gingeras, one of the study’s many senior scientists.

And what’s in the remaining 20 percent? Possibly not junk either, according to Ewan Birney, the project’s Lead Analysis Coordinator and self-described “cat-herder-in-chief”. He explains that ENCODE only (!) looked at 147 types of cells, and the human body has a few thousand. A given part of the genome might control a gene in one cell type, but not others. If every cell is included, functions may emerge for the phantom proportion. “It’s likely that 80 percent will go to 100 percent,” says Birney. “We don’t really have any large chunks of redundant DNA. This metaphor of junk isn’t that useful.” *

This gives rise to three obvious conclusions:








* Quote from here.

  1. The difference now seen between chimps and humans is so large, it is absolutely impossible that mutation could have produced it from a common ancestor in 6 million (or even 6 billion) years.
  2. Evolutionists can no longer accuse creationists of being unable to predict anything. For 40 years the latter have been saying ‘junk DNA’ would turn out to have purpose – even against the mass of evolutionists saying the opposite.
  3. The argument that creation should be banned in schools, colleges and universities because it is an obstacle against true science is now turned on its head: it is evolution that has been obstructing the advance of science by its insistence that 95% of our DNA has no purpose, while creation encouraged research into this area.


Let us look at these three issues in more detail.

1 Chimp-human difference is too high for both to have descended from a common ancestor.

The number of base pairs in human DNA is 3,164,700,000:* just over 3 billion. A chimp has at least 10% more DNA than a human, and in the rest there is a difference between them of around 2%. This means that in total there is at least a 12% difference in the DNA of humans and chimps. Since evolutionists claim that they divided from a common ancestor about 6 million years ago, and usually accept a generation span to be around 20 years, it is a simple calculation to work out how much DNA had to change per generation to produce the difference we now see.

If we assume the same amount of change took place in the chimp line as in the human line, then 632.94 base pairs had to change on average in every generation in both lines.* This is over double the maximum amount that has been observed to change per generation in humans.

So even apart from any other consideration, the amount of change necessary for evolution to be responsible for the rise of chimps and humans is impossibly high. However, there are other significant difficulties:



* According to the Human Genome Project web site




* Calculations:

12% of 3,164,700,000 = 379,764,000 base pairs

379,764,000 / 2 =  189,882,000 base pairs

6 million years / 20 = 300,000 generations

189,882,000 base pairs/ 300,000 generations = 632.94 base pairs per generation.



* Calculations: As there are four different base pairs, the number of possible combinations with one pair is 4; with two pairs is 16; with three pairs is 64. So one has to multiply by four the same number of times as there are base pairs for the possible different combinations. Multiplying by 4, 632 times results in approximately 10400, which is 1 followed by 400 zeros.

** 189,882,000 pairs / 2 = 94,941,000 mutations
94,941,000 x 20 years = 1,898,820,000 years

* See here for my description of it (scroll down to where it is at the end of the introduction). Note: this double mutation was not Darwinian, microbe-to-man evolution, as it was a reduction in specified complexity, not an increase.

** Calculations:

1,898,820,000 x 33,000 = 60,000,000,000,000 years (approx.)

60,000,000,000,000 / 13,700,000,000 = 4,574 times (approx.)

* See here for more details of ‘Haldane’s Dilemma’.

  • According to the theory of evolution, change takes place much slower than this and it would take several generations for any mutation to become established in a population before another could be added to it. This massively increases the number of base pairs required to change in every mutation over 6 million years.
  • A mutation of 632.94 base pairs with all of them accurately coding could never take place. The chances of randomly achieving any specific combination are approximately 1 in 10400.* Even if there were 1 billion viable combinations, this simply reduces the chances to 1 in 10391. In other words it is absolutely impossible to take place even once, never mind in every single generation for 6 million years.
  • The maximum size of any advantageous mutation that has ever been observed to be preserved by natural selection is two base pairs. Even if this took place in every single generation, it would take 1,898,820,000 years (nearly 1.9 billion years) to reach the necessary number of changes to produce 18,882,000 mutated base pairs.**

    However, in Lenski’s experiment * where the double mutation was observed, it did not take place until after 33,000 generations, and then only in one of twelve different populations. So if the rate of change in chimps/humans was the same as that of E coli in Lenski’s experiment, it would take 33,000 times longer than 1.9 billion years; or approximately 60 trillion years,** which is about 4,574 times the evolutionists’ estimated age of the universe! However, even this is a considerable underestimate, since Lenski’s experiment showed a 1 in 12 chance of the double mutations taking place, where these calculations assume it can happen every time. One must also remember that the population size was far higher than could ever have been the case during the evolution from common ancestor to chimps/humans; and the DNA of E coli is significantly smaller than chimps/humans. So for both of these reasons, all possible mutations could take place very much faster in E coli than chimps/humans.
  • Of course, these difficulties have been understood for many years. The famous evolutionary geneticist J.B.S. Haldane (1892–1964) * drew attention to the problem in his paper in 1957—the ‘cost of substitution’. The evolutionists have been avoiding it by the claim that 95% of our DNA has no purpose, so can be discounted from any calculations. They can no longer hide from the problem is this way.

There is a huge damage-limitation exercise now taking place, with evolutionists claiming either most of it still is junk, or that they never said it was junk in the first place. Unfortunately for them, there is too much in print to be able to get away with it! For example, Richard Dawkins said:

…it is a remarkable fact that the greater part (95 percent in the case of humans) of the genome might as well not be there, for all the difference it makes.*

This could not be clearer: according to Dawkins the 95% of human DNA, popularly called ‘junk’, has absolutely no function and might as well not exist. His book was published in 2009, just three years before the ENCODE project released its full findings, but two years after it had began its research, when already papers were being published showing that parts of this 95% did have a function. I find it extraordinary that he could have blundered so spectacularly by clinging to such a ‘mistake’ when so much evidence was emerging to the contrary, even at the time he was making the claim.* Just one page earlier he said:




* p333, The Greatest Show on Earth.





* A point I made in my response to his book soon after its publication. It is at the end of my comments on chapter ten.



* p332, The Greatest Show on Earth.

What pseudogenes are useful for is embarrassing creationists.
It stretches even their creative ingenuity to make up 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.*

Well, now it is the evolutionists who are embarrassed – or certainly should be. For 40 years, ever since Susumu Ohno introduced the term in 1972, they have been waving ‘junk DNA’ in the face of creationists, asking why their Creator-God would have produced DNA with only 5% that had any function. Now they know, or are beginning to find out, that it wasn’t that it was without function, but simply that they knew too little about it to be aware of what it did. In fact this mirrors exactly the blunder they made 100 years ago or so, when they claimed over 100 human organs were vestigial: remnants of our evolutionary past that were no longer functional. They were wrong with vestigial organs 100 years ago, and they have been wrong for the past 40 years with junk DNA. Will they never learn?

It appears not, because, contrary to their claim that they are totally unbiased, simply following scientific discoveries where they lead, at least some of them are still fighting to try to put the genie back in the bottle and pretend ‘junk DNA’ is still junk. For example, University of Toronto biochemistry professor Larry Moran is on record as saying:

“The creationists are going to love this. You blew it Ed Yong. ... ‘Almost every nucleotide ...’? Gimme a break. Don’t these guys read the scientific literature? This is going to make my life very complicated… * The public now believes that the concept of junk DNA has been rejected by scientists and that our huge genome really is full of wonderful sophisticated control elements regulating the expression of every gene. It’s going to take a lot of effort to undo the damage caused by scientists like Ean Birney.” **

Dr Ewan Birney, of the European Bioinformatics Institute near Cambridge, is one of the principal investigators in the Encode project.


* Quoted from here.


** Quoted from here.

“The Encode consortium’s 442 researchers, situated in 32 institutes around the world, used 300 years of computer time and five years in the lab to get their results,” *

...and yet Larry Moran wants us to believe that their research is fundamentally flawed because it flies in the face of his religious belief that God played no part in our creation. Note that his automatic reaction is not to say, “442 researchers, spending 300 computer-years investigating areas not previous studied seriously before, have shown areas we previously thought as useless to be functional: therefore we must consider these findings carefully.” No! He effectively says, “The reports of these people support creationism, therefore we must oppose them.” This is not unbiased scientific reasoning, but typical of the prejudice that has left many valid scientists unpublished because, regardless of the quality of their research, they are known creationists and therefore black-listed. His reaction shows very clearly the serious implications of this report for the theory of evolution: if it made no difference, then he would not be reacting so strongly.


* Quoted from here.

It is certainly impossible for evolutionary scientists now to pretend they never said that the vast majority of our DNA is useless. For example:

“Humans, chimpanzees, and gorillas are within two percentage points of one another genetically, even if not obviously any other way.” (Jonathan Marks, Department of Sociology and Anthropology, University of North Carolina at Charlotte.) *

“Six years ago I jumped at an opportunity to join the international team that was identifying the sequence of DNA bases, or “letters,” in the genome of the common chimpanzee (Pan troglodytes). As a biostatistician with a long-standing interest in human origins, I was eager to line up the human DNA sequence next to that of our closest living relative and take stock. A humbling truth emerged: our DNA blueprints are nearly 99 percent identical to theirs. That is, of the three billion letters that make up the human genome, only 15 million of them—less than 1 percent—have changed in the six million years or so since the human and chimp lineages diverged.” (Katherine S. Pollard; May 2009 Scientific American.) *  

The only way these people could claim such a close relationship in the DNA of chimps and humans is by discounting the 95% DNA they called ‘junk’. However, even this unrealistically modest claim of 15 million letters needing to change is impossible. It requires 50 to change on average in every generation.* The chances of getting any particular combination of 50 letters by mutation is 1 in 838 (8 followed by 38 noughts).** Even if there were one billion valid combinations the chance of getting one would still be 1 in 829, which is so low the likelihood of it happening even once in the entire history of the world is remote in the extreme.




* Quoted from here.





* Quoted from here.



* Calculations:

6 million years/ 20 years = 300,000 generations

15,000,000 letters/ 300,000 generations = 50 base pairs per generation

** 1 multiplied by 4, 50 times = 838

Additionally, this contradicts the theory of evolution, which requires natural selection to favour beneficial mutations over others. Therefore several generations must come and go in order for natural selection to operate. How many generations? At a mutation, there is a population of one - the mutant. If the population doubles in every generation, then it will be 20 generations before one million new ‘mutants’ will have lived, and even this is less than most geneticists would accept is required for a new mutation to become established fully. This is ‘Haldane’s dilemma’ and has never been resolved.

As a part of the damage-limitation exercise, some evolutionists are continuing their ‘blind-eye-turning’ and telling us that the ENCODE results still only show purpose for a small part of DNA, and the rest is useless junk, even though one of the principal investigators says...

“I still think we’re at the start of this journey, we’re still in the warm-up, the first couple of miles of this marathon.” (Dr Ewan Birney) *

We are told it will take decades at least to sift through the 3 billion plus base pairs of our DNA, and perhaps we’ll never ever be able to identify every part of it. Yet, like the leopard that cannot change its spots, these evolutionists persist in telling us that it’s junk. Well, the first 12 years of this new millennium have produced arguably one of the greatest turn-arounds we have yet seen in the creation/evolution debate, and there is absolutely no doubt at all in my mind that there are many more revelations to come.

Through their religious belief that God does not exist, they still persist in assuming DNA arose randomly by chance mutations. The fact is that, as Bill Gates said:


* Quoted from here.

“DNA is like a computer program but far, far more advanced than any software ever created. Indeed, rather than being the hodgepodge that Kenneth Miller claims it to be, DNA appears to be the most complex, ingenious and awe-inspiring information system that mankind will ever behold.” *

So it does not occur to them that our Intelligent Designer may have designed our DNA with the knowledge that it would be attacked by mutation and therefore included sections that would not be necessary for the immediate needs of life, but for integrity maintenance, helping to minimise the damage that mutation always causes.* Obviously, if every part was necessary for life, then at the first event of mutation, life would end. Over 1,000 human ailments are the result of mutation, but the fact that we are still here, albeit with some problems, is evidence of how well our DNA was designed. It is also evidence that we could not possibly have been around for hundreds of thousands, or even millions of years. The observed mutation rate would certainly have resulted in our extinction long before now.



* B. Gates, The Road Ahead, Penguin Group, New York,    p. 188, 1995.


* For example, in New Scientist 14th February 2013, Paul Marks explains how the ‘self-repairing’ computer, called a ‘systemic’ computer, contains “multiple copies of its instructions distributed across its many systems, so if one system becomes corrupted the computer can access another clean copy to repair its own code.” It is quite possible that our ‘Intelligent Designer’ did something similar in our DNA. If so, you can be sure it will prove to be far more complex, and therefore more difficult to discover, than anything found in these latest computers.



* See How did He do that, for example.

It is also clearly the case that there are many organs in our bodies that are not essential to life, but nevertheless improve efficiency. The list is almost endless, but you can manage perfectly well without some (or all?) of your teeth, your appendix, your tonsils, etc. Yet a function is known for all of these things, which either make life easier for us, or are used at a particular stage in our life. It is very likely that some, or much, of our DNA comes into the same category.

All of this is speculation, however, since, as Bill Gates pointed out, it is a fantastically complex system of information, and has been designed by a mind that is infinitely greater than our own.* So any guesses I may make are likely to be a very long way from the truth.

2 Creation is not science because it can make no predictions.

This is a common criticism, and, just like the junk DNA myth, is completely untrue.

Creation predicts that it is impossible for inanimate matter ever to change into a living organism without intelligent intervention. Evolution predicts that it can. Every observation shows creation is correct.

Creation predicts that undirected mutation can never increase the specified complexity of a genome. Evolution predicts that it has done so billions of times over. No-one can offer a single observation that shows specified complexity increasing.

Creation predicts that apart from damage from mutation, all of our DNA will have purpose. The ENCODE project supports this prediction.


3 Creation should be banned from classrooms and universities.

This is the ultimate sting. Evolutionists have increasingly become vocal in their campaign to remove all trace of Christianity and creation from the education system because, they say, it is an obstacle to true science. Yet it is they who have been telling scientists for 40 years that 95% of our DNA has no purpose and can be ignored.

Earlier I quoted a few evolutionists in print with the notion of junk DNA. Let me give one more, from no less than the Natural History Museum, London. In November 2008 they published a book called “99% Ape: How Evolution Adds Up.” * I wonder how many people will now be prepared to part with £14.99 to buy this book with a title that is based on an unscientific, totally inaccurate myth?

Now we hear from the ENCODE project that not only have they found the essential part that some of this 95% plays, but the discovery may lead the way to the treatment of some serious human ailments. It is surely beyond dispute that the ‘junk DNA’ theory has held back research into what is now proving to be a vital area.





* See here for their advert.

Although very catchy, the term "junk DNA" repelled mainstream researchers from studying noncoding genetic material for many years. After all, who would like to dig through genomic garbage? *

Had researches listened to such evolutionists as Richard Dawkins, we would still have absolutely no idea what goes on in that 95% of our DNA. Had they listened to creationists, they would have begun their investigations as soon as the tools to do so became available. So who was the greater obstacle to science, evolutionists or creationists?

100 years ago, evolutionists told the world that over 100 human organs were useless vestiges from the past. Creationists said they must have some function. Who delayed the advance of medical science in this area, evolutionists or creationists?


* Wojciech Makalowski, a Pennsylvania State University biology professor and researcher in computational evolutionary genomics. Scientific American, February 12, 2007

Historically it has been Christian creationists who have been at the forefront of scientific advancement and the promotion of education.*

It is time the modern infatuation with atheism was abandoned, for the sake of the unfettered advancement of science, education and wholesome living. It is inevitable that the theories of Darwin, Dawkins and other promoters of the unscientific idea of evolution of species will eventually be abandoned in the same dustbin of history as the flat earth society. Let us not delay the inevitable but make it sooner rather than later!

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* See here for a list of creation-scientists, past and present.