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Published: Jan 2017
Updated:December 15, 2018

Predictions of Junk versus Functional DNA

"As someone who has studied the concept of 'junk DNA' for over twenty years, I am dismayed by two statements that appear repeatedly on various blog sites discussing evolution: 'No one ever asserted that junk DNA is without function...it was long suspected that these sequences have important roles in the cells.'" — evolutionary biologist Richard Sternberg[[sternberg-2009]]

"I have noticed that there are some creationists who are jumping on [the 2012 ENCODE results] 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."Richard Dawkins[[dawkins-jonathan-sacks]]

Overview

Proponents of evolutionary theory predicted that most DNA in organisms with large genomes and low reproductive rates would be junk.  Meanwhile, Intelligent Design (ID) proponents predicted that most DNA would turn out to be functional.

This table shows notable scientists who advocated junk DNA and their reasons for doing so. The placement of X's is conservative, since not every work by each author has been surveyed:

Authors and Year

Neutral Theory

Genetic Load

Selfish Genes

Trial / Error

C-Value

Seems Unused

How much DNA is junk?

Mootoo Kimura, 1968[[kimura-1968]]

x

"many"

Jack King & Thomas Jukes, 1968[[king-jukes-1969]]

x

"99 percent"

David E. Comings, 1972[[comings-1972]]


x



x


1 to 10% is striclty functional.  
80 to 93% is junk

Susumu Ohno, 1972[[ohno-1972]]

x

x

x

x

94% +

Ford Doolittle, 1980[[doolittle-1980]]

x

x

x

x

?

Francis Crick & Leslie Orgel, 1980[[crick-1980]]

x

x

x

"much DNA... has no specific function"

Carl Sagan, 1993[[sagan-1993]]

x

x

"some, maybe even most"

Kenneth Miller, 1994[[miller-1994]]

x

genomes are "full of junk"

Sydney Brenner, 1998[[brenner-1998]]

x

x

?

Joseph Felsenstein, 2003[[felsenstein-2003]]

x



"much of the DNA"

Francis Collins, 2006[[collins-2006]]

x

x

45% is useless ancient repetitive elements, total junk % not given.

Michael Shermer, 2006[[shermer-2006]]

x

x

"only a tiny percentage" is not junk.

PZ Myers, 2008[[myers-2008]] [[myers-2015]]

x

x

97% (only about 30,000 genes not junk)

Richard Dawkins, 1976, 1998,  2009[[dawkins-1976]] [[dawkins-1998]] [[dawkins-2009]]

x

x

95% "might as well not be there"

John Avise, 2010[[avise-2010]]

x

x

"50% and probably much more"

Dan Graur, 2012, 2013[[graur-2012]] [[graur-2013]]

x

x

x

x

x

x

< 91% junk.  "approximately 9%... is certain to be functional"

Don Prothero, 2013[[prothero-2013]]

x

"80-90%"

T. Ryan Gregory, & Alexander Palazzo, 2014[[gregory-2014]] 

x

x

x

x

x

"at least 90% of the genome"

The following sections describe the fascinating history of this debate. 

Proponents of Evolutionary Theory Predicted Junk DNA

There were at least six reasons why proponents of evolutionary theory predicted most DNA in large genomes would be junk, four of which are based on evolutionary theory itself.  In other words, if evolutionary theory is true these are the reasons we should expect that most DNA in large genomes is junk:

1. Neutral theory

The neutral theory of evolution claims that most of the DNA differences between larger genome organisms is by chance, and not because natural selection favored organisms having those mutations.  The reasoning is as follows:  

  1. In typical populations of complex organisms, natural selection can only help spread or remove mutations that have a strong effect.  Otherwise, random chance is the dominant factor in deciding which organisms reproduce and pass on their genes.
  2. Since most mutations have very little effect on an organism, [[eyre-walker-2007]] [[lind-2010]] neutral theory is a mathematical reality. [[lynch-2006]] "[T]he revolution is over. Neutral and nearly neutral theory won," as biologist PZ Myers described.[[myers-2014]]

In humans and other large mammals, greater than 99.98% of mutations would spread through the population by chance rather than because of natural selection.[[dodson-1962]] [[moran-2014b]]

Only about 5 to 10% of DNA is shared between humans and more distantly related mammals such as horses, dogs, and mice.[[meader-2010]]  Therefore if these animals all evolved from a common ancestor, given neutral theory, the large majority of DNA not shared by these animals would have come about by chance and not natural selection.  Since DNA that exists only by chance will have a random sequence, it is therefore highly unlikely to be functional.


Dan Graur, 2012
Evolutionary and molecular biologist.

...there exists a misconception among functional genomicists that the evolutionary process can produce a genome that is mostly functional.[[graur-2012]]

If the human genome is indeed devoid of junk DNA as implied by the ENCODE project, then a long, undirected evolutionary process cannot explain the human genome.[[graur-2013]]


T. Ryan Gregory, 2014
Evolutionary and genome biologist.

We would expect that natural selection would be powerless to stop the accumulation of certain genomic alterations over the entirety of metazoan [meaning animal] evolution.[[gregory-2014]]

2. Genetic load

Genetic load (also called mutational load) is the average number of deleterious (harmful) mutations per organism in a population.  If the genetic load is too high, the population will not survive.

Organisms with more DNA genreally have more mutations, since the number of errors increases as more is copied.  If most of the DNA in large genome organisms (e.g. mammals) is functional, then these mutations will usually break important functions.  And if evolution could not even maintain these large amounts of DNA, then it could not have created it.

But if most DNA does nothing, or does not have specific information, then most mutations will be harmless.  Therefore because of this genetic load problem, evolutionary theory both predicts and requires only a small amount of DNA in large genome organisms will be functional.

Motoo Kimura, 1968
Influential population geneticist, introduced neutral theory.

Calculating the rate of evolution in terms of nucleotide substitutions seems to give a value so high that many of the mutations involved must be neutral ones.[[kimura-1968]]

Jack King and Thomas Jukes, 1969
King and Jukes (pictured) were evolutionary biologists known (along with Kimura) for originating neutral theory.

Either 99 percent of mammalian DNA is not true genetic material, in the sense that it is not capable of transmitting mutational changes, which affect the phenotype, or 40,000 genes is a gross underestimate of the total gene number... it is clear that there cannot be many more than 40,000 genes.[[king-jukes-1969]]

David E. Comings, 1972
Medical doctor, author, and atheist

The mutational load would be too great to allow survival if all the DNA of most eukaryotes carry was composed of essential genes [...]

Taking into consideration this frequency of spontaneous mutations and the maximal mutational load, Muller estimated the number of functioning gene loci in mammals to be approximately 3 x 104, or about 1% of the genome [...]

Even if the estimate of 3 x 104 is off by a factor of 10, this would still account for only 10% of the genome. [[comings-1972]]

Susumu Ohno, 1972
Geneticist and evolutionary biologist, first proposed gene duplication as a major factor in evolution

The moment we acquire 105 gene loci, the overall deleterious mutation rate per generation becomes 1.0 which appears to represent an unbearably heavy genetic load [...] Even if an allowance is made for the existence in multiplicates of certain genes, it is still concluded that at the most, only 6% of our DNA base sequences is utilized as genes[[ohno-1972]]

By "genes" Ohno does not necessarily only protein coding regions, but rather any functional region of DNA.  Just as Ford Doolittle used the term in his 1980 paper.[[doolittle-1980]]

Ford Doolittle, 1980
Biochemist and member of the National Academy of Sciences.

Middle-repetitive DNAs together comprise too large a fraction of most eukaryotic genomes to be kept accurate by Darwinian selection operating on organismal phenotype.[[doolittle-1980]]

Joseph Felsenstein, 2003
Theoretical population geneticist and member of the National Academy of Sciences.

If much of the DNA is simply “spacer” DNA whose sequence is irrelevant, then there will be a far smaller mutational load. But notice that the sequence must be truly irrelevant, not just of unknown function... Thus the mutational load argument seems to give weight to the notion that this DNA is nonspecific in sequence.[[felsenstein-2003]]

Dan Graur, 2012
Evolutionary and molecular biologist, prominent junk DNA proponent, atheist

Thus, according to the ENCODE Consortium, a biological function can be maintained indefinitely without selection, which implies that at least 80 – 10 = 70% of the genome is perfectly invulnerable to deleterious mutations, either because no mutation can ever occur in these “functional” regions, or because no mutation in these regions can ever be deleterious. This absurd conclusion was reached through various means [...] only sequences that can be shown to be under selection can be claimed with any degree of confidence to be functional... The absurd alternative... is to assume that no deleterious mutations can ever occur in the regions they have deemed to be functional.[[graur-2012]]

If the human genome is indeed devoid of junk DNA as implied by the ENCODE project, then a long, undirected evolutionary process cannot eplain the human genome... If ENCODE is right, evolution is wrong.[[graur-2013]]

T. Ryan Gregory, 2014
Evolutionary and genome biologist

If the rate at which these mutations are generated is higher than the rate at which natural selection can weed them out, then the collective genomes of the organisms in the species will suffer a meltdown as the total number of deleterious alleles increases with each generation... [This is] incompatible with the view that 80% of the genome is functional in the sense implied by ENCODE.[[gregory-2014]]

Larry Moran, 2014
Biochemist, textbook author, atheist, and well known ID critic

It should be no more than 1 or 2 deleterious mutations per generation [...] If the deleterious mutation rate is too high, the species will go extinct.[[moran-2014]]

Humans get about 56 to 160 mutations per generation.[[moran-2013]]  If any more than a small percentage of DNA has a meaningful sequence, such a mutation rate causes more than 1-2 harmful mutations per generation, and evolution becomes primarily a destructive process.

PZ Myers, 2015
Developmental biologist, atheist, and well known ID critic

 there is an upper bound to the number of genes we can possibly carry, and it happens to be in the neighborhood of the number of genes estimated in the human genome project  [...] this is why some of us go all spluttery and cross-eyed at any mention of the ENCODE project. They just blithely postulated orders of magnitude more functioning elements in the genome than could be tolerated by any calculation of the genetic load.[[myers-2015]]

The human genome project found about 30,000 genes,[[human-genome-2003]] which would comprise perhaps 3% of human DNA.  Myers says that If much more than this is functional, evolution becomes primarily a destructive process.

John Sanford, 2015
Population geneticist.  Invented the gene gun leading to most of the world's GMO crops. Christian and young earth creationist.

Most people in the field [of theoretical genetics] think the human genome is clearly degenerating, but they dismiss this as merely arising due to relaxed selection. But those who have examined it most closely realize that even with intense selection there is still a profound problem.[[sanford-2015]]

3. Selfish genes

Some sequences of DNA, called transposons or mobile-elements, have the ability to make copies of themselves within DNA.  Transposons range in size from a few hundred to tens of thousands of letters of DNA.[[britannica-transposon]]  The selfish gene theory proposed that among such sequences, those best at copying themselves will produce more copies of themselves than those that copy less frequently.

Most complex organisms have hundreds of millions to billions of letters of DNA. Since having slightly more DNA has a negligible effect on one's ability to survive and reproduce, natural selection does not differentiate between organisms where transposons have produced several more copies.  Since "only very precise deletion can be non-lethal,"[[doolittle-1980]] these copying sequences spread much faster than they are removed.  Because of this process, proponents of evolutionary theory proposed that the bulk of large genomes are made up of such selfish genes:


Richard Dawkins, 1976

The simplest way to explain the surplus DNA is to suppose that it is a parasite, or at best a harmless but useless passenger.[[dawkins-1976]]


Ford Doolittle, 1980
Biochemist and member of the National Academy of Sciences.

It is inevitable that natural selection of the special sort we call non-phenotypic will favor the development within genomes of DNAs whose only "function" is survival within genomes.[[doolittle-1980]]


Sydney Brenner, 1998
Biologist, nobel laureate for his work on the genetic code.

the molecular processes generating extra DNA outpace those getting rid of it.[[brenner-1998]]


John Avise, 2010
Evolutionary geneticist, member of the National Academy of Sciences.

[Mobile elements] have come to be present in such great abundance because they have found mechanistic ways to proliferate within host genomes.[[avise-2010]]


Dan Graur, 2012
Evolutionary and molecular biologist

the vast majority of transposons in the human genome are merely parasites, parasites of parasites, and dead parasites.[[graur-2012]]

4. Trial and Error

Evolution must "try" many useless sequences of DNA before it can find a few successful ones, and these failed remnants will remain genomes because (like selfish genes) selection to remove them is very weak:


Susumu Ohno, 1972

The creation of every new gene must have been accompanied by many other redundant copies [...] Triumphs as well as failures of nature's past experiments appear to be contained in our genome.[[ohno-1972]]


Ken Miller, 1994
Cell and molecular biologist, activist against intelligent design.

In fact, the genome resembles nothing so much as a hodgepodge of borrowed, copied, mutated, and discarded sequences and commands that has been cobbled together by millions of years of trial and error against the relentless test of survival.[[miller-1994]]


Dan Graur, 2012
Evolutionary and molecular biologist

The tinkerer [of evolution] […] manages with odds and ends. What he ultimately produces is generally related to no special project, and it results from a series of contingent events, of all the opportunities he had to enrich his stock with leftovers."[[graur-2012]]

Large amounts of junk DNA were also argued for two reasons that do not directly relate to evolutionary theroy:

5. The C-value paradox

A C-value is the quantity of all DNA in an organism's genome.  Some organisms have genomes much larger or smaller than other organisms of similar complexity, so it was assumed the extra DNA in large genomes wasn't necessary:

David E. Comings, 1972

Some organisms have an unreasonable excess of DNA, clearly more than they require.[[comings-1972]]


Francis Crick, 1980

It seems totally implausible that the number of radically different genes needed in a salamander is 20 times that in a man.[[crick-1980]]


Carl Sagan, 1993

The DNA instructions for making a human being comprise some 4 billion nucleotide pairs, while those for a one-celled amoeba contain 300 billion nucleotide pairs.  There is little evidence that amoebae are almost a hundred times more "advanced" than humans"[[sagan-1993]]


Dan Graur, 2012
Evolutionary and molecular biologist

Why does an onion need a genome that is about five times larger than ours?"[[graur-2012]]


T. Ryan Gregory, 2014
Evolutionary and genome biologist

A human genome contains eight times more DNA than that of a pufferfish but is 40 times smaller than that of a lungfish.[[gregory-2014]]

6. "It seems unused"

Only around 1.5 to 2.9% of the DNA in mammals directly specifies which amino acids to assumble into proteins.  It was assumed that most of the remaining DNA wasn't copied into RNA, and in places where RNA was produced it was often assumed the RNA didn't do anything.  Some argued (and still argue) that repetitive sequences and transposons fall into this category:

Francis Crick, 1980

The majority of DNA sequences in most higher organisms do not code for protein since they do not occur at all in messenger RNA.  Nor is it very plausible that all this extra DNA is needed for gene control, although some portion of it surely must be.[[crick-1980]]


Michael Shermer, 2006
Historian of evolutionary theory, chief editor of Skeptic Magazine.

Rather than being intelligently designed, the human genome looks more and more like a mosaic of mutations, fragment copies, borrowed sequences, and discarded strings of DNA that were jerry-built over millions of years of evolution.[[shermer-2006]]


PZ Myers, 2008
Developmental biologist, well known ID critic

Go for the gusto and ask them what their god was thinking when he loaded up your genome with the molecular equivalent of styrofoam packing peanuts[[myers-2008]]


T. Ryan Gregory, 2014

The majority of human DNA consists of repetitive, mutationally degraded sequences.[[gregory-2014]]

Skeletal DNA

However not all proponents of evolutionary theory argued that genomes were mostly junk.  A minority argued that large amounts of DNA were useful as "skeletal DNA"--to increase the size of the cell nucleus as well as spacing between functional regions.  Although being used as spacer is not how most biologists define DNA function.


Thomas Cavalier-Smith, 1980

It seems more reasonable to suppose that large cells actually require more DNA than do small ones... larger cells require more rRNA transport to the cytoplasm per cell cycle than do smaller cells [...] This could be done by increasing the amount of skeletal DNA so as to increase the nuclear surface area and the number of nuclear pores [...] much of it may be selfish in the restricted sense of having no sequence-specific function.[[cavalier-smith-1980]]


Gabriel Dover, 1980

it is known from several species groups that chromosome arms increase proportionally in length as species accumulate more DNA, e.g. in salamanders.  This might be a reflection of some process [...] that requires that certain regions of the genome should be kept as separable unique entities [...] we should not abandon all hope of arriving at an understanding of the manner in which some sequences might affect the biology of organisms in completely novel and somewhat unconventional ways.[[dover-1980]]

But it seems no notable proponents of evolutionary theory argued that anything more than a small percentage of DNA had specific sequences or was used for anything more than a spacer.  If it can be shown otherwise this article will be amended.

ID proponents predicted very little junk DNA

In recent years much more function has been discovered in human DNA.  Genomicist and ENCODE researcher John Stamatoyannopoulos wrote in 2012, "I don’t think anyone would have anticipated even close to the amount of sequence that ENCODE has uncovered that looks like it has functional importance."[[stamatoyannopoulos-2012]]  Yet proponents of intelligent design predicted that genomes would contain very little junk DNA long before then:

Michael Denton, 1986
Biochemist and early modern intelligent design proponent

As it is, even without any sort of recombinational expansion, there is sufficient DNA in higher organisms to specify for more than one million genes.  With so much DNA it is obvious that, by exploiting recombinational possibilities, the total number of genes could be expanded to a figure far in excess of one million.[[denton-1986]]

We now know there's certainly not one million protein-coding genes, but Denton's use of "gene" refers to a functional region of DNA in general, just as Ford Doolittle used the term in his 1980 paper.[[doolittle-1980]]

Denton predicted again in 2002:

if it were true that the genomes of higher organisms contained vast quantities of junk, then the whole argument of this book would collapse. Teleology would be entirely discredited.  On any teleological model of evolution, most, perhaps all, the DNA in a genome of higher organisms should have some function [...]  While there is no doubt that at present no specific function can be attributed to most of the DNA in higher organisms, the idea that it is really junk is now under increasing attack.[[denton-2002]]


Forest M Mims III, 1994
A prolific[[Schlesinger-2008]] amateur scientist

A do-nothing string of NOPs [no operations] might appear as "junk code" to the uninitiated, but, when inserted in a program loop, a string of NOPs can be used to achieve a precise time delay.  Perhaps the "junk DNA" puzzle would be solved more rapidly if a few more computer scientists would make the switch to molecular biology.[[mims-1994]]


Michael Behe, 1996
Behe is a biochemist and leading intelligent design proponent. He wrote in response to Ken Miller's argument for junk DNA:

because we have not yet discovered a use for a structure does not mean that no use exists[[behe-1996]]


William Dembski, 1998
Mathematician and philosopher, among the earliest modern intelligent design proponents

On an evolutionary view we expect a lot of useless DNA. If, on the other hand, organisms are designed, we expect DNA, as much as possible, to exhibit function.[[dembski-1998]]


David Snoke, 2001
Physicist

A theory of design can in principle be predictive and quantitative [...] The good-design assumption leads to specific predictions and applications, e.g., the prediction that it is unlikely to find wires which take up metal and space but serve no purpose, with the application that studying any particular wire is likely to be useful.  A bad-design assumption (e.g. that the chip maker made many random circuits and then just picked out the ones that worked) would give very different predictions.[[snoke-2001]]

ID critics affirm that intelligent design predicts function

Some ID critics agree that intelligent design does indeed predicts that most DNA will be functional, and that such a prediction is the opposite of what's expected under evolutionary theory.


Ken Miller, 1994

The human genome is littered with pseudogenes, gene fragments, "orphaned" genes, "junk" DNA, and so many repeated copies of pointless DNA sequences that it cannot be attributed to anything that resembles intelligent design. If the DNA of a human being or any other organism resembled a carefully constructed computer program, with neatly arranged and logically structured modules each written to fulfill a specific function, the evidence of intelligent design would be overwhelming.[[miller-1994]]


Michael Shermer, 2006

We have to wonder why the Intelligent Designer added to our genome junk DNA, repeated copies of useless DNA, orphan genes, gene fragments, tandem repeats, and pseudo­genes, none of which are involved directly in the making of a human being.[[shermer-2006]]


PZ Myers, 2008

Much of our makeup is entirely by accident, and evolution is a story of filtered accidents. Creationists don’t like that — one of their central assumptions is that everything is purposeful — but don’t pander to their beliefs. Go for the gusto and ask them what their god was thinking when he loaded up your genome with the molecular equivalent of styrofoam packing peanuts[[myers-2008]]


Dan Graur, 2013

Turning the genome into a well oiled efficient machine in which every last nucleotide has a function is the dream of every creationist and IDiot (intelligent designer), so the frequent killing of junk DNA serves no good purpose.[[graur-2013b]]

If on the other hand organisms are designed, then all DNA, or as much as possible, is expected to exhibit function.[[graur-2013]]

How much functional DNA does ID predict?

The Abundant Functional DNA as Design Evidence article defines "strictly" and "loosely" functional DNA.

Under many ID models (especially those that reject common descent) it makes sense for most DNA to be at least loosely functional, and the amount of strictly functional DNA would likely be not far behind.  If evolution primarily degrades function, the percentage of functional DNA depends on how fast and how long it has been degrading.

The Age of Humans

This table shows the time estimated by various creation and ID groups since humans were created.

Age of Humans Groups
6,000 (years) Answers in Genesis, Creation Ministries International, Institute for Creation Research, and most other young earth creation groups.
50,000 to 150,000 Reasons to Believe,[[reasons-adam]] an old earth creation group
2,000,000 Casey Luskin and David Klinghoffer writing for the Discover Institute[[klinghoffer-2012]] (although views within the Discovery Institute vary).

A Simple Model

To calculate how much strictly functional human DNA has not already been destroyed, suppose the following:

  1. 25 years per human generation.
  2. 3 million functional units of 1000 nucleotides each, making a 3 billion DNA-letter genome.  Humans have two copies of each gene, so alternatively that would make 6 billion if we count both copies of each gene.
  3. 50 haploid (affecting one only set of genes) mutations per generation.  The total mutation rate is 100 mutations per generation,[[moran-2013]] so we divide that by two.
  4. 45 haploid mutations that persist from one generationto the next, assuming 5 are removed by natural selection.[[gibson-2011]]
  5. A 10% chance a mutation within a gene will destroy that gene.  Many mutations are neutral--having no effect on function, and others only slightly degrade the function of a gene.
  6. Most mutations are either neutral or only slightly deleterious,[[eyre-walker-2007]] [[lind-2010]] causing genes to slowly degrade across the entire population.  Then when a gene becomes entirely non-functional, selection is largely blind to the difference between it and a hightly degraded version of the same gene.

Multiplying the 45 haploid mutations times the 10% chance a mutaiton will destroy a gene gives 4.5 genes being destroyed each generation.  From there we can extrapolate:

Age of Humans Generations  Genes destroyed  Functional haploid genome Functional diploid genome
6,000 (years) 240 1,080 99.96% 99.999984%
10,000 400 1,800 99.94% 99.999964%
100,000 4,000 18,000 99.4% 99.9964%
1,000,000 40,000 180,000 94% 99.64%
6,000,000 240,000 1,080,000 66.67% 88.89%

The "functional diploid genome" column shows the odds of having both pairs in a set of genes broken.  If one among a pair of a genes is still functional, the gene is considered functional.

Caveats with These Models

  1. The results become more skewed further into the past, since when only 66% of the genome is functional, the deleterious mutation rate is reducted to 50 times 66%.
  2. Genes work together in complex, interacting networks.  Knocking out one pair of genes could make the entire network non-functional.  Conversely, unrelated genes may kick in to perform the same task as other genes that have failed.  This model accounts for neither phenomenon.

Other Models

In the Journal of Creation in 2008, botanist Alex Williams makes a more pessimistic estimate.   Based on estimated rates of gene loss and the percentage of critical genes, Williams calculates between 1200 and 1.5 million until humans accumulate too many mutations to survive.[[williams-2008]]

However, a less-involved form of design could give very different predictions. Perhaps a designer only seeded the first cells on earth, or that chemistry itself was designed to greatly increase the odds of life forming from non-living matter?  And then unguided evolution proceeded from there to create most of the life forms we see today.  If a designer only played such a modest role, then the bulk of larger genomes could be junk.

Perspectives change

As new research revealed higher-than-expected levels of function, some former junk DNA proponents changed their minds:


Francis Collins, 2010
Francis Collins was the former head of the human genome project and currently heads the National Institutes of Health. He wrote:

The discoveries of the past decade, little known to most of the public, have completely overturned much of what used to be taught in high school biology.  If you thought the DNA molecule comprised thousands of genes but far more 'junk DNA', think again.[[collins-2010]]

Also in 2015:

I would say, in terms of junk DNA, we don't use that term any more 'cause I think it was pretty much a case of hubris to imagine that we could dispense with any part of the genome as if we knew enough to say it wasn't functional. There will be parts of the genome that are just, you know, random collections of repeats, like Alu's, but most of the genome that we used to think was there for spacer turns out to be doing stuff and most of that stuff is about regulation and that's where the epigenome gets involved, and is teaching us a lot.[[collins-2015]]

Richard Dawkins, 2012

I have noticed that there are some creationists who are jumping on [the 2012 ENCODE results] 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 [...] we thought only a minority of the genome was doing something, mainly that minority which only codes for protein, and now we find that actually the majority of it is doing something.  What it's doing is calling into action the protein coding genes. [...] The program that's calling them into action is the rest that had previously been written off as junk.[[dawkins-jonathan-sacks]]

Thomas Gingeras, 2012
A lead ENCODE researcher (paraphrased in the New York Times)

The thought before the start of the [ENCODE] project, was that only 5 to 10 percent of the DNA in a human being was actually being used. The big surprise was not only that almost all of the DNA is used but also that a large proportion of it is gene switches.[[kolata-2012]]

Richard Dawkins' own selfish gene theory led to the expectation that most of the human genome was junk,[[dawkins-1976]] [[doolittle-1980]] [[avise-2010]] [[graur-2012]] while neutral theory and the problem of genetic load require it outright.  So it doesn't make sense for Dawkins to say "it's exactly what a Darwinist would hope for."

Even shortly before the landmark ENCODE phase 2 announcement of 80% function in 2012, biochemist and junk DNA proponent Larry Moran blogged that most evolutionary biologists he meets no longer share his view:

In my opinion, the evidence for massive amounts of junk DNA in our genome is overwhelming but I struggle to convince other scientists of this ... I recently attended a meeting of evolutionary biologists and I'm pretty sure that the majority still don't feel very comfortable with the idea that 90% of our genome is junk.[[moran-2012]]

Other functional genome researchers expect even more functions to be found in the future:

Ewan Birney, 2012

Birney led the analysis group for the ENCODE project.

It’s likely that 80 percent [estimate of functional human DNA] will go to 100 percent. We don’t really have any large chunks of redundant DNA. This metaphor of junk isn’t that useful.[[yong-2012]]

John Mattick, 2013

John Mattick is a non-coding DNA researcher who heads the Garvan Institute in Australia, a lab of ~750 staff.

Where tested, these [differentially expressed] noncoding RNAs usually show evidence of biological function in different developmental and disease contexts, with, by our estimate, hundreds of validated cases already published and many more en route, which is a big enough subset to draw broader conclusions about the likely functionality of the rest.[[mattick-2013]]

The junk DNA mindset impeded scientific progress

Because evolutionary theory predicted that the majority of large genomes would be non-functional, researchers rarely studied DNA beyond that which directly created proteins.  Many now recognize how this harmed scientific progress, such as in understanding the genetic causes of disease:


W. Wyat Gibbs

The failure to recognize the full implications of this--particularly the possibility that the intervening noncoding sequences may be transmitting parallel information in the form of RNA molecules--may well go down as one of the biggest mistakes in the history of molecular biology.[[gibbs-2003]]

Wojciech Makalowski, 2007
Molecular biologist

[T]he term "junk DNA" repelled mainstream researchers from studying noncoding genetic material for many years[[makalowski-2007]]


Mark Mehler, 2008
Clinical neurologist

"The math just doesn't add up...There's just not enough molecular diversity" in proteins to create the complexity of the brain. "For a while, I despaired of ever being able to even think about this in my lifetime in a rational way," Mehler says. Then he heard about noncoding RNA.[[mehler-2008]]


Edward Trifonov, 2010
Molecular biophysicist known for discovering additional codes in DNA.  From a presentation:

I consider that these publications [the 1980 papers advocating junk DNA by Doolittle, Sapienza, Crick, and Orgel] are bordering with crime [borderline-criminal] because they completely misled scientific community so that all the messages carrying by the noncoding sequences have been ignored since then--30 years.[[trifonov-2010]]

 Trifonov's accompanying slide read:

These two papers inflicted an immense damage to biological sciences.[[trifonov-2010]]


Lawrence Hurst, 2013
Evolutionary geneticist

Intergenic DNA was dismissed as irrelevant junk and many transcripts are presumed to be just so much noise... Early gene therapy trials were, for example, halted owing to unforeseen knock-on consequences of gene insertion.[[hurst-2013]]

Although others (including many of the junk DNA proponents quoted above) still maintain that the large majoirty of human DNA is non-functional.

Abundant Functional DNA is Evidence of Design
This companion article presents data indicating humans have large amounts of functional DNA and that evolution cannot account for it.

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