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 / |
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. |
||||
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" |
|||||
Christian de Duve, 1995[^duve-1995] |
x | x | x | "eukaryotic genome is made mostly of noncoding DNA without obvious function... Less than 5 percent of the human DNA has a coding function" | |||
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. |
||||
Philip Kitcher, 2007[^kitcher-2007] |
x |
x |
genomes are "full of" 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 describes 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:
- 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.
- 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.
Mootoo Kimura, 1968
|
|
|
Dan Graur, 2012
|
|
T. Ryan Gregory, 2014 Evolutionary and genome biologist.
|
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.
Jack King and Thomas Jukes, 1969 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
|
|
Susumu 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
|
|
Joseph Felsenstein, 2003
|
|
Dan Graur, 2012
|
|
T. Ryan Gregory, 2014
|
|
Larry 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
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
|
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
|
|
Ford Doolittle, 1980
|
Christian de Duve, 1995 To quote Dawkins: "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."[^duve-1995] Here Duve is citing the words of Dawkins. |
|
|
Sydney Brenner, 1998
|
John Avise, 2010
|
|
Dan 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
|
|
Ken Miller, 1994
|
|
Philip Kitcher, 2007
|
|
|
Dan 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
|
|
|
Francis Crick, 1980
|
|
Carl Sagan, 1993
|
Christian de Duve, 1995 Less than 5 percent of the human DNA has a coding function. Salamanders do much better--or worse, depending on one’s point of view. Some of these animals have twenty times more DNA than we have, with those in the west of the United States beating those in the east by severalfold.[^duve-1995] Duve seems to be echoing the words of Dawkins. |
|
|
Dan Graur, 2012
|
|
T. Ryan 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
|
|
Christian de Duve, 1995
Here Duve is citing the words of Dawkins. |
|
|
Michael Shermer, 2006
|
|
PZ Myers, 2008
|
|
T. Ryan 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
|
Gabriel 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
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:
|
|
|
Carl Wieland, 1994
|
|
Forest M Mims III, 1994
|
|
Michael Behe, 1996
|
|
William Dembski, 1998
|
|
David Snoke, 2001
|
|
Jonathan Sarfati, 2003
|
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
|
|
Michael Shermer, 2006
|
Philip Kitcher, 2007
|
|
|
PZ Myers, 2008
|
|
Dan 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-adam] | Reasons to Believe, an old earth creation group |
2,000,000 | Casey Luskin and David Klinghoffer writing for the Discovery 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:
- 25 years per human generation.
- 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.
- 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.
- 45 haploid mutations that persist from one generationto the next, assuming 5 are removed by natural selection.[^gibson-2011]
- 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.
- 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
- 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%.
- 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
Botanist Alex Williams makes a more pessimistic estimate in a 2008 Journal of Creation article. 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
Also in 2015:
|
Richard Dawkins, 2012
|
|
Thomas Gingeras, 2012 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, 2012Birney 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, 2013John Mattick is a non-coding DNA researcher who is the CEO of Genomics England, which runs the 100,000 genomes project. 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] In 2018, Mattick noted that more biologists were coming around to the idea that most DNA is not junk: While not everyone yet agrees with me, the evidence is very strong and my thesis is more widely accepted than it once was.[^mattick-2018] |
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:
John Mattick, 2003The failure to recognise the implications of the non-coding DNA will go down as the biggest mistake in the history of molecular biology.[^catalyst-2003] Mattick recognizes himself as: [T]he first to recognise that the human genome is not largely junk, but rather (that the 98.5% that does not code for proteins) specifies a massive hidden layer of regulatory RNAs that organise our development and provides the platform for brain function.[^mattick-2018] |
|
|
Wojciech Makalowski, 2007
|
|
Mark Mehler, 2008
|
|
Edward Trifonov, 2010
Trifonov's accompanying slide read:
|
|
Lawrence 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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Michael Lynch is a highly respected population geneticist. He
writes: "The neutral (or nearly neutral) theory that emerged from this work still
enjoys a central place in the field of molecular evolution" and "it is difficult to
reject the hypothesis that the basic embellishments of the eukaryotic gene originated
largely as a consequence of nonadaptive processes operating contrary to the expected
direction of natural selection."
Mirrors: Archive.is
- [^myers-2014]:Myers, PZ.
"The
state of modern evolutionary theory may not be what you think it is."
Pharyngula Blog. 2014.
PZ Myers is a developmental biologist well known for his criticisms of
Intelligent Design. Myers writes: "the revolution is over. Neutral and
nearly neutral theory won."
Mirrors: Archive.is - [^dodson-1962]:Dodson, Edward O.
"Note on the Cost of
Natural Selection." The American Naturalist. 1962.
JBS Haldane was an evolutionary biologist well known for his work
in developing the modern evolutionary synthesis. Calculating the implications of
Haldane's model, Dodson explains: "Haldane (1957) has published calculations which
indicate that it takes no less than 300 generations to replace a gene by ordinary
selection pressures, and that this evolutionary process cannot be speeded up by
simultaneous selection for more than one gene....we arrive at a maximum of something
over 200 gene substitutions over the past million years for the genus Homo." Since
on average the mutation rate is the fixation rate, 300 generations with about 100
mutations per generation would give 30,000 neutral mutations per 1 beneficial
mutation that fixes. 29,999 / 30,000 is 99.997% of fixed
mutatiosn being netural.
Mirrors: Local screenshot - [^moran-2014b]:Moran, Larry. Comment on "Breaking news: Creationist Vincent Torley lies and moves goalposts." Sandwalk Blog. 2014. Joe Felsenstein is a well known population geneticist who has published a criticism of Haldane's limit. When he and biochemist Larry Moran (both Intelligent Design critics) were asked to estimate the number of beneficial versus netural differences between human and chimps, they replied: "Updated numbers suggest 44 million point mutations and something like 2 million insertions/deletions for a grand total of 46 million mutations. We don't know how many of those were beneficial (adaptive) leading to ways in which modern chimps are better adapted than the common ancestor. (Same for humans.) My guess would be only a few thousand in each lineage." 1 - 3000 / 23,000,000 is 99.987% of fixed mutations being neutral.
- [^myers-2015]:Myers, PZ. "The Genetic Load Problem." Science Blogs. 2015.
- [^human-genome-2003]:"The Human Genome Project Completion: Frequently Asked Questions." National Human Genome Research Institute. 2003. The project estimated "30,000 genes" in the human genome, which would comprise about 3% of human DNA.
- [^gibson-2011]:Gibson et al. "Can Purifying Natural Selection Preserve Biological Information? " World Scientific. 2011. The authors simulate: "With a mutation rate of 10, almost half of all deleterious mutations were retained."
- [^sanford-2015]:Sanford, John. Response to Gerald Jellison. Amazon. 2015.
- [^comings-1972]:Comings, David E. "Advances in Human Genetics Volume 3, Chapter 5: The structure and function of chromatin." Springer. 1972.Mirrors: Local screenshot
- [^mattick-2013]:Mattick, John S. and Marcel E. Dinger. "The extent of functionality in the human genome." HUGO. 2013. Mirrors: Archive.is | Local excerpt with notes
- [^yong-2012]:Yong, Ed. "ENCODE: the rough guide to the human genome." Discover Magazine. 2012.
- [^kolata-2012]:Kolata, Gina. "Bits of Mystery DNA, Far From 'Junk,' Play Crucial Role." New York Times. 2012.
- [^duve-1995]:Duve, Christian de. "Vital Dust: Life as a Cosmic Imperative." 1995. Pages 222-223. Mirrors: Local screenshot
- [^kitcher-2007]:Kitcher, Philip. "Living With Darwin: Evolution, Design, and the Future of Faith." Oxford University Press. 2007. Pages 57-58. Mirrors: Local screenshot
- [^sarfati-2003]:Sarfati, Jonathan. "DNA: marvellous messages or mostly mess?" Creation Magazine. 2003.
- [^mattick-2018]:Mattick, John. "Meet Professor John Mattick, CEO at Genomics England." 2018. Mirrors: Archive.org
- [^wieland-1994]:Wieland, Carl. "Junk Moves Up in the World." Creation ex nihilo Technical Journal. 1994. Mirrors: Archive.org, Archive.is