A word about "junk DNA".

“It seems as though ‘junk DNA’ has become a legitimate jargon in a glossary of molecular biology. Considering the violent reactions this phrase provoked when it was first proposed in 1972, the aura of legitimacy it now enjoys is amusing, indeed.”

- Ohno and Yomo, 1991


The origin of “junk DNA”

Two main problems struck Susumu Ohno as particularly important in his seminal work on the genetics of evolutionary diversification. The first was the lack of correspondence between genome size (amount of DNA) and morphological complexity (taken as a proxy for gene number), which was a prominent topic of discussion in the early 1970s. As he noted in 1972, “If we take the simplistic assumption that the number of genes contained is proportional to the genome size, we would have to conclude that 3 million or so genes are contained in our genome. The falseness of such an assumption becomes clear when we realize that the genome of the lowly lungfish and salamanders can be 36 times greater than our own” (Ohno 1972a). In fact, Ohno and his colleagues were well aware that much of the DNA in the mammalian genome could not code for proteins, lest the mutational load become fatally high (e.g., Comings 1972; Ohno 1972b, 1974).

The second problem related to the conservative force of purifying selection and the limitations it places on the diversification of species. Ohno (1973) attempted to kill both of these vexatious birds with a single conceptual stone:

The points I wish to make are: 1) Natural selection is an extremely conservative force. So long as a particular function is assigned to a single gene locus in the genome, natural selection only permits trivial mutations of that locus to accompany evolution. 2) Only a redundant copy of a gene can escape from natural selection and while being ignored by natural selection can accumulate meaningful mutation to emerge as a new gene locus with a new function. Thus, evolution has been heavily dependent upon the mechanism of gene duplication. 3) The probability of a redundant copy of an old gene emerging as a new gene, however, is quite small. The more likely fate of a base sequence which is not policed by natural selection is to become degenerate. My estimate is that for every new gene locus created about 10 redundant copies must join the ranks of functionless DNA base sequence. 4) As a consequence, the mammalian genome is loaded with functionless DNA.

The corpulent genomes of dipnoans and urodele amphibians were similarly thus accounted for under this view: “Lungfish and salamanders clearly show the tragic consequences of exclusive dependence upon tandem duplication” (Ohno 1970, p.96). Of course, this differs from current thinking about lungfish and salamander genome size, but that’s another story.

To Ohno, this situation not only permitted, but also paralleled, the evolution of life at large. As he put it, “The earth is strewn with fossil remains of extinct species; is it any wonder that our genome too is filled with the remains of extinct genes?” (Ohno 1972a). The primary outcome of this gene duplication mechanism would not be the generation of new genes, but the deactivation of redundant copies – just as extinction has been the fate of more than 99% of species that have ever lived (Raup 1991). Once purifying selection ceased to shelter gene sequences from change, they would be free to mutate and, if one imagines a set of three gene copies initially sharing the same sequence, it is likely that “in a relatively short time, two of the three duplicates would join the ranks of ‘garbage DNA’” (Ohno 1970, p.62).

In Ohno’s usage, as in the vernacular, “garbage” refers to both the loss of function and the lack of any further utility (it was once useful, but now it isn’t). “Garbage DNA” proved to be an unsuccessful meme, but its essence remains
in the wildly popular term coined by Ohno two years later – “junk DNA”. Thus, as Ohno (1972b) stated, “at least 90% of our genomic DNA is ‘junk’ or ‘garbage’ of various sorts”. Interestingly, Ohno mentioned “junk DNA” only in the titles of two of his papers (1972a, 1973), and invoked the term only once in passing in a third (1972b). Comings (1972), on the other hand, gave what must be considered the first explicit discussion of the nature of “junk DNA”, and was the first to apply the term to all non-coding DNA.

There are several independent mechanisms by which non-coding DNA can accumulate in the genome. Gene duplication and deactivation is one such mechanism, but this, we now know, applies to only a minority of the non-coding sequences. Nevertheless, the term “junk DNA” was used in some early general descriptions of non-coding elements, including heterochromatin. For example, Comings (1972) noted that:

It has frequently been suggested that the DNA of genetically inactive heterochromatin represents the degenerate and useless DNA of the genome. However, heterochromatin rarely constitutes more than 20% of the genome. This suggests that there are two categories of junk DNA, (1) DNA of constitutive heterochromatin which is neither transcribed nor translated, and (2) nonheterochromatic junk DNA which is probably transcribed, but not translated. This distinction adds one more dimension to the mystery of heterochromatic DNA. Why is it singled out to be nontranscribable when being nontranslatable seems adequate for most of the junk DNA? Perhaps there is clustered junk (heterochromatic DNA) and nonclustered junk, just as there is clustered repetitious DNA (satellite DNA) and nonclustered repetitious DNA.


Later, Ohno himself began applying the term “junk” to heterochromatic, intergenic, and intronic sequences: “Much of this junk DNA occurs as large heterochromatin blocks, often localized in pericentric regions of mammalian chromosomes, or as intergenic spacers and intervening sequences within genes.” (Ohno 1985).

It is clear, however, that Ohno (1982) believed all these sequences were produced by gene duplication:

This great preponderance of intergenic spacers in the euchromatic region is due mostly to the extreme inefficacy of the mechanism of gene duplication as a means of creating new genes with altered active sites. For every redundant copy of the pre-existent gene that emerged triumphant as a new gene, hundreds of other copies must have degenerated to join the rank of junk DNA.


This mechanism alone was considered capable of explaining the vast intergenic regions of eukaryotic genomes. According to Ohno (1985):


Indeed, the abundance of pseudogenes (recent degenerates) attests to the inefficacy of gene duplication as a means of acquiring new genes with novel functions. The net consequence of hundreds of millions of years of continuous gene duplication is the desertification of the euchromatic region of modern vertebrates; the average distance between still functioning gene loci becoming progressively longer.


Junk DNA, function, and non-function

“Junk DNA” had a specific meaning when it first was formulated. It was meant to describe the loss of protein-coding function by deactivated gene duplicates, which in turn were believed to constitute the bulk of eukaryotic genomes. As different types of non-coding DNA were identified, the concept of gene duplication as their source – and therefore “junk DNA” as their descriptor – found new and broader application. However, it is now clear that most non-coding DNA is not produced by this mechanism, and is therefore not accurately described as “junk” in the original sense.

The term “pseudogene” — the technical term for functionless gene copies — was not coined until 1977 (Jacq et al. 1977), and the more explicit definition of these sequences that specified non-function in terms of protein-coding emerged almost a decade later. So, although Ohno’s original description of “junk DNA” obviously involved what are now called “pseudogenes”, there was no initial requirement for non-function. As Comings (1972) put it, “Being junk doesn’t mean it is entirely useless. Common sense suggests that anything that is completely useless would be discarded.” (This is what Sydney Brenner meant by the distinction between “trash” or “rubbish”, which one throws away, and “junk”, which one keeps; Brenner 1998). Of course, Ohno did reject the notion of protein-coding function for the extinct genes. As he described it, “a functional gene locus is defined as that DNA base sequence which may sustain deleterious mutations”, and from this it followed that “a DNA base sequence in which all sorts of mutational changes are permissible is obviously not contributing to the well-being of an organism, and for this very reason, it has no function” (Ohno 1973). On the other hand, and in the same publication, Ohno (1973) suggested a different role for non-coding DNA: “The bulk of functionless DNA in the mammalian genome may serve as a damper to give a reasonably long cell generation time (12 hours or so instead of several minutes)”.

From the very beginning, the concept of “junk DNA” has implied non-functionality with regards to protein-coding, but left open the question of sequence-independent impacts (perhaps even functions) at the cellular level. “Junk DNA” may now be taken to imply total non-function and is rightly considered problematic for that reason, but no such tacit assumption was present in the term when it was coined.

Two groups of people, though maximally divergent in their reasons for so doing, have been driven by a philosophical need to identify functions for all n
on-coding DNA. The first includes strict adaptationists, among whom it was often assumed that all non-coding DNA, by virtue of its very existence, must be endowed with some as-yet-unknown function of critical importance: “The very fact that amplified sequences have been maintained, withstanding rigours of selection, indicates some adaptive significance” (Sharma 1985).

We may also consider the following discussion comments recorded at the end of Ohno (1973):

Yunis: “This is what I emphasized earlier, that this DNA must have a functional value since nothing is known so widespread and universal in nature that has proven useless.”

Fraccaro: “Well, there is an exception to that rule. A lot of us have permanent positions at the University but are considered by others (mainly by students) meaningless and of no utility whatsoever.”


These examples aside, it seems likely that most evolutionary biologists today could tolerate a conclusion, if such were rendered, that a significant fraction of non-coding DNA is functionless
. This is not true of the second group in question, compared to whom the passion for function is unrivaled. As Dawkins (1999) suggested, “creationists might spend some earnest time speculating on why the Creator should bother to litter genomes with untranslated pseudogenes and junk tandem repeat DNA”. In fact, many have done so (e.g., Gibson 1994; Wieland 1994; Batten 1998; Jerlström 2000; Walkup 2000; Woodmorappe 2000; Bergman 2001). Although apparently “not enough is yet known about eukaryotic genomes to construct a comprehensive creationist model of pseudogenes” (Woodmorappe 2000), the theme that undergirds all of these discussions is that all non-coding DNA must, a priori, be functional.

To satisfy this expectation, creationist authors (borrowing, of course, from the work of molecular biologists, as they do no such research themselves) simply equivocate the various types of non-coding DNA, and mistakenly suggest that functions discovered for a few examples of some types of non-coding sequences indicate functions for all (see Max 2002 for a cogent rebuttal to these creationist confusions). Case in point: a few years ago, much ado was made of Beaton and Cavalier-Smith’s (1999) titular proclamation, based on a survey of cryptomonad nuclear and nucleomorphic genomes, that “eukaryotic non-coding DNA is functional”. The point was evidently lost that the function proposed by Beaton and Cavalier-Smith (1999) was based entirely on coevolutionary interactions between nucleus size and cell size.

Those who complain about a supposed unilateral neglect of potential functions for non-coding DNA simply have been reading the wrong literature. In fact, quite a lengthy list of proposed functions for non-coding DNA could be compiled (for an early version, see Bostock 1971). Examples include buffering against mutations (e.g., Comings 1972; Patrushev and Minkevich 2006) or retroviruses (e.g., Bremmerman 1987) or fluctuations in intracellular solute concentrations (Vinogradov 1998), serving as binding sites for regulatory molecules (Zuckerkandl 1981), facilitating recombination (e.g., Comings 1972; Gall 1981; Comeron 2001), inhibiting recombination (Zuckerkandl and Hennig 1995), influencing gene expression (Britten and Davidson 1969; Georgiev 1969; Nowak 1994; Zuckerkandl and Hennig 1995; Zuckerkandl 1997), increasing evolutionary flexibility (e.g., Britten and Davidson 1969, 1971; Jain 1980; reviewed critically in Doolittle 1982), maintaining chromosome structure and behaviour (e.g., Walker et al. 1969; Yunis and Yasmineh 1971; Bennett 1982; Zuckerkandl and Hennig 1995), coordingating genome function (Shapiro and von Sternberg 2005), and providing multiple copies of genes to be recruited when needed (Roels 1966).

Does non-coding DNA have a function? Some of it does, to be sure. Some of it is involved in chromosome structure and cell division (e.g., telomeres, centromeres). Some of it is undoubtedly regulatory in nature. Some of it is involved in alternative splicing (Kondrashov et al. 2003). A fair portion of it in various genomes shows signs of being evolutionarily conserved, which may imply function (Bejerano et al. 2004; Andolfatto 2005; Kondrashov 2005; Woolfe et al. 2005; Halligan and Keightley 2006). On the other hand, the largest fraction is comprised of transposable elements — some of which become co-opted by the host genome, some of which play major role in generating genomic variation, some of which may be involved in cellular stress response, and yet others of which remain detrimental to host fitness (Kidwell and Lisch 2001; Biémont and Vieira 2006). The upshot is that some non-coding DNA is most certainly functional — but when it is, this usually makes sense only in an evolutionary context, particularly through processes like co-option. More broadly, those who would attribute a universal function for non-coding DNA must bear the following in mind: any proposed function for all non-coding DNA must explain why an onion or a grasshopper needs five times more of it than anyone reading this sentence.

Should “junk” be thrown out?

There is nothing wrong with a word taking on a new meaning as knowledge changes – that is, unless reference to an original (and outmoded) sense lingers as a source of confusion, or the term expands so much as to lose contact with an initially accurate definition. Indeed, even the term “evolution” is technically a misnomer since its etymology implies an “unfolding”, as of a pre-determined developmental program (see Bowler 1975). The objection raised here is not to terms that change in usage per se, but to those whose shifting usage involves collecting or retaining unwanted conceptual baggage. This is especially relevant when the baggage is toted surreptitiously (note that no serious biologist takes “evolution” to mean a pre-determined unfolding but that ideas of inherent “progress” have been almost impossible to shake; see Gould 1996; Ruse 1996).

“Junk DNA”, which originally was coined in reference to now-functionless gene duplicates (i.e., true broken-down “junk”), is now used as “a catch-all phrase for chromosomal sequences with no apparent function” (Moore 1996). Its current usage also implies a lack of function which is accurate by definition for pseudogenes in regard to protein-coding, but which does not hold for all non-coding elements. The term has deviated from or outgrown its original use, and its continued invocation is non-neutral in its expression – and generation – of conceptual biases.

“Junk DNA” is not the only offender. Non-coding DNA has been called by many names that have had the same pejorative undertones (intentional or not) implying uselessness, if not outright wastefulness. Examples include excess DNA (Zuckerkandl 1976; Doolittle and Sapienza 1980), surplus or nonessential or degenerate or silent DNA (Comings 1972; Gilbert 1978), quiet DNA (Lefevre 1971), garbage DNA (Ohno 1970), non-informational or nonsense DNA (Ohno 1972b), worthless DNA (Ohno 1973), trivial DNA (Ohno 1974), vestigial DNA (Loomis 1973), redundant DNA (Vinogradov 1998), supplementary DNA (Hutchinson et al. 1980), secondary DNA (Hinegardner 1976), and incidental DNA (Jain 1980).

As Gould (2002, p.503) stated, “A rose may retain its fragrance under all vicissitudes of human taxonomy, but never doubt the power of a name to shape and direct our thoughts”. Because it is generally no longer applied in its original meaningful sense, because the type of DNA to which it actually relates now has a more descriptive name (pseudogenes), and because of its connotations of total phenotypic inertness, the term “junk DNA” should probably be abandoned in favour of less subjective terminology. “Non-coding DNA” serves this purpose quite well.

Concluding remarks

It is an exciting time in genome biology. Aspects of genomic form and function that were largely inconceivable only a few decades ago are now being revealed on a daily basis. It should come as no surprise (and indeed, it probably does not) that new roles are being discovered for non-coding DNA and that some of yesterday’s buzzwords — including “junk DNA” — are destined for the dustbin. However, extrapolating each report that a given small segment of DNA may be functional to mean that all non-coding DNA is vital is as counterproductive as dismissing non-coding DNA as totally non-functional. Genomes are complex, and there is little use in approaching them from a simplistic point of view.

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Update: At Sandwalk, Larry Moran argues that the term “junk DNA” is “a good term”, “an accurate term”, and “a useful term”. You can read my response in the comments section of the original post or in my re-post on this blog.



12 comments to A word about "junk DNA".

  • Chris Harrison

    This clears up a lot of things for me Dr. Gregory. Looking forward to more of your posts.
    Thanks.

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  • TR Gregory

    You’re quite welcome. I poached this from something I had written years ago but never published, so it’s pretty formal and full of quotes. I intend to do more user-friendly discussions of junk DNA and other issues in the near future, once I can find some time to prepare them.

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  • edhensley

    Thank you for your excellent explanation of junk DNA and the history of the term. I look forward to reading your blogs in the future.

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  • Steve Murphy MD

    All that junk DNA and no comment on copy number variation. What do think we will say about junk DNA 20-30 years from now when we know more about CNV?
    Steve
    http://www.thegenesherpa.blogspot.com

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  • TR Gregory

    As far as we know thus far, copy number variants (CNVs) account for at most a 0.5% differences in genome size among individuals. I wrote about them here.

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  • Dr. Andras J. Pellionisz

    The “Junk” DNA expression as a scientific term is “officially dead at 35 years”. (After the announcement of the results of the pilot (1%) program of ENCODE; see also featured at http://www.junkdna.com )

    Dr. Gregory’s contribution is greatly appreciated not only from the viewpoint of history, but particularly his reduction of the former “c-value paradox” to “c-value enigma” and with his 2001 paper to “c-value explanation”.

    Perhaps one addition may be appropriate to Dr. Gregory’s analysis. Most believe that one of the synonymes of “junk DNA”; “regulatory DNA” is something that evolved AFTER Dr. Onho’s coining the “junk DNA” phrase in 1972.

    Fact is, that “regulatory DNA” (that was “non-coding”) appeared much earlier than the “framing” that Dr. Ohno did on the Genome.

    Most notable is the 1961 discovery (and 1965 Nobel) for regulatory “Operons” (by Jacob and Monod) – but one may go as far back as in the 1920-30 period of Barbara Mcclintock’ “transposons” -althought her official recognition by Nobel was much delayed; to a large extent precisely because modern Genetics framed “non-genes” as “junk”.

    Personal recognition is not the issue. “Framing science” is a more important problem (as it also happened, e.g. when Artificial Intelligence “framed” Neural Networks and thus retarded its development as a robust field of research).

    Finally, in case of “Junk DNA” the truly inexcusable delay cost the lives of uncounted millions of people who actually suffered and died of “junk DNA diseases” – their research was set back by decades. (See http://www.junkdna.com/junkdna_diseases.html)

    pellionisz_at_junkdna.com

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  • Andras

    In “The Scientist” (July) Editor-in-Chief Richard Gallagher published an Editorial, titled “Junk Worth Keeping”: http://www.the-scientist.com/2007/7/1/15/1/
    (subscription only, but it is also available at http://www.junkdna.com)

    Clearly, Gallagher retires “Junk DNA” as a scientific term, but suggests to keep it as a catchy moniker.

    While one would agree on his point as a journalist (“keep things interesting”), how about those suffering from “junk DNA diseases”?

    IMHO it is in the interest of the general public, since any of us at any time may be affected by some of these dreadful diseases, that the “non-gene”, “post-gene” (or whatever you call the 98.7% of human DNA) gets proper attention via dedicated funding.

    IPGS http://www.postgenetics.org serves as an instrument to collectively better achieve our goals.

    pellionisz_at_junkdna.com

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  • Anonymous

    What does “lest the mutational load become fatally high” mean? Is this implying some maximum number of proteins an organism can make? Or does it mean that the observed variation due to junk DNA would be impossible for coding DNA?

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  • Dane

    The position of L. J. Gibson and many other creationists is mischaracterized in the following statement:

    “[T]he theme that undergirds all of these [creationist] discussions is that all non-coding DNA must, a priori, be functional.”

    In the Gibson article you reference he states:

    “In retrospect, it seems perfectly reasonable to expect most DNA sequences, as well as organs, to have some function. One of the rules of nature seems to be that structures that are not useful tend to become lost. This is not to say that all DNA sequences must have a function. Copying errors, unequal crossing over and disruptive transposition all may contribute to the accumulation of useless DNA sequences. Many pseudogenes may indeed be junk DNA. However, the argument that particular DNA sequences must not have a function because we haven’t discovered any function for them is an argument from silence. To conclude that pseudogenes are junk DNA seems premature.” (the Gibson article referenced is freely available on the web at: http://www.grisda.org/origins/21091u.htm)

    Creationists may have an expectation of functionality (at least at one time) in DNA sequences, but this is not effectively different from the adaptationist approach of many evolutionary biologists. This expectation of functionality has been explored and questioned in creationist literature. For example, see: http://www.grisda.org/origins/53007.pdf. One big question relates to how “function” is defined. Richard Dawkins’ “Selfish Gene” hypothesis simply moves the function from the fitness of the organisms to the propagation of DNA sequences. Creationists eschew this reductionist approach and tend to argue that the function of a DNA sequence most likely ORIGINALLY played some function related to fitness, although presupposing the intentions of God may assume more than is knowable.

    Dawkins responds with theological arguments based on two presuppositions: 1) When the function of a DNA sequences is unknown, it genuinely has no adaptive function (thus it is “selfish DNA” and nothing else) and 2) God would not have included DNA sequences that do not contribute to fitness. Both presuppositions are open to question, as is the strawman argument that from a creationist perspective, “all non-coding DNA must, a priori, be functional.”

    Junk DNA is well accommodated within creationist thinking by noting that God can do whatever He likes. It is only when a very specific theology is applied to God, one in which He does only what we think He should do, that issues may arise. Further more, most Christian creationists embrace a theological view in which a once perfect creation is now damaged as a result of sin. Thus, after the perfect creation genuine junk DNA can well have accumulated cluttering up genomes.

    Ultimately the whole concept of junk DNA hinges on a very difficult argument from a negative. The temptation to brandish junk DNA as evidence for evolution and against creation has proven too much for many and leaves their arguments vulnerable to every published instance of functionality in once junk DNA.

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