#and my prof told me to look at 2-3 examples to prove my points

[hashtag-anthems]

alright we're doing it lads we are writing an academic paper about bg3

[judgestarling]

The Origin of the Term “Junk DNA”: A Historical Whodunnit (Second Edition)

As textbooks would have it, the term “junk DNA” was coined in 1972 by Susumu Ohno as part of his work on the role of gene and genome duplication. I met Susumu Ohno at a meeting in Crete many years ago, and the way I remember, he told me that he “deliberately” chose a “provocative term” to emphasize the “uselessness” of this DNA fraction. (Indeed, the term “junk” comes with a “semantic baggage” since it used as a synonym for heroin and male genitalia—two terms that are verboten in polite company.) At a dinner, Ohno also told me (and other newbies) that rosé wine is produced by mixing red and white wines.

I no longer believe either of these historical “narratives.”

It all started with my obsession to read very thoroughly every article that I quote, instead of relying on indirect references. In this day and age, in which articles are signed by hundreds of authors, the vast majority of whom don’t even bother to read their “own” publications, I stand out like a nigella seed in mayonnaise. This disorder is probably due to my association with Mina Graur, who is a historian who only trusts “primary sources.” Indeed, so strong is her belief in primary sources, that I am quite certain she wouldn’t even trust a textbook description of the double helix—she would want to read Watson and Crick’s (1953) article, as well as their notebooks, correspondences, and preliminary drafts, and if possible interview each and every one associated with the lab in Cambridge including the janitors. What can I say? She does NOT trust “secondary” sources!

For a few years, I engaged in a bitter fight with the quacks of the ENCODE Project over “junk DNA,” and to my dismay, I realized that I cannot find a copy of Susumu Ohno’s (1972) article “So much ‘junk’ DNA in our genome.” So, I started searching the net for the article. My searches led me to discover three publications from 1972 that mention “junk DNA.” The above-mentioned paper by Susumu Ohno, an article by David Comings, and a New Scientist commentary by Tim Hunt.

Solving the origin of Comings’ “junk DNA” was easy. He got it from Susumu Ohno, who was his colleague at City of Hope National Medical Center in Duarte, California. Indeed, Comings quotes two “in press” papers by Ohno. The most interesting thing about Comings’ article, however, is that his treatment of junk DNA is much more thorough and much more informative and much more considerate than Ohno’s cryptic article, in which the term “junk” is only mentioned in the title.

The origin of Tim Hunt’s “junk DNA” proved to be much more interesting. In 1972, the future Nobelist was a 29-year-old researcher at Cambridge trying to understand messenger RNA and the great amounts of DNA that never produce mRNA. In time, his research led him into a different area of study, and in 2001, Tim Hunt shared the Nobel Prize in Physiology and Medicine with Paul Nurse and Leland Hartwell. The work for which he was conferred the highest accolade in the sciences had nothing to do with either mRNA or junk DNA—the Nobel was in recognition of his discovery of proteins that control cell division.

In his 1972 commentary, Tim Hunt uses the term “junk DNA” to refer to “the large amount of nucleic acid that never finds its way out of the nucleus, which does not fit in with the old categories of genes and messages.” Note that Hunt’s 1972 “junk DNA” employs a mechanistic definition of junk DNA that is different from but not at odds with our current understanding of junk DNA as “useless and harmless.”

Where did Tim Hunt get the term? I sent him the following email.

“I have recently realized that although the late Susumu Ohno is credited solely with the coinage ‘junk DNA,’ he was not the only person to have used the term in 1972. In your ‘How mammals get the message’ in New Scientist, you have an entire section entitled ‘Why all that junk?’ In this section you mention “junk DNA.” I am curious whether (1) you got the term from Susumu Ohno, (2) he got it from you, (3) you coined it independently, or (4) you got it from a third person. I would greatly appreciate your help with this historical puzzle.”

The reply by Dr. Hunt was surprising.

“Gosh, yes! I did write that piece, and I never met Ohno. I got it from Sydney Brenner and/or Francis Crick—it was certainly current in Cambridge at the time. Maybe they got it from Ohno? You should ask Sydney.”

So, I wrote Dr. Brenner. The first sentence of his reply made the puzzle even more profound.

“I can confirm that we were using the idea of “junk” in the genome in the sixties at Cambridge.”

Really? The sixties? If the term was indeed current in the sixties, it is entirely possible that the term may have found its way into the literature and hasn’t been detected thus far. If it was there, I was determined to find it.

Enter Google Ngram, with which one can find short phrases in over 5.2 million books (published between 1500 and 2008) that have been digitized by Google.

With Google Ngram, I struck gold, a 1963 paper by Charles Ehret and Gérard de Haller entitled “Origin, development, and maturation of organelles and organelle systems of the cell surface in Paramecium.” The paper which was published in Journal of Ultrastructure Research is huge—42 pages and 86 figures. On page 39 it is written:

“While current evidence makes plausible the idea that all genetic material is DNA (with the possible exception of RNA viruses), it does not follow that all DNA is competent genetic material (viz. ‘junk’ DNA), nor that all Feulgen-positive material is active DNA.”

This was completely unexpected. Nine years before Susumu Ohno, two authors wrote about “junk DNA” in a casual manner without even bothering to explain what junk DNA is. If we assume that non-”competent genetic material” is the same as nonfunctional DNA, then their use of “junk DNA” was entirely modern. The problem was that I have never heard of the authors before. Who was Charles F. Ehret? Who was Gérard de Haller?

A little more digging revealed that Charles F. Ehret was a very important person, as evidenced by the fact that The Washington Post published an obituary on his death in 2007.

“Charles F. Ehret, 83, a scientist whose study of circadian rhythms led to a widely popular anti-jet lag regimen that improved the trips of untold numbers of world travelers, died February 24 of multiple illnesses at his home in Grayslake, Ill.

In more than 35 years of experimentation, Dr. Ehret found that the headaches, nausea, disorientation, fatigue, and malaise suffered by globe-trotters had almost nothing to do with thin air and the dizzying effects of supersonic speed, as was commonly assumed. Rather, jet lag is a matter of crossing too many time zones too quickly for the body to adjust. It can be ameliorated by adjusting eating, activity and sleep schedules according to a strict system that Dr. Ehret developed.”

A search of the literature revealed that the paper in Journal of Ultrastructure Research represented quite a detour in the scientific life of Dr. Ehret. With the exception of a 1948 paper in The Anatomical Record, entitled “The mating reaction of multimicronuclear monstrosities in Paramecium bursaria,” his entire research program dealt with circadian rhythms, jet lag, and light exposure.

Interestingly, Dr. Ehret worked on many different organisms which, according to The Washington Post, included “single-celled organisms, rats, his eight children, and volunteers.” Rats and eight children? That sounds like a winning combination!

The amount of information I could find on Gérard de Haller was quite minimal. He became Professor of Protistology at the University of Geneva in 1969. He mostly published in French, and the last known address for him was the Molecular Systematics Group at the University of Geneva. As far as I could ascertain, he published his last paper in 1993. In October, 2013, I wrote to the head of the Molecular Systematics Group, Jan Wojciech Pawlowski. He replied promptly.

“Prof. Gérard de Haller is a Honorary Professor of the University of Geneva. He was one of the jurors of my PhD thesis and the head of Protistology Laboratory since 1969. His specialty was the biology of ciliates. As far as I know he is still alive, although he is not scientifically very active since his retirement. I saw him last time about 2 years ago when he came to the University to participate in a ceremony for one of his younger assistants. He is still on the list of University Professors.

I was looking for more information about him but could not find anything more. However, I can easily find someone from his family who live in Geneva if this is necessary.”

In the end, the person who managed to find Gérard de Haller was Robert Hirt, Professor of Evolutionary Parasitology at Newcastle University. In May 2014, I got an email from Prof. de Haller.

“As far as I can remember, the first time we spoke of junk DNA was at a seminar with Werner Arber around 1958 or so, and I know that Eduard Kellenberger's department, where Werner was working, was in close contact with the big bosses of the raising DNA science [at Cambridge]. Unfortunately, that’s all I can remember, except that these were great times!

I asked Werner Arber, but he couldn’t add anything. He mentioned Francis Crick as a possible "inventor" of the term.”

At this point, I was quite certain that Ehret and de Haller did not invent the term “junk DNA.” They used it properly and in the right context, but it wasn’t theirs.

I wrote about my findings in my blog, and ended the article with an appeal.  

“In the manner of the appeals by Oxford English Dictionary, I would like to ask the readers: Do you have an earlier record of the term “junk DNA”? Please submit your evidence by email.”

Soon afterwards, an anonymous reader found an example of “junk DNA” from 1960.

“Following your example, I've been trying to find earlier "junk DNA" quotes using Google. I found this quote in the Year Book of the Carnegie Institution, Washington July 1, 1959- June 30, 1960 (Volume 59, page 278).

‘It is much more difficult to imagine how the different DNA’s could act as templates for the similar RNA’s. This is the problem that can be avoided most easily by considering a large part of the DNA to be junk.’”

The authors, however, did not like the concept of “junk DNA’, although they admitted that there were precedents.

“The idea that a large part of the nucleic acid is nonfunctional is repugnant. It seems unlikely that such an inefficient mechanism would have survived through evolution, although it must be remembered that enzyme molecules are very large in comparison with their active centers.”

The Carnegie Institution report was written by eight members of the Biophysics Group within the Department of Terrestrial Magnetism. Yes, “Terrestrial Magnetism”!

Several names stood out. Sadly, Richard Roberts died in 1980, Ellis Bolton in 2006, and Roy Britten in 2012. The person with which I was most familiar with was Roy Britten, who was was the discoverer of repeated DNA sequences in the genomes of eukaryotic organisms, and later studied their effects on the evolution of genomes. I have met Britten several times at scientific meetings, and if there was one thing clear, it was the fact that he was not a fan of “junk DNA.” When Roy Britten died in 2012 at the age of 92, his obituary in the journal Science was written by his close collaborator Eric Davidson.

So, I wrote to Eric Davidson, and got the following email.

“First off, I wouldn't exactly consider that citation as related to the later nonsense about junk DNA of the Leslie Orgel/Francis Crick variety. At Carnegie they were strictly concerned that year with the protein coding sequence load of the DNA, as seen through the lens of ribosome structure/function, without considering the function of mRNA and tRNA.

As for Roy, you are right, he couldn't stand the idea of junk DNA, but that was in reference to the Crick usage (which we heard about verbally all the time from him and others of his circle; in those days, late 60s and early 70s Roy and I were hotly involved in arguments about the organization of animal genomic DNA). Anyway, Roy could not possibly have been responsible for the Year Book citation you sent because that particular report concerned the year Roy wasn't even at Carnegie; he was in Denmark working on yeast. The Biophysics report then and in the succeeding few years at the Department of Terrestrial Magnetism was written by the senior people, Bolton and Roberts, I think mainly Bolton (with whom Roy did not get along particularly well in intellectual terms). Roy was then very junior in the hierarchy and he wrote his own report on that year's activity; it is very doubtful he could have inserted anything like that even ex post facto. So, I don't think it is a likely hypothesis that Roy originated that term in any way shape form or manner, then or later.”

Is it possible that Davidson was wrong and one of the authors of the Carnegie report did coin the term “junk DNA” as a pejorative? One such precedent comes to mind. In 1955, British cosmologist Fred Hoyle derided a theory by American physicist George Gamow and called it a ridiculous "Big Bang." The name stuck. As far as “junk DNA” is concerned, however, there is little evidence for the pejorative-nickname hypothesis.

Why did the Biophysics group at the Department of Terrestrial Magnetism at Carnegie found the concept of “junk DNA” to be repugnant in 1959? The historical context was explained to me by Alexander Palazzo from the University of Toronto.

“To understand this report, you need to remember that it was written two years before the discovery of mRNA. Back then it was believed that each gene made a separate RNA that got incorporated into a ribosome (i.e., ribosomal RNA). Thus, according to this model, each ribosome contained information within it to make a single protein. Of course, today we understand that ribosomes are only enzymes, and that the protein-information is contained in mRNA. But considering that >90% of cellular RNA is rRNA, their old faulty model is understandable.

The Roberts’ group was analyzing the length of E. coli rRNA. In the discussion they write about the size of proteins and note that some of these are very small. In contrast, there was too much rRNA in each ribosome. This discrepancy indicated that in these cases the additional RNA was likely non-functional. Interestingly, Roberts missed a critical fact that was pointed out by others—that rRNA was not large enough to code for certain large proteins (beta-galactosidase, for example).

Roberts' group also noted that all rRNAs looked the same, whereas the nucleotide composition of DNA varied considerably. Thus, some DNA must not code for ribosomal RNA and this is where they invoke the idea of junk DNA.

Note that a new form of RNA (messenger RNA) was recognized in a landmark paper by Brenner, François Jacob and Matthew Meselson in 1961 making this whole discussion moot. (And yes, I'm aware that James Watson's group also demonstrated the existence of mRNA…)”

How should I summarize my current understanding on the origin of “junk DNA”—the term and the concept?

First, there is evidence that the term “junk DNA” was already in use in the early 1960s (e.g., Aronson et al. 1960; Ehret and de Haller 1963). I am, however, almost certain that none of these authors coined the term. All clues point to Cambridge in the late 1950s. My guess is that the term originated with Francis Crick, but at present I have no evidence for this claim.

And what about Susumu Ohno? I was reminded by a reader that “a conceptual discovery is usually ascribed to one who first stuck his/her neck out to push the viewpoint.” It doesn't really matter who said what first. “We remember Charles Darwin, not because he discovered natural selection (and sexual selection) or because he was the first to propose that adaptive evolution is due to selection. Others, e.g., William Charles Wells, Patrick Matthew, James Cowles Prichard, William Lawrence, and John Sebright, may (or may not) have recognized evolution by natural selection long before him. It was Darwin, however, who staked his reputation on what was considered at the time a grave heresy. It is, of course, interesting that Hunt, Brenner, De Haller, Roberts and perhaps others toyed explicitly with the idea of "junk DNA" before 1972, not to mention others who may have entertained the same idea without calling it "junk." However, it was Susumu Ohno who stuck his neck out and put his reputation on the line by advocating a very unpopular and contentious idea.

In my latest book, I decided on the following phrasing:

“We have written evidence that the term “junk DNA” was already in use in the early 1960s (e.g., Aronson et al. 1960; Ehret and de Haller 1963); however, it was Susumu Ohno (1972, 1973) who formalized its meaning and provided an evolutionary rationale for its existence.”

Literature

Aronson AI, Bolton ET, Britten RJ, Cowie DB, Duerksen JD, McCarthy BJ, McQuillen K, Roberts RB. 1960. Biophysics. pp. 229–289. In: Year Book: Carnegie Institution of Washington. Volume 59. Lord Baltimore Press, Baltimore, MD.

Comings DE. 1972. The structure and function of chromatin. Adv. Hum. Genet. 3:237–431.

Ehret CF, G. Haller G. 1963. Origin, development and maturation of organelles and organelle systems of the cell surface in Paramecium. J. Ultrastruct. Res. 23:S1–S42.

Hunt T. 1972. How mammals get the message. New Scientist 18 May:373–375.

Ohno S. 1972. So much “junk” DNA in our genome. In: Smith HH (ed.) Evolution of Genetic Systems: Brookhaven Symposia in Biology. Gordon and Breach, New York. 23:366–370.  Ohno, S. 1973. Evolutional reason for having so much junk DNA. In: Pfeiffer RA (ed.) Modern Aspects of Cytogenetics: Constitutive Heterochromatin in Man. Schattauer Verlag, Stuttgart, Germany. pp. 169–180.

Watson JD, Crick F.HC. 1953. Molecular structure of nucleic acids: A structure for deoxyribose nucleic acid. Nature 171:737–738.