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Monday, October 21, 2013

Jukes to Crick on Junk DNA

Dan Graur discovered that the term "junk DNA" was commonly used in the 1960's—long before Susumu Ohno used "junk" in the title of his 1972 paper. This makes a lot of sense. Apparently the term was quite commonly used in Cambridge by people like Francis Crick and Sydney Brenner. (Perhaps you've heard of them?)

Graur found a 1963 paper that refers to "junk" DNA. This is the earliest known refencee to junk in the scientific literature. Read about his sleuthing at: The Origin of Junk DNA: A Historical Whodunnit.

Meanwhile, a person named "ShadiZl" commented on one my posts and pointed me to a letter from Thomas Jukes to Francis Crick in 1979. Jukes, you might recall, was no Darwinian. He was a proponent of Neutral Theory and random genetic drift. The letter is archived on the National Library of Medicine (USE) site under a section devoted to The Francis Crick Papers: Letter from Thomas H. Jukes to Francis Crick.

The letter is interesting because it reveals how casually the "insiders" talked about junk DNA and about the adaptationist misconception even as far back as 1979. This was when Gould and Lewontin published the "spandrels" paper. It also reveals how misguided the creationists are when it comes to the history of junk DNA. They still think that it was "Darwinists" who "predicted" junk DNA based on their view of natural selection. (Do not read this letter if you are irony-deficient. It will only confuse you.)
December 20, 1979

Dear Francis:

I am sure that you realize how frightfully angry a lot of people will be if you say that much of the DNA is junk. The geneticists will be angry because they think that DNA is sacred. The Darwinian evolutionists will be outraged because they believe every change in DNA that is accepted in evolution is necessarily an adaptive change. To suggest anything else is an insult to the sacred memory of Darwin.

This additive is so pervasive that if no reason can be found for an evolutionary change, it is necessary to invent one. Kimura points out that one author attributed the pink color of flamingos to protective coloration against the setting sun. This type of thinking carries over into people who sequence mRNA. They claim that differences between rabbit and human globin mRNAs are because each species has its own requirements for secondary structure.

Various people have tried to think up possible functions for the regions of DNA that do not code for anything as far as is known. Roy Britten says that such DNA has a regulatory function.

Actually, the scheme proposed by Britten about ten years ago was that occasionally events of saltatory duplication, took place, so that a great many copies of a short piece of DNA were made. As time went by, the composition of a family of identical copies became changed by drift, until the copies no longer closely resemble each other. Figure 55 of the article by Britten shows a diagram of a sort of "junk DNA generating system". I note that he says on page 105 "the rate of increase in DNA content per cell resulting from saltatory replication alone may prove to be embarrassingly large and a mechanism for the loss of DNA may have to be invoked". I gather that you agree with this.

I quoted you on drift in DNA in a talk that I gave at the symposium for Emil Smith (see enclosure). Your concept of "junk DNA" presumably includes this idea. I shall look forward to hearing more about it, and I have been asked by Die Naturwissenschaften to write an article on silent changes, so I hope I can include mention of your new manuscript when I start to write mine.

With best regards,

Thomas H. Jukes


Claudiu Bandea said...

I previously made the point that, when discussing the evolution of genome size, C-value enigma and "junk DNA", it would make sense to refer to the work and the ideas developed by the scholars in this field, including Michael Bennett, Thomas Cavalier-Smith, Ford Doolittle and Ryan Gregory. These scientists have dedicated most of their career to these issues, so they are in position to offer some relevant insights into these highly important issues. That doesn’t mean that their ideas and hypotheses should not be questioned, but they should be used as references in any informed discussions.

For example, in regard to the use and implications of the term “junk DNA”, here is what Ryan wrote:

“Not only is “junk DNA” an inappropriate moniker for noncoding DNA in general because of the minority status of pseudogenes within genome sequences, but it also has the unfortunate consequence of instilling a strong a priori assumption of total nonfunction.”

Ryan T. Gregory, The Evolution of the Genome, Elsevier/Academic Press, 2005 (

Newbie said...

Don't be naive! Evolutionists need "junk DNA" or people like Dan Graur will have no choice but to become creationists and Larry will have to rewrite his textbooks... lol

Mikkel Rumraket Rasmussen said...

Really? Did you even read the paper in the blogpost? How come the "Darwinists" despise the idea of junk DNA ?

Anonymous said...

No Louise, "evolutionists" don't need junk DNA (more about it below). Creationists, on the other hand, may or may not need junk not to be. It works ether way because creationists also have choices, only they don't realize it. Since creationism is about magic, whatever ad hoc explanation would work. It's only their false perception that evolutionists need junk that has them blind to the availability of their magic tricks. After all, gods are all about magic, and junk might as well be a magic trick. So what?

Evolution does not stand on its shoes for the presence or absence of junk. It is more that Darwin proposed natural selection, and the explanatory power of natural selection was an eye opener. I was blinded myself by the huge amounts of light coming from it. Wow! A huge amount of understanding came into my brain all of a sudden. No magic tricks needed at all! All by natural phenomena I could attest to exist myself. Yet, this very power made many of us, me included, expect that every aspect of nature would show signs of natural selection, and I rejected the idea of junk DNA for that very reason, because I could not understand how natural selection would allow for junk DNA to be there. It was until I properly understood that not everything has a selectionable effect that I understood how junk could accumulate regardless of natural selection, and that natural selection is but one aspect of evolutionary outcomes. Lots of details missing from my explanation, but you guys have it wrong. In my case, I could not care one bit if you reject your reason in exchange for god-did-it. I find the god hypothesis useless, retrograde, and obviously flawed. So, I care about how and how much junk there is for reasons that have nothing to do with IDiocy, but with science. If there was zero junk, then we would have an interesting puzzle. One leading to your god? Nah. That's not an explanation, but rather an excuse to keep yourself in the darkness.

See ya.

W. Benson said...

Larry, The guy pointed out by Kimura and cited by Jukes as a "Darwinist" who proposed that the pink coloration of flamingos is camouflage was an early 20th century naturalist-artist who, according to S. J. Gould, was considered "controversial", with "absurd" ideas regarding protective coloration in zebras and flamingos (see Roy R. Behrens. 2009. Philosophical Transactions of the Royal Society, B, 364: 497-501, Free). Because he rejected adaptationist interpretatins such as warning coloration (think wasps and coral snakes) and sexual displays (think peacocks), Thayer became bizarrely inventive. Quoting something like this as an argument against "Darwinists" certainly qualifies as "poisoning the well". We can do better than this, can´t we?