The onion test.

I am not sure how official this is, but here is a term I would like to coin right here on my blog: “The onion test”.

The onion test is a simple reality check for anyone who thinks they have come up with a universal function for junk DNA. Whatever your proposed function, ask yourself this question: Can I explain why an onion needs about five times more non-coding DNA for this function than a human?

The onion, Allium cepa, is a diploid (2n = 16) plant with a haploid genome size of about 17 pg. Human, Homo sapiens, is a diploid (2n = 46) animal with a haploid genome size of about 3.5 pg. This comparison is chosen more or less arbitrarily (there are far bigger genomes than onion, and far smaller ones than human), but it makes the problem of universal function for non-coding DNA clear1.

Further, if you think perhaps onions are somehow special, consider that members of the genus Allium range in genome size from 7 pg to 31.5 pg. So why can A. altyncolicum make do with one fifth as much regulation, structural maintenance, protection against mutagens, or [insert preferred universal function] as A. ursinum?

Left, A. altyncolicum (7 pg); centre, A. cepa (17 pg); right, A. ursinum (31.5 pg).


There you have it. The onion test. To be applied to any ambitious claims that a universal function has been found for non-coding DNA.

____________

1 Some non-coding DNA certainly has a function at the organismal level, but this does not justify a huge leap from “this bit of non-coding DNA [usually less than 5% of the genome] is functional” to “ergo, all non-coding DNA is functional”.


64 comments to The onion test.

  • this didn’t help because i just the answer about how much DNA does an onion have

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  • “I think this will come to be a classic story of orthodoxy derailing objective analysis of the facts, in this case for a quarter of a century,” Mattick says. “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.” = John S. Mattick quoted in W. Wayt Gibbs, “The Unseen Genome, Gems Among the Junk,” Scientific American, November, 2003

    Although catchy, the term ‘junk DNA’ for many years repelled mainstream researchers from studying noncoding DNA. Who, except a small number of genomic clochards, would like to dig through genomic garbage? However, in science as in normal life, there are some clochards who, at the risk of being ridiculed, explore unpopular territories. Because of them, the view of junk DNA, especially repetitive elements, began to change in the early 1990s. Now, more and more biologists regard repetitive elements as a genomic treasure.” – Wojciech Makalowski, “Not Junk After All,” Science, Vol. 300(5623):1246-1247, May 23, 2003

    “It has recently been shown that many proteins are unfolded in their functional state. In addition, a large number of stretches of protein sequences are predicted to be unfolded. It has been argued that the high frequency of occurrence of these predicted unfolded sequences indicates that the majority of these sequences must also be functional. These sequences tend to be of low complexity. It is well established that certain types of low-complexity sequences are genetically unstable, and are prone to expand in the genome. It is possible, therefore, that in addition to these well-characterised functional unfolded proteins, there are a large number of unfolded proteins that are non-functional. Analogous to ‘junk DNA’ these protein sequences may arise due to physical characteristics of DNA. Their high frequency may reflect, therefore, the high probability of expansion in the genome. Such ‘junk proteins’ would not be advantageous, and may be mildly deleterious to the cell.” – Simon C Lovell, “Are non-functional, unfolded proteins (‘junk proteins’) common in the genome?,” FEBS Letters, Vol. 554(3):237-239, November 20, 2003

    Science Daily article from May 21 titled, “‘Junk’ DNA Has Important Role, Researchers Find,” found a function or transposons, which of course are another common type of repetitive DNA:

    Researchers from Princeton University and Indiana University who have been studying the genome of a pond organism have found that junk DNA may not be so junky after all. They have discovered that DNA sequences from regions of what had been viewed as the “dispensable genome” are actually performing functions that are central for the organism. They have concluded that the genes spur an almost acrobatic rearrangement of the entire genome that is necessary for the organism to grow.

    It all happens very quickly. Genes called transposons in the single-celled pond-dwelling organism Oxytricha produce cell proteins known as transposases. During development, the transposons appear to first influence hundreds of thousands of DNA pieces to regroup. Then, when no longer needed, the organism cleverly erases the transposases from its genetic material, paring its genome to a slim 5 percent of its original load.

    A May 30 news article on Science Daily observes that “tandem repeats” are now thought to have function, even though we used to think they were “useless trash”:

    “Scientists used to believe that most of the DNA outside of genes, the so-called non-coding DNA, is useless trash that has sneaked into our genome and refuses to leave. One commonly known example of such ‘junk DNA’ are the so-called tandem repeats, short stretches of DNA that are repeated head-to-tail. “At first sight, it may seem unlikely that this stutter-DNA has any biological function,” says Marcelo Vinces, one of the lead authors on the paper. “On the other hand, it seems hard to believe that nature would foster such a wasteful system.”

    “A geneticist, Susumu Ohno, was the first to coin the term “junk” DNA in 1972.He used the term to refer to pseudogenes (commonly thought of as defunct relatives of known genes that do not code for proteins), but with time its meaning broadened to include all non-coding DNA (DNA that does not contain genes and does not produce proteins).1 Ohno stated, “The earth is strewn with fossil remains of extinct species; is it a wonder that our genome too is filled with the remains of extinct genes?”1 Due to his evolutionary presupposition, he assumed that non-coding DNA was merely a “genetic fossil” that may have been useful somewhere in our evolutionary past but had been discarded as we evolved into more complex, higher organisms. Since this “junk” DNA was no longer needed, it would not be under selective pressure, and mutations could accumulate without any harm to the organism.

    Unfortunately, for many years this notion that non-coding DNA was not functional (“junk”) actually inhibited science. Many scientists didn’t spend their time studying it because of their evolutionary presuppositions that it was worthless DNA. It is rather an ironic situation, since many times creationists are accused of inhibiting science because of their presuppositions (the God-did-it-so-there’s-nothing-more-to-study idea; but in reality, it’s just the opposite—“God did it” so we have every reason to study it!). Creationists for many years have argued that non-coding DNA is not junk (see “Junk” DNA Is Not Junk) because of their presupposition that God intelligently designed all DNA and it does have a purpose (granting that DNA has been negatively affected by the curse and some of its original functions may have been lost).” – Dr. Georgia Purdom on August 22, 2007

    https://answersingenesis.org/genetics/junk-dna/junk-dna-past-present-and-future-part-1/

    Evolution theory has held back the advancement of genetics because of the materialistic view evolutionists have of all things biological and their denial of design. Because of this, they believe that almost all of the DNA is junk, and despite the amazing array of discoveries that verify that there is no part of the genome of any organism that is actually junk, evolutionists continue to cling to this absurd and grossly outdated, scientifically refuted concept.

    “The molecular taxonomists. who have been drawing up evolutionary histories (phylogeny) for nearly every kind of life, are going to have to undo all of their years of “Junk DNA”-based historical reconstructions and wait for the full implications to emerge before they try again.” – Linda Walkup, molecular biologist, referring to junk DNA and retroviruses

    “The human genome is pervasively transcribed, such that the majority of its bases are associated with at least one primary transcript and many transcripts link distal regions to established protein-coding loci.” – Identification and analysis of functional elements in 1% of the human genome by the ENCODE pilot project, Nature 447, 799-816 (14 June 2007) | doi:10.1038/nature05874; Received 2 March 2007; Accepted 23 April 2007
    http://www.nature.com/nature/journal/v447/n7146/full/nature05874.html

    “Should we be retiring the phrase “junk DNA” now? Yes, I really think this phrase does need to be totally expunged from the lexicon. It was a slightly throwaway phrase to describe very interesting phenomena that were discovered in the 1970s. I am now convinced that it’s just not a very useful way of describing what’s going on.” – Ewan Birney of the European Bioinformatics Institute in Cambridge, England, led the analysis by the more than 400 ENCODE scientists who annotated the genome http://www.scientificamerican.com/article.cfm?id=hidden-treasures-in-junk-dna

    An integrated encyclopedia of DNA elements in the human genome
    http://www.nature.com/nature/journal/v489/n7414/full/nature11247.html
    The vast majority (80.4%) of the human genome participates in at least one biochemical RNA- and/or chromatin-associated event in at least one cell type. Much of the genome lies close to a regulatory event: 95% of the genome lies within 8?kilobases (kb) of a DNA–protein interaction (as assayed by bound ChIP-seq motifs or DNase I footprints), and 99% is within 1.7?kb of at least one of the biochemical events measured by ENCODE.

    In 1988 two papers were published in Nature, one by Leslie Orgel and Francis Crick, and one by Carmien Sopience and Carlisle Doolittle, which claimed that most of the human DNA was junk, largely because it does not code for protein.

    In 1998 Eugenie Scott made the claim that speudogenes are non-functional.

    Prior to 1998 evolutionists called sequences of DNA that had no apearent function “pseudogenes and declared them to be “junk DNA”. This has been proven false since 1998 as it has been learned that what have been called “pseudogenes” by evolutionists are not sequences of DNA that have no function.

    Fruit Fly gene DSCAM produces 38,016 different proteins.

    “We now know based on both genetic studies, based on experimental studies that many so-called psedugenes don’t code for proteins but they have important function in chromosome biology, such as the way a chromosome fiber folds, and they may also code for RNAs which are spliced and regulate other RNAs which make other proteins.” – Richard Sternberg, geneticist

    According to Dr. John Greally of the Albert Einstein College of Medicine, New York, ‘It would now take a very brave person to call non-coding DNA junk.’ Andy Coghlan, ‘Junk’ DNA Makes Compulsive Reading, New Scientist 13 June 2007.

    Some sequences of information once called “junk DNA” are now known to necessary for the correct growth of embryo to baby and the subsequent correct working of the body is the timing of protein production: the right genes must be switched on at the right times so as to produce the right amount of the right proteins when they are needed. Increasingly, it is being discovered that the DNA controlling the use of genes lies in areas formerly deemed ‘junk’.

    It is now known that one gene often produces many different proteins, and the ‘junk DNA’ interspersed within the gene contains information needed to facilitate this (p. 41). Moreover, ‘junk DNA’ can modify the way chromosomes (packages of DNA) are organized, thus changing the way the DNA functions (p. 44). Some genes, formerly deemed to be functionless and therefore labeled ‘pseudogenes’, have now been found to function, and actually produce proteins. Other ‘pseudogenes’ are now known to switch off genes when they are not needed, or to increase their use, when more proteins are required.

    Many ‘junk DNA’ sequences have been found to be the same in very different creatures. For example, some sequences are the same in both humans and mice. Evolutionists would say that humans and mice have these similar sequences because they inherited them from a common ancestor. However, if they were really junk it is most unlikely that they would have retained their similarity over millions of years of independent evolution. This is because, again, natural selection would not act on junk so as to preserve it from degradation by mutation

    “First, our studies provide convincing evidence that the genome is pervasively transcribed, such that the majority of its bases can be found in primary transcripts, including non-protein-coding transcripts, and those that extensively overlap one another.”
    Gina Kolata, “Bits of mystery DNA, far from ‘junk,’ play crucial role,” The New York Times, September 5, 2012.

    Ewan Birney, ENCODE’s Lead Analysis Coordinator, said, “It’s likely that 80 percent will go to 100 percent.”
    Ed Yong, “ENCODE: the rough guide to the human genome,” Discover Magazine, September 5, 2012.

    Decades ago, Orgel and Crick wrote: “In summary, then, there is a large amount of evidence which suggests, but does not prove, that much DNA in higher organisms is little better than junk.”

    “The complexity of our biology resides not in the number of our genes but in the regulatory switches,” – Eric Green, director of the National Human Genome Research Institute and collaborator on the ENCODE project, in a press briefing September 5, 2013

    ENCODE Project Writes Eulogy for Junk DNA http://www.sciencemag.org/content/337/6099/1159.summary

    ENCODE – The Junk DNA concept must be consigned to history http://www.arn.org/blogs/index.php/literature/2012/09/10/encode_the_junk_dna_concept_must_be_cons

    “These findings reveal there are secrets within the genomes of humans and other animals that scientists are still uncovering, and the old belief that life has useless junk DNA is more false than ever, scientists added.” http://science.nbcnews.com/junk-dna

    Weird molecular hoops dispel ‘junk DNA’ myth http://science.nbcnews.com/_news/2013/03/01/17147699-weird-molecular-hoops-dispel-junk-dna-myth?lite

    “Junk” DNA Holds Clues to Common Diseases http://www.scientificamerican.com/article.cfm?id=junk-dna-encode

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