Junk DNA: The original ‘onion test’ is a biological non-sequitur

_{Denyse O'Leary

October 10, 2011

'Junk DNA', Darwinism}

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Probably in response to Nick Matzke here and here, proposing among other things an onion test. A friend of UD News writes to say,

Those who employ “the onion test” should recall that the test — as originally formulated by geneticist T. Ryan Gregory — asks for a “universal function” for non-coding DNA. Is this a biologically reasonable question to ask? No. As Jonathan Wells writes, in The Myth of Junk DNA (pp. 85-86):

The “onion test,” according to Gregory, “is a simply reality check for anyone who thinks they have come up with a universal function for non-coding 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?” [1]

Gregory directs his challenge to “anyone who thinks they have come up with a universal function for non-coding DNA.” Yet there probably is no such person. As we have seen, scientists know of many functions for non-protein-coding DNA. Nobody claims that there is “a universal function” that applies both to mammals and to onions. Based on the evidence, scientists have proposed that non-protein-coding intronic DNA helps to regulate alternative splicing in brain cells, and that non-protein-coding repetitive DNA plays a role in placental development. Why should those scientists justify their proposals by referring to onions, which have neither brains nor placentas?

See also: Thoughts on the “C-Value Enigma”, the “Onion Test” and “Junk DNA”

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Comments

You haven't been reading what I've written, I've already laid out the two major ideas in the scientific community, see here: https://uncommondescent.com/junk-dna/thoughts-on-the-c-value-enigma-the-onion-test-and-junk-dna/comment-page-1/#comment-402595 and here: https://uncommondescent.com/darwinism/the-original-onion-test-is-a-biological-non-sequitur/comment-page-1/#comment-402687NickMatzke_UD_{October 10, 2011
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Nick that is far from the ONLY question, and in my view is secondary to the question of what epigenetic mechanism is driving the variance.
You can't just toss around the word "epigenetics" like it means whatever poorly-specified notion is in your head. Saying that epigenetics determines genome size is a contradiction in terms -- epigenetics is what happens on top of the genome, e.g. methylation. If the genome size changes, that's genetics, straight-up.NickMatzke_UD_{October 10, 2011
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Nick this is OT, but in case your interested, Holly Ordway, a former atheist, is interviewed by Apologetics315 here; http://www.youtube.com/watch?v=uA4pho7QfVwbornagain77_{October 10, 2011
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Nick,
The only interesting question is whether or not some higher-level factor like selection favors particular genome sizes, and thus spreads insertions in some genomes, and deletions in others
You've just finished calling it junk. Maybe you're right. But why would selection favor either junk or specific genome sizes? If that were the case, then by definition the extra genes would be advantageous, therefore functional. This is true even if you overlook the circular logic that cannot distinguish between advantage and selection. Are you redefining natural selection so that it can "select" was does not affect differential reproduction? Or are you admitting that it's a tautology, defined as whatever survives, including enlarged genomes? Or are you saying that the enlarged genomes actually do provide a selectable advantage, contradicting everything you've just said before?ScottAndrews_{October 10, 2011
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Here's the answer to the onion test: Namely, that not all introns are functional. Many introns are functionless. Nevertheless, under a teleological perspective, the first introns were functional. Not all introns are functional because of whole-genome duplications. Let's say we have an onion with a small genome size. That genome is duplicated. There is no selective pressure to preserve the function of the duplicated introns (just like duplicated genes can often tolerate far more mutations than the original gene), and so the duplicated introns become functionless. Repeat this process several times and you have an onion population with a large genome size and large chunks of functionless introns. Nevertheless, the first introns were functional. This answers the onion test from a teleological context.LivingstoneMorford_{October 10, 2011
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Now who is being the lawyer Nick???bornagain77_{October 10, 2011
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as to this comment:
The only interesting question is whether or not some higher-level factor like selection
Nick that is far from the ONLY question, and in my view is secondary to the question of what epigenetic mechanism is driving the variance. For you to presuppose the variance is completely random is to completely ignore where the cutting edge science is at right now (Shapiro for one cite), And indeed I would hold you position to be a science stopper!bornagain77_{October 10, 2011
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I am just opposing the numerous statements of the ID movement to the effect that junk DNA was a stupid idea, that the genome is "chock-full" of digital code, and that most/all of the genome is functional. Gregory is making a narrow point about the confusing history of the term. He certainly does not, though, think it is valid to declare or assume that most/all of the genome has organismal function, especially some kind of sexy, informational function, which is what IDists usually imply. When I use the word "junk", I am referring to the "no very important function" position. The primary, and very, very, good, evidence for this position, is that it is manifestly true that some organisms have way more DNA than is really required to build them, and we know this for a fact because basically similar organisms (even the same genus, or sister species) have much, much less DNA. And atheist philosophy? Puh-lease. The Gnu Atheists bash me worse than you guys for not being on their side.NickMatzke_UD_{October 10, 2011
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This is true, but I believe the onion genome sizes are all haploid values, i.e. it is not a matter of diploids vs. tetraploids vs. hexaploids etc. The usual explanation for dramatic differences in genome size is self-replication of the repetitive elements. LINES, SINES, etc. can easily get copied again and again in the genome, blowing up its size. Genome size is determined by a balance between genome-growing elements such as LINES and SINES, and removal mechanisms like deletion. The only interesting question is whether or not some higher-level factor like selection favors particular genome sizes, and thus spreads insertions in some genomes, and deletions in others, or whether genome size is just a byproduct of e.g. population size, where extra DNA is always deleterious, but very mildly so, such that only in very large populations with rapid generation time is selection strong enough to favor the very weakly beneficial deletions.NickMatzke_UD_{October 10, 2011
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Petrushka, let's assume for a moment this is correct. What does it tell us about junk DNA generally? Not much. No-one disputes that duplications occur. This issue is that the iconic myth of "junk DNA" in humans has been shouted from the rooftops, over and over and over again, as a wonderful example of bad design and a confirmation of Darwinian evolution. That assessment has turned out to be spectacularly wrong, which, according to the Darwinists' own logic then, must operate as a *refutation* of the Darwinian mechanism. You can't have it both ways. Either junk DNA is irrelevant and never did support Darwinism in the first place, or it is relevant and has refuted Darwinism in the case of human junk DNA. Now the Darwinist lobby moves on to another example of what they think is junk DNA, in Nick's case, apparently misrepresenting what Gregory intended to say and making pronouncements without having the faintest idea whether the DNA is junk or not. The real kicker is that ID proponents don't dispute that machines break down, that code can get messed up, that errors can occur in the history of life. In contrast, the materialist cannot accept even a single example of design in the history of life, or his whole materialistic enterprise goes up in smoke. Some of us are willing to look at the world, realize some things are designed and others aren't, and then delve into the interesting question of whether and how we can detect which things are designed. The materialist can never even grasp this interesting question, because it lies beyond his philosophical blinders.Eric Anderson_{October 10, 2011
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Then why in blue blazes are you using the word 'junk DNA' to further your atheistic philosophy, instead of using “non-coding DNA” so Gregory suggests. But then again it is not about the science is it Nick??? It is about your religion!!!bornagain77_{October 10, 2011
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I myself noted this on the other thread: https://uncommondescent.com/junk-dna/thoughts-on-the-c-value-enigma-the-onion-test-and-junk-dna/comment-page-1/#comment-402596NickMatzke_UD_{October 10, 2011
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Blas, as with Petrushka's cite, all you are ever going to get from neo-Darwinists is misdirection that never addresses core questions such as what is the functionality for why the genome size is at it is.bornagain77_{October 10, 2011
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Perhaps a little thinking outside of the 'central dogma' box?
Picture: Thinking Outside The Box http://www.crystalinks.com/outsidebox.jpg
Notes:
Modern Synthesis of Neo-Darwinism (Genetic Reductionism) Is Dead - Paul Nelson - video http://www.metacafe.com/watch/5548184/
Also of interest in the following paper other than the quote that is excerpted, on page 22, is a simplified list of the ‘epigentic’ information flow in the cell that directly contradicts what was expected from the central dogma (Genetic Reductionism/modern synthesis) model of neo-Darwinism.
Revisiting the Central Dogma in the 21st Century - James A. Shapiro - 2009 Excerpt (Page 12): Underlying the central dogma and conventional views of genome evolution was the idea that the genome is a stable structure that changes rarely and accidentally by chemical fluctuations (106) or replication errors. This view has had to change with the realization that maintenance of genome stability is an active cellular function and the discovery of numerous dedicated biochemical systems for restructuring DNA molecules.(107–110) Genetic change is almost always the result of cellular action on the genome. These natural processes are analogous to human genetic engineering,,, (Page 14) Genome change arises as a consequence of natural genetic engineering, not from accidents. Replication errors and DNA damage are subject to cell surveillance and correction. When DNA damage correction does produce novel genetic structures, natural genetic engineering functions, such as mutator polymerases and nonhomologous end-joining complexes, are involved. Realizing that DNA change is a biochemical process means that it is subject to regulation like other cellular activities. Thus, we expect to see genome change occurring in response to different stimuli (Table 1) and operating nonrandomly throughout the genome, guided by various types of intermolecular contacts (Table 1 of Ref. 112). http://shapiro.bsd.uchicago.edu/Shapiro2009.AnnNYAcadSciMS.RevisitingCentral%20Dogma.pdf
Eugene Koonin also agrees that the modern evolutionary synthesis (Genetic Reductionism/Central dogma) is devastated.
The Origin at 150: is a new evolutionary synthesis in sight? - Koonin - Nov. 2009 Excerpt: The edifice of the modern synthesis has crumbled, apparently, beyond repair. http://www.arn.org/blogs/index.php/literature/2009/11/18/not_to_mince_words_the_modern_synthesis
Dr. Sternberg has also come out very hard against 'neo-Darwinian narratives';
On the roles of repetitive DNA elements in the context of a unified genomic-epigenetic system. - Richard Sternberg Excerpt: It is argued throughout that a new conceptual framework is needed for understanding the roles of repetitive DNA in genomic/epigenetic systems, and that neo-Darwinian “narratives” have been the primary obstacle to elucidating the effects of these enigmatic components of chromosomes. http://www.ncbi.nlm.nih.gov/pubmed/12547679
Further notes:
Deep Genomics: In the Case of DNA, the Package Can Be as Important as Its Contents, New Work With Fruit Flies Reveals - January 2011 http://www.sciencedaily.com/releases/2011/01/110113102158.htm Gene Regulatory Networks in Embryos Depend on Pre-existing Spatial Coordinates - Jonathan Wells - July 2011 Excerpt: The development of metazoan embryos requires the precise spatial deployment of specific cellular functions. This deployment depends on gene regulatory networks (GRNs), which operate downstream of initial spatial inputs (E. H. Davidson, Nature 468 [2010]: 911). Those initial inputs depend, in turn, on pre-existing spatial coordinate systems. In Drosophila oocytes, for example, spatial localization of the earliest-acting elements of the maternal GRN depends on the prior establishment of an anteroposterior body axis by antecedent asymmetries in the ovary. Those asymmetries appear to depend on cytoskeletal and membrane patterns rather than on DNA sequences,,, http://www.discovery.org/scripts/viewDB/filesDB-download.php?command=download&id=7751 “Live memory” of the cell, the other hereditary memory of living systems - 2005 Excerpt: To understand this notion of “live memory”, its role and interactions with DNA must be resituated; indeed, operational information belongs as much to the cell body and to its cytoplasmic regulatory protein components and other endogenous or exogenous ligands as it does to the DNA database. We will see in Section 2, using examples from recent experiments in biology, the principal roles of “live memory” in relation to the four aspects of cellular identity, memory of form, hereditary transmission and also working memory. http://www.ncbi.nlm.nih.gov/pubmed/15888340
verse and music:
Psalm 139:13 For you created my inmost being; you knit me together in my mother's womb. Live - Heaven (official video) http://www.youtube.com/watch?v=Ff3NUP-xzqQ
bornagain77_{October 10, 2011
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Whole genome duplications are common in plants, and have occurred in animals. http://en.wikipedia.org/wiki/PolyploidPetrushka_{October 10, 2011
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Shouldn´t darwinist explain first how one onion specie has 7 times the genome size of other onion specie from a common ancestor via RM + NS?Blas_{October 10, 2011
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Nick, Your statements are deeply rooted in assumptions. Maybe they are accurate assumptions. But why not question them?
If you’re going to claim, as ID advocates have again and again and again, that junk DNA is a crock, scientists were idiots for ever believing in such a thing, and most/all DNA is functional, you need to explain why some onions need multiple human genome’s worth of DNA more than other onions
You assume that there are only two possibilities. Either the onion needs the extra DNA to function, or it is junk. That assumption naturally follows from other assumptions. Maybe you're right on both counts. But it's odd that in a field dependent on boundless imagination that's all you can come up with.ScottAndrews_{October 10, 2011
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This is a interesting comment from Gregory, the originator of the onion test, at the bottom of the page:
The onion test. by T. Ryan Gregory, on April 25th, 2007 Excerpt: 1) I do not endorse the use of the term “junk DNA”, which I think has deviated far too much from its original meaning and is now little more than a loaded buzzword; the descriptive term “non-coding DNA” is what I use to refer to the majority of eukaryotic sequences (of various types) that do not encode protein products. - http://www.genomicron.evolverzone.com/2007/04/onion-test/
Are you listening Nick???bornagain77_{October 10, 2011
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Interesting. When the facts start getting inconvenient, bring out the lawyerly hair-splitting. Unfortunately the facts are still inconvenient for you. Most of the difference in genome sizes is typically due to repetitive elements. Gene counts etc. don't change very much even between genomes with hugely different sizes. If you're going to claim, as ID advocates have again and again and again, that junk DNA is a crock, scientists were idiots for ever believing in such a thing, and most/all DNA is functional, you need to explain why some onions need multiple human genome's worth of DNA more than other onions, and why onions in general have genomes many times the size of the human genome. Otherwise, the argument that a lot of the DNA in organisms with large genome isn't doing much is pretty strong. After all, you can build an onion with a few human genomes worth of DNA, so clearly building an onion with 20 human genomes worth of DNA is not strictly necessary.NickMatzke_UD_{October 10, 2011
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