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Onion Test

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The onion test is a way of assessing the validity of an argument for a functional role for non-coding DNA, sometimes called "junk DNA". It relates to the paradox that would emerge if the majority of eukaryotic non-coding DNA would be assumed to be functional and the difficulty of reconciling that assumption with the diversity in genome sizes among species.[1] The term "onion test" was originally proposed[2] informally in a blog post by T. Ryan Gregory in order to help clarify the debate about junk DNA. The term has been mentioned in newspapers and online media,[3][4] scientific journal articles,[5][6][7][8] and a textbook.[9] The test is defined as:

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?

Onions and their relatives vary dramatically in their genome sizes,[10] without changing their ploidy, and this gives an exceptionally valuable window on the genomic expansion junk DNA. Since the onion (Allium cepa) is a diploid organism having a haploid genome size of 15.9 Gb,[10] it has 4.9x as much DNA as does a human genome (3.2 Gb). Other species in the genus Allium vary hugely in DNA content without changing their ploidy. Allium schoenoprasum (chives) for example has a haploid genome size of 7.5 Gb, less than half that of onions, yet Allium ursinum (wild garlic) has a haploid genome size of 30.9 Gb, nearly twice (1.94x) that of onion and over four times (4.1x) that of chives. This extreme size variation between closely related species in the genus Allium is also part of the extended onion test rationale as originally defined:[2]

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?

C-value paradox

Some researchers argue that the onion test is related to wider issues involving the C-value paradox and is only valid if one can justify the presumption that genome size has no bearing on organismal physiology.[11] According to Larry Moran, the onion test is not an argument for junk DNA, but an approach to assessing possible functional explanations for non-coding DNA. According to him, it asks why allium species need so much more of that proposed function than do humans, and why so much more (or less) than other closely related species of allium and does not address the variation in genome size (C-value) among organisms itself.[12]

Criticism

According to Jonathan McLatchie, the onion test is only valid if one can justify the presumption that genome size has no bearing on organismal physiology. Long sequences of repetitive DNA can be highly relevant to an organism and can contribute to transcription delays and developmental timing mechanisms for an organism. Furthermore, he argues that there is a positive correlation between genome size and cell volume for unicellular eukaryotes like plants and protozoa and so the larger amount of DNA thus provides a selective advantage by contributing to the skeleton and volume of the nucleus of these cells.[11] McLathcie's representation of the onion test which refers to intelligent design advocate Jonathan Wells' The Myth of Junk DNA was published on the web pages of the anti-evolution/intelligent design-creationist Discovery Institute has been refuted by Larry Moran who was actually addressed in McLathie's post:[13]

[the onion test is] designed as a thought experiment to test a hypothesis about the possible function of large amounts of noncoding DNA. If you think you have an explanation for why most of the human genome has a function then you should explain how that accounts for the genomes of onions. Ryan Gregory knew that most so-called explanations look very silly when you try using them to account for genome size in onion species.

McLatchie made similar arguments at Uncommondescent.com another ID-creationist web site to which Nick Matzke replied:[14]

[...] the onion test is a challenge to the large group of people — lots of creationists/IDists, lots of journalists, some scientists, some cranks — who make bold declarations about how most/all DNA is functional and how stupid scientists were to ever think that a lot of it was junk. Your proposed function(s) had better be able to pass the Onion Test, or else you really haven’t got any evidence that most DNA is functional.

Ewan Birney (then head of the ENCODE Project) explained the difference as a product of polyploidy,[15][16] and therefore not relevant to the discussion of humans.

(re: onions etc); polyploidy and letting your repeats "go crazy" (bad piRNAs anyone) mean your genome can be v. big

Similar claims were made by John Mattick in an article defending the ENCODE project against arguments disputing the main finding of the project:[17]

The other substantive argument that bears on the issue, alluded to in the quotes that preface the Graur et al. article, and more explicitly discussed by Doolittle, is the so-called ‘C-value enigma’ , which refers to the fact that some organisms (like some amoebae, onions, some arthropods, and amphibians) have much more DNA per cell than humans, but cannot possibly be more developmentally or cognitively complex, implying that eukaryotic genomes can and do carry varying amounts of unnecessary baggage. That may be so, but the extent of such baggage in humans is unknown. However, where data is available, these upward exceptions appear to be due to polyploidy and/or varying transposon loads (of uncertain biological relevance), rather than an absolute increase in genetic complexity. Moreover, there is a broadly consistent rise in the amount of non-protein-coding intergenic and intronic DNA with developmental complexity, a relationship that proves nothing but which suggests an association that can only be falsified by downward exceptions, of which there are none known.

A reader left the following comment:[17]

IMO T. Ryan Gregory's onon test cited by Mattick is not so much about the fact that onion genomes are bigger than the human genome but rather about the fact that the sizes of the smallest and the biggest onion genomes differ by a factor of 5. One would have to claim different complexities for these onion species if one beleaves that most sequences are functional.

Some Allium species are tetraploid; however, the species often described in the onion test, including the onion itself, are diploid like humans. In the original extended onion test rationale,[2] Gregory used A. altyncolicum as an example of an exceptionally small (7pg, 6.9 Gb) Allium genome. This species is most likely tetraploid,[10] but this perhaps makes the case for highly variable genome size even more strongly, and could be easily replaced with other diploid species such as Allium schoenoprasum (chives,7.5 Gb).

References

  1. ^ Palazzo, Alexander F.; Gregory, T. Ryan (2014-05-08). Akey, Joshua M. (ed.). "The Case for Junk DNA". PLoS Genetics. 10 (5): e1004351. doi:10.1371/journal.pgen.1004351. ISSN 1553-7404. PMC 4014423. PMID 24809441. In summary, the notion that the majority of eukaryotic noncoding DNA is functional is very difficult to reconcile with the massive diversity in genome size observed among species, including among some closely related taxa. The onion test is merely a restatement of this issue, which has been well known to genome biologists for many decades.{{cite journal}}: CS1 maint: unflagged free DOI (link)
  2. ^ a b c "The onion test. « Genomicron". www.genomicron.evolverzone.com. Retrieved 2019-02-13.
  3. ^ Moran, Laurence A. (2011-10-12). "Sandwalk: A Twofer". Sandwalk. Retrieved 2019-02-13.
  4. ^ Zimmer, Carl (March 8, 2015). "Is most of our DNA garbage?". The New York Times Magazine.
  5. ^ Palazzo, Alexander F.; Gregory, T. Ryan (2014-05-08). Akey, Joshua M. (ed.). "The Case for Junk DNA". PLoS Genetics. 10 (5): e1004351. doi:10.1371/journal.pgen.1004351. ISSN 1553-7404. PMC 4014423. PMID 24809441.{{cite journal}}: CS1 maint: unflagged free DOI (link)
  6. ^ Freeling, Michael; Xu, Jie; Woodhouse, Margaret; Lisch, Damon (2015). "A Solution to the C-Value Paradox and the Function of Junk DNA: The Genome Balance Hypothesis". Molecular Plant. 8 (6): 899–910. doi:10.1016/j.molp.2015.02.009. PMID 25743198.
  7. ^ Germain, Pierre-Luc; Ratti, Emanuele; Boem, Federico (2014). "Junk or functional DNA? ENCODE and the function controversy". Biology & Philosophy. 29 (6): 807–831. doi:10.1007/s10539-014-9441-3. ISSN 0169-3867.
  8. ^ Graur, D.; Zheng, Y.; Price, N.; Azevedo, R. B. R.; Zufall, R. A.; Elhaik, E. (2013-03-26). "On the Immortality of Television Sets: "Function" in the Human Genome According to the Evolution-Free Gospel of ENCODE". Genome Biology and Evolution. 5 (3): 578–590. doi:10.1093/gbe/evt028. ISSN 1759-6653. PMC 3622293. PMID 23431001.
  9. ^ Graur, Dan (2016). Molecular and genome evolution. Sunderland, Massachusetts: Oxford University Press. ISBN 9781605354699. OCLC 951474209.
  10. ^ a b c Ricroch, A; Yockteng, R; Brown, S C; Nadot, S (2005). "Evolution of genome size across some cultivated Allium species". Genome. 48 (3): 511–520. doi:10.1139/g05-017. ISSN 0831-2796. PMID 16121247.
  11. ^ a b "Why the "Onion Test" Fails as an Argument for "Junk DNA"". Evolution News. 2011-11-02. Retrieved 2019-02-12.
  12. ^ Moran, Laurence A. (12 October 2011). "Sandwalk: A Twofer". Sandwalk.
  13. ^ Moran, Larry (2011-11-02). "Sandwalk: Jonathan M Flunks the Onion Test, Again". Sandwalk. Retrieved 2020-07-22.
  14. ^ "Thoughts on the "C-Value Enigma", the "Onion Test" and "Junk DNA" – Uncommon Descent". Retrieved 2020-07-22.
  15. ^ "https://twitter.com/ewanbirney/status/243497615134687232". Twitter. Retrieved 2020-07-20. {{cite web}}: External link in |title= (help)
  16. ^ "https://twitter.com/leonidkruglyak/status/243495391692197888". Twitter. Retrieved 2020-07-20. {{cite web}}: External link in |title= (help)
  17. ^ a b Mattick, John S.; Dinger, Marcel E. (2013-07-15). "The extent of functionality in the human genome". The HUGO Journal. 7 (1): 2. doi:10.1186/1877-6566-7-2. ISSN 1877-6566. PMC 4685169.{{cite journal}}: CS1 maint: unflagged free DOI (link) Text was copied from this source, which is available under a Creative Commons Attribution 2.0 (CC BY 2.0) license.
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