Evolution Icon Evolution

The Onion Test Is a Red Herring

YellowOnions.jpg

Editor’s note: With the famous "Onion Test" back in the news (see here and here), readers may find useful the following excerpt from Jonathan Wells’s book, The Myth of Junk DNA (2011, Discovery Institute Press). For details of the references cited below, please consult the book.

In 2007, Canadian biologist T. Ryan Gregory wrote: "Some non-coding DNA is proving to be functional, but this is still a minority of the noncoding DNA, and there is always the issue of the onion test when considering all non-coding DNA to be functional."[22] The "onion test," according to Gregory, "is a simple 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?"[23]

The difference between the DNA content of an onion cell and that of a human cell is one piece of a larger puzzle called the "C-value paradox" or "C-value enigma."[24-�30] Biologists have long known that the DNA content (the "C-value") of eukaryotic cells varies by a factor of several thousand, with no apparent correlation to organismal complexity or to the number of protein-coding genes. There is a strong positive correlation, however, between the amount of DNA and the volume of a cell and its nucleus — which affects the rate of cell growth and division.[31-�32] Furthermore, in mammals there is a negative correlation between genome size and the rate of metabolism.[33] Bats have very high metabolic rates and relatively small genomes.[34�-35] In birds, there is a negative correlation between C-value and resting metabolic rate.[36�-37] In salamanders, there is also a negative correlation between genome size and the rate of limb regeneration.[38]

Gregory has written extensively on the C-value enigma,[39-�42] and various hypotheses have been proposed to explain it.[43-�48] One of those hypotheses attempts to explain the enigma by the accumulation of "junk DNA" or "selfish DNA," but — as Gregory himself has pointed out — that explanation cannot make sense of the correlations noted above.[49] "Under the traditional junk DNA and selfish DNA theories," Gregory wrote in 2005, "the relationship between genome size and cell size is considered purely coincidental." Since this approach is incapable of explaining the correlation between C-value and cell size, "the strictly coincidental interpretation has been rejected."[50]

But if Gregory rejects the accumulation of "junk DNA" as an explanation for the C-value enigma, why does he use the "onion test" to defend the notion that most non-protein-coding DNA is nonfunctional? Something peculiar is going on here. Let’s take a closer look at his reasoning.

First, 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?

Second, Gregory makes it clear that his true goal is to defend Darwinian evolution and attack intelligent design. One way he does this is by misrepresenting the latter. The same year he proposed the onion test he wrote that in order for ID to be considered scientific its proponents must "specify the basis for assuming that all non-coding DNA must be functional."[51] But ID proponents do not assume that all non-coding DNA must be functional. They infer that it is unlikely that most of our DNA would be nonfunctional; therefore, scientists should continue looking for functions.[52-�53]

Gregory misrepresents not only ID but also the logic of the argument. In 2007 he wrote: "It is commonly suggested by anti-evolutionists that recent discoveries of function in non-coding DNA support intelligent design and refute ‘Darwinism.’"[54] But Dawkins, Futuyma, Shermer, Collins, Kitcher, Miller, Coyne, and Avise argue exactly the opposite: They all claim that non-protein-coding DNA supports Darwinism and refutes intelligent design. It is THEIR claim that is the issue here — and "recent discoveries of function in non-coding DNA" refute it. Gregory stands the debate on its head.

So the onion test is a red herring. Why onion cells have five times as much DNA as human cells is an interesting question, but it poses no challenge to the growing evidence against the myth of junk DNA.

References Cited:

22. T. Ryan Gregory, “Junk DNA: let me say it one more time,” Genomicron (September 16, 2007). Freely accessible (2011) at http://www.genomicron.evolverzone.com/2007/09/junk-dna-let-me-say-itone-more-time/

23. T. Ryan Gregory, “The onion test,” Genomicron (April 25, 2007). Freely accessible (2011) at http://www.genomicron.evolverzone.com/2007/04/onion-test/

24. Roger Vendrely & Colette Vendrely, “La teneur du noyau cellulaire en acide d�soxyribonucl�ique � travers les organes, les individus et les esp�ces animales: Techniques et premiers resultants,” Experientia 4 (1948): 434-436.

25. A. E. Mirsky & Hans Ris, “The Desoxyribonucleic Acid Content of Animal Cells and Its Evolutionary Significance,” Journal of General Physiology 34 (1951): 451-462. Freely accessible (2011) at http://www.ncbi.nlm.nih.gov/pmc/articles/PMC2147229/pdf/451.pdf

26. C. A. Thomas, Jr., “The Genetic Organization of Chromosomes,” Annual Review of Genetics 5 (1971): 237-256.

27. Joseph G. Gall, “Chromosome Structure and the C-Value Paradox,” Journal of Cell Biology 91 (1981): 3s-14s. Freely accessible (2011) at http://jcb.rupress.org/content/91/3/3s.full.pdf

28. Gordon P. Moore, “The C-Value Paradox,” BioScience 34 (July/August 1984): 425-429.

29. Wen-Hsiung Li, Molecular Evolution (Sunderland, MA: Sinauer Associates, 1997), pp. 379-384.

30. Daniel L. Hartl, “Molecular melodies in high and low C,” Nature Reviews Genetics 1 (2000): 145-149.

31. Thomas Cavalier-Smith, “Nuclear volume control by nucleoskeletal DNA, selection for cell volume and cell growth rate, and the solution of the DNA C-value paradox,” Journal of Cell Science 34 (1978): 247-278. Freely accessible (2011) at http://jcs.biologists.org/cgi/reprint/34/1/247

32. Thomas Cavalier-Smith, “Cell Volume and the Evolution of Eukaryotic Genome Size,” pp. 105-184 in Thomas Cavalier- Smith (editor), The Evolution of Genome Size (Chichester, UK: John Wiley & Sons, 1985).

33. Alexander E. Vinogradov, “Nucleotypic Effect in Homeotherms: Body-Mass-Corrected Basal Metabolic Rate of Mammals Is Related to Genome Size,” Evolution 49 (1995): 1249-1259.

34. R. A. Van Den Bussche, J. L. Longmire & R. J. Baker, “How bats achieve a small C-value: frequency of repetitive DNA in Macrotus,” Mammalian Genome 6 (1995): 521-525.

35. Austin L. Hughes & Marianne K. Hughes, “Small genomes for better flyers,” Nature 377 (1995): 391.

36. Alexander E. Vinogradov, “Nucleotypic Effect in Homeotherms: Body-Mass Independent Resting Metabolic Rate of Passerine Birds Is Related to Genome Size,” Evolution 51 (1997): 220-225.

37. T. Ryan Gregory, “A bird’s-eye view of the C-value enigma: genome size, cell size, and metabolic rate in the class aves,” Evolution 56 (2002): 121-130.

38. Stanley K. Sessions & Allan Larson, “Developmental Correlates of Genome Size in Plethodontid Salamanders and their Implications for Genome Evolution,” Evolution 41 (1987): 1239-1251.

39. T. Ryan Gregory & Paul D. N. Hebert, “The Modulation of DNA Content: Proximate Causes and Ultimate Consequences,” Genome Research 9 (1999): 317-324. Freely accessible (2011) at http://genome.cshlp.org/content/9/4/317.full.pdf+html

40. T. Ryan Gregory, “Genome size and developmental complexity,” Genetica 115 (2002): 131-146.

41. T. Ryan Gregory, “The C-value Enigma in Plants and Animals: A Review of Parallels and an Appeal for Partnership,” Annals of Botany 95 (2005): 133-146. Freely accessible (2011) at http://aob.oxfordjournals.org/content/95/1/133.full.pdf+html

42. T. Ryan Gregory & J. S. Johnston, “Genome size diversity in the family Drosophilidae,” Heredity 101 (2008): 228-238.

43. Emile Zuckerkandl, “Gene control in eukaryotes and the c-value paradox ‘excess’ DNA as an impediment to transcription of coding sequences,” Journal of Molecular Evolution 9 (1976): 73-104.

44. Sean Luke, “Evolutionary computation and the c-value paradox,” Proceedings of the 2005 conference on Genetic and Evolutionary Computation (2005): 91-97.

45. Thomas Cavalier-Smith, “Economy, speed and size matter: evolutionary forces driving nuclear genome miniaturization and expansion,” Annals of Botany 95 (2005): 147-175.

46. Ryan J. Taft, Michael Pheasant & John S. Mattick, “The relationship between nonprotein- coding DNA and eukaryotic complexity,” BioEssays 29 (2007): 288-299.

47. L. I. Patrushev & I. G. Minkevich, “The Problem of the Eukaryotic Genome Size,” Biochemistry (Moscow) 73 (2008): 1519-1552. Freely accessible (2011) at http://protein.bio.msu.ru/biokhimiya/contents/v73/full/73131519.html

48. Eduard Kejnovsky, Ilia J. Leitch & Andrew R. Leitch, “Contrasting evolutionary dynamics between angiosperm and mammalian genomes,” Trends in Ecology and Evolution 24 (2009): 572-582.

49. T. Ryan Gregory, “Coincidence, coevolution, or causation? DNA content, cell size, and the C-value enigma,” Biological Reviews of the Cambridge Philosophical Society 76 (2001): 65-101.

50. T. Ryan Gregory, “Genome Size Evolution in Animals,” pp. 3-87 in T. Ryan Gregory (editor), The Evolution of the Genome(Amsterdam: Elsevier, 2005), pp. 48-49.

51. T. Ryan Gregory, “An opportunity for ID to be scientific,” Genomicron (July 10, 2007). Freely accessible (2011) at http://www.genomicron.evolverzone.com/2007/07/opportunity-for-id-to-bescientific/

52. William A. Dembski, Intelligent Design: The Bridge Between Science and Theology (Downer’s Grove, IL: InterVarsity Press, 2002), p. 150.

53. William A. Dembski, The Design Revolution (Downer’s Grove, IL: InterVarsity Press, 2004), p. 272.

54. T. Ryan Gregory, “Function, nonfunction, some function: a brief history of junk DNA,” Genomicron (June 14, 2007). Freely accessible (2011) at http://www.genomicron.evolverzone.com/2007/06/function-non-function-some-function/

Image by Jon Sullivan [Public domain], via Wikimedia Commons.