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Friday, February 12, 2021

The 20th anniversary of the human genome sequence:
5. 90% of our genome is junk

This is the fifth (and last) post in celebration of the 20th anniversary of publishing the draft sequence. The first four posts dealt with: (1) the way Science chose to commemorate the occasion [Access to the data]; (2) finishing the sequence; (3) the number of genes; and (4) the amount of functional DNA in the genome.

Back in 2001, knowledgeable scientists knew that most of the human genome is junk and the sequence confirmed that knowledge. Subsequent work on the human genome over the past 20 years has provided additional evidence of junk DNA so that we can now be confident that something like 90% of our genome is junk DNA. Here's a list of data and arguments that support that claim.

  • Evolutionary theory; Modern evolutionary theory includes Nearly-Neutral Theory and the importance of random genetic drift. This accommodates the presence of large amounts of junk DNA and removes the old objection that natural selection would have removed non-functional DNA.
  • The C-value paradox: The fact that different related species can have very different genome sizes was a paradox 50 years ago but it is easily explained by junk DNA. The Onion Test is now a powerful tool in refuting most claims of function in our genome.
  • Transposons: The human genome sequence is littered with fragments of defective transposons that take up as much as two-thirds of the genome. These fragments are obvioulsy mutated versions of once-active transposons that became established millions of years ago and subsequently degenerated. They are junk.
  • Introns: About 25% of our genome is located in introns and introns are almost entirely junk DNA.
  • Sequence conservation: No more than 12% of the genome is conserved and the best current estimate is about 8%. Since sequence conservation is our best measure of function, this means that less than 10% of the genome is functioal.
  • Genetic load: Our species cannot survive if the number of deleterious/lethal mutations per generation is too high. The resulting genetic load (mutation load) would soon lead to extinction if there were more than a few deleterious mutations per individual per generation. Geneticists have known for more than 70 years that, given the best estimates of mutation rate, the human genome is too large if all of the genome is functional and that led to predictions that we only have about 30,000 genes and much of our genome is non-functional so that mutations in that fraction do not contribute to mutation load. These predictions turned out to be correct; our species is viable because most of our genome is junk.

11 comments :

  1. Are you scared of predators Larry? - "occasion [Access to the data]; (2) finishing the sequnece; (3) the number of genes; and (4) the amount of functinal DNA in the genome." So "Sequence" mutates to "Sequnece" and "Functional" mutates to "Functinal." Now the intracellular predators' strategy is to mutate towards host self as long as they can get away with it. So it becomes advantageous for potential hosts to generate diversionary near-self sequences as a barrier against such progressive, step-by-step, mutation by potential intracellular pathogens. The immunologists discovered this positive selection towards self sequences during thymus development long, long, ago. Happy Valentines!

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    1. I appreciate people who point out typos so I can correct them but in this case I couldn't find the typos you mention. Could you be more specific?

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    2. They can be found in the links leading to the previous posts (in this post's first paragraph)

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    3. @Fukuda

      Did YOU find them? I couldn't.

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    4. I could. "Sequnece" in point 2, and "functinal" in point 4.

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  2. Does that theory work by assuming that the immune system recognizes as self the somewhat mutated sequences that were around when it was developing, but the "predator" sequences have arrived later than that and so are not seen to be "self"?

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  3. The mutations occur and are screened against self over evolutionary-time and so are innate, "junk," DNA. In a somatic-time emergency there can be pervasive transcription, with some RNAs even translated. It is hoped that the cause of the emergency (an intracellular predator) might, perchance, react specifically with the unusual RNAs or proteins that have been invoked. So all hands on deck, the regular crew being supported by the "junk" rest, who, as Sydney pointed out long ago, are so different from "garbage" in that they might be useful one day.

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    1. Why do lungfish need so much more of this DNA than humans and why do pufferfish need so much less? How do you address the fact that your speculation doesn't pass the Onion Test? How do you deal with the fact that your speculation isn't supported by evidence?

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  4. Be it on pufferfish, onions or the noble pine tree, and be they in prose or poetry, Larry and Daniel have kindly accommodated my responses in their respective blogs. Some examples follow:
    ________________________________

    On Perplexity that Pine should have Seven Times more DNA than You or Me

    Daniel Graur is so annoyed,
    Mum and Dad made him diploid.
    Didn’t make his genome svelte,
    Gorged with braces and with belt!

    Why two DNAs when one will do?
    Junk should be flushed down the loo!
    If two’s OK, then three or four,
    Five or six, and more and more?

    Noble pine on wind-swept shore,
    Diminish’d returns is not the law!
    Lots of “junk” suites pine just right,
    Suites it best in Nature’s fight.

    Just how so, ‘s not hard to see,
    ‘Tis all a matter of degree.
    For one, small may be enough,
    Other looks for right trade-off.

    One has four tyres and no spare,
    Put’s its bets on quick repair,
    For which it totes patch and glue,
    Quite enough to get it through.

    Other tries a different barter,
    Doesn’t need to be much smarter.
    No patch and glue, yet hasn’t blundered,
    Has four tyres plus spares a hundred.

    Multiple ways to reach same goal,
    Multiple ways to ford each shoal.
    Humble pine, or you or me,
    Each to his own on life’s journey.
    _________________________________

    Sandwalk Blog 4 March 2015

    Some cars escape sans dent,
    But strategies are different.
    Some alas have accident,
    And not just bumper bent.

    Same for tyres that go flat,
    That get us into such a spat.
    Some carry just one spare,
    Others far from base,
    Trail a hundred just in case.

    Others have tricks und' belt,
    No baggage, we go svelt.
    So we use our humble wit,
    Zero tyres, just repair kit.

    Others in land of sun,
    With tube empty,
    Take air from three,
    To give to one!

    No one-fits-all,
    No excess fattegy,
    But what recalls,
    Evolution’s strategy!

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    1. "The Camel's hump is an ugly lump
      Which well you may see at the Zoo;
      But uglier yet is the hump we get
      From having too little to do.

      Kiddies and grown-ups too-oo-oo,
      If we haven't enough to do-oo-oo,
      We get the hump --
      Cameelious hump --
      The hump that is black and blue!"

      How the Camel Got His Hump
      Rudyard Kipling

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