'Junk DNA' Evolution

Researcher: Dark DNA raises fundamental questions about evolution

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From Adam Hargreaves at New Scientist,

No doubt you have heard of dark matter, which is thought to make up over a quarter of the universe. We know it’s there; we just haven’t been able to detect it. Well, something similar is afoot in the genome. My colleagues and I have dubbed this elusive genetic matter “dark DNA”. And our investigations into the sand rat are starting to reveal its nature.

The discovery of dark DNA is so recent that we are still trying to work out how widespread it is and whether it benefits those species that possess it. However, its very existence raises some fundamental questions about genetics and evolution. We may need to look again at how adaptation occurs at the molecular level. Controversially, dark DNA might even be a driving force of evolution. (paywall) More.

Indeed. As evolution becomes more history and less religion, the driving forces of evolution are becoming as numerous and varied as those of World War II.

The obvious question is not whether dark DNA matters. If we are not diehard fans of Darwinian “junk DNA” (the supposed vast heaps of rubbish left over from random evolution*), we will simply assume that dark DNA matters.

The question with evolution, seen as a history, is one of mechanism. As Michael Behe would ask, what exactly does dark DNA do? For example, does it assist epigenetics, horizontal gene transfer, hybridization, convergent evolution, devolution… Or another, as yet undiscovered, function?

See also: Could “dark DNA” change the way we think about evolution?

Researcher: Best educated guesses fail with plant evolution “There is still a lot we don’t know about why life is the way it is and how most biological process originated,” said Dr. Cardona. “Sometimes our best educated guesses don’t even come close to representing what really happened so long ago.”

and

What the fossils told us in their own words

Also:

* See also: “Junk” RNA helps regulate metabolism

Junk DNA defender just isn’t doing politeness any more.

Anyone remember ENCODE? Not much junk DNA? Still not much. (Paper is open access.)

Yes, Darwin’s followers did use junk DNA as an argument for their position.

Another response to Darwin’s followers’ attack on the “not-much-junk-DNA” ENCODE findings

5 Replies to “Researcher: Dark DNA raises fundamental questions about evolution”

  1. 1
    forexhr says:
    March 12, 2018 at 11:57 am

    The definitive way to debunk both evolution and abiogenesis: https://biospecificity.wordpress.com/

  2. 2
    LocalMinimum says:
    March 12, 2018 at 1:44 pm

    An interesting thing, about the 99.whatever% similarities and “junk”. We look to the protein coding sections, as if they define the whole of the function.

    Perhaps it’s as fallacious as comparing programming languages on the basis of their basic operators. The great variety of programming languages share a great deal of arithmetic and other operators. Most OOP capable languages these days follow or at least accommodate a C++ style syntax.

    However, the larger differences emerge out of sight of the “business end” of the code. Differences in structure emerging from subtle differences in syntax, pointer mechanics, implicit features of objects. The real features of a language are often to be found in standard libraries, referenced only by names of functions, macros, and variables/constants; the entire scope of use of a language can be defined by libraries that can’t even be written in that language.

    An “it’s all the same because it looks the same” or “I can’t conceive of why this is like this so it’s junk” would be a plainly blockheaded approach to investigating a human written piece of code, especially if that code stood independent from any external library.

    Whether one believes it’s Darwin’s magic algorithm or an intelligence that wrote the genetic code, surely it’s going to be sufficiently alien to our eyes to require at least as much suspension of a smug sense of familiarity as human works.

  3. 3
    PaV says:
    March 12, 2018 at 9:45 pm

    Try this to get at the article in New Scientist.

    I suspect James Shapiro must be happy because this sure looks like another NGE instance.

  4. 4
    Nonlin.org says:
    March 15, 2018 at 1:17 pm

    This is the full article: https://theconversation.com/introducing-dark-dna-the-phenomenon-that-could-change-how-we-think-about-evolution-82867

    “We know GC-rich sequences cause problems for certain DNA-sequencing technologies. This makes it more likely that the genes we were looking for were hard to detect rather than missing.”

    – then get better technologies.
    And how about the DNA being overrated: http://nonlin.org/dna-not-essence-of-life/ ?

  5. 5
    PaV says:
    March 16, 2018 at 10:43 am

    From the New Scientist article:

    Even more intriguing is how dark DNA might influence evolution. Most textbooks describe evolution as a two-step process. First, a steady trickle of random genetic mutation creates variation in an organism’s DNA. Then, natural selection acts like a filter, deciding which mutations are passed on. This usually depends on whether they confer some sort of advantage, although not everything produced over the course of evolution is an adaptation. So, natural selection is the sole driving force pushing the direction in which organisms evolve. But add dark DNA to the picture, and that’s not necessarily the case. If genes contained within these mutation hotspots have a greater chance of mutating than those elsewhere, they will display more variation on which natural selection can act, so the traits they confer will evolve faster. In other words, dark DNA could influence the direction of evolution, giving a driving role to mutation. Indeed, my colleagues and I have suggested that mutation rates in dark DNA may be so rapid that natural selection cannot act fast enough to remove deleterious variants in the usual way. Such genes might even become adaptive later on, if a species faces a new environmental challenge.

    We’re headed towards James Shapiro’s “Natural Genetic Engineering,” with this ‘mutational complex’ part of a cell’s engineering capacity.

    Here’s a link you may like.

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