Dark DNA

[Sriram]

Hi everyone,

Here is an interesting article about Dark DNA...that is the DNA that seems to be missing but appears to influence evolution nevertheless.

https://explorebiotech.com/dark-dna-will-make-question-concept-evolution/

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Certain genes have been found missing in animal species, which is present in other similar species and must be present to keep the animals alive. These missing genes are known as “dark DNA”. And its existence will change the concept of evolution.

This makes it more likely that the genes we were looking for were hard to detect rather than missing. This is why we call the hidden sequence “dark DNA” as a reference to dark matter, the stuff that we think makes up about 25% of the universe but has not been proven.

Natural selection... determines whether mutations are kept and passed on or not, usually depending on whether they result in higher reproductive success. In short, mutation creates the variation in an organism’s DNA, natural selection decides whether it stays or if it goes, and so biases the direction of evolution. But the hotspots of high mutation within a genome mean genes in certain locations have a higher chance of mutating than others.

It means that such hotspots could be an underappreciated mechanism which could also bias the direction of evolution, meaning natural selection may not be the sole driving force.

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Cheers.

Sriram

[Stranger]

Here is an interesting article about Dark DNA...that is the DNA that seems to be missing but appears to influence evolution nevertheless.

https://explorebiotech.com/dark-dna-will-make-question-concept-evolution/

Bit of a sloppy article that is partially lifted from an article by one of the researchers (Introducing ‘dark DNA’) of the actual paper (Genome sequence of a diabetes-prone rodent reveals a mutation hotspot around the ParaHox gene cluster).

What it actually boils down to is that there seem to be parts of the genome that are hard to detect and that are especially prone to mutation. So what is described in the article you linked as something that "will change the concept of evolution" is described in the paper as "...the discovery of a localized chromosomal region subject to elevated mutation suggests that mutational heterogeneity within genomes could influence the course of evolution."

Such is journalistic hype even in science reporting.   

Why isn't this in the Science and Technology section?

[Gordon]

Why isn't this in the Science and Technology section?

Moderator:

It is now.

[SteveH]

I did a bit of exploring around that site. All of the articles are written in slightly bizarre English, as if by someone for whom it is not the first language. I also got the impression, though I might be wrong, that there's an Intelligent-design agenda lurking in the background.

[Harrowby Hall]

I did a bit of exploring around that site. All of the articles are written in slightly bizarre English, as if by someone for whom it is not the first language. I also got the impression, though I might be wrong, that there's an Intelligent-design agenda lurking in the background.

Indeed Steve, on the page that the article in question appeared, there was a box which, when clicked, let directly to an article endorsing intelligent design.

[Sriram]

Indeed Steve, on the page that the article in question appeared, there was a box which, when clicked, let directly to an article endorsing intelligent design.

Which probably means that all scientists don't necessarily take a hard and extreme stand against such grey areas.

[torridon]

Which probably means that all scientists don't necessarily take a hard and extreme stand against such grey areas.

'Intelligent Design' is not science, it is fake science masquerading as real science, conceived to lure the unwary into irrational beliefs.  It doesn't usually take much digging to find that its proponents have a religious agenda, rather than empirical or epistemic truth.

[Sriram]

'Intelligent Design' is not science, it is fake science masquerading as real science, conceived to lure the unwary into irrational beliefs.  It doesn't usually take much digging to find that its proponents have a religious agenda, rather than empirical or epistemic truth.

That is just an assertion.

If we find that there is some sort of an Intelligence (or even a bias) at work in evolution there is no point in going on and on with the chance hypothesis.

And that does not necessarily mean that it is any form of religious belief.  You must realize that we have to find secular ways of factoring in Consciousness and Intelligence into all aspects of life....including evolution.

[Stranger]

That is just an assertion.

Not it isn't. ID is not a science. The claim that it is was literally thrown out of court.

If we find that there is some sort of an Intelligence (or even a bias) at work in evolution there is no point in going on and on with the chance hypothesis.

There has been no such finding and the very well tested theory of evolution by natural selection is not a 'chance hypothesis'.

You must realize that we have to find secular ways of factoring in Consciousness and Intelligence into all aspects of life....including evolution.

All the evidence is that intelligence or consciousness are products of evolution.

[Enki]

That is just an assertion.

If we find that there is some sort of an Intelligence (or even a bias) at work in evolution there is no point in going on and on with the chance hypothesis.

And that does not necessarily mean that it is any form of religious belief.  You must realize that we have to find secular ways of factoring in Consciousness and Intelligence into all aspects of life....including evolution.

With reference to your last sentence:

And you must realise that we only do this on the basis of evidence, and so far there is no evidence that there is a 'Consciousness and Intelligence' pervading  any aspects of life, other than that appertaining to the living things that life has produced. Evolution has constantly increasing evidence that no such consciousness is needed for life to develop.

Not sure why you decided to focus on your particular link for discussing 'dark dna' as it shows a bias towards intelligent design. You could have delved a little further perhaps and looked at this description:

https://www.nature.com/articles/d41586-018-00920-x

which is far more balanced and from a clearly recognised peer reviewed source.

Or, indeed, shown the article that Stranger referred to in Message 1.

[Sriram]

I don't see why I shouldn't!! It is not exactly a religious site or anything....it is a science site too.

Even the New Scientist article (whatever little I can read without paying) says '....is forcing us to rethink some basics of evolution'.... and.... '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.'

https://www.newscientist.com/article/mg23731680-200-dark-dna-the-missing-matter-at-the-heart-of-nature/

[Enki]

I don't see why I shouldn't!! It is not exactly a religious site or anything....it is a science site too.

Even the New Scientist article (whatever little I can read without paying) says '....is forcing us to rethink some basics of evolution'.... and.... '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.'

https://www.newscientist.com/article/mg23731680-200-dark-dna-the-missing-matter-at-the-heart-of-nature/

And even in this short extract, no sign of anything to do with your 'Consciousness and Intelligence' at all, just an acceptance that there are things about evolution we do not know enough about. And, of course, I accept that completely.

[Sriram]

I did not bring in Intelligent design into the conversation. Others did! 

[Stranger]

Even the New Scientist article (whatever little I can read without paying) says '....is forcing us to rethink some basics of evolution'.... and.... '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.'

https://www.newscientist.com/article/mg23731680-200-dark-dna-the-missing-matter-at-the-heart-of-nature/

I was going to say that I didn't know why you were quoting yet another pop-science articles when I'd pointed you at the actual paper, but I guess I know exactly why: you're just trawling for quotes that suggest that the basic mechanism of evolution might be in question.

Anyway, the "Significance" section in the published paper (which is how all the researchers presented their findings to their peers) says (in full):

"A core question in evolutionary biology is how mutation and selection adapt and constrain species to specialized habitats. We sequenced the genome of the sand rat, a desert rodent susceptible to nutritionally induced diabetes, and discovered an unusual chromosome region skewed toward G and C nucleotides. This region includes the Pdx1 homeobox gene, a transcriptional activator of insulin, which has undergone massive sequence change, likely contributing to diabetes and adaptation to low caloric intake. Our results imply that mutation rate varies within a genome and that hotspots of high mutation rate may influence ecological adaptation and constraint. In addition, we caution that divergent regions can be omitted by conventional short-read sequencing approaches, a consideration for existing and future genome sequencing projects."

So as I said, this is about a region of the genome that has a higher rate of mutation and that may indeed affect the course of evolution. However, there really is no suggestion that the basic mechanism of evolution (variation and mutation acted on by natural selection) is being questioned. The full New Scientist article says: "If genes contained within these mutational 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."

Of course the difficulty in detecting 'dark DNA' may also have an impact on current understanding of individual instances of evolution because some genes may not have been detected by certain sequencing techniques.

There is a little more hype in the full New Scientist article but even at its most speculative, it only suggests that "...mutation rates in dark DNA may be so rapid that natural selection cannot act fast enough to remove deleterious variations in the usual way. Such genes might even become adaptive later on, if a species faces a new environmental challenge." Which I guess is possible but hardly very probable.