Where are all the mutations?

That’s a good question to explore, though the way you phrase it, it almost sounds like you view it as some kind of scale – like if we keep piling mutations higher and higher on the scale it will reach a tipping point and collapse. I don’t think that’s an accurate description of what’s going on. This is not my area of expertise, but I’ll encourage you to continue engaging with others here who’ve pointed you to articles and resources that better explain it.

Thanks Mervin, it does get a bit confusing after lots of messages back and forth :slight_smile:

Thanks cheers.

These two posts from an expert in the field can be helpful:

This is true. We each accumulate about 100 more mutations than our parents so “why aren’t we dead 100 times over?”. There is probably no such thing as a neutral mutation, at best most are slightly detrimental but below the selection threshold, and gain of function mutations are several orders of magnitude less common than detrimental ones… Kimura in his “neutral theory” didn’t even bother to include gain of function mutations.

Since we now know that most of the genome is functional we can’t appeal to most of the mutations being hidden in junk DNA.

As Behe and Sanford have concluded Darwin devolves; it’s down not up.

An evolutionary algorithm is just a glorified trial and error solution which can be good for optimising something that already works to some extent, but it doesn’t produce true novelty.

That statement is certainly subject to further examination. I assume you are quoting the ENCODE project, which defined functional in such a way that makes no real sense. Sort of like saying all rocks are functional, when most are only functional as fill when what you want to use the rock for is to cut and put in an engagement ring.
Here is an article discussing it further:At least 75 per cent of our DNA really is useless junk after all | New Scientist

I read the article which includes ‘We don’t know how much of our DNA has a non-sequence-related function, says Ryan Gregory of the University of Guelph in Canada. Some regions of DNA are useful without having an important sequence, so mutations in these areas probably don’t matter. But even taking this into account, most DNA is probably junk, says Gregory.’ Note the words ‘we dont know’ and ‘probably don’t matter’ and ‘probably junk’. Maybe it does matter and maybe it’s not ‘junk’. Scientists come to their conclusions not neutrally but in accordance with their worldview - we all do.

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Well, no, That’s how scientists speak. “Most DNA is probably junk” means that the evidence to date implies that most DNA is junk. Which is correct – all the evidence I’ve ever seen supports the idea that most human DNA has no sequence-relevant function or effect on fitness, and I have seen precisely zero evidence that most human DNA does have a function.

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What’s true? Most of what you say after this is false.

No, there’s no reason at all to think that most mutations are slightly detrimental. I presented evidence (linked to in the preceding post) that slightly detrimental and slightly beneficial mutations are equally common.

Kimura never suggested that beneficial mutations don’t occur or aren’t responsible for adaptive evolution. His claim, which was radical at the time, was that most mutations were neutral – which they are.

Where did you get that idea? The ENCODE project concluded that mutations in ~10% of the genome would affect fitness.

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That’s an interesting way of looking at it Chris. And an interesting question. What are the limitations of evolutionary algorithms, and what are the implications of those limitations for the explanatory power of biological evolution?

Can you provide any links to peer reviewed research in answer to this question?

Well fill is functional when you need fill; you wouldn’t use diamonds.
I see from the article “Graur’s team have now calculated how many children a couple would need to conceive so evolution could weed out enough bad mutations from our genomes as fast as they arise.” Graur never accepted the EDCODE results from the day they were published. It’s basically just a rehashing of the “why aren’t we dead 100 times over” argument.

On the other hand we have " This week’s “we thought it was junk but it turned out to be crucial” study comes with the added bonus that the so-called “junk” is also species-specific / taxonomically restricted.

Despite a vigorous rearguard action by Graur et al function continues to be found in the “junk” when they look for it.

As I already pointed out, the ENCODE results don’t say at all what you think they say.

Despite all of the chatter, the amount of the human genome that is junk is still estimated to be around 90%. This estimate really hasn’t changed at all. If you have any evidence that mutations in more of the genome affect fitness, please present it. Right now you’re just making patently false statements.

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Since the ENCODE project results were published in 2012 more and more functions have been found in what was once regarded as junk. Here’s a sample.

Sex Determination Depends on Non-Coding DNA (original paper behind paywall)

Only 2% of human DNA contains the ‘code’ to produce proteins, key building blocks of life. The remaining 98% is ‘non-coding’ and was once thought to be unnecessary ‘junk’ DNA, but there is increasing evidence that it can play important roles.

The latest study adds to this evidence, showing that a small piece of DNA called enhancer 13 (Enh13), located over half a million bases away from the Sox9 gene, boosts SOX9 protein production at the right moment to trigger testes development. When the team genetically removed Enh13 from male (XY) mice, they developed ovaries and female genitalia.

Not Junk: ‘Jumping Gene’ is Critical for Early Embryo

A so-called “jumping gene” that researchers long considered either genetic junk or a pernicious parasite is actually a critical regulator of the first stages of embryonic development, according to a new study in mice led by UC San Francisco scientists and published June 21, 2018 in Cell

Understanding how to control ‘jumping’ genes

For years, they had been thought of as useless or ‘junk’ DNA,” Zhang said. “However, it has been recently known that transposons also play very important roles in gene regulation and evolution regardless of the potential deleterious effect.”

Scientists discover a role for ‘junk’ DNA

Researchers have determined how satellite DNA, considered to be ‘junk DNA,’ plays a crucial role in holding the genome together.

Imaging in living cells reveals how ‘junk DNA’ switches on a gene

Researchers have captured video showing how pieces of DNA once thought to be useless can act as on-off switches for genes.

These pieces of DNA are part of over 90 percent of the genetic material that are not genes. Researchers now know that this “junk DNA” contains most of the information that can turn on or off genes.

In the mammalian genome, there are an estimated 200,000 to 1 million enhancers, and many are located far away on the DNA strand from the gene they regulate, …

There have been quite a few other articles that I have read over the years but I don’t have the enthusiasm to find them all; do your own research.

Yes, I know – I do try to keep up with my own field (well, at least a little). That’s quite irrelevant. The amount of functional DNA isn’t estimated by totting up all the bits whose function we know; it’s estimated by identifying the portion that shows signs of being under purifying selection.

Whoever wrote this doesn’t know the history of the field. “Junk DNA” never meant “noncoding DNA”.

Satellite DNA wasn’t included in the analysis of the fraction of the genome that’s functional; it’s generally been left out of “complete” genomes because it’s difficult to assemble.

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Sadly, that includes a number of scientists (probably not aware of the history in their fields) and writers/journalists.

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I have found no compelling evidence to show how this vast diversity we see in nature came about through random mutations, in such a short period of time since the Cambrian Explosion.

For me, the best explanation of this diversity comes in an analogy. God created the clay and He invited all the artists of Heaven to surprise HIm. The diversity of our natural world is only a shadow of the diversity in Heaven, and all of its creative residents.

Oh well that explains it; just because it has function doesn’t mean it’s functional.

Umm… No. That’s not what @glipsnort wrote. If you total all the bits whose function we know you are only setting a lower limit on the amount of functional DNA. There are proxies that give better estimates of the actual percentage.

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Umm…Yes. That IS what @glipsnort is saying. His definition allows him to reject function as a criteria of functionality and instead say you have to prove that it is under purifying selection. This allows him to delay admitting that much of DNA is actually functional. It is a self serving definition.

So let ME be clear. It is functional if it has function. Anything else is a nonsense.