[BroJoeK]

Kalamata: "Did you actually read those articles?
The Wisegeek article doesn’t really say anything."

Did you read it?
It says 95% of DNA is non-coding, aka "junk".
It also says:

"By looking at the differences in junk DNA between organisms, researchers have been able to learn more about when these organisms diverged from common ancestors.
The fact that noncoding DNA has been preserved for millions of years would seem to indicate that it has some sort of function, perhaps in the role of gene regulation, gene repair, or gene evolution.
Noncoding DNA also appears to act as a buffer in the genetic code which may play a role in DNA replication.

"There is some evidence that some of the sections in junk DNA were once active genes, leading researchers to refer to these sections as 'pseudogenes.'
At some point in evolutionary history, these genes were deemed unimportant or superseded by other genes, but they quietly remained in the background."

Kalamata: "Dan Graur is, above all else, a far left whack job — seriously!
He makes the nutty Lawrence Krauss look like a choir boy."

So you know him personally?
This article makes the entirely reasonable point that "junk" depends wholly on your definitions.
The original definition of "junk" meant simply all non-coding DNA, which remains today 98% of the total.
Then researchers began to find some activity in the "junk", but what was that activity, exactly?
In most cases they don't know, but to some people it didn't matter, they just wanted to get rid of the term "junk" and so claimed any activity at all was reason enough to call "junk" something else.

But non-coding DNA is still 98%, whether you call it "junk" or something else.

Page's article on Graur begins with the headline: "At Least 75% of our DNA really is useless junk after all".
In the article's body it uses other numbers, from 92% to 86%, again depending entirely on how, exactly, you define "junk".

"The heart of the issue is how you define functional.
ENCODE defined DNA as such if it showed any “biochemical activity”, for instance, if it was copied into RNA.
But Graur doesn’t think a bit of activity like this is enough to prove DNA has a meaningful use.
Instead, he argues that a sequence can only be described as functional if it has evolved to do something useful, and if a mutation disrupting it would have a harmful effect."

Key point: a DNA sequence is not "junk" if a mutation to it will cause a harmful effect.
But if the mutation has no bad effect, then the sequence can legitimately be called "junk".

Kalamata: "The 2017 article by Graur that Le Page referenced is only one of his many attacks on the ENCODE project, which he claims: 1) provides support for intelligent design, and 2) doesn’t take into account the primary tenent of his religion, which is “everything is shaped by evolution”.
“If ENCODE is right,” according to Graur, “then evolution is wrong.”
I don’t disagree on that point..."

None of that is in the article I posted, so I have to assume that, as usual, you misrepresent someone because you dislike him.
That's sort of your thing, FRiend.

Kalamata: "...even he claims the functionality of Junk DNA is as high as 25%."

Or at least that's what Page's headline said.
The article itself argues that "functionality" is ill defined and so anything outside the 8% of coding-or-functioning DNA is suspect of being non-coding "junk".

Kalamata quoting Zimmer, NYTimes: " 'Most of the DNA that scientists once thought was just taking up space in the genome,' Collins said, ‘turns out to be doing stuff.’ "

But how much "doing stuff"?
Turns out, not much because:

"On average, each baby is born with roughly 100 new mutations.
If every piece of the genome were essential, then many of those mutations would lead to significant birth defects, with the defects only multiplying over the course of generations; in less than a century, the species would become extinct."

Right, 100 new mutation per generation and yet the vast majority of us are born as healthy as our parents.
Clearly that suggests the label "junk" is not so inappropriate for non-coding DNA.

"He expects that as we examine the genome more closely, we’ll find many [figurative] bottle caps and nails.
It’s a prediction based, he and others argue, on the deep evolutionary history of our genome.
Over millions of years, essential genes haven’t changed very much, while junk DNA has picked up many harmless mutations.
Scientists at the University of Oxford have measured evolutionary change over the past 100 million years at every spot in the human genome.
“I can today say, hand on my heart, that 8 percent, plus or minus 1 percent, is what I would consider functional,” Chris Ponting, an author of the study, says.
And the other 92 percent? “It doesn’t seem to matter that much,” he says"

So, despite ENCODE's claims, many scientists in the field are not convinced that "junk DNA" is anything but.

"It’s no coincidence, researchers like Gregory argue, that bona fide creationists have used recent changes in the thinking about junk DNA to try to turn back the clock to the days before Darwin.
(The recent studies on noncoding DNA “clearly demonstrate we are ‘fearfully and wonderfully made’ by our Creator God,” declared the Institute for Creation Research.)
In a sense, this debate stretches back to Darwin himself, whose 1859 book, “On the Origin of Species,” set the course for our understanding natural selection as a natural “designer.”
Later in his life, Darwin took pains to stress that there was more to evolution than natural selection.
He was frustrated to see how many of his readers thought he was arguing that natural selection was the only force behind life’s diversity."

Kalamata: "Worse for the evolutionist, this 2018 article states that 95% of the human genome is restrained, that is, it cannot evolve:"

No, your link is highly technical however, no surprise, it doesn't say what you claim.
What it does say is this:

"The exact proportion of the genome that is influenced by selection is still the source of an intense debate (Bernstein et al., 2012; Rands et al., 2014; Graur, 2017; Kern and Hahn, 2018).
Here, we show that up to 80–85% of the human genome is probably affected by background selection (BGS), an effect that is not subtle (Reed et al., 2005) and that is visible from single individuals genomes (Figure 1—figure supplement 5A).
Even though our estimate of the fraction of the human genome influenced by BGS matches relatively well with that reported to be biochemically functional by the ENCODE consortium (Bernstein et al., 2012), our results do not imply that 80–85% of the human genome is functional.
They rather show that functional sites that are the direct target of purifying selection in both coding and non-coding regions (potentially representing 8–15% of the genome, Rands et al. (2014); Graur, 2017) have an important but indirect influence on most of the genome."

So, 8-15% of our genome "matters", the rest is fairly called "junk".

Kalamata: "It is meaningless. Genetics has moved on."

Not nearly as much as you'd wish, FRiend.

Kalamata: "That is over-generalized.
Real science is observable and repeatable.
Even forces, such as gravity, are observable, or at least their results are.
Charlie did it backwards.
He took observable science (adaptation and speciation,) and extrapolated it into unobservable, untestable, unrepeatable conjecture (common descent).
That is not science."

Nonsense, that is certainly science -- observed, tested & repeated, Darwin's hypothesis is now strongly confirmed theory.
It will never be "fact" because the past cannot be observed directly, but every indirect vision we have into the past (i.e., fossils, DNA, geology, radiometric dating, morphological comparisons, etc.), all confirm what evolution theory predicts.

Darwin's basic idea has never been falsified.

[Kalamata]

>>[The Wisegeek article] says 95% of DNA is non-coding, aka “junk”.

This is the quote:

“In humans, for example, 95% of the genome is composed of noncoding DNA. Junk DNA appears to explain a large part of the differences in genome size between different organisms, as some plants and animals have a great deal of junk DNA, while others have less.”

That is ancient history, based on an old evolutionism myth. Try to stay current.

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>>It also says: “By looking at the differences in junk DNA between organisms, researchers have been able to learn more about when these organisms diverged from common ancestors.

That is what it says, but it is story-telling, not science.

***********************
>>The fact that noncoding DNA has been preserved for millions of years would seem to indicate that it has some sort of function, perhaps in the role of gene regulation, gene repair, or gene evolution.

It is NOT a fact that “noncoding DNA has been preserved for millions of years”. That is more story-telling.

There is no need for you to quote profusely from an article I have already read. Just give me your interpretation, and I will tell you why it is wrong.

***********************
>>So you know him personally?

No sane person wants to know him personally. It is burden enough to read his ideologically-driven rampages.

Seriously, you need better sources.

***********************
>>This article makes the entirely reasonable point that “junk” depends wholly on your definitions.

What else can they say now that the ENCODE project has exposed their made-up “evidence” for evolution.

***********************
>>The original definition of “junk” meant simply all non-coding DNA, which remains today 98% of the total.

The definition was abused by those desperately seeking evidence for evolution, and against intelligent design.

***********************
>>Then researchers began to find some activity in the “junk”, but what was that activity, exactly? In most cases they don’t know, but to some people it didn’t matter, they just wanted to get rid of the term “junk” and so claimed any activity at all was reason enough to call “junk” something else.”

That is slanderous. You are accusing the ENCODE researchers, most or all of which are evolutionists, of faking their results.

***********************
>>But non-coding DNA is still 98%, whether you call it “junk” or something else.

The rule-of-thumb for real scientists is, “Don’t call it junk, unless you know it is junk.”

***********************
>>Page’s article on Graur begins with the headline: “At Least 75% of our DNA really is useless junk after all”.
In the article’s body it uses other numbers, from 92% to 86%, again depending entirely on how, exactly, you define “junk”.<<

There are some who agree with him, and there are plenty who do not.

***********************
>>ENCODE defined DNA as such if it showed any “biochemical activity”, for instance, if it was copied into RNA.
But Graur doesn’t think a bit of activity like this is enough to prove DNA has a meaningful use.

And the ENCODE biomedical researchers obviously thought it did.

***********************
>>Instead, he argues that a sequence can only be described as functional if it has evolved to do something useful, and if a mutation disrupting it would have a harmful effect.”

That would require evidence that evolution can occur.

***********************
>>Key point: a DNA sequence is not “junk” if a mutation to it will cause a harmful effect. But if the mutation has no bad effect, then the sequence can legitimately be called “junk”.

Maybe, or maybe not.

***********************
>>None of that is in the article I posted, so I have to assume that, as usual, you misrepresent someone because you dislike him. That’s sort of your thing, FRiend.”

Of course I don’t like him. He is a belligerent jackass. But everything I quoted can be found in the literature, some of which can be found in this article:

“Graur’s atheism inflamed his anger at ENCODE. He perceives an echo of intelligent design in the consortium’s ‘80% claim,’ which he takes to imply that most of the genome exists because it serves a purpose. ‘What ENCODE researchers did not take into account,’ he contends, ‘is that everything is shaped by evolution.’ And evolution is slow to weed out useless features.” [Yudhijit Bhattacharjee, “The Vigilante.” Science, Vol.343, Iss.6177; March 21, 2014, p.1307]

https://science.sciencemag.org/content/343/6177/1306.summary

More came from here. In my post, I left out the part about Graur resorting to circular science:

“We read the paper, and looked over Graur’s accompanying PowerPoint. We’re not impressed by theoretical population genetics because it is based on neo-Darwinian assumptions rather than biological realities. Basically, he is using that circular science to add a quantitative gloss to his fundamental position, namely that if ENCODE is right then evolution is wrong, and evolution can’t be wrong, so ENCODE can’t be right.” [”Dan Graur, Anti-ENCODE Crusader, Is Back.” Evolution News & Science Today, July 28, 2017]”

https://evolutionnews.org/2017/07/dan-graur-anti-encode-crusader-is-back/

***********************
>>The article itself argues that “functionality” is ill defined and so anything outside the 8% of coding-or-functioning DNA is suspect of being non-coding “junk”.

Yes, that is what he claims.

***********************
>> But how much “doing stuff”? Turns out, not much because: “On average, each baby is born with roughly 100 new mutations. If every piece of the genome were essential, then many of those mutations would lead to significant birth defects, with the defects only multiplying over the course of generations; in less than a century, the species would become extinct.”

Have you read that mutations within Junk DNA can cause cancer?

BTW, I read Zimmer’s 2015 article a long while back, so there is no need for you to copy paste from it.

***********************
>>No, your link is highly technical however, no surprise, it doesn’t say what you claim.
What it does say is this: “The exact proportion of the genome that is influenced by selection is still the source of an intense debate (Bernstein et al., 2012; Rands et al., 2014; Graur, 2017; Kern and Hahn, 2018).” . . . So, 8-15% of our genome “matters”, the rest is fairly called “junk”.. .

Perhaps you misinterpreted. This report from the AAAS of a release by the Swiss Institute of Bioinformatics states:

“Models used to reconstruct the history of a species or to discover how populations are related to one another rely on a key assumption: that the genome regions under scrutiny are made of”neutral” snippets of DNA, i.e. parts that have evolved randomly rather than being selected for or against. But these regions might actually not be as neutral as previously thought, according to a recent finding by scientists at SIB and the University of Bern: “What we find is that less than 5% of the human genome can actually be considered as “neutral””, says Fanny Pouyet, lead author of the study. “This is a striking finding: it means that 95% of the genome is indirectly influenced by functional sites, which themselves represent only 10% to 15% of the genome”, she concludes. These functional sites encompass both genes and regions involved in gene regulation.” [”A Genome Under Influence: The faulty yardstick in genomics studies and how to cope with it.” Swiss Institute of Bioinformatics, Oct 9, 2018]

That clearly states, “What we find is that less than 5% of the human genome can actually be considered as ‘neutral’”.

https://www.eurekalert.org/pub_releases/2018-10/siob-agu100918.php
https://www.sciencedaily.com/releases/2018/10/181010105536.htm

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>>Nonsense, that is certainly science — observed, tested & repeated, Darwin’s hypothesis is now strongly confirmed theory. It will never be “fact” because the past cannot be observed directly, but every indirect vision we have into the past (i.e., fossils, DNA, geology, radiometric dating, morphological comparisons, etc.), all confirm what evolution theory predicts. Darwin’s basic idea has never been falsified.

It has never been confirmed, or even observed. It is a theory on life support, perpetuated by suppression of opposing theories. It is dead, for all practical purposes. We are just biding our time until the “Planck Doctrine” kicks in:

“A new scientific truth does not triumph by convincing its opponents and making them see the light, but rather because its opponents eventually die, and a new generation grows up that is familiar with it.” [Max Planck, “Scientific Autobiography And Other Papers.” Williams and Norgate, 1968, pp.33-34]

Mr. Kalamata