[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.

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>>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.

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>>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.

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>>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.

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>>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.

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>>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.

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>>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.”

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>>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.

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>>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.

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>>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.

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>>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.

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>>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/

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>>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.

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>> 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.

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>>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

[BroJoeK]

I have some time today, will pick up where left off and see how far we get...

Kalamata on WiseGEEK's "junk DNA" article: "That is ancient history, based on an old evolutionism myth.
Try to stay current."

The WiseGEEK article is undated and the site began in 2003, but there's no reason to think the article does not reflect the latest data & ideas.

For perspective, the ENCODE project began in 2003, issued a major report in 2012, phase four began in 2017.
The Carl Zimmer NY Times article is from 2015.
The New Scientist piece is from 2017.

To summarize the debate:

1. Less than 2% of total DNA encodes functional proteins.

2. Of the remaining 98% about 6% is recognized as being functional, which gives us the number 8% of DNA recognized as critical to human life.

3. Beginning in 2003 the ENCODE project researched the remaining 92% to see how much had some sort of functionality.
   They found up to 80% did, but their definition of "function" has been widely criticized.

4. The chief criticism starts here: does a mutation in this region cause some harm to the individual?
   If the answer is "no", then it has no practical "function".

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

Says Danny the-denier Kalamata.
We should notice that the ENCODE project was not anti-evolutionist and does not consider its results to somehow "oppose" evolution.

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

Right, not an observed fact, but a theory confirmed by (among other things) results from projects like ENCODE.

Kalamata "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."

Says Danny I-don't-see-no-stinkin'-facts Kalamata.

Kalamata on Dan Graur: "No sane person wants to know him personally.
It is burden enough to read his ideologically-driven rampages."

So, you read his book?

Kalamata: "Seriously, you need better sources."

Did you say you read Graur's book?

Kalamata on defining "junk DNA": "The definition was abused by those desperately seeking evidence for evolution, and against intelligent design."

The ENCODE project is in no way anti-evolution:

"A total of 5% of the bases in the genome can be confidently identified as being under evolutionary constraint in mammals; for approximately 60% of these constrained bases, there is evidence of function on the basis of the results of the experimental assays performed to date."

ENCODE (not Graur!) says that only 5% of human bases are identified as "under evolutionary constraint", meaning mutations there cause harm.

"Surprisingly, many functional elements are seemingly unconstrained across mammalian evolution.
This suggests the possibility of a large pool of neutral elements that are biochemically active but provide no specific benefit to the organism.
This pool may serve as a 'warehouse' for natural selection, potentially acting as the source of lineage-specific elements and functionally conserved but non-orthologous elements between species."

That is ENCODE speaking, not Graur, not yours truly and certainly not "ancient history".

Kalamata post #162: "95% of the human genome is restrained, that is, it cannot evolve:"

Nonsense.
First of all, the word is "constrained", not "restrained".
Second, ENCODE tells us that only 5% of DNA is "constrained" by evolution, the rest has no effect on natural selection.
Third, and to your point: "constrained" does not mean "no evolution", rather it means mutations there are normally harmful so eventually deleted by natural selection -- by evolution!

Kalamata on the term "junk DNA": "That is slanderous.
You are accusing the ENCODE researchers, most or all of which are evolutionists, of faking their results."

Nonsense, but ENCODE did define "functioning DNA" as any discernable activity, whether it produced results or not.
That number is around 80%, which makes so-called "junk" 20%.
However, ENCODE found that only 5% of DNA is "constrained" by evolution, meaning mutations there are usually harmful.

Kalamata: "The rule-of-thumb for real scientists is, 'Don’t call it junk, unless you know it is junk.' "

So far it's never been demonstrated that any beyond the ~8% of known functioning DNA is anything other than "junk".

Kalamata on Graur's opinions: "There are some who agree with him, and there are plenty who do not."

Reasonable people, even scientists, can disagree reasonably.
It all depends on your definition of "junk".

Kalamata quoting Le Page's 2017 article: "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."

Kalamata: "And the ENCODE biomedical researchers obviously thought it did."

ENCORE researchers are evolutionists who also said only 5% of DNA is constrained by evolution.
They don't label the other 95% as "junk", they don't need to.

Kalamata on harmful mutations: "That would require evidence that evolution can occur."

Evidence which, unlike self-blinded Kalamata, ENCORE researchers had no trouble seeing.

Kalamata on harmful mutations are not "junk": "Maybe, or maybe not."

There's no dispute that a harmful mutation is not to "junk", but if the mutation is harmless, then "junk" sounds about right.

Kalamata on Graur: "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...."

That article is not available without a subscription, so no way to tell if you've only cherry-picked a hyperbolic quote.
Regardless, even ENCORE says that only 5% of human DNA is "constrained" by evolution.

Kalamata: "In my post, I left out the part about Graur resorting to circular science:"

That link is available, so a quick review of it shows the following:

"ENCODE determined a range of possible functional sequences of 20-80 percent.
It would not be a surprise, given the above considerations, that the percentage of our genome that is functional may be double what Graur estimates.
This places the percentage of junk DNA considerably lower than it was historically thought to be, and well within the range found by ENCODE."

Again, the question here is how, exactly, to define "functional".
Even ENCODE admits, "functional" may be as low as 20%, leaving 80% by their own definition "junk".

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

Maybe, in select cases, maybe not.

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

But your article gives no specifics, none, on how non-"neutral" assumptions might change previous results.

Kalamata on evolution theory: "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. "

Complete nonsense.
So here is another place where your reckless use of words like "confirmed", "observed" and "theory" tell me you never did get any, ah, edumacation and so have no clue to what those terms actually mean.
Or, if you ever did know sometime in the past, what they meant, you've suppressed the memories in order to replace them with your new theological opinions.

So, once again by definition: what can be observed is a fact.
Scientific explanations of facts are hypotheses and when confirmed theories.
A theory cannot normally ever become "fact" unless, as in the case of the globe-shaped Earth, it is eventually observed directly.

The evolution hypothesis is now a theory confirmed by two different methodologies:

1. Predictions from theory later observed as facts.

2. Failure to falsify.