Replies

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:

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

Predictions from theory later observed as facts.
Failure to falsify.

>>Joe the Denier says, “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”

The page was a VLS propaganda piece promoting the Evolutionism Party line. There is no science to be found in it.

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>>Joe the Denier says, “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.”

So, who do we believe: Francis Collins and the highly professional ENCODE staff, or those of the ilk that gave us Haeckel, Piltdown, Peppered Moth, Vestigial Organs, fake radiometric dating, fake horse and whale evolution, and, of course, Junk DNA?

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>>Joe the Denier says, “Less than 2% of total DNA encodes functional proteins. 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. 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. 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”.

Again, who do you trust: the professional ENCODE scientists, or a few rabid ideologues of a dead theory propped up by lies, inneundo, suppression of opposing ideas, and downright fraud?

The dirty little secret is the evolutionism cult made up the Junk DNA myth out of thin air, like every other “proof” they trumpet or have trumpeted. They can’t let this one go because there is nothing left to cling to — there is not a shred of observable evidence in any field that supports evolutionism.

>>Joe the Denier says, “We should notice that the ENCODE project was not anti-evolutionist and does not consider its results to somehow “oppose” evolution.”

Don’t tell Dan Graur that! It is true that every scientist on the project was probably an evolutionist, including Collins. So, if anything, they were biased toward evolutionism.

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>>Joe the Denier says, “Right, not an observed fact, but a theory confirmed by (among other things) results from projects like ENCODE.”

How did anyone confirm DNA was millions of years old, as the Wisegeek bunch claimed? (This I have to see.)

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>>Joe the Denier says, “So, you read [Graur’s] book?

Not that one. I have Graur & Li, “Fundamentals of molecular evolution”, 1st & 2nd editions. Of course, I have many other books on the subject, for reference.

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>>Joe the Denier says, 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”.

I believe you are quoting from a 2007 Encode Pilot Project report, which concluded:

“At the outset of the ENCODE Project, many believed that the broad collection of experimental data would nicely dovetail with the detailed evolutionary information derived from comparing multiple mammalian sequences to provide a neat ‘dictionary’ of conserved genomic elements, each with a growing annotation about their biochemical function(s). In one sense, this was achieved; the majority of constrained bases in the ENCODE regions are now associated with at least some experimentally derived information about function. However, we have also encountered a remarkable excess of experimentally identified functional elements lacking evolutionary constraint, and these cannot be dismissed for technical reasons. This is perhaps the biggest surprise of the pilot phase of the ENCODE Project, and suggests that we take a more ‘neutral’ view of many of the functions conferred by the genome.” [”Identification and analysis of functional elements in 1% of the human genome by the ENCODE pilot project.” Nature, 447; June 14, 2007, p.812]

That was the year Francis Collins released the paperback version of his book, “Language of God,” in which he wrote:

“Some of these may have been lost in one species or the other, but many of them remain in a position that is most consistent with their having arrived in the genome of a common mammalian ancestor, and having been carried along ever since. Of course, some might argue that these are actually functional elements placed there by the Creator for a good reason, and our discounting of them as”junk DNA” just betrays our current level of ignorance. And indeed, some small fraction of them may play important regulatory roles. But certain examples severely strain the credulity of that explanation.” [Collins, Francis, “The Language of God.” 2007, Gen 1:12, p.136]

So, Collins was in harmony with the pilot project report. However, in 2015, Collins had changed his tune, as previously quoted from the 2015 Zimmer article:

“In January, Francis Collins, the director of the National Institutes of Health, made a comment that revealed just how far the consensus has moved. At a health care conference in San Francisco, an audience member asked him about junk DNA. “We don’t use that term anymore,” Collins replied. “It was pretty much a case of hubris to imagine that we could dispense with any part of the genome—as if we knew enough to say it wasn’t functional.” Most of the DNA that scientists once thought was just taking up space in the genome, Collins said, ‘turns out to be doing stuff.’” [Carl Zimmer, “Is Most of Our DNA Garbage?” New York Times, 2015]

https://www.nytimes.com/2015/03/08/magazine/is-most-of-our-dna-garbage.html

Have you read this article on Graur’s interpretation of ENCODE (hint: “it is ‘evolution-free’”)?

“A recent slew of ENCyclopedia Of DNA Elements (ENCODE) Consortium publications, specifically the article signed by all Consortium members, put forward the idea that more than 80% of the human genome is functional. This claim flies in the face of current estimates according towhich the fraction of the genome that is evolutionarily conserved through purifying selection is less than 10%. Thus, according to the ENCODE Consortium, a biological function can be maintained indefinitely without selection, which implies that at least 80-10=70% of the genome is perfectly invulnerable to deleterious mutations, either because no mutation can ever occur in these ‘functional’ regions or because no mutation in these regions can ever be deleterious.” [Graur et al, “Human Genome According to the Evolution-Free Gospel of ENCODE.” Genome Biology and Evolution, 5(3), Feb 20, 2013]

https://academic.oup.com/gbe/article/5/3/578/583411

Yes, I would say that Graur was none-to-happy with the results published by the consortium. It got much
worse for Graur with this AAAS (American Association for the Advancement of Science) report on a Swiss study:

“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, October 9, 2018]

https://www.eurekalert.org/pub_releases/2018-10/siob-agu100918.php

Geneticist Jeffrey Tomkins reported on those results in this manner (he mentions Graur in the main article):

“According to the popular neutral model of evolutionary theory, much of the human genome is nothing but randomly evolving junk. All of this so-called neutral DNA that is allegedly not under any ‘selective restraint’ only serves as fodder for functional new genes and traits to somehow magically arise and thus provide the engine of evolution... Global data among diverse people groups for DNA sequence variability across the human genome was inputted into a statistical model of neutral evolution. It was discovered that, at most, only 5% of the human genome could randomly evolve and not be subject to the alleged forces of selection. Fanny Pouyet, the lead author of the published study stated, ‘What we find is that less than 5% of the human genome can actually be considered as ‘neutral.’’ Oops, so much for human evolution!... This study is just one more example in a long line of failures where the theoretical models of evolution have completely collapsed in light of real-world data. And in this case, the failure was even more spectacular because the statistical model that was used was based on theoretical evolutionary assumptions.” [Jeffrey P. Tomkins, “95% of Human Genome Can’t Evolve.” Institute for Creation Research, 2018]

https://www.icr.org/article/ninety-five-percent-of-human-genome-cant-evolve

If I understand that correctly, the only human ancestors are other humans.

Tomkins references an article he wrote on the GENOME project, which references this report:

“According to ENCODE’s analysis, 80 percent of the genome has a ‘biochemical function’. More on exactly what this means later, but the key point is: It’s not ‘junk’. Scientists have long recognised that some non-coding DNA has a function, and more and more solid examples have come to light [edited for clarity – Ed]. But, many maintained that much of these sequences were, indeed, junk. ENCODE says otherwise. ‘Almost every nucleotide is associated with a function of some sort or another, and we now know where they are, what binds to them, what their associations are, and more,’ says Tom Gingeras, one of the study’s many senior scientists. And what’s in the remaining 20 percent? Possibly not junk either, according to Ewan Birney, the project’s Lead Analysis Coordinator and self-described ‘cat-herder-in-chief’. He explains that ENCODE only (!) looked at 147 types of cells, and the human body has a few thousand. A given part of the genome might control a gene in one cell type, but not others. If every cell is included, functions may emerge for the phantom proportion. ‘It’s likely that 80 percent will go to 100 percent,’ says Birney. ‘We don’t really have any large chunks of redundant DNA. This metaphor of junk isn’t that useful.’” [Ed Yong, “ENCODE - the rough guide to the human genome.” Discover Magazine, Sept 5, 2012]

http://blogs.discovermagazine.com/notrocketscience/2012/09/05/encode-the-rough-guide-to-the-human-genome/#.XRUkEHtKgkJ

100% function? Wow!

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>>Joe the Denier says, “First of all, the word is “constrained”, not “restrained”.

Jeffrey Tomkins used that phrase in his article (above), but added quotes. It is possible he took the phrase from this blog post that was based on the work of Dan Graur, Alexander F. Palazzo and T. Ryan Gregory, in which the authors state that human genome is under “selective restraint”:

“The relevance of this to junk DNA is that most of the human genome (~90%) accumulates mutations in this way and that the effective historic size of the human population is small, close to 10’000 which means much of the genome changes unnoticed by natural selection, including viral insertions and other indels. These change the size of the human genome, usually by making it larger than it needs to be. Other research on genome conservation has largely confirmed the predictions of neutral theory. Current estimates looking at comparisons of many related mammalian genomes have shown that about ~9% of the human genome is under some selective restraint, with 5% being highly conserved and another 4% being conserved in a lineage dependant manner. The rest can be assaulted by random mutation with little effect.” [Wallis & Rhiannon, “Junk DNA, Bunk.” Synthetic Duo, Jan 24, 2016]

https://syntheticduo.wordpress.com/2016/01/24/junk-dna-bunk/comment-page-1/

I have seen the phase in other papers.

BTW, I believe Jeffrey Tomkins is the one who explained the human-chimp genome comparison in this manner:

“Where it is similar, it is 98% similar”. LOL!

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>>Joe the Denier says, “So far it’s never been demonstrated that any beyond the ~8% of known functioning DNA is anything other than “junk”.

You do not know it is junk. Your imagination is running wild.

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>>Joe the Denier says, “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. Evidence which, unlike self-blinded Kalamata, ENCORE researchers had no trouble seeing.

Again, you are quoting from the 2007 Pilot Project report.

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>>Joe the Denier says, “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.

This is the same paragraph, sandwiched between the previous and next:

“Graur is given to intemperate griping over whatever he finds silly or stupid or wrong. By his own admission, he has a streak of vigilantism: On occasion he’ll produce a serious paper that debunks someone else’s finding. In 2001, he and a colleague at Tel Aviv University published a genetic analysis showing that a bacterium claimed to be 250 million years old was likely just a modern strain. Another team confirmed that Graur was right. When we met in December, he was getting ready to publish a study designed to poke statistical and analytical holes in a claim that the last common male ancestor of humans walked on Earth 338,000 years ago. On his personal blog, labeled Judge Starling (Judge is ‘Dan’ in Hebrew; Graur is ‘starling’ in Romanian), he regularly excoriates science in his field that he deems shoddy or hyped.

“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.

“Genetic mutations—the drivers of evolution—occur at random, and those that are deleterious are weeded out, sometimes over many generations. Other mutations, salubrious and inconsequential alike, get passed down to progeny. As a result, species like humans and elephants that have a small effective population size are expected to accumulate a lot of junk in their genomes.”

[Yudhijit Bhattacharjee, “The Vigilante.” Science, Vol.343, Iss.6177; March 21, 2014, p.1307]

You really should consider dropping the 5% nonsense.

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>>Joe the Denier says, “But your article gives no specifics, none, on how non-”neutral” assumptions might change previous results.”

The paper is cited by both AAAS and Science Daily reports, with a link provided by the latter:

Pouyet F et al. Background selection and biased gene conversion affect more than 95% of the human genome and bias demographic inferences. eLife 2018;7:e36317 doi: 10.7554/eLife.36317

https://elifesciences.org/articles/36317

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>>Joe the Denier says, “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.

It take more faith to be an evolutionist, since all of its so-called evidence is extrapolated and/or imagined. I know; I used to be an evolutionist.

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>>Joe the Denier says, “The evolution hypothesis is now a theory confirmed by two different methodologies: Predictions from theory later observed as facts. Failure to falsify.

It is not falsifiable.

Mr. Kalamata