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Junk DNA: Darwinism evolves swiftly in real time

June 20, 2018

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male (XY) mouse with female genitalia and female (XX) mouse/Greta Keenan, Francis Crick Institute

From David Klinghoffer at ENST, on Darwinism and the recent find that junk DNA can alter genitalia:

The “junk” view, once a prized piece of evidence for neo-Darwinian theory, is thus reduced to the province of the benighted, the reactionaries who “still refer to [it] as ‘junk’ DNA,” after science has already passed them by. Having volumes of garbage lying around was a logical prediction of Darwinism that is in the process of being falsified. Now, it seems likely that non-coding regions have not trivial but “drastic effects.”

This reversal helps explain why evolutionists like Richard Dawkins have radically revised a key claim. Dawkins himself, in the space of three years, went from assuring us that junk validates Darwinism to claiming that function is what it expects. What a theory! It can never, ever be wrong. More.

Dawkins here:

I have noticed that there are some creationists who are jumping on [the ENCODE results] because they think that’s awkward for Darwinism. Quite the contrary it’s exactly what a Darwinist would hope for, to find usefulness in the living world…. [2012]

vs.

Dawkins here:

Back in 2009, in The Greatest Show on Earth (pp. 332-333), he was presenting the supposed junkiness of the vast majority of the genome as an assured scientific reality and one that is, in the specific case of “pseudogenes,” “useful for. . . embarrassing creationists.”

Believe Dawkins if you want. We understand that there is currently a sale price offered for universal swivel joints for the mind…

See also: Junk DNA can actually change genitalia. Junk DNA played the same role in defending Darwinian evolution as claims that Neanderthal man was a subhuman did: The vast library of junk genes and the missing link made Darwin’s story understandable to the average person and the missing link even became part of popular culture. With Darwinism so entrenched, the fact that these beliefs are not based on fact will be difficult to root out of the culture. Darwin-only school systems are part of the problem.

(2012)

39 Responses to Junk DNA: Darwinism evolves swiftly in real time

1

KasJune 20, 2018 at 10:06 am

I’ve been saying for years that Darwinism is non-falsifiable, and it looks like the evidence in support of that contention is mounting.

__________________

Darwin made it impossible to be an intellectually fulfilled atheist.
2

ETJune 20, 2018 at 11:31 am

Kas- Darwinism is untestable
3

Silver AsiaticJune 20, 2018 at 12:29 pm

Even within the tests that Darwinists use there is a lot of deception.

Any p-value that is greater than 0.05 means the results are not statistically significant. Even .06 – not significant. It’s not a question of “really close”. It either is or isn’t at a 95% confidence level, which is how they set up the test.

500 different ways that contributors to scientific journals have used language to obscure their results
https://mchankins.wordpress.com/2013/04/21/still-not-significant-2/

some highlights …

a certain trend toward significance (p=0.08)
approached the borderline of significance (p=0.07)
at the margin of statistical significance (p<0.07)
close to being statistically signi?cant (p=0.055)
fell just short of statistical significance (p=0.12)
just very slightly missed the significance level (p=0.086)
near-marginal significance (p=0.18)
only slightly non-significant (p=0.0738)
provisionally significant (p=0.073)
quasi-significant (p=0.09)
4

AmblyrhynchusJune 20, 2018 at 2:12 pm

This whole post (and he journalisic cliche in the press release) seems to based entirely on conflating non-coding DNA with junk DNA.

SA,

Those comments sort of illustrate the wierdness of null hypothesis testig, but there is no indication on that page these are from evolutionary biologists, much less “Darwinists”.
5

LatemarchJune 20, 2018 at 2:19 pm

The ‘Just So’ stories continue. It’s all proof of evolution.

What’s amazing is that they aren’t embarrassed by any of this.
“But of course we have changed our minds. Science is self correcting.”
As if science (See SA@3) was what they were doing all along.

Ambly@4:

Those comments sort of illustrate the wierdness of null hypothesis testig,[sic] but there is no indication on that page these are from evolutionary biologists, much less “Darwinists”.

No, probably not from either evolutionary biologists or Darwinists. Neither hardly ever stoops to using a non-materialist mathematics to support their science.
6

Silver AsiaticJune 20, 2018 at 2:42 pm

Amblyrhynchus @4

That distinction was added later in the scientific conversation as yet another attempt to salvage some credibility. When researchers find some new functionality for what was previously considered Junk DNA, then Darwinists can still claim, “yes, it’s functional but it’s still non-coding”.

Now that discoveries are showing functions for the supposed junk, evolutionists like Dawkins can say “of course, it must have a function, that’s what evolution would select for”.

Now, as above to avoid some embarrassment. “We never said Junk DNA was non-functional, only that it was non-coding”.

Right. If any biological feature doesn’t code for genes then we should call it junk?

As for the fudging of statistics – yes, perhaps evolutionary biologists are the only scientists who do not use such tactics. I’ve read enough of their papers and personal opinions over the years to draw my own conclusion.
7

AmblyrhynchusJune 20, 2018 at 2:47 pm

That distinction was added later in the scientific conversation as yet another attempt to salvage some credibility. When researchers find some new functionality for what was previously considered Junk DNA, then Darwinists can still claim, “yes, it’s functional but it’s still non-coding”.

This is not true at all, do you just make this stuff up or what?
8

bornagain77June 20, 2018 at 2:57 pm

Actually, Richard Dawkins can’t slip out from the ‘prediction’ of junk DNA so easily.

The ‘prediction’ of junk DNA came from population genetics itself. That is why Dan Graur and Larry Moran were so flustered by the results of ENCODE and is exactly why they fought so hard against the ENCODE results.

Revisiting the genetic load argument with Dan Graur – Larry Moran – JULY 14, 2017
Excerpt: The deleterious mutation rate is calculated using the lowest possible mutation rate and the smallest percentage of deleterious mutations (4%). Under these conditions, the human population could survive with a fertility value of 1.8 as long as less than 25% of the genome is functional (i.e. 75% junk) (red circle). That’s the UPPER LIMIT on the functional fraction of the human genome.
But that limit is quite unreasonable. It’s more reasonable to assume about 100 new mutations per generation with about 10% deleterious. Using these assumptions, only 10% of the genome could be functional with a fertility value of 1.8 (green circle).
Whatever the exact percentage of junk DNA it’s clear that the available data and population genetics point to a genome that’s mostly junk DNA. If you want to argue for more functionality then you have to refute this data.
http://sandwalk.blogspot.com/2.....-with.html

Maybe Moran and Graur need a refresher course on how science actually works:

The Scientific Method – Richard Feynman – video
Quote: ‘If it disagrees with experiment, it’s wrong. In that simple statement is the key to science. It doesn’t make any difference how beautiful your guess is, it doesn’t matter how smart you are who made the guess, or what his name is… If it disagrees with experiment, it’s wrong. That’s all there is to it.”
https://www.youtube.com/watch?v=OL6-x0modwY

The ENCODE Embroilment, – part 3
Excerpt: A Great Divorce
Critics like Dan Graur charge that ENCODE is guilty of “divorcing genomic analysis from its evolutionary context”22—and that’s exactly right. ENCODE’s empirically based finding that the vast majority of our genome is functional has withstood theoretical, evolution-based objections from critics. Maybe a divorce from evolutionary thinking is exactly what we need to liberate biology from bad evolutionary assumptions and explain what’s happening inside our cells.,,,
http://www.salvomag.com/new/ar.....rt-III.php

Dan Graur, Darwin’s Reactionary – June 21, 2017
Excerpt: In 2013, biologist Dan Graur criticized the “evolution-free gospel of ENCODE” and accused its researchers of “playing fast and loose with the term ‘function,’ by divorcing genomic analysis from its evolutionary context.”81 In a lecture at the University of Houston, Graur argued that “if the human genome is indeed devoid of junk DNA as implied by the ENCODE project, then a long, undirected evolutionary process cannot explain the human genome.” In other words: “If ENCODE is right, then evolution is wrong.” But for Graur, evolution can’t be wrong. His solution to the problem? “Kill ENCODE.”82,,,
Lots of evolutionists think that way but only the rare Darwinian atheist materialist is willing to state the matter as nakedly as this. No wonder Dr. Graur is among a list of individuals thanked by Dr. Wells in his Acknowledgments for “making embarrassingly candid or unwittingly humorous statements.”
https://evolutionnews.org/2017/06/dan-graur-darwins-reactionary/
9

goodusernameJune 20, 2018 at 3:13 pm

SA,

That distinction was added later in the scientific conversation as yet another attempt to salvage some credibility.

So what is the time period where no such distinction was made? I remember in the 1980s biologists regularly attempting to explain that not all non-coding dna is considered junk, as there’s non-coding dna that has functions, such as various regulatory roles. The media never seems to get the memo though.

I believe the distinction is even in the 1972 paper that coined the term “junk dna”.

For how many years (decades) has Larry Moran been predicting that the amount of dna in our genome will be about 90%?
I think currently we know of about 1% of non-coding dna has a function of some kind. In other words, we need to find about 10x more functional non-coding dna that what’s currently known. Maybe in another 100 years or so of finding more and more functional non-coding dna we’ll start getting close to his 90% prediction.
10

AmblyrhynchusJune 20, 2018 at 3:30 pm

I’m afraid you don’t understand what these words mean, SA.

Now, as above to avoid some embarrassment. “We never said Junk DNA was non-functional, only that it was non-coding”.

Junk DNA is by definition non-functional. Non-coding DNA is DNA that doesn’t make a protein.

As Goodusername points out, the paper introducing the term Junk DNA explicitly includes regulatory sequences (like the enhancer in the paper that precipitated this post…) in the functional (i.e. non-junk) part of the genome. So this distinction is as old as the term.
11

AmblyrhynchusJune 20, 2018 at 3:30 pm

I’m afraid you don’t understand what these words mean, SA.

Now, as above to avoid some embarrassment. “We never said Junk DNA was non-functional, only that it was non-coding”.

Junk DNA is by definition non-functional. Non-coding DNA is DNA that doesn’t make a protein.

As Goodusername points out, the paper introducing the term Junk DNA explicitly includes regulatory sequences (like the enhancer in the paper that precipitated this post…) in the functional (i.e. non-junk) part of the genome. So this distinction is as old as the term.
12

Silver AsiaticJune 20, 2018 at 3:45 pm

GUN

I think currently we know of about 1% of non-coding dna has a function of some kind.

To call the remaining 99% “non-functional” is a misnomer then, in that case. That’s how scientific predictions are supposed to work. When the statement is made “this is non-functional” and that is used as evidence which supports the theory that supposedly predicted such, when it is later discovered that there is, indeed, function present there — then the prediction/theory is falsified.
13

Silver AsiaticJune 20, 2018 at 3:52 pm

Amblyrhynchus @10

Junk DNA is by definition non-functional. Non-coding DNA is DNA that doesn’t make a protein.

As mentioned above, to identify regions as being Junk DNA is to state that they are non-functional. When functions are later discovered in Junk DNA, then the original claim was falsified.
So, on what basis should we continue to accept that the rest is necessarily Junk DNA/non-functional?
14

AmblyrhynchusJune 20, 2018 at 3:55 pm

Who identified this region as junk DNA?
15

Silver AsiaticJune 20, 2018 at 4:01 pm

There is a deeper level to the sleight of hand than merely a confusion of terms. That’s my concern.

You proclaim a theory. It predicts something. It makes an affirmative statement about what should be observed.
Then the prediction is shown to be false.
Have some courage.
Just say it. The theory is wrong.
16

goodusernameJune 20, 2018 at 4:06 pm

SA,

To call the remaining 99% “non-functional” is a misnomer then, in that case.

Who on earth is doing that?

Why do you think that even one of the champions of the term “junk dna,” Larry Moran, is “only” saying that about 90% of the genome is junk? It’s because “non-coding” does not imply “non-functional”, and there’s undoubtedly many, many, regions of dna which have a function that we don’t know about yet.

…the theory that supposedly predicted such…

The theory didn’t predict such. When it was discovered that there were (apparently) regions of dna that didn’t have function, it came as a surprise. Even the discovery that there’s dna that doesn’t code for protein came as a surprise. What geneticists were predicting was that chromosomes would be one gene after another like beads on a string.

Sure, there are many that have attempted to explain the presence of junk dna by invoking Darwinism, but it was not a prediction.
17

Silver AsiaticJune 20, 2018 at 4:10 pm

Amblyrhynchus @13

I’m sorry, I may have worded that incorrectly. I meant to follow what Nitzan Gonen, Chris R. Futtner, Sophie Wood, S. Alexandra Garcia-Moreno, Isabella M. Salamone, Shiela C. Samson, Ryohei Sekido, Francis Poulat, Danielle M. Maatouk, Robin Lovell-Badge said …

Our study also highlights the important role of what some still refer to as ‘junk’ DNA …

You’ve defined Junk DNA as “non-functional”.
But the researchers looked at what was referred to as Junk DNA and found an “important role (function)”.

So, since there is function found in Junk DNA, then your definition that “Junk DNA is non-functional” is false.
18

Silver AsiaticJune 20, 2018 at 4:17 pm

GUN

there’s undoubtedly many, many, regions of dna which have a function that we don’t know about yet.

Then how do you know which ones are non-functional?

Sure, there are many that have attempted to explain the presence of junk dna by invoking Darwinism, but it was not a prediction.

Ok, that’s a very safe way to proceed but a failure to make predictions is almost as bad as making false predictions. It makes the weakness of the theory very evident. (As do various “surprises” that occur).
19

AmblyrhynchusJune 20, 2018 at 4:27 pm

You haven’t answered the question though, who identified this region as junk DNA?

These researchers seem to conflate non-coding and junk DNA too. But that doesn’t mean the distinction doesn’t exist (as I’ve shown, the distinction is as old as the term junk DNA).
20

Silver AsiaticJune 20, 2018 at 5:09 pm

Amblyrhynchus

You haven’t answered the question though, who identified this region as junk DNA?

Who? The researchers called them “some”.

Who they were precisely? That would be everybody who considered the region to be non-functional. So, the entire biological/genetic research community that accepts the concept of Junk DNA. That was a region, referred to by them, as non-functional. That is what the researchers stated.

These researchers seem to conflate non-coding and junk DNA too. But that doesn’t mean the distinction doesn’t exist (as I’ve shown, the distinction is as old as the term junk DNA.

As stated earlier, in order to observe the existence of “non-functional DNA” one has to know that it does not serve a function in the cell. We find new discoveries of function in non-coding regions frequently. So, how could we know with certainty that any non-coding regions are necessarily non-functional?
21

AmblyrhynchusJune 20, 2018 at 5:29 pm

How do you get from

Who? The researchers called them “some”.

Who they were precisely? That would be everybody who considered the region to be non-functional

to

So, the entire biological/genetic research community that accepts the concept of Junk DNA

There is no link that I can find. I very much doubt anyone ever called this particular region junk. These researchers seem to be making the same mistake as you, conflating “junk” with “non-coding”.
22

Nonlin.orgJune 20, 2018 at 5:45 pm

ET and Kas,

Actually, Darwinism and its neo is very much testable and it fails all tests:
Gradualism fails – http://nonlin.org/gradualism/
Natural selection fails – http://nonlin.org/natural-selection/
Divergence of character fails – http://nonlin.org/evotest/
Speciation fails – http://nonlin.org/speciation-problems/
DNA “essence of life” fails – http://nonlin.org/dna-not-essence-of-life/
Randomness fails – http://nonlin.org/random-abuse/
Abiogenesis fails – http://nonlin.org/warmpond/
etc., etc.

And let’s test it again and make sure it fails again and again: http://nonlin.org/evotest/
23

SeverskyJune 20, 2018 at 7:27 pm

From New Scientist 17 July 2017

At least 75 per cent of our DNA really is useless junk after all

[…]

The grandest claim came in 2012, when a consortium of genomics researchers called ENCODE declared that, according to their project, a huge 80 per cent of the DNA in the human genome has a function. “They had spent $400 million, they wanted something big to say,” says Dan Graur of the University of Houston.

Graur is one of many researchers who didn’t believe ENCODE’s claim. 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

[…]

Following Graur’s logic, if most of our DNA is functional, we would accumulate a large proportion of harmful mutations in important sequences. But if most of our DNA is junk, the majority of mutations would have no effect.

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. If the entire genome was functional, couples would need to have around 100 million children, and almost all would have to die. Even if just a quarter of the genome is functional, each couple would still have to have nearly four children on average, with only two surviving to adulthood, to prevent harmful mutations building up to dangerous levels.

Taking into account estimates of the mutation rate and average prehistorical reproduction rate, Graur’s team calculated that only around 8 to 14 per cent of our DNA is likely to have a function.

This ties in nicely with a 2014 study that compared our genome with other species and concluded that around 8 per cent of it is functional.

“The findings are entirely supportive of one another,” says one of the authors of the 2014 study, Chris Ponting of the University of Edinburgh, UK. “We are walking around with a genome where only 1 in 10 bases actually matters.”
24

DATCGJune 20, 2018 at 9:16 pm

Richard Dawkins comparison 2009 – 2012…

Dawkins in 2009:

“It stretches even their creative ingenuity to make a convincing reason why an intelligent designer should have created a pseudogene — a gene that does absolutely nothing and gives every appearance of being a superannuated version of a gene that used to do something — unless he was deliberately setting out to fool us…

Leaving pseudogenes aside, it is a remarkable fact that the greater part (95 percent in the case of humans) of the genome might as well not be there, for all the difference it makes.”

“(95 percent in the case of humans)… “might as well not be there”

Dawkins in 2012:

“I have noticed that there are some creationists who are jumping on [the ENCODE results] because they think that’s awkward for Darwinism. Quite the contrary it’s exactly what a Darwinist would hope for, to find usefulness in the living world….

Whereas we thought that only a minority of the genome was doing something, namely that minority which actually codes for protein, and now we find that actually the majority of it is doing something.

What it’s doing is calling into action the protein-coding genes. So you can think of the protein-coding genes as being sort of the toolbox of subroutines which is pretty much common to all mammals — mice and men have the same number, roughly speaking, of protein-coding genes and that’s always been a bit of a blow to self-esteem of humanity. But the point is that that was just the subroutines that are called into being; the program that’s calling them into action is the rest [of the genome] which had previously been written off as junk.”

From, “might as well not be there” to “now we find the majority is now doing something” and “program… calling… rest [of the genome] which had previously been written off as JUNK”

Amazing turnabout by Dawkins and waffle, waffle, rewrite Darwinist history crowd.

95% or 98% myth of JUNK DNA exist because yes, many neo-Darwinist believed it for decades and pushed it as factual and truth, then routinely turned around and beat people over the head if any dare to think otherwise as dumb and stupid.

Seversky quotes Graur @22, who cannot give up his religious convictions and predicts at least 75% junk based upon blind, unguided evolutionary assumptions. He must have that 75% or his blind assumptions fail. But his belief drives him, not science. It’s the final breath of a failed and flawed theory based much upon ignorance over the last century and a half.

The antiquated neo-Darwinist faithful seemingly cannot give up their own religion.

We shall see if Dan Graur is correct or not.

Time does not stop and more function is found daily, 24/7 around the globe in former regions dedicated as “JUNK” DNA, once thought by Dawkins to “might as well not be there” and many scientist like him.
25

DATCGJune 20, 2018 at 9:46 pm

the pseudogene junk?

I’ve said this before. A Darwinist called me stupid and dumb for daring to think a pseudogenes might have function.

So, Dawkins(quoted above #23) as many Darwinist faithful believed pseudogenes had no purpose. But his opinion and speculation was based upon ignorance, not objective, scientific research.

Turns many do have functions. They support gene expression and turn up in regulatory controls of the parent genes. Very important scientific research as a deleterious mutation can lead to disease.

So far from “writing off” pseudogenes or “junk” as not needing to be there at all, it turns out to be extremely important in solving and curing disease.

So how does a Darwinist spin this? Miraculous resurrection story 😉 Pseudogenes have function and “JUNK” DNA started by Ohno 1972…

Not So Pseudo Anymore: Pseudogenes as Therapeutic Targets

Abstract
Pseudogenes are junk DNA gene remnants generated by inactivating mutations or the loss of regulatory sequences, often following gene duplication or retrotransposition events. These pseudogenes have previously been considered to be molecular fossils derived from once-coding genes. In many cases, pseudogenes confer no observable selective advantage to the host organism and may be on a path towards removal from the genome.

However, pseudogenes can also serve as raw material for the exaptation of novel functions, particularly in relation to the regulation of gene expression. Many pseudogenes are resurrected as noncoding RNA genes, which function in RNA-based gene regulatory circuits.

As such, functional pseudogenes might simply be considered as ‘genes’.

Here, we discuss the role of these pseudogene-derived RNAs as regulators of gene expression in the context of human disease. In particular, we consider the manipulation of pseudogene transcripts through the use of antisense oligonucleotides, siRNAs, aptamers or classical gene therapy approaches as novel pharmacological strategies.

Keywords: epigenetics, lncRNAs, long noncoding RNAs, microRNA, miRNA, pseudogenes, therapeutics

A pseudogene is a genomic DNA sequence that is closely related to a paralogous parent gene but is deficient with respect to the parent gene function [1,2]. Typically, these are gene copies that have lost their protein-coding potential. Pseudogenes were first identified in Xenopus laevis [3] and have since been found in a range of organisms, including bacteria, plants and animals [4].

The estimated number of pseudogenes in the human genome is comparable to that of protein-coding genes(~20,000) [5,6].

What if? What if just half the number of pseudogenes(~10k) turn out to have function?

“JUNK” DNA, Ohno, “JUNK” DNA, “Trash…”

In a classic 1972 essay, Ohno proposed the concept of junk DNA to explain the dramatic differences in genome sizes between organisms of similar levels of complexity/occupying similar niches (the so-called C-value paradox) [7].

The sequencing of the human genome subsequently demonstrated that protein-coding genes constitute only approximately 1% of the genome [8,9], and the remainder was assumed to be noncoding junk. Junk DNA has often been considered nonfunctional ‘trash’ and, by extension, pseudogenes have been dismissed as failed copes of genes that contribute nothing to the survival of the organism.

However, Ohno was prescient enough to propose that junk DNA could also serve as a raw material for evolutionary innovation (similar ideas were also proposed by Britten and Davidson at approximately the same time [10,11]).(miracle Darwinist resurrection story)

Some pseudogenes are clearly nonfunctional ‘dying’ genes. For example, comparative genomic studies in mammals have revealed a great diversity in the number of functional and pseudo-genized olfactory receptor genes [12]. Indeed, all olfactory receptor genes in the dolphin (Stenella coeruleoalba) genome are pseudogenes [13].

Similarly, the ancient gene ACYL3 has been lost from the human lineage, but retained as a pseudogene [14]. Conversely, other pseudogenes have been ‘resurrected’(see – miracle!) as long noncoding RNA (lncRNA) genes that adopt new functions, as in the case of XIST, the noncoding RNA initiator of X chromosome inactivation [15].

In this article, we discuss those pseudogenes that have evolved functions(miracle resurrection!) related to human disease and discuss the therapeutic potential of manipulating their expression.

Darwinism is a religion with it’s own “resurrection” story 😉
26

DATCGJune 20, 2018 at 9:52 pm

from the paper quoted in #24 above, more evidence of function in formerly named “Trash” and “Junk” DNA regions…

Although pseudogenes are generally considered to be evolving neutrally, many show evidence of evolutionary conservation [35–37]. specifically, Svensson et al. identified 30 transcribed pseudogenes that were conserved between humans and mice [37]. Khachane and Harrison showed that whereas only approximately 3% of transcribed pseudogenes were conserved between humans and mice, the conservation between humans and rhesus monkeys was much higher (~50%) [35].

Similarly, transcribed pseudogenes show evidence of being under selection pressure in these monkeys, and 68 transcribed pseudogenes were found to be syntenic between humans and at least two other mammals [35]. Additionally, pseudogenes that show higher levels of evolutionary constraint show a greater tendency towards being transcribed [38].

Taken together, these studies suggest that many pseudogenes have evolved under positive selective pressure, consistent with biological functionality. The fact that many of these pseudogene sequences are conserved but restricted to certain mammals (or specific to the primate lineage) suggests that they may represent relatively recent evolutionary innovations.

There are interesting parallels with studies that show that the amount of noncoding DNA (corrected for ploidy) scales with organismal complexity [39], whereas the number of protein-coding genes does not [40].

It is tempting to speculate that some of the novel gene-regulatory functions that result from exapted(unexplained transformation miracle happens – Evolution did it story) pseudogene sequences may account for the differences between organisms with similar coding gene repertoires.

The functionality of many lncRNA transcripts often manifests through the formation of secondary structure motifs that can act as binding domains for proteins or other nucleic acids. Positive selection may be acting to conserve these structural features, but this would not be apparent at the primary sequence level [41]. As a result, sequence based evolutionary comparisons and analysis could be misleading. As templates for lncRNAs, pseudogenes may be subject to this type of selection, although a structure-based view of conservation analysis would be required to detect this.

Transcribed pseudogenes show tissue-specific patterns of expression [23,38] and multiple studies have reported testis-specific pseudogene transcription [21,23,42,43]. In some cases, pseudogenes are expressed in tissues in which the parent gene is not. For example, the 5-HT7 receptor (HRT7) has a pseudogene that is expressed in liver and kidney, which are tissues that do not express the parent HTR7 gene [44,45]. Further more, expression of some pseudogenes is dynamic and responds to physiological signals, such as cell stress [43].

Pseudogene expression has also been implicated in the control of neuronal differentiation[46]. These observations are indicative of tightly regulated expression of pseudogene transcription, consistent with biological function.

However, it could equally be argued that regulated pseudogene transcription is a consequence of differential transcription factor expression, leading to tissue-specific or stress-responsive ‘leaky’ transcription.

Very interesting reading for anyone reviewing history. How misleading some can be and how wrong Darwinist and neo-Darwinist were for quite some time. Thus the need for an Extended Synthesis, but not revisionist history.

Clearly JUNK DNA was pushed by many scientist, including Mr. Public Scientist himself – Dawkins. And was required by Dr. Ohno.

Whether Graur’s assumptions are correct may still turn out to be wrong and based upon ignorance, not science.
27

DATCGJune 20, 2018 at 10:29 pm

Lovely, there are so many new discoveries every day in former “JUNK” declared regions. Don’t have the time to keep reading, reviewing, and posting but how fascinating it is to make such crucial and important discoveries in what many Darwinist wrote off as non-important DNA regions, or what was it?

“Might as not well be there, for all the difference it makes.” Richard Dawkins

https://www.ncbi.nlm.nih.gov/pmc/articles/PMC5829750/

We found that the 34 translated pseudogenes have peptides identified from on average two out of 30 tissues (including cell lines) surveyed in the human proteomic data.

The corresponding number (28) is much larger for their parental genes. Furthermore, the protein expression tissues of each translated pseudogene are a subset of those of its parental gene. The translated pseudogenes appear in 64 tissues in total (a tissue is counted as many times as the number of pseudogenes found translated in the tissue), including 6 times in testis and 58 times in other tissues. This ratio of 6/58 = 0.1 is greater than the corresponding ratio (0.04) for their parental genes with marginal significance (P = 0.07, Fisher’s exact test). A ratio of 0.7 was found among the translated pseudogenes with ? significantly smaller than 1. The preferred translation of pseudogenes in testis may be explained by the hyper-transcription hypothesis, which states that, in haploid germ cells of the testis, an overall permissive chromatin and abundant RNA polymerase II complexes promote widespread gene expression (Schmidt 1996; Soumillon et al. 2013).

The detection of purifying selection acting on five translated pseudogenes of humans raises the question of whether these pseudogenes were misannotated.

Strictly speaking, the answer is yes, because by definition they are not pseudogenes if they are subject to purifying selection. A more practical question is whether their annotations as pseudogenes followed the commonly used guideline. The answer is also yes, because there was no evidence for their mRNA or protein expression at the time of annotation.

Given that they are transcribed and translated and are under purifying selection, they should be reannotated as genes. These cases illustrate the point that neither ORF disruption nor presumed loss of promoter activity upon retroposition proves that a gene is nonfunctional.

… very interesting last paragraph, how much more to find, learn and maybe be “reannotated” based upon new research.
28

DATCGJune 20, 2018 at 10:41 pm

“The more sophisticated an organism, the higher the percentage of junk DNA it contains.”
Nessa Carey, Junk DNA: A Journey Through the Dark Matter of the Genome

http://www.nessacarey.co.uk

“heretical…”

There are lots of situations where two things are genetically identical, but which aren’t the same.

This is the field of epigenetics, and it tells us that there must be more to us than just our DNA code. The science is weird, heretical and fascinating.

If the genes that code for proteins are so important, why do they comprise only 2% of the human genome? For years(decades), the rest(98%) was dismissed as unimportant “junk DNA”.

But now we know that these neglected regions have a huge range of important functions.

Both epigenetics and junk DNA affect huge amounts of life on earth and have a big impact on human health.

( ) emphasis mine

No kidding, but… no one used “junk” DNA in the past to write off large portions of DNA? Please, that is revisionist history.
29

bornagain77June 21, 2018 at 5:06 am

The mathematics of Population Genetics has not been kind to Darwinian claims in the least. First off, because of the “waiting time problem”, Darwinists were forced to cast natural selection, Charles Darwin’s supposed ‘designer substitute’, by the wayside.

The waiting time problem in a model hominin population – 2015 Sep 17
John Sanford, Wesley Brewer, Franzine Smith, and John Baumgardner
Excerpt: The program Mendel’s Accountant realistically simulates the mutation/selection process,,,
Given optimal settings, what is the longest nucleotide string that can arise within a reasonable waiting time within a hominin population of 10,000? Arguably, the waiting time for the fixation of a “string-of-one” is by itself problematic (Table 2). Waiting a minimum of 1.5 million years (realistically, much longer), for a single point mutation is not timely adaptation in the face of any type of pressing evolutionary challenge. This is especially problematic when we consider that it is estimated that it only took six million years for the chimp and human genomes to diverge by over 5 % [1]. This represents at least 75 million nucleotide changes in the human lineage, many of which must encode new information.
While fixing one point mutation is problematic, our simulations show that the fixation of two co-dependent mutations is extremely problematic – requiring at least 84 million years (Table 2). This is ten-fold longer than the estimated time required for ape-to-man evolution. In this light, we suggest that a string of two specific mutations is a reasonable upper limit, in terms of the longest string length that is likely to evolve within a hominin population (at least in a way that is either timely or meaningful). Certainly the creation and fixation of a string of three (requiring at least 380 million years) would be extremely untimely (and trivial in effect), in terms of the evolution of modern man.
It is widely thought that a larger population size can eliminate the waiting time problem. If that were true, then the waiting time problem would only be meaningful within small populations. While our simulations show that larger populations do help reduce waiting time, we see that the benefit of larger population size produces rapidly diminishing returns (Table 4 and Fig. 4). When we increase the hominin population from 10,000 to 1 million (our current upper limit for these types of experiments), the waiting time for creating a string of five is only reduced from two billion to 482 million years.
http://www.ncbi.nlm.nih.gov/pm.....MC4573302/

“Darwinism provided an explanation for the appearance of design, and argued that there is no Designer — or, if you will, the designer is natural selection. If that’s out of the way — if that (natural selection) just does not explain the evidence — then the flip side of that is, well, things appear designed because they are designed.”
Richard Sternberg – Living Waters documentary
Whale Evolution vs. Population Genetics – Richard Sternberg and Paul Nelson – (excerpt from Living Waters video)
https://www.youtube.com/watch?v=0csd3M4bc0Q

And when looking at Natural Selection from the physical perspective of what is actually going on, that is to say when looking at Natural Selection with empirical evidence, then it is very easy to see exactly why Natural Selection is grossly inadequate as the supposed ‘Designer substitute’ that Darwinists have falsely imagined it to be.

The abject failure of Natural Selection on two levels of physical reality – video (2016) (princess and the pea paradox & quarter power scaling)
https://youtu.be/ISu-09yq2Gc

Genome-wide analysis of a long-term evolution experiment with Drosophila – 2010
Excerpt of concluding paragraph: “Despite decades of sustained selection in relatively small, sexually reproducing laboratory populations, selection did not lead to the fixation of newly arising unconditionally advantageous alleles. This is notable because in wild populations we expect the strength of natural selection to be less intense and the environment unlikely to remain constant for ~600 generations. Consequently, the probability of fixation in wild populations should be even lower than its likelihood in these experiments.”
http://www.homepages.ed.ac.uk/.....202010.pdf

“The Third Way” – James Shapiro, Denis Noble, and etc.. etc..,,,
excerpt: “some Neo-Darwinists have elevated Natural Selection into a unique creative force that solves all the difficult evolutionary problems without a real empirical basis.”
http://www.thethirdwayofevolution.com/

“the uncritical acceptance of natural selection as an explanatory force for all aspects of biodiversity (without any direct evidence) is not much different than invoking an intelligent designer”
Michael Lynch – The Origins of Genome Architecture, p 368

Since natural selection has been cast by the wayside, Darwinists now claim, via neutral theory, that the vast majority of the amazing integrated complexity found in life is the result of pure chance instead of the result of natural selection.

In the following article Larry Moran quotes Austin Hughes who states, ‘Darwinism asserts that natural selection is the driving force of evolutionary change. It is the claim of the neutral theory, on the other hand, that the majority of evolutionary change is due to chance.’

Austin Hughes and Neutral Theory – Laurence A. Moran – June 19, 2017
Excerpt: Originally proposed by Motoo Kimura, Jack King, and Thomas Jukes, the neutral theory of molecular evolution is inherently non-Darwinian. Darwinism asserts that natural selection is the driving force of evolutionary change. It is the claim of the neutral theory, on the other hand, that the majority of evolutionary change is due to chance.
http://sandwalk.blogspot.com/2.....heory.html

“many genomic features could not have emerged without a near-complete disengagement of the power of natural selection”
Michael Lynch – The Origins of Genome Architecture, intro

“a relative lack of natural selection may be the prerequisite for major evolutionary advance”
Mae Wan Ho – Beyond neo-Darwinism – Evolution by Absence of Selection

Thus, with Natural selection being tossed aside by the mathematics of population genetics, and by empirical evidence, as the explanation for the ‘appearance of design’ that we see in life, Darwinists did not accept such a devastating finding from mathematics as an outright falsification for their theory, as they should have done, but are instead now reduced to arguing that the ‘appearance of design’ that we see in life is, basically, the result of pure chance with natural selection now playing a very negligible role if any role at all.
To call such a move on the part of Darwinists disingenuous would be an understatement.

As William Murray comments on this development within Darwin’s theory,

“One wonders what would have become of evolution had Darwin originally claimed that it was simply the accumulation of random, neutral variations that generated all of the deeply complex, organized, interdependent structures we find in biology? Would we even know his name today?
What exactly is Darwin really famous for now? Advancing a really popular, disproven idea (of Natural Selection), along the lines of Luminiferous Aether?
Without the erroneous but powerful meme of “survival of the fittest” to act as an opiate for the Victorian intelligentsia and as a rationale for 20th century fascism, how might history have proceeded under the influence of the less vitriolic maxim, “Survival of the Happenstance”?”
– William J Murray

Secondly, as mentioned previously, the mathematics of population genetics has forced Darwinists to claim, against all common sense and the results of ENCODE, that the vast majority of our DNA is junk.

Revisiting the genetic load argument with Dan Graur – Larry Moran – JULY 14, 2017
Excerpt: The deleterious mutation rate is calculated using the lowest possible mutation rate and the smallest percentage of deleterious mutations (4%). Under these conditions, the human population could survive with a fertility value of 1.8 as long as less than 25% of the genome is functional (i.e. 75% junk) (red circle). That’s the UPPER LIMIT on the functional fraction of the human genome.
But that limit is quite unreasonable. It’s more reasonable to assume about 100 new mutations per generation with about 10% deleterious. Using these assumptions, only 10% of the genome could be functional with a fertility value of 1.8 (green circle).
Whatever the exact percentage of junk DNA it’s clear that the available data and population genetics point to a genome that’s mostly junk DNA. If you want to argue for more functionality then you have to refute this data.
http://sandwalk.blogspot.com/2.....-with.html

To put is kindly, anyone who claims the vast majority of our DNA is junk in not playing with a full deck.

Genes and Organisms: Improvising the Dance of Life – Stephen L. Talbott – Nov. 10, 2015
Excerpt: The performances of countless cells in your body are redirected and coordinated as part of a global narrative for which no localized controller exists. This redirection and coordination includes a unique choreography of gene expression in each individual cell. Hundreds or thousands of DNA sequences move (or are moved) within vast numbers of cell nuclei, and are subjected to extraordinarily nuanced, locally modulated chemical activity so as to contribute appropriately to bodily requirements that are nowhere codified — least of all in those DNA sequences.,,,
DNA in its larger matrix
You may recall from my earlier article, “Getting Over the Code Delusion” (Talbott 2010), that packing DNA into a typical cell nucleus is like packing about 24 miles of very thin, double-stranded string into a tennis ball, with the string cut up (in the normal human case) into 46 pieces, corresponding to our 46 chromosomes.
To locate a protein-coding gene of typical size within all that DNA is like homing in on a one-half-inch stretch within those 24 miles. Or, rather, two relevant half-inch stretches located on different pieces of string, since we typically have two copies of any given gene. Except that sometimes one copy differs from the other and one version is not supposed to be expressed, or one version needs to be expressed more than the other, or the product of one needs to be modified relative to the other. So part of the job may be to distinguish one of those half-inch stretches from the other. “Decisions” everywhere, it seems.
But no such decisions are made in a vacuum. As it happens, the chromosome does not consist of a naked DNA double helix. Our DNA, rather, is bound up with a massive, intricate, and dynamic protein-RNA-small molecule complex (called chromatin) that is as fully “informative” for the cell as the DNA sequence itself — and, you might say, much more active and directive.,,,
the cell, by managing the shifting patterns of the chromatin infrastructure within which DNA is embedded, brings our chromosomes into movement on widely varying scales. These include large looping movements that put particular genes into connection with essential regulatory sequences and with other, related genes (that is, with other one-half inch stretches of our “24 miles of string in a tennis ball”).,,,
A gene is not in any case the kind of rigidly defined entity one might hope to calculate with. As a functional unit appropriate to current circumstances, it must be cobbled together by the cell according to the needs of the moment. There is no neatly predefined path to follow once the cell has located the “right” half inch or so of string, or once it has done whatever is necessary to bring that locus into proper relation with other chromosomal loci participating in the same “dance”.
One issue has to do with the fact that there are two strands in the DNA double helix and, starting from any particular point, it is possible to transcibe either of two DNA sequences in either of two directions: “forward” along one strand, or “backward” along the other. This yields two completely different products. One of them is very likely not even a protein-coding RNA, and yet it may still play a vital role in gene expression and in cellular processes more generally.
And even when the cell would proceed in one particular direction, it must “choose” the exact point in the genetic sequence at which to begin. Different starting points can yield functionally distinct results. “Many studies focusing on single genes have shown that the choice of a specific transcription start site has critical roles during development and cell differentiation, and aberrations in . . . transcription start site use lead to various diseases including cancer, neuropsychiatric disorders, and developmental disorders”.8,,,
The (protein) enzyme that transcribes DNA into RNA is RNA polymerase12. The enzyme certainly does not work alone, however, and its task is by no means cut-and-dried. To begin with, its critical interactions with various elements of the pre-initiation complex help determine whether and exactly where transcription will begin, if it is to begin at all. Then, after those “decisions” have been made, RNA polymerase moves along the double helix transcribing the sequence of genetic “letters” into the complementary sequence of an RNA.
Throughout this productive journey, which is called elongation, the RNA polymerase still keeps good and necessary company. Certain co-activators modify it during its transit of a genetic locus, and these modifications not only enable transcription elongation to begin, but also provide binding sites for yet other proteins that will cooperate throughout the transcription journey.,,,
Finally — and mirroring all the possibilities surrounding initiation of gene transcription — there are the issues relating to its termination. Again, they are far too many to mention here. Transcription may conclude at a more or less canonical terminus, or at an alternative terminus, or it may proceed altogether past the gene locus, even to the point of overlapping what, by usual definitions, would be regarded as a separate gene farther “downstream”. The cell has great flexibility in determining what, on any given occasion, counts as a gene, or transcriptional unit.
The last part of the transcribed gene is generally non-protein-coding, but nevertheless contains great significance. Examining this region in a single gene, a research team recently identified “at least 35 distinct regulatory elements” to which other molecules can bind.13 Further regulatory potentials arise from yet more binding sites on the customized “tail” that the cell adds to the RNA immediately upon conclusion of its transcription.
Proteins and other molecules that bind to the various regulatory elements of the non-protein-coding portion of the transcript do so in a context-sensitive manner, where cell and tissue type, phase of the cell cycle, developmental stage, location of the RNA within the cell, and environmental factors, both intra- and extra-cellular, may all play a role. These converging influences can change the stability of the RNA, change its localization within the cell, and change the efficiency of its translation into protein, among other possibilities.,,,
What is generally considered the post-transcriptional modulation of gene expression actually begins during transcription proper. A prime example has to do with what happens partly as a result of the pauses during elongation.
Cells don’t just passively accept the RNAs that emerge from the transcription process, but rather “snip and stitch” them via an elaborate procedure known as RNA splicing. It happens that the cutting out and knitting together of selected pieces typically begins before the RNA is fully transcribed, and the rhythm of pauses during elongation has an important influence upon which pieces form the mature transcript.
This splicing operation, which is applied to nearly all human RNAs, is performed by the spliceosome, consisting of a few non-protein-coding RNAs and over 300 cooperating proteins, and is hardly less exacting in its requirements than, say, brain surgery.
For the vast majority of human genes the operation can be performed in different ways, yielding distinct proteins (called isoforms) from a single RNA derived from a single DNA sequence. This is called alternative splicing, and it would be hard to find anything in human development, disease etiology, or normal functioning that is not dependent in one way or another on the effectiveness of this liberty the cell takes with its gene products.
But RNA splicing is hardly the end of it. Through RNA editing the cell can add, delete, or substitute individual “letters” of the RNA sequence.15 Or, leaving the letters in place, the cell can chemically modify them in any of over one hundred different ways.16 ,,,
Eventually, a protein-coding RNA needs to be translated into protein. This happens by means of large molecular complexes called “ribosomes”. Just as with gene transcription, there are many associated factors that must work together to bring about the initiation of translation, many that cooperate with the ribosome during translation, and yet others that play a role in modifying, localizing, or otherwise regulating the newly produced protein.
The overall picture of gene expression is one of unsurveyable complexity in the service of remarkably effective living processes.,,,
A decisive problem for the classical view of DNA is that “as cells differentiate and respond to stimuli in the human body, over one million different proteins are likely to be produced from less than 25,000 genes”.30 Functionally, in other words, you might say that we have over a million genes.,,,
http://www.natureinstitute.org.....nes_29.htm
30

bornagain77June 21, 2018 at 5:18 am

On top of all that, the mathematics of population genetics goes even further than just throwing natural selection overboard as to undermining the Darwinian worldview from within. In this following video and article, Donald Hoffman has, through numerous computer simulations of population genetics shown that if Darwinian evolution were actually true then all our observations of reality would be unreliable.

Donald Hoffman: Do we see reality as it is? – Video – 9:59 minute mark
Quote: “fitness does depend on reality as it is, yes.,,, Fitness is not the same thing as reality as it is, and it is fitness, and not reality as it is, that figures centrally in the equations of evolution. So, in my lab, we have run hundreds of thousands of evolutionary game simulations with lots of different randomly chosen worlds and organisms that compete for resources in those worlds. Some of the organisms see all of the reality. Others see just part of the reality. And some see none of the reality. Only fitness. Who wins? Well I hate to break it to you but perception of reality goes extinct. In almost every simulation, organisms that see none of reality, but are just tuned to fitness, drive to extinction that perceive reality as it is. So the bottom line is, evolution does not favor veridical, or accurate perceptions. Those (accurate) perceptions of reality go extinct. Now this is a bit stunning. How can it be that not seeing the world accurately gives us a survival advantage?”
https://youtu.be/oYp5XuGYqqY?t=601

The Evolutionary Argument Against Reality – April 2016
The cognitive scientist Donald Hoffman uses evolutionary game theory to show that our perceptions of an independent reality must be illusions.
Excerpt: “The classic argument is that those of our ancestors who saw more accurately had a competitive advantage over those who saw less accurately and thus were more likely to pass on their genes that coded for those more accurate perceptions, so after thousands of generations we can be quite confident that we’re the offspring of those who saw accurately, and so we see accurately. That sounds very plausible. But I think it is utterly false. It misunderstands the fundamental fact about evolution, which is that it’s about fitness functions — mathematical functions that describe how well a given strategy achieves the goals of survival and reproduction. The mathematical physicist Chetan Prakash proved a theorem that I devised that says: According to evolution by natural selection, an organism that sees reality as it is will never be more fit than an organism of equal complexity that sees none of reality but is just tuned to fitness. Never.”
https://www.quantamagazine.org/20160421-the-evolutionary-argument-against-reality/

Thus, in what should be needless to say, a worldview that undermines the scientific method itself by holding all our observations of reality are unreliable is NOT a worldview that can ever be firmly grounded within the scientific method!

Steps of the Scientific Method
Observation/Research
Hypothesis
Prediction
Experimentation
Conclusion
http://www.sciencemadesimple.c.....ethod.html

Moreover, completely contrary to what Donald Hoffman found from the mathematics of population genetics,, conscious observation, far from being unreliable, is experimentally found to be far more integral to reality, i.e. far more reliable of reality, than the mathematics of population genetics had predicted. In the following experiment, it was found that reality doesn’t exist without an observer.

New Mind-blowing Experiment Confirms That Reality Doesn’t Exist If You Are Not Looking at It – June 3, 2015
Excerpt: The results of the Australian scientists’ experiment, which were published in the journal Nature Physics, show that this choice is determined by the way the object is measured, which is in accordance with what quantum theory predicts.
“It proves that measurement is everything. At the quantum level, reality does not exist if you are not looking at it,” said lead researcher Dr. Andrew Truscott in a press release.,,,
“The atoms did not travel from A to B. It was only when they were measured at the end of the journey that their wave-like or particle-like behavior was brought into existence,” he said.
Thus, this experiment adds to the validity of the quantum theory and provides new evidence to the idea that reality doesn’t exist without an observer.
http://themindunleashed.org/20.....at-it.html

Apparently science itself could care less if Darwinists are forced to believe, because of the mathematics of population genetics, that their observations of reality are unreliable!

Moreover, as if all that was not bad enough, Darwinian evolution, since it is based on ‘reductive materialism’, denies the reality of the immaterial realm. That is to say, there simply is no place for the immaterial, “Platonic”, realm of mathematics to find grounding for its reality within the reductive materialism that undergirds Darwinian thought.

What Does It Mean to Say That Science & Religion Conflict? – M. Anthony Mills – April 16, 2018
Excerpt: In fact, more problematic for the materialist than the non-existence of persons is the existence of mathematics. Why? Although a committed materialist might be perfectly willing to accept that you do not really exist, he will have a harder time accepting that numbers do not exist. The trouble is that numbers — along with other mathematical entities such as classes, sets, and functions — are indispensable for modern science. And yet — here’s the rub — these “abstract objects” are not material. Thus, one cannot take science as the only sure guide to reality and at the same time discount disbelief in all immaterial realities.
https://www.realclearreligion.org/articles/2018/04/16/what_does_it_mean_to_say_that_science_and_religion_conflict.html

Platonic World vs Physical World
https://i2.wp.com/abyss.uoregon.edu/~js/images/platonic_physical.gif

Therefore, besides Darwinian evolution already being shown to be mathematically impossible (by Sanford, Dembski, Marks, Axe, Behe, Durston etc.. etc..), Darwinian evolution is further falsified by mathematics as being a scientific theory since Darwinism denies the very reality of one the thing it most needs, i.e. mathematics, in order to be considered scientific in the first place.

Darwinian Evolution vs Mathematics – video
https://www.youtube.com/watch?v=q3gyx70BHvA
31

Silver AsiaticJune 21, 2018 at 6:36 am

20
Amblyrhynchus

There is no link that I can find. I very much doubt anyone ever called this particular region junk.

You could be right, and true, I do not have a link to any specific person. But I hope you’re not trying to draw a distinction between Junk DNA and non-functional DNA. You stated earlier that the two are equivalent.
If anyone states that 75% (for example) of DNA is Junk (non-functional), they are referring to something. They are identifying regions. What regions?
That’s the problem that I’m pointing to, and I believe you are echoing the same problem.
It’s a very big risk for anyone to state, definitively, that any specific region is non-functional/Junk.
In fact, these researchers use the phrase “of what some still refer to as ‘junk’ DNA …”

The word I highlighted is significant. They’re saying “There are still some who think they can call regions ‘non-functional’ but they do so at a big risk of being proven wrong”.

Now, you state that nobody ever called this region non-functional (equivalent term to junk DNA by your definition).

I put the challenge back to anyone: What regions, specifically, are you claiming to be non-functional? How do you know that no function will be found there?

Facing those questions, I believe most geneticists will realize that to claim that non-functional/Junk DNA even exists at all anywhere, is a predictive-risk that is not worth taking. Already, we see it here: “some are still claiming that there is Junk DNA”.

So, there’s a problem. From Ohno’s paper through the gradual findings of function for pseudogenes through the following decades, you’ll find the answer to your question of “who called this region ‘Junk’.” You’re saying nobody did. The researchers who made the discovery said “some” did.

DATCG’s post @23 quotes Richard Dawkins:

Whereas we thought that only a minority of the genome was doing something, namely that minority which actually codes for protein, and now we find that actually the majority of it is doing something.

He may answer your question as to “who called this region ‘Junk’?” Dawkins said “we” did. He’s referring to himself and his fellow “Darwinists” (his term). As I said, the entire evolutionary biology community who accepted the concept of Junk DNA are the ones who said this, and except for functions already known in non-coding regions, they believed it was 95% of the genome.

If they didn’t know of a function at that moment in time for any region – they called that region Junk.
They were proven wrong, and most likely will continue to be proven wrong (and they will probably claim “we never called it ‘Junk'”).
32

ETJune 21, 2018 at 6:44 am

At least 75 per cent of our DNA really is useless junk after all

That is based on ignorance and nothing else.

Did the histone octamers evolve to spool up and organize all of that junk along with the functional DNA?
33

PearlmanJune 21, 2018 at 11:51 am

Nice article. Shared.
RCCF comments: As far as testable predictions, that pass or falsify, Neo-Darwin doctrine (NDT) a failed hypothesis long ago when the critical mass of transitional fossils predicted are known not to exist.
Appreciating ‘junk’ is just more icing on the cake, that NDT falsified and a religious like blind faith based dogmatic doctrine only, not science. So should be barred from the public classroom due to the establishment clause. True scientists would want to stick to the science, not the deep-time dependent doctrine dogma. Refrerence and references in: RCCF framework for understanding science.
34

MungJune 21, 2018 at 12:10 pm

ET:

That is based on ignorance and nothing else.

So?
35

Silver AsiaticJune 21, 2018 at 1:17 pm

I recall the days when resident Darwinist trolls here would argue endlessly on this topic. Like Dawkins’ comments cited in post #24 here – it’s pathetic.
36

AmblyrhynchusJune 21, 2018 at 3:50 pm

If anyone states that 75% (for example) of DNA is Junk (non-functional), they are referring to something. They are identifying regions. What regions?

This not true at all. The best evidence that much of our genome, and the genomes of many other organisms, are not essential for normal biological function doesn’t depend on declaring this or that region. Instead, you want to look at the evidence from genetic load and the inverse correlation between the power of selection and genome size.

Now, you can use a little bit of evolutionary biology to narrow down which parts of the non-coding sequence are likely to functional. For instance, functional regions tend to be conserved within and among-species. If you read the paper that started this discussion you’ll see the enhancer they knock out to reverse sex determination is unusually highly conserved comparing mice to primates. So, not only was this region never determined to be junk, evolutionary biology gave us a reason to suspect it wasn’t.
37

bornagain77June 21, 2018 at 6:57 pm

As was mentioned in post 29, population genetics, via ‘the waiting time problem’, has shown that Natural Selection, Darwin’s supposed ‘Designer substitute’, to be grossly inadequate.

As was also shown, in post 29, since natural selection has been cast by the wayside, Darwinists now claim, via neutral theory, that the vast majority of the amazing integrated complexity being found in life is the result of pure chance instead of being the result of natural selection.

That is to say that Darwinists now claim, basically, that random mutations, all by their lonesome, with virtually no help from natural selection, created all the amazing integrated complexity, i.e. ‘appearance of design’, that we see in life.

Small problem with this heavy reliance on ‘random’ mutations that Darwinists have, mutations are now, empirically, shown to NOT be random mutations but to be directed mutations:

How life changes itself: the Read-Write (RW) genome. – 2013
Excerpt: Research dating back to the 1930s has shown that genetic change is the result of cell-mediated processes, not simply accidents or damage to the DNA. This cell-active view of genome change applies to all scales of DNA sequence variation, from point mutations to large-scale genome rearrangements and whole genome duplications (WGDs). This conceptual change to active cell inscriptions controlling RW genome functions has profound implications for all areas of the life sciences.
http://www.ncbi.nlm.nih.gov/pubmed/23876611

WHAT SCIENTIFIC IDEA IS READY FOR RETIREMENT? Fully Random Mutations – Kevin Kelly – 2014
Excerpt: What is commonly called “random mutation” does not in fact occur in a mathematically random pattern. The process of genetic mutation is extremely complex, with multiple pathways, involving more than one system. Current research suggests most spontaneous mutations occur as errors in the repair process for damaged DNA. Neither the damage nor the errors in repair have been shown to be random in where they occur, how they occur, or when they occur. Rather, the idea that mutations are random is simply a widely held assumption by non-specialists and even many teachers of biology. There is no direct evidence for it.
On the contrary, there’s much evidence that genetic mutation vary in patterns. For instance it is pretty much accepted that mutation rates increase or decrease as stress on the cells increases or decreases. These variable rates of mutation include mutations induced by stress from an organism’s predators and competition, and as well as increased mutations brought on by environmental and epigenetic factors. Mutations have also been shown to have a higher chance of occurring near a place in DNA where mutations have already occurred, creating mutation hotspot clusters—a non-random pattern.
http://edge.org/response-detail/25264

Duality in the human genome – November 28, 2014
Excerpt: The results show that most genes can occur in many different forms within a population: On average, about 250 different forms of each gene exist. The researchers found around four million different gene forms just in the 400 or so genomes they analysed. This figure is certain to increase as more human genomes are examined. More than 85 percent of all genes have no predominant form which occurs in more than half of all individuals. This enormous diversity means that over half of all genes in an individual, around 9,000 of 17,500, occur uniquely in that one person – and are therefore individual in the truest sense of the word.
The gene, as we imagined it, exists only in exceptional cases. “We need to fundamentally rethink the view of genes that every schoolchild has learned since Gregor Mendel’s time.,,,
According to the researchers, mutations of genes are not randomly distributed between the parental chromosomes. They found that 60 percent of mutations affect the same chromosome set and 40 percent both sets. Scientists refer to these as cis and trans mutations, respectively. Evidently, an organism must have more cis mutations, where the second gene form remains intact. “It’s amazing how precisely the 60:40 ratio is maintained. It occurs in the genome of every individual – almost like a magic formula,” says Hoehe.
http://medicalxpress.com/news/.....enome.html

Thus, with both natural selection and random mutations shown to virtually non-existent, the primary presuppositions that undergird the entire neo-Darwinian edifice are now shown to false.

If Darwinian evolution were a normal science, this SHOULD render it to the garbage heap of failed scientific hypothesis. But alas, Darwinian evolution never really has been a real science since it has always been, at least in the eyes of faithful Darwinists, impervious to empirical falsification:

Darwin’s Theory vs Falsification – video
https://www.youtube.com/watch?v=8rzw0JkuKuQ

i.e. Darwinian evolution is, in reality, a unfalsifiable pseudoscience, that functions more like a religion for atheists than a testable science that is open to falsification.

CHARLES DARWIN: VICTORIAN MYTHMAKER By A.N. Wilson (Book Review By Jonathan Wells) – – Wednesday, January 31, 2018
Excerpt: Darwin called “The Origin of Species” “one long argument,” and it was a theology-laden argument against creation by design. Many people have the mistaken impression that Darwin’s theory was accepted because he provided so much scientific evidence for it (he didn’t). Instead, his theory was accepted because it fit the increasingly secular spirit of the times.,,,
So Darwinian evolution is not so much a scientific theory as it is a secular creation myth. According to Mr. Wilson, “Darwinism, as is shown by the current state of debate, is resistant to argument because it is resistant to fact. The worship of Darwin as a man, the attribution to him of insights and discoveries which were either part of the common scientific store of knowledge or were the discoveries of others, this is all necessary to bolster the religion of Darwinism.”
Mr. Wilson’s book is not flawless, but on this point he’s right.
https://www.washingtontimes.com/news/2018/jan/31/book-review-charles-darwin-by-an-wilson/
38

bornagain77June 21, 2018 at 8:20 pm

To continue on in the falsification of the Darwinian presupposition of ‘randomness’ within biology, it is now found that there is far less ‘randomness’ and/or ‘random thermodynamic jostling’ within molecular biology than was presupposed by Darwinists:

At the 6:52 minute mark of the following video, Jim Al-Khalili states:

“To paraphrase, (Erwin Schrödinger in his book “What Is Life”), he says at the molecular level living organisms have a certain order. A structure to them that’s very different from the random thermodynamic jostling of atoms and molecules in inanimate matter of the same complexity. In fact, living matter seems to behave in its order and its structure just like inanimate matter cooled down to near absolute zero. Where quantum effects play a very important role. There is something special about the structure, about the order, inside a living cell. So Schrodinger speculated that maybe quantum mechanics plays a role in life”.
Jim Al-Khalili – Quantum biology – video
https://www.youtube.com/watch?v=zOzCkeTPR3Q

In fact, advances in quantum biology have now falsified the entire reductive materialistic foundation of Darwinian thought:

Darwinian Materialism vs. Quantum Biology – video
https://youtu.be/LHdD2Am1g5Y

And to touch on the genetic load argument,

Here is a 2011 Oxford job description which stated,,, Grand theories in physics are usually expressed in mathematics. Newton’s mechanics and Einstein’s theory of special relativity are essentially equations. Words are needed only to interpret the terms. Darwin’s theory of evolution by natural selection has obstinately remained in words since 1859. … and goes on to state,,, The mainstream of mathematical population geneticists since about 1964 has emphatically rejected the claim that fitness is maximised. … and goes on to state,,, mathematical population geneticists mainly deny that natural selection leads to optimization of any useful kind.

Oxford University Seeks Mathemagician — May 5th, 2011 by Douglas Axe
Excerpt: In the Oxford job description [1], under the heading Extracts from the grant application to the St John’s Research Centre, subheading Objectives:
1. To construct a mathematical framework, with appropriate theorems, to represent fully the core argument in Darwin’s Origin of Species, namely that the purely mechanical processes of inheritance and reproduction can give rise through natural selection to the appearance of design.
–- Under the same heading, subheading Summary:
Grand theories in physics are usually expressed in mathematics. Newton’s mechanics and Einstein’s theory of special relativity are essentially equations. Words are needed only to interpret the terms. Darwin’s theory of evolution by natural selection has obstinately remained in words since 1859. …
Under the same heading, subheading Detailed Application:
The idea that organisms maximise their fitness as a result of natural selection is extremely important in many areas of biology. The explanatory apparatus of most whole organism, behavioural ecology, work would make no sense without it. However, the logical basis for the idea is in considerable doubt. The mainstream of mathematical population geneticists since about 1964 has emphatically rejected the claim that fitness is maximised. …
There has been essentially no formal consideration of the kind of optimisation that emerges so naturally from verbal arguments such as those of Darwin (1859) and Dawkins (1976).
In the main job description, under the heading The Deep Mathematical Theory of Selfish Genes, subheading About the project:
,,,However, mathematical population geneticists mainly deny that natural selection leads to optimization of any useful kind. This fifty-year old schism is intellectually damaging in itself, and has prevented improvements in our concept of what fitness is.…
http://www.biologicinstitute.o.....hemagician

And if you doubt that mainstream mathematical population geneticists mainly deny that natural selection leads to optimization of any useful kind then just remember that many leading Darwinists, such as Dan Graur and Larry Moran, because of the math of population genetics, and via the genetic load argument, insist that upwards to 90% of DNA must be junk:

Revisiting the genetic load argument with Dan Graur – Larry Moran – July 14, 2017
Excerpt: I’ve discussed genetic load several times on this blog (e.g. Genetic Load, Neutral Theory, and Junk DNA) but a recent paper by Dan Graur provides a good opportunity to explain it once more. The basic idea of Genetic Load is that a population can only tolerate a finite number of deleterious mutations before going extinct. The theory is sound but many of the variables are not known with precision.,,,
Let’s look at the first line in this table. The deleterious mutation rate is calculated using the lowest possible mutation rate and the smallest percentage of deleterious mutations (4%). Under these conditions, the human population could survive with a fertility value of 1.8 as long as less than 25% of the genome is functional (i.e. 75% junk) (red circle). That’s the UPPER LIMIT on the functional fraction of the human genome.
But that limit is quite unreasonable. It’s more reasonable to assume about 100 new mutations per generation with about 10% deleterious. Using these assumptions, only 10% of the genome could be functional with a fertility value of 1.8 (green circle).
Whatever the exact percentage of junk DNA it’s clear that the available data and population genetics point to a genome that’s mostly junk DNA.
http://sandwalk.blogspot.com/2.....-with.html

I hold Moran’s 10% estimate for deleterious mutations, that he used in his calculation in the preceding paper, to be far too conservative, and thus the percentage of junk DNA, according to his own calculation, should actually be much higher than his 90% estimate,,, As Michael Behe stated in the following paper,, we had already known that the great majority of mutations that have a visible effect on an organism are deleterious. Now, surprisingly, it seems that even the great majority of helpful mutations degrade the genome to a greater or lesser extent

“The First Rule of Adaptive Evolution”: Break or blunt any functional coded element whose loss would yield a net fitness gain – Michael Behe – December 2010
Excerpt: In its most recent issue The Quarterly Review of Biology has published a review by myself of laboratory evolution experiments of microbes going back four decades.,,, The gist of the paper is that so far the overwhelming number of adaptive (that is, helpful) mutations seen in laboratory evolution experiments are either loss or modification of function. Of course we had already known that the great majority of mutations that have a visible effect on an organism are deleterious. Now, surprisingly, it seems that even the great majority of helpful mutations degrade the genome to a greater or lesser extent.,,, I dub it “The First Rule of Adaptive Evolution”: Break or blunt any functional coded element whose loss would yield a net fitness gain.
http://behe.uncommondescent.co.....evolution/
39

bornagain77June 21, 2018 at 8:21 pm

Moreover, as John Sanford showed in his book Genetic Entropy and the following paper, the unselectable ‘near neutral’ mutations, which Dr Moran classified as perfectly neutral in his calculation, should, in reality, all be classified as slightly deleterious mutations that will build up over time instead of being classified as perfectly neutral.,,,

Can Purifying Natural Selection Preserve Biological Information? – May 2013 –
Paul Gibson, John R. Baumgardner, Wesley H. Brewer, John C. Sanford
In conclusion, numerical simulation shows that realistic levels of biological noise result in a high selection threshold. This results in the ongoing accumulation of low-impact deleterious mutations, with deleterious mutation count per individual increasing linearly over time. Even in very long experiments (more than 100,000 generations), slightly deleterious alleles accumulate steadily, causing eventual extinction. These findings provide independent validation of previous analytical and simulation studies [2–13]. Previous concerns about the problem of accumulation of nearly neutral mutations are strongly supported by our analysis. Indeed, when numerical simulations incorporate realistic levels of biological noise, our analyses indicate that the problem is much more severe than has been acknowledged, and that the large majority of deleterious mutations become invisible to the selection process.,,,
http://www.worldscientific.com.....08728_0010

Kimura’s Distribution
http://dl0.creation.com/articl.....-white.jpg

Correct Distribution
http://dl0.creation.com/articl.....-white.jpg

Thus, even though Moran used unrealistic estimates for deleterious mutations in his calculation, Moran was still only able to calculate that 10% of the genome may be functional. Moreover, these leading Darwinists insisted that most of the genome must be junk in spite of overwhelming empirical evidence to the contrary from ENCODE, and from other sources

New Book on “Junk DNA” Surveys the Functions of Non-Coding DNA – April 29, 2015
Excerpt: Carey,, goes on to explain how today we now believe that, far from being irrelevant, it’s the “junk DNA” that is running the whole show:
“The other shock from the sequencing of the human genome was the realisation that the extraordinary complexities of human anatomy, physiology, intelligence and behaviour cannot be explained by referring to the classical model of genes. In terms of numbers of genes that code for proteins, humans contain pretty much the same quantity (around 20,000) as simple microscopic worms. Even more remarkably, most of the genes in the worms have directly equivalent genes in humans.
http://www.evolutionnews.org/2.....95611.html

,,, and they also held it to be mostly junk in spite of the fact that DNA is now known to be, by far, the most efficient information storage device known to man,,,

Information Storage in DNA by Wyss Institute – video
https://vimeo.com/47615970
Quote from preceding video:
“The theoretical (information) density of DNA is you could store the total world information, which is 1.8 zetabytes, at least in 2011, in about 4 grams of DNA.”
Sriram Kosuri PhD. – Wyss Institute

Indeed, all of biology is turning out to be, contrary to Darwinian expectations, optimized in a way that is ‘more perfect than we imagined’. William Bialek states “Scientists have identified and mathematically anatomized an array of cases where optimization has left its fastidious mark, among them;,,,,, In each instance, biophysicists have calculated, the system couldn’t get faster, more sensitive or more efficient without first relocating to an alternate universe with alternate physical constants.”

William Bialek: More Perfect Than We Imagined – March 23, 2013
Excerpt: photoreceptor cells that carpet the retinal tissue of the eye and respond to light, are not just good or great or phabulous at their job. They are not merely exceptionally impressive by the standards of biology, with whatever slop and wiggle room the animate category implies. Photoreceptors operate at the outermost boundary allowed by the laws of physics, which means they are as good as they can be, period. Each one is designed to detect and respond to single photons of light — the smallest possible packages in which light comes wrapped.
“Light is quantized, and you can’t count half a photon,” said William Bialek, a professor of physics and integrative genomics at Princeton University. “This is as far as it goes.” …
Scientists have identified and mathematically anatomized an array of cases where optimization has left its fastidious mark, among them;,, the precision response in a fruit fly embryo to contouring molecules that help distinguish tail from head;,,, In each instance, biophysicists have calculated, the system couldn’t get faster, more sensitive or more efficient without first relocating to an alternate universe with alternate physical constants.
http://darwins-god.blogspot.co.....an-we.html

Thus, far from being mostly junk, or failing to have ‘optimization of any useful kind’, the fact of the matter is that much of molecular biology is found to be ‘optimized’ to the maximum extent possible.

I hate to break it to Larry Moran and Dan Graur, but in empirical science evidence trumps theory every time. As Richard Feynman stated,

The Scientific Method – Richard Feynman – video
Quote: ‘If it disagrees with experiment, it’s wrong. In that simple statement is the key to science. It doesn’t make any difference how beautiful your guess is, it doesn’t matter how smart you are, who made the guess, or what his name is… If it disagrees with experiment, it’s wrong. That’s all there is to it.”
https://www.youtube.com/watch?v=OL6-x0modwY

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Junk DNA: Darwinism evolves swiftly in real time

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