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)
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.
Kas- Darwinism is untestable
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.
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)
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”.
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:
No, probably not from either evolutionary biologists or Darwinists. Neither hardly ever stoops to using a non-materialist mathematics to support their science.
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.
This is not true at all, do you just make this stuff up or what?
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.
Maybe Moran and Graur need a refresher course on how science actually works:
SA,
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.
I’m afraid you don’t understand what these words mean, SA.
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.
I’m afraid you don’t understand what these words mean, SA.
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.
GUN
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.
Amblyrhynchus @10
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?
Who identified this region as junk DNA?
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.
SA,
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 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.
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 …
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.
GUN
Then how do you know which ones are non-functional?
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).
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).
Amblyrhynchus
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.
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?
How do you get from
to
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”.
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/
From New Scientist 17 July 2017
[…]
[…]
Richard Dawkins comparison 2009 – 2012…
Dawkins in 2009:
“(95 percent in the case of humans)… “might as well not be there”
Dawkins in 2012:
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.
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
What if? What if just half the number of pseudogenes(~10k) turn out to have function?
“JUNK” DNA, Ohno, “JUNK” DNA, “Trash…”
Darwinism is a religion with it’s own “resurrection” story 😉
from the paper quoted in #24 above, more evidence of function in formerly named “Trash” and “Junk” DNA regions…
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.
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/
… very interesting last paragraph, how much more to find, learn and maybe be “reannotated” based upon new research.
“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…”
( ) 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.
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.
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.
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.’
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,
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.
To put is kindly, anyone who claims the vast majority of our DNA is junk in not playing with a full deck.
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.
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!
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.
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.
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.
20
Amblyrhynchus
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:
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'”).
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?
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.
ET:
So?
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.
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.
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:
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:
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.
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:
In fact, advances in quantum biology have now falsified the entire reductive materialistic foundation of Darwinian thought:
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.
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:
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
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.,,,
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
,,, 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,,,
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.”
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,