Predictions, predictions: ID predicts overlapping codes, Darwinism predicts “junk DNA”

_{Denyse O'Leary

January 8, 2020

'Junk DNA', Genetics, Information, Intelligent Design}

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Overlapping genes, or “nested coding,” was anticipated by microbiologist Siegfried Scherer, as Meyer points out. Why? Because human coders layer codes on top of codes, for various reasons including improved storage. Therefore a designing agent, operating behind the veil of biology, would likely do so as well. And so it is.
David Klinghoffer, “Meyer on “Nested Coding”: Another Successful Design Prediction” at Evolution News and Science Today

And, as Klinghoffer reminds us, the Darwinists predicted lots of “junk DNA,” mindless and meaningless evolution’s scrap heap.

Hat tip: Philip Cunningham

Comments

@38 Silver Asiatic: 'Evolutionary theory has changed the world, changed (destroyed) large aspects of human culture, even causing some theologians to change teachings on God, causing many other people to become atheists — it has had an enormous and devastating impact.' That was the plan. All along. And that is why they can not stand people fighting back. Destroying God (and consequently harming almost irreparably humanity) is the atheist evolutionists life-purpose (although life is 'purposeless' they affirm. Purpose is an 'illusion'. So they waste their lives pursuing something that does not exist. And then they tell theists: 'thou shall not waste your lives pursuing and illusion-'god'). LOL. The champions of 'reason' and 'logic'.Truthfreedom_{January 11, 2020
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Bob O'H
Well, I’m sorry. When we don’t know things precisely, it’s better to be imprecise.
I think that when evolutionary theory does not offer accuracy, then evolutionists should say that they are just guessing. To your credit, you said this. But I am talking about evolutionary theory in general. It makes the most extraordinary claim to have an explanation for the development of all life on earth beginning from the first life-form. To publish papers using the concept of Junk DNA, while at the same time knowing these papers are guesswork, is deceptive. The public is told that evolutionary theory has the answers. The theory is "more certain than gravity". Well, it needs to be held to the same standards of precision as scientific theories are.
Again, I’m sorry. I wasn’t aware that observations had to be predictive.
They do not need to be predictive. But if evolutionary claims are merely observations, then we do not need the theory. Anybody can observe things. The theory does nothing. "We observe this and that". Evolutionary papers do this all the time. They observe something and then describe what is observed. Evolution provided nothing in that process. In the rare cases where the theory actually predicts something, it is ambiguous and can be interpreted in contradictory ways in order to avoid falsification. So again, if evolution merely offers observations of what we see in nature, then the theory is useless.
But evolutionary theory is supposed to lead the process and enable the discovery. Says who?
It's just the nature of a theory. An idea is proposed - a theory. It is predictive: "The universe is expanding and galaxies are moving a away from a central point" … or some such. This is then subject to rigorous testing, measurement and comparison. Whatever is observed it matched with the theory. If the observation matches the theory, then the prediction is confirmed. But what I was getting at is that evolutionary theory does not work this way. Darwin proposed mechanisms that caused the development of all life on earth. But as we discovered that those mechanisms do not work, other mechanisms are proposed. But there's no mathematical or logical precision to this. We then have evolutionists saying that "some" Junk DNA is non-functional. But is that what they really said? There is no precision. Dawkins said this: “creationists might spend some earnest time speculating on why the Creator should bother to litter genomes with untranslated pseudogenes and junk tandem repeat DNA.” But what Dawkins did not say is "we're really just making a wild guess about what Junk DNA does because we don't even know what it is". What Dawkins also did not say was "of course, we all know that Junk DNA has some function". ENCODE comes along later and says that Junk DNA is at least 80% functional. Would Dawkins then say "it's ok, I already knew Junk DNA had function". I don't think so. He used Junk DNA to attack creationism, even though what he claimed he knew was based on guesswork, and nobody even knew what Junk DNA was at that point. So, ENCODE says it's 80% functional.
Apparently some of those researchers are backing away from ENCODE’s initial claims that 80 percent of the human genome is functional, and now claim that it’s more like 50 percent functional.
ENCODE's estimates were attacked and they "backed away" from the claim. This is not even a matter of predictives, but can evolutionists even understand what they observe?
University of Houston molecular evolutionary biologist Dan Graur probably shook up the ENCODE proponents. Graur and others vocally attacked ENCODE proponents in both the scientific literature and on blogs for their “hype” and claimed that only 8-20 percent of our genome is functional.
Did Dan Graur explain that he doesn't even know what Junk DNA is and that his estimate is a "guess"? I don't think so. He's trying to make the observation match the unstated prediction of evolutionary theory.
Graur's reasoning followed from evolution-based considerations like the percent conservation.
This was more guesswork and an indication about how evolutionary theory is built on a false assumption in the null hypothesis (based on sequence conservation and therefore assuming parts of the genome are non-functional on that basis).
In this case, the null hypothesis would be that these parts of the genome are non-functional and have properties, be it on the basis of conservation or biochemical activity, that would be expected of such regions based on our general understanding of molecular evolution and biochemistry. According to these critics, until a region in question has been shown to have additional features, beyond what is expected of the null hypothesis, it should provisionally be labelled as non-functional.
So ENCODE then adjusts their estimates down to 50% function.
Here’s what I wonder: Do any of them appreciate that even the 50 percent of our genome that they already believe is functional refutes unguided evolution according to Graur’s infamous quip, “If ENCODE is right, then Evolution is wrong“? So whether it’s 50 percent functionality or 80 percent functionality, that’s bad for unguided evolutionary models! Why? Because if those ENCODE people are right that about 50 percent of the genome is functional, that’s still a lot higher than Graur et al.‘s percentage. It also seems that many are already prepared to reject at least some of Graur’s evolution-based arguments.
At least Graur is willing to risk evolutionary theory on the basis of what is observed. But that's why the theory is a prediction and not merely and explanation of observations. Graur is willing to claim that "evolution is wrong" if ENCODE's findings are correct. That is why, when we find more function for Junk DNA - it is a very big deal.
in a Nature article titled “Celebrate the Unknowns,” Philip Ball writes about ENCODE: [T]he current picture of how and where evolution operates, and how this shapes genomes, is something of a mess. … But we are grown-up enough to be told about the doubts, debates and discussions that are leaving the putative ‘age of the genome’ with more questions than answers. Tidying up the story bowdlerizes the science and creates straw men for its detractors. Simplistic portrayals of evolution encourage equally simplistic demolitions.”2
That's a choice comment. The picture of how evolution operates is "a mess". Anyone "tidying up the story" is going to encourage "demolitions" of the theory. But what I was getting at is that if there is little or no precision and only ambiguous or no predictive power, then the story itself is confused.
Aside from Ball’s admission that ENCODE leaves evolutionary genomics in “a mess,” don’t miss his last two sentences. In referring to “detractors” who demolish “simplistic portrayals of evolution,” he has advocates of intelligent design in mind. ID proponents point out that ENCODE refutes evolutionary models that predicted a junk-filled genome. Now that those predictions have failed, the best way to save evolution from ENCODE is to disavow the old models by calling them “simplistic” or “straw men.”
Some will accept that evolutionary models predicted something. Others will claim that there was no prediction.
And how could we have made a prediction about the amount of non-coding DNA before we knew what it was?
I think this question can be extended to evolutionary theory in general. "How can we claim that evolutionary mechanisms explain the development of all life on earth when we don't even know what is going on within the genome"? Exactly. The theory was supposed to explain all of life. People still think that it does. But evolutionists do not even understand what they have observed so far, as Junk DNA proves.
I have to ask, how much do you know about what scientists do? Have you ever done any research? Have you published many papers? Or have you studied the philosophy or sociology of science, and thus have some expertise from that?
I am not a professional microbiologist. I have not published any peer-reviewed papers. I have argued with evolutionists on the web for over 15 years and I've read evolutionists books and papers over that time. So I think I have some level of expertise on these questions. I work in the field of data science, but I'm sure that will not be considered the field of science. In any case, I am not questioning your credentials. I'm assuming you work in the field somehow. Have you published papers on microbiology or Junk DNA? If it is enough to say that I am not a biologist, then I accept that. You've been good enough to engage in the conversation. I also respect your honesty about these matters and I'm not questioning your personal integrity. You might think that I'm holding evolutionary theory to an unfair standard, but again, the claims of the theory are overwhelming. I think anything said about evolution must be challenged and after all of the hype and from the thousands of biologists who claim victory for evolution, the theory must be held up to the most rigorous standards. Evolutionary theory has changed the world, changed (destroyed) large aspects of human culture, even causing some theologians to change teachings on God, causing many other people to become atheists -- it has had an enormous and devastating impact. For the same evolutionists to come back later and say "we made some guesses" and when those guesses are proven wrong to say "it's ok, we can always adjust the theory to new information" -- that just destroys credibility of the whole evolutionary enterprise.Silver Asiatic_{January 11, 2020
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These farcical liars (atheist evolutionists) do not longer 'adhere' to the 'falsification' criteria. 'Oh no, we are not doing Popper anymore'. They twist science to support their crazy evil philosophy.Truthfreedom_{January 10, 2020
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Besides Darwinists refusing to adhere to the criteria of falsification for their supposed scientific theory, by any other reasonable measure that one may wish to judge whether Darwinian evolution even qualifies as a science or not, as is shown in the following video, Darwinian evolution fails to meet those other criteria as well:
“There are five standard tests for a scientific hypothesis. Has anyone observed the phenomenon — in this case, Evolution — as it occurred and recorded it? Could other scientists replicate it? Could any of them come up with a set of facts that, if true, would contradict the theory (Karl Popper’s “falsifiability” tests)? Could scientists make predictions based on it? Did it illuminate hitherto unknown or baffling areas of science? In the case of Evolution… well… no… no… no… no… and no.” – Tom Wolfe – The Kingdom of Speech – page 17 Darwinian Evolution Fails the Five Standard Tests of a Scientific Hypothesis – video https://www.youtube.com/watch?v=L7f_fyoPybw
Simply put, Darwinian evolution simply fails to qualify as a rigorous and testable science by any reasonable measure one may wish to invoke and is therefore more properly classified as a pseudoscience, even as a religion for atheists, rather than ever being classified as a real and testable science. Moreover, contrary to what many people have been falsely led to believe by Darwinian atheists, about Intelligent Design supposedly being a pseudo-science, the fact of the matter is that all of science, every nook and cranny of it, is based on the presupposition of intelligent design and is certainly not based on the presupposition of methodological naturalism.
From the essential Christian presuppositions that undergird the founding of modern science itself, (namely that the universe is rational and that the minds of men, being made in the ‘image of God’, can dare understand that rationality), to the intelligent design of the scientific instruments and experiments themselves, to the logical and mathematical analysis of experimental results themselves, from top to bottom, science itself is certainly not to be considered a ‘natural’ endeavor of man. Not one scientific instrument would ever exist if men did not first intelligently design that scientific instrument. Not one test tube, microscope, telescope, spectroscope, or etc.. etc.., was ever found just laying around on a beach somewhere which was ‘naturally’ constructed by nature. Not one experimental result would ever be rationally analyzed since there would be no immaterial minds to rationally analyze the immaterial logic and immaterial mathematics that lay behind the intelligently designed experiments in the first place.
Again, all of science, every nook and cranny of it, is based on the presupposition of intelligent design and is certainly not based on the presupposition of methodological naturalism. Moreover, following the artificial restriction of methodological naturalism that Darwinian Atheists try to artificially impose on science before any investigation has even begun, that is to say, following the presumption that only natural, material, and/or physical causes are allowed to be given in order to explain any given effect in science, leads to the catastrophic epistemological failure of science itself.
Basically, because of reductive materialism (and/or methodological naturalism), the atheistic materialist is forced to claim that he is merely a ‘neuronal illusion’ (Coyne, Dennett, etc..), who has the illusion of free will (Harris), who has unreliable, (i.e. illusory), beliefs about reality (Plantinga), who has illusory perceptions of reality (Hoffman), who, since he has no real time empirical evidence substantiating his grandiose claims, must make up illusory “just so stories” with the illusory, and impotent, ‘designer substitute’ of natural selection (Behe, Gould, Sternberg), so as to ‘explain away’ the appearance (i.e. illusion) of design (Crick, Dawkins), and who must make up illusory meanings and purposes for his life since the reality of the nihilism inherent in his atheistic worldview is too much for him to bear (Weikart), and who must also hold morality to be subjective and illusory since he has rejected God (Craig, Kreeft). Who, since beauty cannot be grounded within his materialistic worldview, must hold beauty itself to be illusory. Bottom line, nothing is truly real in the atheist’s worldview, least of all, beauty, morality, meaning and purposes for life.,,, Darwinian Materialism and/or Methodological Naturalism vs. Reality – video https://www.youtube.com/watch?v=CaksmYceRXM
Thus, although the Darwinist may firmly believe that he is on the terra firma of science (in his appeal, even demand, for methodological naturalism), the fact of the matter is that, when examining the details of his materialistic and/or naturalistic worldview, it is found that Darwinian materialists are adrift in an ocean of fantasy and imagination with no discernible anchor for reality to grab on to. Again, It would be hard to fathom a worldview that turns out to be more antagonistic towards modern science, indeed more antagonistic towards reality itself, than the presumption of methodological naturalism has turned out to be.
2 Corinthians 10:5 Casting down imaginations, and every high thing that exalteth itself against the knowledge of God, and bringing into captivity every thought to the obedience of Christ;
Bottom line, without God nothing turns out to be truly real in the atheist’s worldview. Not even the atheist himself turns out to be a real person in his materialistic worldview. Much less can Bob (and weave) O'Hara, since he is not even a real person in his materialistic Darwinian worldview, ever truly be a 'real' scientist as he falsely fancies himself to be. Of supplemental note, in her very first article on UD, Emily Morales notes that Darwin himself blatantly ignored Bacon’s method of “repeated experimentation” (inductive reasoning)
Darwin, in his day was excoriated by Adam Sedgewick (his mentor of the past) for abandoning the tram-road of inductive thinking (Baconian methodology) in favor of embracing the methodologies associated with deductive reasoning carried out by the likes of Aristotle. Sedgewick was not alone in his criticism of Darwin. Louis Agassiz, at Harvard similarly rebuked Darwin for a thesis having no support in the known fossil record (refer to Stephen Meyer’s book Darwin’s Doubt). Note that neither of these men pushed back against Darwin because they were creationists – it was rather that Darwin drew some conclusions on the diversity of life and origin of species that were presumptuous to say the least. As it turns out, Bacon addressed the dangers of this manner of “logic” and “reasoning,” at length, warning us of its ability to stifle scientific inquiry two hundred and thirty years before Darwin’s published work. Bacon today, would not be impressed with where the brave new world of science is heading. Rather than holding on to those facts that are the fruit of repeated experimentation or steadied observation, society is clinging to fallacies that are oftentimes the fruit of a past college professor’s wild imagination. https://uncommondescent.com/intelligent-design/welcome-to-the-brave-new-world-of-science/#comment-690388
In fact, Charles Darwin himself honestly admitted to Asa Gray, professor of biology at Harvard University, that “I am quite conscious that my speculations run quite beyond the bounds of true science.” and “What you hint at generally is very, very true: that my work is grievously hypothetical, and large parts are by no means worthy of being called induction.”
Anti-Science Irony Excerpt: In response to a letter from Asa Gray, professor of biology at Harvard University, Darwin declared: “I am quite conscious that my speculations run quite beyond the bounds of true science.” When questioned further by Gray, Darwin confirmed Gray’s suspicions: “What you hint at generally is very, very true: that my work is grievously hypothetical, and large parts are by no means worthy of being called induction.” Darwin had turned against the use of scientific principles in developing his theory of evolution. http://www.darwinthenandnow.com/2011/10/anti-science-irony/
bornagain77_{January 10, 2020
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In fact there is currently up to a 10 million dollar prize being offered for the first person that can “Show an example of Information that doesn’t come from a mind. All you need is one.”
The Origin of Information: How to Solve It - Perry Marshall Where did the information in DNA come from? This is one of the most important and valuable questions in the history of science. Cosmic Fingerprints has issued a challenge to the scientific community: “Show an example of Information that doesn’t come from a mind. All you need is one.” “Information” is defined as digital communication between an encoder and a decoder, using agreed upon symbols. To date, no one has shown an example of a naturally occurring encoding / decoding system, i.e. one that has demonstrably come into existence without a designer. A private equity investment group is offering a technology prize for this discovery (up to 10 million dollars). We will financially reward and publicize the first person who can solve this;,,, To solve this problem is far more than an object of abstract religious or philosophical discussion. It would demonstrate a mechanism for producing coding systems, thus opening up new channels of scientific discovery. Such a find would have sweeping implications for Artificial Intelligence research. http://cosmicfingerprints.com/solve/
Imre Lakatos, who was a student of Karl Popper, and who is also regarded as another prominent philosopher of science in the 20th century, stated that "nobody to date has yet found a demarcation criterion according to which Darwin can be described as scientific"
Imre Lakatos - Pseudoscience - Darwin's Theory According to the demarcation criterion of pseudoscience originally proposed by Lakatos, a theory is pseudoscientific if it fails to make any novel predictions of previously unknown phenomena, in contrast with scientific theories, which predict novel fact(s).[21] Progressive scientific theories are those which have their novel facts confirmed and degenerate scientific theories are those whose predictions of novel facts are refuted. As he put it: "A given fact is explained scientifically only if a new fact is predicted with it....The idea of growth and the concept of empirical character are soldered into one." See pages 34–5 of The Methodology of Scientific Research Programmes, 1978. Lakatos's own key examples of pseudoscience were Ptolemaic astronomy, Immanuel Velikovsky's planetary cosmogony, Freudian psychoanalysis, 20th century Soviet Marxism,[22] Lysenko's biology, Niels Bohr's Quantum Mechanics post-1924, astrology, psychiatry, sociology, neoclassical economics, and Darwin's theory. Darwin's theory In his 1973 LSE Scientific Method Lecture 1[23] he also claimed that "nobody to date has yet found a demarcation criterion according to which Darwin can be described as scientific". Almost 20 years after Lakatos's 1973 challenge to the scientificity of Darwin, in her 1991 The Ant and the Peacock, LSE lecturer and ex-colleague of Lakatos, Helena Cronin, attempted to establish that Darwinian theory was empirically scientific in respect of at least being supported by evidence of likeness in the diversity of life forms in the world, explained by descent with modification. She wrote that "our usual idea of corroboration as requiring the successful prediction of novel facts...Darwinian theory was not strong on temporally novel predictions.." https://en.wikipedia.org/wiki/Imre_Lakatos#Pseudoscience
Lakatos also went on to state that “In degenerating programmes, however, theories are fabricated only in order to accommodate known facts”
Science and Pseudoscience (transcript) – “In degenerating programmes, however, theories are fabricated only in order to accommodate known facts” – Imre Lakatos (November 9, 1922 – February 2, 1974) a philosopher of mathematics and science, , quote as stated in 1973 LSE Scientific Method Lecture http://www.lse.ac.uk/philosophy/science-and-pseudoscience-overview-and-transcript/
And another prominent philosopher of science of the 20th century, Thomas Kuhn, who introduced the term 'paradigm shift' into popular culture, also noted that when faced with an anomaly, a theory's defenders "will devise numerous articulations and ad hoc modifications of their theory in order to eliminate any apparent conflict."
Thomas Kuhn Excerpt: Thomas Samuel Kuhn (/ku?n/; July 18, 1922 – June 17, 1996) was an American physicist, historian and philosopher of science whose controversial 1962 book The Structure of Scientific Revolutions was influential in both academic and popular circles, introducing the term paradigm shift, which has since become an English-language idiom.,,, https://en.wikipedia.org/wiki/Thomas_Kuhn Inquiry-Based Science Education -- on Everything but Evolution - Sarah Chaffee - January 22, 2016 Excerpt: As Thomas Kuhn wrote in The Structure of Scientific Revolutions, when faced with an anomaly, a theory's defenders "will devise numerous articulations and ad hoc modifications of their theory in order to eliminate any apparent conflict." http://www.evolutionnews.org/2016/01/inquiry-based_s102534.html
And in regards to a theory making predictions that are shown to be false and then making up ad hoc theories to try to cover up those falsified predictions, then by that ‘predictability’ falsification criteria set out by Lakatos and Kuhn, Darwinian evolution more than qualifies as a pseudoscience rather than a real science. Here is a site, that was put together by Dr. Cornelius Hunter, that goes over many of the failed predictions of Darwinian evolution.
Darwin’s (Failed) Predictions – Cornelius Hunter https://sites.google.com/site/darwinspredictions/
As Dr. Hunter states in the following article,,, “With each new absurdity another new complicated just-so story is woven into evolutionary theory. As Lakatos explained, some theories simply are not falsifiable. But as a result they sacrifice realism and parsimony.”
Here’s That Algae Study That Decouples Phylogeny and Competition – June 17, 2014 Excerpt: “With each new absurdity another new complicated just-so story is woven into evolutionary theory. As Lakatos explained, some theories simply are not falsifiable. But as a result they sacrifice realism and parsimony.” – Cornelius Hunter http://darwins-god.blogspot.com/2014/06/heres-that-algae-study-that-decouples.html
But in regards to falsification in particular (Popper) which is considered the gold standard to judge whether a theory is truly scientific or not, even though Darwinian evolution is not mathematically structured on a universal law so as to make it easily susceptible to empirical testing and/or falsification (as ‘real’ theories of science are set up), Darwinian evolution can, nevertheless, be falsified. It just takes a bit more effort to do so than usual. And yet, even though Darwinian evolution can be rigorously falsified (and has been falsified by numerous lines of evidence), Darwinists still simply refuse to accept falsification of their theory. Thus once again demonstrating that we are not dealing with a real science but are instead dealing with a pseudoscience (Lakatos, Kuhn), even a religion for atheists that Darwinists defend with all the fervor of fundamentalists. Here are a few falsifications of Darwin's theory that Darwinists simply refuse to ever accept as falsifications of their theory:
Darwin’s theory holds mutations to the genome to be random. The vast majority of mutations to the genome are not random but are now found to be ‘directed’. Darwin’s theory holds that Natural Selection is the ‘designer substitute’ that produces the ‘appearance’ and/or illusion of design. Natural Selection, especially for multicellular organisms, is found to grossly inadequate as the ‘designer substitute. Darwin’s theory holds that mutations to DNA will eventually change the basic biological form of any given species into a new form of a brand new species. Yet, biological form is found to be irreducible to mutations to DNA, nor is biological form reducible to any other material particulars in biology one may wish to invoke. Darwin’s theory holds there to be an extremely beneficial and flexible mutation rate for DNA which was ultimately responsible for all the diversity and complexity of life we see on earth. The mutation rate to DNA is overwhelmingly detrimental. Detrimental to such a point that it is seriously questioned whether there are any truly beneficial, information building, mutations whatsoever. Charles Darwin himself held that the gradual unfolding of life would (someday) be self-evident in the fossil record. Yet, from the Cambrian Explosion onward, the fossil record is consistently characterized by the sudden appearance of a group/kind in the fossil record(disparity), then rapid diversity within the group/kind, and then long term stability and even deterioration of variety within the overall group/kind, and within the specific species of the kind, over long periods of time. Of the few dozen or so fossils claimed as transitional, not one is uncontested as a true example of transition between major animal forms out of millions of collected fossils. Moreover, Fossils are found in the “wrong place” all the time (either too early, or too late). Darwin’s theory, due to the randomness postulate, holds that patterns will not repeat themselves in supposedly widely divergent species. Yet thousands of instances of what is ironically called ‘convergent evolution’, on both the morphological and genetic level, falsifies the Darwinian belief that patterns will not repeat themselves in widely divergent species. Charles Darwin himself stated that “If it could be demonstrated that any complex organ existed which could not possibly have been formed by numerous, successive, slight modifications, my theory would absolutely break down.” Yet as Doug Axe pointed out, “Basically every gene and every new protein fold, there is nothing of significance that we can show that can be had in that gradualistic way. It’s all a mirage. None of it happens that way.” Charles Darwin himself stated that “If it could be proved that any part of the structure of any one species had been formed for the exclusive good of another species, it would annihilate my theory, for such could not have been produced through natural selection.” Yet as Wolf-Ekkehard Lönnig pointed out, “in thousands of plant species often entirely new organs have been formed for the exclusive good of more than 132,930 other species, these ‘ugly facts’ have annihilated Darwin’s theory as well as modern versions of it.” Charles Darwin himself stated that, ““The impossibility of conceiving that this grand and wondrous universe, with our conscious selves, arose through chance, seems to me the chief argument for the existence of God. Yet ‘our conscious selves’ are certainly not explainable by ‘chance’ (nor is consciousness explainable by any possible reductive materialistic explanation in general), i.e. ‘the hard problem of consciousness’. Besides the mathematics of probability consistently showing that Darwinian evolution is impossible, the mathematics of population genetics itself has now shown Darwinian evolution to be impossible. Moreover, ‘immaterial’ mathematics itself, which undergirds all of science, engineering and technology, is held by most mathematicians to exist in some timeless, unchanging, immaterial, Platonic realm. Yet, the reductive materialism that Darwinian theory is based upon denies the existence of the immaterial realm that mathematics exists in. i.e. Darwinian evolution actually denies the objective reality of the one thing, i.e. mathematics, that it most needs in order to be considered scientific in the first place! Donald Hoffman has, via population genetics, shown that if Darwin’s materialistic theory were true then all our observations of reality would be illusory. Yet the scientific method itself is based on reliable observation. Moreover, Quantum Mechanics itself has now shown that conscious observation must come before material reality, i.e. falsification of ‘realism’ proves that our conscious observations are reliable!. The reductive materialism that undergirds Darwinian thought holds that immaterial information is merely ’emergent’ from a material basis. Yet immaterial Information, via experimental realization of the “Maxwell’s Demon” thought experiment, is now found to be its own distinctive physical entity that, although it can interact in a ‘top down’ manner with matter and energy, is separate from matter and energy. Darwinists hold that Darwin’s theory is true. Yet ‘Truth’ itself is an abstract property of an immaterial mind that is irreducible to the reductive materialistic explanations of Darwinian evolution. i.e. Assuming reductive materialism and/or Naturalism as the starting philosophical position of science actually precludes ‘the truth’ from ever being reached by science! Darwinists, due to their underlying naturalistic philosophy, insist that teleology (i.e. goal directed purpose) does not exist. Yet it is impossible for Biologists to do biological research without constantly invoking words that directly imply teleology. i.e. The very words that Biologists themselves use when they are doing their research falsifies Darwinian evolution.
Verse:
1 Thessalonians 5:21 Test all things; hold fast what is good.
bornagain77_{January 10, 2020
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How cute, Bob (and weave) O'Hara wants to pretend that he is a real scientist. (Bet he even has a degree on the wall and a lab coat :) )
"I have to ask, how much do you know about what scientists do? Have you ever done any research? Have you published many papers? Or have you studied the philosophy or sociology of science, and thus have some expertise from that?"
Apparently little does Bob (and weave) know that being a Darwinist in and of itself precludes him from ever being a real scientist. Karl Popper is generally regarded as one of the 20th century's greatest philosophers of science.
Karl Popper Sir Karl Raimund Popper (28 July 1902 – 17 September 1994) was an Austrian-British philosopher and professor.[8][9][10] He is generally regarded as one of the 20th century's greatest philosophers of science.[11][12][13] Popper is known for his rejection of the classical inductivist views on the scientific method, in favour of empirical falsification: A theory in the empirical sciences can never be proven, but it can be falsified, meaning that it can and should be scrutinized by decisive experiments. https://en.wikipedia.org/wiki/Karl_Popper
Karl Popper stated that "In so far as a scientific statement speaks about reality, it must be falsifiable; and in so far as it is not falsifiable, it does not speak about reality."
"In so far as a scientific statement speaks about reality, it must be falsifiable; and in so far as it is not falsifiable, it does not speak about reality." Karl Popper - The Two Fundamental Problems of the Theory of Knowledge (2014 edition), Routledge
Early in his career, Popper noted that Darwinian evolution itself is set up in a way that makes it impervious to empirical falsification. Specifically, Popper called evolution via natural selection “almost a tautology” and “not a testable scientific theory but a metaphysical research program.” Popper was attacked by Darwinists for these criticisms. So Popper, in approx 1978 for the most part, took his criticisms of Darwinism back. But when John Horgan interviewed Popper in 1992, Horgan noted that Popper apparently changed his mind again and “blurted out that he still found Darwin’s theory dissatisfying. “One ought to look for alternatives!” Popper exclaimed, banging his kitchen table.”
Dubitable Darwin? Why Some Smart, Nonreligious People Doubt the Theory of Evolution - John Horgan - July 6, 2010 Excerpt: Early in his career, the philosopher Karl Popper ,, called evolution via natural selection “almost a tautology” and “not a testable scientific theory but a metaphysical research program.” Attacked for these criticisms, Popper took them back (in approx 1978). But when I interviewed him in 1992, he blurted out that he still found Darwin’s theory dissatisfying. “One ought to look for alternatives!” Popper exclaimed, banging his kitchen table. http://blogs.scientificamerican.com/cross-check/dubitable-darwin-why-some-smart-nonreligious-people-doubt-the-theory-of-evolution/
Tom Bethell also interviewed Karl Popper after the Darwinian backlash and Popper once again reiterated his claim that Darwinism was not a testable scientific theory.
Tom Bethell on Karl Popper's rejection of Darwinian Evolution as a testable scientific theory - 5:54 minute mark https://youtu.be/MLdZzf8HoUU?t=352
Darwinian Evolution simply lacks any of the rigor that one usually encounters with a typical scientific theory. As David Berlinski notes: “On the other hand, I disagree that Darwin’s theory is as `solid as any explanation in science.; Disagree? I regard the claim as preposterous. Quantum electrodynamics is accurate to thirteen or so decimal places; so, too, general relativity. A leaf trembling in the wrong way would suffice to shatter either theory. What can Darwinian theory offer in comparison?”
“On the other hand, I disagree that Darwin’s theory is as `solid as any explanation in science.; Disagree? I regard the claim as preposterous. Quantum electrodynamics is accurate to thirteen or so decimal places; so, too, general relativity. A leaf trembling in the wrong way would suffice to shatter either theory. What can Darwinian theory offer in comparison?” - David Berlinski, “A Scientific Scandal?: David Berlinski & Critics,” Commentary, July 8, 2003
The primary reason why Darwinian evolution lacks any of the rigor that is usually associated with the hard sciences is because Darwinian evolution has no mathematical model to test against. As Dr. Robert Marks states “Hard sciences are built on foundations of mathematics or definitive simulations. ,,, there exists no model successfully describing undirected Darwinian evolution. According to our current understanding, there never will be.,,,”
“There exists no model successfully describing undirected Darwinian evolution. Hard sciences are built on foundations of mathematics or definitive simulations. Examples include electromagnetics, Newtonian mechanics, geophysics, relativity, thermodynamics, quantum mechanics, optics, and many areas in biology. Those hoping to establish Darwinian evolution as a hard science with a model have either failed or inadvertently cheated. These models contain guidance mechanisms to land the airplane squarely on the target runway despite stochastic wind gusts. Not only can the guiding assistance be specifically identified in each proposed evolution model, its contribution to the success can be measured, in bits, as active information.,,,”,,, “there exists no model successfully describing undirected Darwinian evolution. According to our current understanding, there never will be.,,,” – Robert J. Marks II – Top Ten Questions and Objections to ‘Introduction to Evolutionary Informatics’ – June 12, 2017 https://evolutionnews.org/2017/06/top-ten-questions-and-objections-to-introduction-to-evolutionary-informatics/
And the primary reason why nobody has ever been able to build a realistic mathematical model for Darwinian evolution to test against is simply because there is no ‘law of evolution’ within the known physical universe for mathematicians and physicists to ever build a realistic mathematical model upon: As Ernst Mayr himself conceded, “In biology, as several other people have shown, and I totally agree with them, there are no natural laws in biology corresponding to the natural laws of the physical sciences.”
The Evolution of Ernst: Interview with Ernst Mayr – 2004 (page 2 of 14) Excerpt: biology (Darwinian Evolution) differs from the physical sciences in that in the physical sciences, all theories, I don’t know exceptions so I think it’s probably a safe statement, all theories are based somehow or other on natural laws. In biology, as several other people have shown, and I totally agree with them, there are no natural laws in biology corresponding to the natural laws of the physical sciences. ,,, And so that’s what I do in this book. I show that the theoretical basis, you might call it, or I prefer to call it the philosophy of biology, has a totally different basis than the theories of physics. https://www.scientificamerican.com/media/pdf/0004D8E1-178C-10EB-978C83414B7F012C.pdf
In the following article, Roger Highfield makes much the same observation as Ernst Mayr and states, ,,, Whatever the case, those universal truths—’laws’—that physicists and chemists all rely upon appear relatively absent from biology.
WHAT SCIENTIFIC IDEA IS READY FOR RETIREMENT? Evolution is True – Roger Highfield – January 2014 Excerpt: If evolutionary biologists are really Seekers of the Truth, they need to focus more on finding the mathematical regularities of biology, following in the giant footsteps of Sewall Wright, JBS Haldane, Ronald Fisher and so on. ,,, Whatever the case, those universal truths—’laws’—that physicists and chemists all rely upon appear relatively absent from biology. Little seems to have changed from a decade ago when the late and great John Maynard Smith wrote a chapter on evolutionary game theory for a book on the most powerful equations of science: his contribution did not include a single equation. http://www.edge.org/response-detail/25468
Professor Murray Eden of MIT, in a paper entitled “Inadequacies of Neo-Darwinian Evolution as a Scientific Theory” stated that “the randomness postulate is highly implausible and that an adequate scientific theory of evolution must await the discovery and elucidation of new natural laws—physical, physico-chemical, and biological.”
“It is our contention that if ‘random’ is given a serious and crucial interpretation from a probabilistic point of view, the randomness postulate is highly implausible and that an adequate scientific theory of evolution must await the discovery and elucidation of new natural laws—physical, physico-chemical, and biological.” Murray Eden, “Inadequacies of Neo-Darwinian Evolution as a Scientific Theory,” Mathematical Challenges to the Neo-Darwinian Interpretation of Evolution, editors Paul S. Moorhead and Martin M. Kaplan, June 1967, p. 109. https://people.eecs.berkeley.edu/~christos/evol/compevol_files/Wistar-Eden-1.pdf
In fact, not only is there no ‘law of evolution’ within the known physical universe for Darwinists to build a realistic mathematical model upon, the second law of thermodynamics, entropy, a law with great mathematical explanatory power in science, almost directly contradicts the primary Darwinian claim that greater and greater levels of functional complexity can easily be had and/or ‘naturally selected’ for over long periods of time. Indeed, entropy’s main claim is that, over long periods of time, everything in the universe will decay into simpler and simpler states until what is termed thermodynamic equilibrium is finally reached.
Why Tornados Running Backward do not Violate the Second Law – Granville Sewell Professor of Mathematics at University of Texas – El Paso – May 2012 – article with video Excerpt: So, how does the spontaneous rearrangement of matter on a rocky, barren, planet into human brains and spaceships and jet airplanes and nuclear power plants and libraries full of science texts and novels, and supercomputers running partial differential equation solving software , represent a less obvious or less spectacular violation of the second law—or at least of the fundamental natural principle behind this law—than tornados turning rubble into houses and cars? Can anyone even imagine a more spectacular violation? https://uncommondescent.com/intelligent-design/why-tornados-running-backward-do-not-violate-the-second-law/
And whereas Darwinian evolution has no known law of nature to appeal to so as to establish itself as a proper, testable, science, (in fact it almost directly contradicts the second law), Intelligent Design does not suffer from such an embarrassing disconnect from physical reality. In other words, Intelligent Design can appeal directly to ‘the laws of conservation of information’ (Dembski, Marks, etc..) in order to establish itself as a proper, testable, and rigorous science.
Conservation of information, evolution, etc – Sept. 30, 2014 Excerpt: Kurt Gödel’s logical objection to Darwinian evolution: “The formation in geological time of the human body by the laws of physics (or any other laws of similar nature), starting from a random distribution of elementary particles and the field is as unlikely as the separation of the atmosphere into its components. The complexity of the living things has to be present within the material [from which they are derived] or in the laws [governing their formation].” Gödel – As quoted in H. Wang. “On `computabilism’ and physicalism: Some Problems.” in Nature’s Imagination, J. Cornwall, Ed, pp.161-189, Oxford University Press (1995). Gödel’s argument is that if evolution is unfolding from an initial state by mathematical laws of physics, it cannot generate any information not inherent from the start – and in his view, neither the primaeval environment nor the laws are information-rich enough.,,, More recently this led him (Dembski) to postulate a Law of Conservation of Information, or actually to consolidate the idea, first put forward by Nobel-prizewinner Peter Medawar in the 1980s. Medawar had shown, as others before him, that in mathematical and computational operations, no new information can be created, but new findings are always implicit in the original starting points – laws and axioms.,,, http://potiphar.jongarvey.co.uk/2014/09/30/conservation-of-information-evolution-etc/
bornagain77_{January 10, 2020
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Bob O'H: 'Well, I’m sorry. When we don’t know things precisely, it’s better to be imprecise'. Evolutionists did not know precisely about 'junk' DNA and yet they precisely labelled it 'junk' and 'useless' for the organism. It fitted well some philosophical agenda (you know, the 'purposeless, blind, un-intelligent' endlessly boring one). Good to know you are going to bite (another) bullet. 'One man's junk is another man's treasure' :)Truthfreedom_{January 10, 2020
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SA @ 28 -
In your case, you start by saying “the guess was that some junk DNA …”. Two problems: 1. You point out that it was “a guess”. But the theory is supposed to tell us and not leave a guess. 2. How much junk DNA had function? “some”. This is hedging the bet. There’s no precision.
Well, I'm sorry. When we don't know things precisely, it's better to be imprecise.
You continue to say that there is “the observation that most junk DNA appear not to have a function”. Again, there’s nothing predictive in this, unless you want to claim it.
Again, I'm sorry. I wasn't aware that observations had to be predictive.
But evolutionary theory is supposed to lead the process and enable the discovery.
Says who?
It’s supposed to tell us how much Junk DNA is functional and be precise about it. Instead, it is ambiguous and avoids predictions.
Again, says who? If we know enough about junk DNA we can make predictions - we'd need to know the rates of duplication of repetitive sequences, and the fitness effects. Then we could make predictions. But if we don't have those we can't. And how could we have made a prediction about the amount of non-coding DNA before we knew what it was? I have to ask, how much do you know about what scientists do? Have you ever done any research? Have you published many papers? Or have you studied the philosophy or sociology of science, and thus have some expertise from that?Bob O'H_{January 10, 2020
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Do not worry, darwinists. Faith conquers it all. You will get over the 'junk' DNA ridicule. Go pray richard dawkins for the salvation of your memes.Truthfreedom_{January 10, 2020
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Silver Asiatic at 28
“All Junk DNA is non-functional. Because, by definition, if it has function it’s not Junk. And also, Junk DNA might or might not exist”.. I think those are pretty solid predictions that we can derive directly from evolutionary theory.
LOL :) ,, got to love how 'specific' Darwinists can be in their 'predictions',,,
Who would have thought that it would be biologists that came up with the first Theory of Everything? Biological divergence? Evolution. Biological convergence? Evolution. Gradual variation? Evolution. Sudden variation? Evolution. Stasis? Evolution. Junk DNA? Evolution. No Junk DNA? Evolution. Tree of life? Evolution. No tree of life? Evolution. Common genes? Evolution. Orfan genes? Evolution. Cell with little more than a jelly-like protoplasm? Evolution. Cell filled with countless, highly-specified nano-machines directed by a software code? Evolution. More hardy, more procreative organisms? Evolution. Less hardy, less procreative organisms? Evolution. - Evolution explains everything. - William J Murray "Being an evolutionist means there is no bad news. If new species appear abruptly in the fossil record, that just means evolution operates in spurts. If species then persist for eons with little modification, that just means evolution takes long breaks. If clever mechanisms are discovered in biology, that just means evolution is smarter than we imagined. If strikingly similar designs are found in distant species, that just means evolution repeats itself. If significant differences are found in allied species, that just means evolution sometimes introduces new designs rapidly. If no likely mechanism can be found for the large-scale change evolution requires, that just means evolution is mysterious. If adaptation responds to environmental signals, that just means evolution has more foresight than was thought. If major predictions of evolution are found to be false, that just means evolution is more complex than we thought." ~ Cornelius Hunter
Apparently it is wise for Darwinists to play fast and loose with how specific they are willing be with their predictions since Darwinists have been burned time and time again when they got too specific with their predictions:
Problem 10: Neo-Darwinism’s Long History of Inaccurate Predictions about Junk Organs and Junk DNA (Part 10 of 10 with links to the other nine problems) – Casey Luskin February 19, 2015 http://www.evolutionnews.org/2015/02/problem_10_neo-091191.html Darwin’s (failed) Predictions – Cornelius G. Hunter – 2015 This paper evaluates 23 fundamental (false) predictions of evolutionary theory from a wide range of different categories. The paper begins with a brief introduction to the nature of scientific predictions, and typical concerns evolutionists raise against investigating predictions of evolution. The paper next presents the individual predictions in seven categories: early evolution, evolutionary causes, molecular evolution, common descent, evolutionary phylogenies, evolutionary pathways, and behavior. Finally the conclusion summarizes these various predictions, their implications for evolution’s capacity to explain phenomena, and how they bear on evolutionist’s claims about their theory. *Introduction Why investigate evolution’s false predictions? Responses to common objections *Early evolution predictions The DNA code is not unique The cell’s fundamental molecules are universal *Evolutionary causes predictions Mutations are not adaptive Embryology and common descent Competition is greatest between neighbors *Molecular evolution predictions Protein evolution Histone proteins cannot tolerate much change The molecular clock keeps evolutionary time *Common descent predictions The pentadactyl pattern and common descent Serological tests reveal evolutionary relationships Biology is not lineage specific Similar species share similar genes MicroRNA *Evolutionary phylogenies predictions Genomic features are not sporadically distributed Gene and host phylogenies are congruent Gene phylogenies are congruent The species should form an evolutionary tree *Evolutionary pathways predictions Complex structures evolved from simpler structures Structures do not evolve before there is a need for them Functionally unconstrained DNA is not conserved Nature does not make leaps *Behavior Altruism Cell death *Conclusions What false predictions tell us about evolution https://sites.google.com/site/darwinspredictions/home Why investigate evolution’s false predictions? Excerpt: The predictions examined in this paper were selected according to several criteria. They cover a wide spectrum of evolutionary theory and are fundamental to the theory, reflecting major tenets of evolutionary thought. They were widely held by the consensus rather than reflecting one viewpoint of several competing viewpoints. Each prediction was a natural and fundamental expectation of the theory of evolution, and constituted mainstream evolutionary science. Furthermore, the selected predictions are not vague but rather are specific and can be objectively evaluated. They have been tested and evaluated and the outcome is not controversial or in question. And finally the predictions have implications for evolution’s (in)capacity to explain phenomena, as discussed in the conclusions. https://sites.google.com/site/darwinspredictions/why-investigate-evolution-s-false-predictions
bornagain77_{January 10, 2020
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Bob O'H
Nope, I’ve no idea where ba77 gets this idea from either.
He provided some analysis that supports his view. Mutations are deleterious. Why should there be any function at all by now? Why should organisms have repair mechanisms? Chemicals have no incentive to be alive. They are just has happy being inert chemicals. When an organism dies it just returns to its former state of chemical compounds. Why should there be any struggle to survive? What benefit is there in the Darwinian world?Silver Asiatic_{January 10, 2020
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Bob O'H
Not really. The guess was that some junk DNA had function, and we’ve been finding out what those functions are. But that still doesn’t negate the observation that most junk DNA appear not to have a function (for the organism, at least).
You're indicating to me, how ambiguous (and deliberately deceptive?) evolutionary theory really is here. In science, especially with a theory that claims so much importance, terminology is essential. Researchers cannot hide behind ambiguity and then claim success later. In your case, you start by saying "the guess was that some junk DNA …". Two problems: 1. You point out that it was "a guess". But the theory is supposed to tell us and not leave a guess. 2. How much junk DNA had function? "some". This is hedging the bet. There's no precision. You continue to say that there is "the observation that most junk DNA appear not to have a function". Again, there's nothing predictive in this, unless you want to claim it. We know this is how "evolutionary theory" (it's not a theory in this case) works. There is an "observation", a claim is made about what things "appear" to be. And then evolution claims that it caused it. But evolutionary theory is supposed to lead the process and enable the discovery. It's supposed to tell us how much Junk DNA is functional and be precise about it. Instead, it is ambiguous and avoids predictions. In your case, we can take it as a prediction: You claim "most Junk DNA does not have a function". Already, the term Junk DNA is "loaded" because if it is functional then it is not Junk. In fact, some of what was even considered non-functional genes proved to code for proteins. So even that was incorrect.
Some of these functions are “protein-based,” meaning the pseudogene actually generates a functional protein.
But to predict both that "most Junk DNA is not functional" and then to say:
Finding another function for some non-coding DNA isn’t really a big deal evolutionarily: we already know a some of it has function.
… doesn't follow. You make a prediction that "most is non-functional". Then you say that if we find more function, it's not a big deal because we know it has function. Again, there's no precision. It's a question of degree. How much function? It's that question that caused evolutionists to fight against the claims that ENCODE made regarding the amount of function. Even after "adjusting" their estimates down from 80% functional to around 50%, there's still a huge range. At the low end, some evolutionists (I'll guess Larry Moran) will claim (hope for) 2% functional. At the high end, ENCODE will claim 50% functional. You're predicting "most is non-functional". So, less than 50%. At the same time, you say that if we find more function, it's not a big deal. But it is a big deal. Your "less than 50%" keeps getting squeezed as we find more function. In fact, ENCODE already conflicts with your prediction. Ok, I'll expect a response: "They said 50% and that is not most". So, you'll hold on to 49.9999999999999999% as validation of your prediction? Better yet, just dismiss ENCODE as being incorrect, which appears to be a very easy thing to do among evolutionary scientists. On another thread, Larry Moran dismissed 3 or 4 peer reviewed papers as being wrong. Thus the uselessness of evolutionary theory is revealed again. Peer reviewed papers can be ignored. In post 18 here, BA77 quotes an article entitled: "Why Are Biologists Lashing Out Against Empirically Verified Research Results?" And as above, research can be opposed if it does not conform with the dominant paradigm. Back to this statement:
The guess was that some junk DNA had function, and we’ve been finding out what those functions are.
We have a "guess" not a theory-based prediction, the claim is "some" with no precision, and finally, you explain that the "change in the 1990s" (that you admitted to) was merely a matter of validation and identification. For you, it was not a question of misunderstanding and underestimating the functional quantity of non-coding DNA, but merely that evolutionists identified what they had predicted they would find. But the Nature Reviews Genetics paper contradicts that claim. The "change that occurred" was that more function was discovered than was expected. In fact, evolutionary theory inhibited scientific research with a mistaken claim of non-function. But even that paper plays both sides. Evolutionary theory is not leading the research, as they admit. But they allow the theory to follow along after observations are made. It's an add-on. "We observe this, therefore evolution did it". That is totally bogus. You're doing the same thing: "We predicted some function. Now we identify it. We called it Junk because some doesn't have function." You go on to add precision about the difference between pseudogenes and transposable elements. In your analogy, there is Australia and non-Australia. Your theory supposedly predicts something about this. When asked how much of the earth is Australia, the answer is "some". That's the prediction. Then you go and measure it and say "See, we told you some of the earth was Australia, and some is not". But with evolution, you don't even know what Junk DNA is, and you make ambiguous claims "some appears to be non-functional". It's "not a big deal" if all of it is functional, because you hedged it - "I said at the time, some 'appeared' to be non-functional and now through evolutionary theory we discovered that it is all functional". ENCODE claimed that 80% was functional. But even that is "not a big deal" in this scenario. But the matter of pseudogenes versus TEs is not relevant to the question of how evolution restricted our understanding, since the same process is used in all matters of Junk DNA. The Scientific American article contradicts your claim that "the changes" in the 1990s were merely a matter of identifying functions that were predicted:
Although very catchy, the term "junk DNA" repelled mainstream researchers from studying noncoding genetic material for many years. After all, who would like to dig through genomic garbage? Thankfully, though, there are some clochards who, at the risk of being ridiculed, explore unpopular territories. And it is because of them that in the early 1990s, the view of junk DNA, especially repetitive elements, began to change. In fact, more and more biologists now regard repetitive elements as genomic treasures. It appears that these transposable elements are not useless DNA. Instead, they interact with the surrounding genomic environment and increase the ability of the organism to evolve by serving as hot spots for genetic recombination and by providing new and important signals for regulating gene expression.
Evolution gave the term Junk DNA. That was a science-stopper. Notice, in the early 1990s, the view of "transposable elements" began to change. What changed? You claimed that we merely identified functions that were predicted. No, not quite. As it says, the claim was that Junk DNA was useless but in reality
It appears that these transposable elements are not useless DNA.
That's what it says. The change was that something initially considered (predicted by the Theory to be) useless actually "are not useless". Again, not pseudogenes here. The evolutionary claim of non-functionality, according to the Nature Reviews Genetics paper
remains the dominant and default perception
This is what they're complaining about. If evolutionary theory had predicted correctly, then this paper wouldn't talk about how there was a dominant limitation in advancing the investigation based on "the prevailing mindset" that those regions are intrinsically non-functional. That's the gross error that is now somewhat being corrected, but without any explanation as to why the evolutionary prediction was wrong, but just merely that it was.
In consideration of their evolutionary origins and inherent limitations in genome annotation practices, we posit that pseudogenes have been classified on a scientifically unsubstantiated basis.
Evolutionary theory is "scientifically unsubstantiated". We know that.
We reflect that a broad misunderstanding of pseudogenes, perpetuated in part by the pejorative inference of the ‘pseudogene’ label, has led to their frequent dismissal from functional assessment and exclusion from genomic analyses.
Evolutionists came up with the label because they claimed there was no function. The same is true of the label Junk DNA. Ohno came up with that because he believed those regions of the genome were non-functional, and that inhibited scientific research.
“with a growing number of instances of pseudogene-annotated regions later found to exhibit biological function, there is an emerging risk that these regions of the genome are prematurely dismissed as pseudogenic and therefore regarded as void of function.”
A growing number of instances. More function is found. The same could be true in all non-coding areas. If it is eventually found that "most Junk DNA has function" then at least your prediction, Bob, will be falsified. But you've protected yourself against that problem by saying no matter what functions we find it won't be a "big deal". I hope you wouldn't conclude in that case, that since we already knew there was "some function" that its the same as saying "most". Or worse, that the term "Junk DNA" refers to non-functional DNA. In that case, I think evolutionary theory would be very safe to predict: "All Junk DNA is non-functional. Because, by definition, if it has function it's not Junk. And also, Junk DNA might or might not exist".. I think those are pretty solid predictions that we can derive directly from evolutionary theory. I'm sure someone will find value in them also, and maybe sell a book or two on that basis.Silver Asiatic_{January 10, 2020
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Now if they were only honest enough to admit that, if Darwinian evolution were true, then ALL of the genome should be non-functional junk.
Nope, I've no idea where ba77 gets this idea from either.Bob O'H_{January 10, 2020
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Likewise, Michael Behe has found the probability of proteins finding new protein-protein binding sites, in order to accomplish new molecular functions, is prohibitive. As Behe states in his book 'The Edge of Evolution",, "the likelihood of developing two binding sites in a protein complex would be the square of the probability for getting one: a double CCC, 10^20 times 10^20, which is 10^40. There have likely been fewer than 10^40 cells in the world in the last 4 billion years, so the odds are against a single event of this variety in the history of life. It is biologically unreasonable."
"The immediate, most important implication is that complexes with more than two different binding sites-ones that require three or more proteins-are beyond the edge of evolution, past what is biologically reasonable to expect Darwinian evolution to have accomplished in all of life in all of the billion-year history of the world. The reasoning is straightforward. The odds of getting two independent things right are the multiple of the odds of getting each right by itself. So, other things being equal, the likelihood of developing two binding sites in a protein complex would be the square of the probability for getting one: a double CCC, 10^20 times 10^20, which is 10^40. There have likely been fewer than 10^40 cells in the world in the last 4 billion years, so the odds are against a single event of this variety in the history of life. It is biologically unreasonable." - Michael Behe - The Edge of Evolution - page 146 Michael Behe - Observed (1 in 10^20) Edge of Evolution - video - Lecture delivered in April 2015 at Colorado School of Mines 25:56 minute quote - "This is not an argument anymore that Darwinism cannot make complex functional systems; it is an observation that it does not." https://www.youtube.com/watch?v=9svV8wNUqvA
Since Darwinian processes have to explain the origin of far more than a single protein-protein binding site, then the probabilities against Darwinian evolution quickly escalate into astronomical proportions. As Bruce Alberts explained, "we now know that nearly every major process in a cell is carried out by assemblies of 10 or more protein molecules."
"But, as it turns out, we can walk and we can talk because the chemistry that makes life possible is much more elaborate and sophisticated than anything we students had ever considered. Proteins make up most of the dry mass of a cell. But instead of a cell dominated by randomly colliding individual protein molecules, we now know that nearly every major process in a cell is carried out by assemblies of 10 or more protein molecules. And, as it carries out its biological functions, each of these protein assemblies interacts with several other large complexes of proteins. Indeed, the entire cell can be viewed as a factory that contains an elaborate network of interlocking assembly lines, each of which is composed of a set of large protein machines.” – Bruce Alberts, “The Cell as a Collection of Protein Machines: Preparing the Next Generation of Molecular Biologists,” Cell, 92 (February 6, 1998): 291-294) https://brucealberts.ucsf.edu/publications/BAPub157.pdf Editor-in-Chief of Science (2009-2013). Dr Alberts served two six-year terms as the president of the National Academy of Sciences
Thus, since "developing two binding sites in a protein complex would be the square of the probability for getting one: a double CCC, 10^20 times 10^20, which is 10^40", then getting protein-protein binding sites for 10 protein molecules in order to accomplish a major process in a cell would be, conservatively, on the order of 1 in 10^200. For comparison, there are held to be only 10^80 subatomic particles in the entire universe. To say Darwinian processes are inadequate to explain the complexity we find in life is a severe understatement. As Jay Homnick wrote, "Once you allow the intellect to consider that an elaborate organism with trillions of microscopic interactive components can be an accident… you have essentially “lost your mind.”",,,
"It is not enough to say that design is a more likely scenario to explain a world full of well-designed things. It strikes me as urgent to insist that you not allow your mind to surrender the absolute clarity that all complex and magnificent things were made that way. Once you allow the intellect to consider that an elaborate organism with trillions of microscopic interactive components can be an accident… you have essentially “lost your mind.” https://evolutionnews.org/2015/11/it_really_isnt/
Thus in conclusion, and to repeat what I stated at the beginning of this post, "I guess we should be grateful that Darwinists are at least honest enough to admit that, if Darwinian evolution were true, then most of the genome should be non-functional junk. Now if they were only honest enough to admit that, if Darwinian evolution were true, then ALL of the genome should be non-functional junk." Unfortunately, rigorous honesty seems to be in very limited supply among die-hard Darwinists.
Ephesians 4:25 Therefore each of you must put off falsehood and speak truthfully to your neighbor, for we are all members of one body.
Music:
Sidewalk Prophets - Smile (Official Lyric Video) https://www.youtube.com/watch?v=15V2sXSJ8Co
bornagain77_{January 10, 2020
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I guess we should be grateful that Darwinists are at least honest enough to admit that, if Darwinian evolution were true, then most of the genome should be non-functional junk. Now if they were only honest enough to admit that, if Darwinian evolution were true, then ALL of the genome should be non-functional junk. In other words instead of the genome being 75% or 90% junk, as Graur and Moran predicted, (post 16), the genome should instead be 100% non-functional junk. The probability of Darwinian processes finding a protein fold, not even an entire functional protein mind you, is in and of itself prohibitive. Douglas Axe found that only "about 1 in 10^77 sequences produce the stably folded structure",,,
(Venema's) Adam and the Genome and Doug Axe’s Research on the Evolution of New Protein Folds - March 7, 2018, Excerpt: Douglas Axe, a protein scientist who has published work on the rarity of new protein folds by doing research on beta-lactamase enzymes. Publishing in the Journal of Molecular Biology, Axe found that only about 1 in 10^77 sequences produce the stably folded structure needed for beta lactamase to work.,,, Axe’s generalization of results follows the tradition of many similar papers, which came to similar conclusions about the rarity of functional protein sequences, and applied their results broadly. For example: * Reidhaar-Olson and Sauer 1990 (published in the journal Proteins), mutated the ?-repressor in coli and found that only one in 10^63 sequences yield a functional repressor fold. They generalized the implications of their results for how we predict protein structure in other cases, writing: “The high level of degeneracy involved in protein folding suggests that the most fruitful approaches to structure prediction will concentrate on those residues that are informationally rich.” * Yockey 1977 (published in the Journal of Theoretical Biology) calculated that the likelihood of generating a functional cytochrome c sequence is one in 10^65. He generalized this result to conclude that many proteins are not evolvable, and even concluded that standard mechanisms of abiogenesis could not produce such features on a reasonable timescale. He wrote that “belief in currently accepted scenarios of spontaneous biogenesis is based on faith, contrary to conventional wisdom.” * Hayashi et al. 2006 (published in PLOS ONE) determined that 10^70 trials would be necessary to acquire the wild-type function of the g3p minor coat protein of the fd phage. They generalized their inferred fitness landscape results to other cases, and wrote: “The landscape structure has a number of implications for initial functional evolution of proteins and for molecular evolutionary engineering.” However, because reaching higher fitness levels required scaling much steeper fitness functions (i.e., functional sequences were very rare), thus concludeD, as a general matter: “In molecular evolutionary engineering, larger library size is generally favorable for reaching higher stationary fitness.” https://evolutionnews.org/2018/03/adam-and-the-genome-and-doug-axes-research-on-the-evolution-of-new-protein-folds/
1 in 10^77 dwarfs the total number of organisms (10^40) that have existed on earth and therefore renders Darwinian explanations untenable. As Stephen Meyer explains, "every replication event in the entire multi-billion year history of life on Earth would not generate or "search" but a miniscule fraction (one ten trillion, trillion trillionth, to be exact) of the total number of possible nucleotide base or amino-acid sequences corresponding to a single functional gene or protein fold. The number of trials available to the evolutionary process (corresponding to the total number of organisms -- 10^40 -- that have ever existed on earth), thus, turns out to be incredibly small in relation to the number of possible sequences that need to be searched.
About a Bike Lock: Responding to Richard Dawkins - Stephen C. Meyer – March 25, 2016 Excerpt: Moreover, given the empirically based estimates of the rarity (of protein folds) (conservatively estimated by Axe3 at 1 in 10^77 and within a similar range by others4) the analysis that I presented in Toronto does pose a formidable challenge to those who claim the mutation-natural selection mechanism provides an adequate means for the generation of novel genetic information -- at least, again, in amounts sufficient to generate novel protein folds.5 Why a formidable challenge? Because random mutations alone must produce (or "search for") exceedingly rare functional sequences among a vast combinatorial sea of possible sequences before natural selection can play any significant role. Moreover, as I discussed in Toronto, and show in more detail in Darwin's Doubt,6 every replication event in the entire multi-billion year history of life on Earth would not generate or "search" but a miniscule fraction (one ten trillion, trillion trillionth, to be exact) of the total number of possible nucleotide base or amino-acid sequences corresponding to a single functional gene or protein fold. The number of trials available to the evolutionary process (corresponding to the total number of organisms -- 10^40 -- that have ever existed on earth), thus, turns out to be incredibly small in relation to the number of possible sequences that need to be searched. The threshold of selectable function exceeds what is reasonable to expect a random search to be able to accomplish given the number of trials available to the search even assuming evolutionary deep time. ------- (3) Axe, Douglas. "Estimating the Prevalence of Protein Sequences Adopting Functional Enzyme Folds." Journal of Molecular Biology 341 (2004): 1295-1315. (4) Reidhaar-Olson, John, and Robert Sauer. "Functionally Acceptable Solutions in Two Alpha-Helical Regions of Lambda Repressor." Proteins: Structure, Function, and Genetics 7 (1990): 306-16; Yockey, Hubert P. "A Calculation of the Probability of Spontaneous Biogenesis by Information Theory," Journal of Theoretical Biology 67 (1977c): 377-98; Yockey, Hubert. "On the Information Content of Cytochrome C," Journal of Theoretical Biology 67 (1977b) 345-376. http://www.evolutionnews.org/2016/03/about_a_bike_lo102722.html
Evolutionists themselves admit that only 10^43 trials are available during the entire history of life on earth for Darwinian processes to find a functional protein. As Cornelius Hunter explains, "Even evolutionists have had to admit that evolution could only have a maximum of 10^43 such experiments. It is important to understand how tiny this number is compared to 10^70. 10^43 is not more than half of 10^70. It is not even close to half. 10^43 is an astronomically tiny sliver of 10^70. Furthermore, the estimate of 10^43 is, itself, entirely unrealistic. For instance, it assumes the entire history of the Earth is available, rather than the limited time window that evolution actually would have had. Even more importantly, it assumes the pre existence of bacteria and, yes, proteins."
Here Are Those Two Protein Evolution Falsifications That Have Evolutionists Rewriting Their Script - Cornelius Hunter - March 2012 Excerpt: Several different studies indicate that, at a minimum, about 10^70 (a one followed by 70 zeros) evolutionary experiments would be needed to get close enough to a workable protein design before evolutionary mechanisms could take over and establish the protein in a population. For instance, one study concluded that 10^63 attempts would be required for a relatively short protein. And a similar result (10^65 attempts required) was obtained by comparing protein sequences. Another study found that 10^64 to 10^77 attempts are required, and another study concluded that 10^70 attempts would be required. This requirement for 10^70 evolutionary experiments is far greater than what evolution could accomplish. Even evolutionists have had to admit that evolution could only have a maximum of 10^43 such experiments. It is important to understand how tiny this number is compared to 10^70. 10^43 is not more than half of 10^70. It is not even close to half. 10^43 is an astronomically tiny sliver of 10^70. Furthermore, the estimate of 10^43 is, itself, entirely unrealistic. For instance, it assumes the entire history of the Earth is available, rather than the limited time window that evolution actually would have had. Even more importantly, it assumes the pre existence of bacteria and, yes, proteins. http://darwins-god.blogspot.com/2012/03/here-are-those-two-protein-evolution.html
Recent work in quantum criticality has further confirmed the rarity of proteins. In the following 2015 paper entitled, “Quantum criticality in a wide range of important biomolecules” it was found that “Most of the molecules taking part actively in biochemical processes are tuned exactly to the transition point and are critical conductors,” and the researchers further commented that “finding even one (biomolecule) that is in the quantum critical state by accident is mind-bogglingly small and, to all intents and purposes, impossible.,, of the order of 10^-50 of possible small biomolecules and even less for proteins,”,,,
Quantum criticality in a wide range of important biomolecules – Mar. 6, 2015 Excerpt: “Most of the molecules taking part actively in biochemical processes are tuned exactly to the transition point and are critical conductors,” they say. That’s a discovery that is as important as it is unexpected. “These findings suggest an entirely new and universal mechanism of conductance in biology very different from the one used in electrical circuits.” The permutations of possible energy levels of biomolecules is huge so the possibility of finding even one (biomolecule) that is in the quantum critical state by accident is mind-bogglingly small and, to all intents and purposes, impossible.,, of the order of 10^-50 of possible small biomolecules and even less for proteins,”,,, “what exactly is the advantage that criticality confers?” https://medium.com/the-physics-arxiv-blog/the-origin-of-life-and-the-hidden-role-of-quantum-criticality-ca4707924552
Quantum criticality is simply inexplicable for Darwinists. As this follow-up paper stated, "There is no obvious evolutionary reason why a protein should evolve toward a quantum-critical state, and there is no chance at all that the state could occur randomly.,,,"
Quantum Critical Proteins – Stuart Lindsay – Professor of Physics and Chemistry at Arizona State University – 2018 Excerpt: The difficulty with this proposal lies in its improbability. Only an infinitesimal density of random states exists near the critical point.,, Gábor Vattay et al. recently examined a number of proteins and conducting and insulating polymers.14 The distribution for the insulators and conductors were as expected, but the functional proteins all fell on the quantum-critical distribution. Such a result cannot be a consequence of chance.,,, WHAT OF quantum criticality? Vattay et al. carried out electronic structure calculations for the very large protein used in our work. They found that the distribution of energy-level spacings fell on exactly the quantum-critical distribution, implying that this protein is also quantum critical. There is no obvious evolutionary reason why a protein should evolve toward a quantum-critical state, and there is no chance at all that the state could occur randomly.,,, http://inference-review.com/article/quantum-critical-proteins Gábor Vattay et al., “Quantum Criticality at the Origin of Life,” Journal of Physics: Conference Series 626 (2015); Gábor Vattay, Stuart Kauffman, and Samuli Niiranen, “Quantum Biology on the Edge of Quantum Chaos,” PLOS One 9, no. 3 (2014)
Moreover, even if we granted Darwinists the existence of proteins, it is still of no help to Darwinists. Darwinists believe that genes/proteins have basically unlimited plasticity in their ability to search for new functional sequences in sequence space. Yet, genes/proteins are instead found to be highly constrained in their ability to search ‘sequence space’ in order to try to find new functional sequences.
Stability effects of mutations and protein evolvability. October 2009 Excerpt: The accepted paradigm that proteins can tolerate nearly any amino acid substitution has been replaced by the view that the deleterious effects of mutations, and especially their tendency to undermine the thermodynamic and kinetic stability of protein, is a major constraint on protein evolvability,, http://www.ncbi.nlm.nih.gov/pubmed/19765975
As Günter Bechly, Brian Miller and David Berlinski explain, "Harvard mathematical biologist Martin Nowak has shown that random searches in sequence space that start from known functional sequences are no more likely to enter regions in sequence space with new protein folds than searches that start from random sequences. The reason for this is clear: random searches are overwhelmingly more likely to go off into a non-folding, non-functional abyss than they are to find a novel protein fold."
Right of Reply: Our Response to Jerry Coyne - September 29, 2019 by Günter Bechly, Brian Miller and David Berlinski Excerpt: Indeed, Harvard mathematical biologist Martin Nowak has shown that random searches in sequence space that start from known functional sequences are no more likely to enter regions in sequence space with new protein folds than searches that start from random sequences. The reason for this is clear: random searches are overwhelmingly more likely to go off into a non-folding, non-functional abyss than they are to find a novel protein fold. Why? Because such novel folds are so extraordinarily rare in sequence space. Moreover, as Meyer explained in Darwin’s Doubt, as mutations accumulate in functional sequences, they will inevitably destroy function long before they stumble across a new protein fold. Again, this follows from the extreme rarity (as well as the isolation) of protein folds in sequence space. Recent work by Weizmann Institute protein scientist Dan Tawfik has reinforced this conclusion. Tawfik’s work shows that as mutations to functional protein sequences accumulate, the folds of those proteins become progressively more thermodynamically and structurally unstable. Typically, 15 or fewer mutations will completely destroy the stability of known protein folds of average size. Yet, generating (or finding) a new protein fold requires far more amino acid sequence changes than that. Finally, calculations based on Tawfik’s work confirm and extend the applicability of Axe’s original measure of the rarity of protein folds. These calculations confirm that the measure of rarity that Axe determined for the protein he studied is actually representative of the rarity for large classes of other globular proteins. Not surprisingly, Dan Tawfik has described the origination of a truly novel protein or fold as “something like close to a miracle.” Tawfik is on Coyne’s side: He is mainstream. https://quillette.com/2019/09/29/right-of-reply-our-response-to-jerry-coyne/
Doug Axe and Ann Gauger have done experimental work exploring just how constrained genes-proteins are in their ability to search sequence space. Their work found that, "Darwin’s mechanism would need a truly staggering amount of time—a trillion trillion years or more—to accomplish the seemingly subtle change in enzyme function that we studied."
When Theory and Experiment Collide — April 16th, 2011 by Douglas Axe Excerpt: Based on our experimental observations and on calculations we made using a published population model [3], we estimated that Darwin’s mechanism would need a truly staggering amount of time—a trillion trillion years or more—to accomplish the seemingly subtle change in enzyme function that we studied. http://www.biologicinstitute.org/post/18022460402/when-theory-and-experiment-collide “Enzyme Families — Shared Evolutionary History or Shared Design?” – Ann Gauger – December 4, 2014 Excerpt: If enzymes can’t be recruited to genuinely new functions by unguided means, no matter how similar they are, the evolutionary story is false.,,, Taken together, since we found no enzyme that was within one mutation of cooption, the total number of mutations needed is at least four: one for duplication, one for over-production, and two or more single base changes. The waiting time required to achieve four mutations is 10^15 years. That’s longer than the age of the universe. The real waiting time is likely to be much greater, since the two most likely candidate enzymes failed to be coopted by double mutations. We have now addressed two objections raised by our critics: that we didn’t test the right mutation(s), and that we didn’t use the right starting point. We tested all possible single base changes in nine different enzymes, Those nine enzymes are the most structurally similar of BioF’s entire family We also tested 70 percent of double mutations in the two closest enzymes of those nine. Finally, some have said we should have used the ancestral enzyme as our starting point, because they believe modern enzymes are somehow different from ancient ones. Why do they think that? It’s because modern enzymes can’t be coopted to anything except trivial changes in function. In other words, they don’t evolve! That is precisely the point we are making. http://www.evolutionnews.org/2014/12/a_new_paper_fro091701.html
bornagain77_{January 10, 2020
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It’s worth poiting out the main reason we now know more about transposbale elements and the like is technological.
that would be my guess. Non-coding DNA caused hell with sequencing in the 90s, because a lot of time would be spent making a YAC or BAC library, essentially libraries of stretches of DNA, and these would have to be sequenced and then assembled into chromosomes. A lot of non-coding DNA is multiple copies of the same sequence, so trying to work out how they fitted together was a pain. It was so bad that the people wanting to sequence wheat gave up, and sequences rice instead (less junk DNA, and the order of the genes along the chromosome was almost the same).Bob O'H_{January 10, 2020
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It's worth poiting out the main reason we now know more about transposbale elements and the like is technological. We have long-read (and longer short-read) sequencing methods that allow us to resolve these repetitive regions of tgenomes and study them, rather than mask them out as un-tractable as we used. The narrative that people ignored non-coding regions and beginning of the genomics era is especially silly, as methods like recombination mapping and GWAS take in the whole genome and do not rely on reserachers choosing targets. The fact these methods mosly uncovered coding regions is evidence that the coding regions are mroe importnat than non-coding ones for the traits people where studying. The contributions of TEs and other non-codign DNA to gene regulation adn genome structure is a very interesting field, and one being lead by evolutionary geneticists. But it's still not the case that msot of the genome is functional.Mimus_{January 9, 2020
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SA @ 19 -
A change occurred – yes. There was a “feeling” that most of it was functionless. Then that changed as more function was discovered. That was a very big deal because of how wrong the evolutionist were.
Not really. The guess was that some junk DNA had function, and we've been finding out what those functions are. But that still doesn't negate the observation that most junk DNA appear not to have a function (for the organism, at least).
I was going to take some time and quote back the paper from Nature Reviews Genetics about how the “misunderstanding” of pseudogenes was a very big deal which inhibited further study, but the whole argument is already nicely laid out here:
Are you aware that only a small proportion of non-coding DNA is pseudo-genes? Most of it is TEs and the like. I'll repeat what I wrote @ 15:
You seem to be unable to understand that ‘junk DNA’ is not a single thing. It’s like splitting the world into Australia and Not Australia. There is a lot of Not Australia, but not every part of Not Australia is the same. So if I claim that some parts of Not Australia are dry, that does not mean that all of Not Australia is dry, and it also doesn’t mean that people who disagree with me think that all of Not Australia is under water.
Bob O'H_{January 9, 2020
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Pardon a personal anecdote, but... One of the few benefits of getting older is getting to see how well or poorly predictions and beliefs of your younger years hold up. Back in the late 80's/early 90's, I participated in a Creation/Evolution discussion forum on the computer service Compuserve*. This was pre-ID, pre-internet, billboards and modems era stuff. I was, of course, arguing from a YEC perspective. At the time, I was an engineer at a steel foundry, and one of my responsibilities was a network of PLC's (programmable logic controllers) that exchanged data over a twisted pair communication line. As such, I got involved a lot with the basics of data communication. On the CrEv board, I used to compare DNA with data being transmitted, and made a number of predictions about DNA based on my understanding of designed data. Anyway, based on my knowledge of data transmission, and believing it not the product of random chance, here were predictions I made at the time would be discovered about DNA: 1) Error detection: almost all data transmission technologies, even in the 80's, utilitize some form of checksum. DNA will have checksums. 2) Error correction: DNA will contain parity bits, duplicate copies of data, and/or some other method of self-correcting corrupt data. 3) Compression: Compression (e.g. pkzip) is used when space constraints are important, either for storage or transmission. However, it imposes a penalty on performance. DNA will implement compression on regions that are rarely used, but will be uncompressed on regions used constantly/frequently. 4) Encryption: The purpose of encryption is to hide secret data. Like compression, it imposes a performance penalty. DNA will not implement encryption - God isn't trying to hide His work. 5) Random changes only break it: self-explanatory. Not long after I made these predictions almost 30 years ago, I added a couple based on my additional understanding of DNA as code (I moved from engineering to software dev.): 6) Reuse: commonly used sections of DNA will be used for multiple purposes. 7) Large regions of rarely/never used code, mostly in compressed regions: it is not uncommon for less than 10% of code in an application to get used - large sections of code get rarely/never called (e.g. try/catch blocks, outlier use-cases, etc.). Most DNA will not get interpreted/used in steady-state living conditions, and will only kick in under extremes/changed environments. I'll leave it to you how well these predictions have held up. * Additional personal anecdote - On one of the boards, I ran into one of my favorite fantasy authors, Raymond Feist. My only quibble with him was to ask him why he had to kill off one of his book characters, Laurie. He responded that he had to - Laurie's agent was asking for too much money to extend his contract...drc466_{January 9, 2020
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My two pence on this, however little I understand in this particular issue, is that evolutionists trying to prove nothing is a big deal for evolution are shooting themselves in the foot because what do you call a hypothesis that cannot be falsified? -- Anything but science.EugeneS_{January 9, 2020
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Bob O'H
There was a feeling that most junk DNA was functionless ...
And thus you engaged in an argument about this, attempting to say something else.
They say that the change occurred in the 90s, so i don’t see that as being inconsistent with what I wrote.
A change occurred - yes. There was a "feeling" that most of it was functionless. Then that changed as more function was discovered. That was a very big deal because of how wrong the evolutionist were.
Finding another function for some non-coding DNA isn’t really a big deal evolutionarily: we already know a some of it has function.
I was going to take some time and quote back the paper from Nature Reviews Genetics about how the "misunderstanding" of pseudogenes was a very big deal which inhibited further study, but the whole argument is already nicely laid out here: https://evolutionnews.org/2020/01/nature-reviews-genetics-pseudogene-function-is-prematurely-dismissed/ The key point for me is that you began with a statement that whatever functions we find for non-coding DNA it will not be a "big deal". So, you tried to minimize the problem. But as noted, "change" had to occur. That conflicts with your view. You then engaged in an argument, attempting to say or prove something like: Nothing we discovered thus far was a big deal, evolutionists were not wrong, the evolutionary claim that most Junk DNA was functionless was not a problem and evolution predicted whatever followed in our understanding of Junk DNA. Again, you're trying to dismiss the problem. The Nature Reviews Genetics paper itself says it was something significant.Silver Asiatic_{January 9, 2020
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Thus, even the mathematical model that Darwinists are using that supposedly shows that 'fitness must always increase' is now known to be wrong. Moreover, even though Larry 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
Why Are Biologists Lashing Out Against Empirically Verified Research Results? - Casey Luskin - July 13, 2015 Excerpt: no publication shook this (ID vs Darwin) debate so much as a 2012 Nature paper that finally put junk DNA to rest--or so it seemed. This bombshell paper presented the results of the ENCODE (Encyclopedia of DNA Elements) Project, a years-long research consortium involving over 400 international scientists studying noncoding DNA in the human genome. Along with 30 other groundbreaking papers, the lead ENCODE article found that the "vast majority" of the human genome shows biochemical function: "These data enabled us to assign biochemical functions for 80 percent of the genome, in particular outside of the well-studied protein-coding regions."3 Ewan Birney, ENCODE's lead analyst, explained in Discover Magazine that since ENCODE studied 147 types of cells, and the human body has a few thousand cell types, "it's likely that 80 percent will go to 100 percent."4 Another senior ENCODE researcher noted that "almost every nucleotide is associated with a function."5 A headline in Science declared, "ENCODE project writes eulogy for junk DNA."6,,, Evolutionists Strike Back Darwin defenders weren't going to take ENCODE's data sitting down.,,, How could they possibly oppose such empirically based conclusions? The same way they always defend their theory: by assuming an evolutionary viewpoint is correct and reinterpreting the data in light of their paradigm--and by personally attacking, (i.e. ad hominem), those who challenge their position.,,, http://www.evolutionnews.org/2015/07/the_encode_embr097561.html 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/2015/04/a_new_book_on_j095611.html
,,, and they (Moran and Graur) also held the genome 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 Demonstrating, Once Again, the Fantastic Information-Storage Capacity of DNA - January 29, 2013 Excerpt: researchers led by molecular biologists Nick Goldman and Ewan Birney of the European Bioinformatics Institute (EBI) in Hinxton, UK, report online today in Nature that they've improved the DNA encoding scheme to raise that storage density to a staggering 2.2 petabytes per gram, three times the previous effort.,,, http://www.evolutionnews.org/2013/01/how_do_you_peta068641.html
I hate to break it to Larry Moran and Dan Graur (and Seversky and Bob O'Hara)), but in empirical science evidence trumps theory every time. As Richard Feynman stated, ‘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.”
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
That Darwinists would blatantly ignore empirical evidence that falsifies their theory, (indeed attack people who provide falsifying evidence to their theory), is par for the course. As Emily Morales pointed out the other day, Darwinists, today and ever since its inception, have blatantly ignored Bacon’s method of “repeated experimentation”
(January 1, 2020) - in her very first article on UD, Emily Morales goes on to note that Darwinists, today and even since its inception, have blatantly ignored Bacon’s method of “repeated experimentation” https://uncommondescent.com/intelligent-design/welcome-to-the-brave-new-world-of-science/#comment-690388
In short, Darwinian evolution, since it ignores, even attacks, any empirical evidence that falsifies its claims, is, in reality, a pseudoscience, even a religion for atheists, rather than it being a real and testable empirical science.
1 Thessalonians 5:21 but test them all; hold on to what is good,
bornagain77_{January 9, 2020
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Darwinists simply have no evidence that the rate of beneficial mutations to deleterious mutations are anywhere near sufficiently high enough to make Darwinian evolution feasible:
The Human Gene Mutation Database The Human Gene Mutation Database (HGMD®) represents an attempt to collate known (published) gene lesions responsible for human inherited disease. Deleterious Mutation total (as of January 9. 2020) – 269419 http://www.hgmd.cf.ac.uk/ac/ Critic ignores reality of Genetic Entropy - Dr John Sanford - 7 March 2013 Excerpt: Where are the beneficial mutations in man? It is very well documented that there are thousands of deleterious Mendelian mutations accumulating in the human gene pool, even though there is strong selection against such mutations. Yet such easily recognized deleterious mutations are just the tip of the iceberg. The vast majority of deleterious mutations will not display any clear phenotype at all. There is a very high rate of visible birth defects, all of which appear deleterious. Again, this is just the tip of the iceberg. Why are no beneficial birth anomalies being seen? This is not just a matter of identifying positive changes. If there are so many beneficial mutations happening in the human population, selection should very effectively amplify them. They should be popping up virtually everywhere. They should be much more common than genetic pathologies. Where are they? European adult lactose tolerance appears to be due to a broken lactase promoter [see Can’t drink milk? You’re ‘normal’! Ed.]. African resistance to malaria is due to a broken hemoglobin protein [see Sickle-cell disease. Also, immunity of an estimated 20% of western Europeans to HIV infection is due to a broken chemokine receptor—see CCR5-delta32: a very beneficial mutation. Ed.] Beneficials happen, but generally they are loss-of-function mutations, and even then they are very rare! http://creation.com/genetic-entropy
As Dr Sanford states In the following article, “It is almost universally acknowledged that beneficial mutations are rare compared to deleterious mutations.,, It appears that beneficial mutations may be too rare to actually allow the accurate measurement of how rare they are.”
Multiple Overlapping Genetic Codes Profoundly Reduce the Probability of Beneficial Mutation George Montañez 1, Robert J. Marks II 2, Jorge Fernandez 3 and John C. Sanford 4 - May 2013 Excerpt: It is almost universally acknowledged that beneficial mutations are rare compared to deleterious mutations [1–10].,, It appears that beneficial mutations may be too rare to actually allow the accurate measurement of how rare they are [11]. 1. Kibota T, Lynch M (1996) Estimate of the genomic mutation rate deleterious to overall fitness in E. coli . Nature 381:694–696. 2. Charlesworth B, Charlesworth D (1998) Some evolutionary consequences of deleterious mutations. Genetica 103: 3–19. 3. Elena S, et al (1998) Distribution of fitness effects caused by random insertion mutations in Escherichia coli. Genetica 102/103: 349–358. 4. Gerrish P, Lenski R N (1998) The fate of competing beneficial mutations in an asexual population. Genetica 102/103:127–144. 5. Crow J (2000) The origins, patterns, and implications of human spontaneous mutation. Nature Reviews 1:40–47. 6. Bataillon T (2000) Estimation of spontaneous genome-wide mutation rate parameters: whither beneficial mutations? Heredity 84:497–501. 7. Imhof M, Schlotterer C (2001) Fitness effects of advantageous mutations in evolving Escherichia coli populations. Proc Natl Acad Sci USA 98:1113–1117. 8. Orr H (2003) The distribution of fitness effects among beneficial mutations. Genetics 163: 1519–1526. 9. Keightley P, Lynch M (2003) Toward a realistic model of mutations affecting fitness. Evolution 57:683–685. 10. Barrett R, et al (2006) The distribution of beneficial mutation effects under strong selection. Genetics 174:2071–2079. 11. Bataillon T (2000) Estimation of spontaneous genome-wide mutation rate parameters: whither beneficial mutations? Heredity 84:497–501. http://www.worldscientific.com/doi/pdf/10.1142/9789814508728_0006
Moreover, as John Sanford outlines in his book ‘Genetic Entropy’ and in 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/doi/pdf/10.1142/9789814508728_0010 Critic ignores reality of Genetic Entropy by Dr John Sanford - 7 March 2013 Excerpt: For deleterious mutations, Kimura and most other population geneticists agree the distribution is essentially exponential. Figure 3c in my book (based upon Kimura) shows an exponential-type distribution of deleterious mutations, with most deleterious mutations being ‘nearly-neutral’ and hence un-selectable (effectively neutral). But, as I point out, Kimura’s picture is not complete, because degeneration is all about the ratio of good to bad mutations. Kimura does not show the beneficial distribution, which is essential to the question of net gain versus net loss! When I show the beneficial distribution (while Kimura did not do this, I suspect he would have drawn it much as I did), anyone can see the problem: the vast majority of beneficial mutations will be un-selectable (Figure 3d). Scott does not appear to contest my representation of the mutational effect distribution, which is the main issue here. Scott should easily be able to see that most mutations fall within the ‘no-selection zone’ and that almost all of them are deleterious. So even with strong selection, this entire zone can only undergo degeneration. Outside this zone, the substantially bad mutations will be selected away, and an occasional rare high-impact beneficial will be amplified (which can explain isolated events such as antibiotic resistance). http://creation.com/genetic-entropy Kimura's Distribution http://dl0.creation.com/articles/p091/c09164/9164-diagram-3c-lge-white.jpg Correct Distribution (from Sanford's book 'Genetic Entropy) http://dl0.creation.com/articles/p091/c09164/9164-diagram-3d-lge-white.jpg
Moreover, Dr. Sanford has also now shown that when realistic rates of detrimental to beneficial mutations are taken into consideration then that falsifies Fisher's belief that fitness must always increase,
Geneticist Corrects Fisher’s Theorem, but the Correction Turns Natural Selection Upside Down - December 22, 2017 | David F. Coppedge Excerpt: Fisher essentially assumed that new mutations arose with a nearly normal distribution – with an equal proportion of good and bad mutations (so mutations would have a net fitness effect of zero). We now know that the vast majority of mutations in the functional genome are harmful, and that beneficial mutations are vanishingly rare. The simple fact that Fisher’s premise was wrong, falsifies Fisher’s corollary. Without Fisher’s corollary – Fisher’s Theorem proves only that selection improves a population’s fitness until selection exhausts the initial genetic variation, at which point selective progress ceases. Apart from his corollary, Fisher’s Theorem only shows that within an initial population with variant genetic alleles, there is limited selective progress followed by terminal stasis.,,, The authors observe that the more realistic the parameters, the more likely fitness decline becomes. https://crev.info/2017/12/geneticist-corrects-fishers-theorem/
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Larry Moran hitched his wagon to Dan Graur. After ENCODE came out, Dan Graur infamously stated that “If ENCODE is right, then evolution is wrong.”, The reason why Graur and Moran insist that ENCODE must be wrong, and that most of the genome must be junk, is because of the mathematics of population genetics. Specifically because of the genetic load argument within population genetics.
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/2017/07/revisiting-genetic-load-argument-with.html
And indeed the genetic load argument is a severe problem, not for ENCODE but for Darwinian evolution:
Human evolution or extinction – (genetic load argument) discussion on acceptable mutation rate per generation (with clips from Dr. John Sanford) - video http://www.youtube.com/watch?v=aC_NyFZG7pM "it would in the end be far easier and more sensible to manufacture a complete man de novo, out of appropriately chosen raw materials, than to try to fashion into human form those pitiful relics which remained… it is evident that the natural rate of mutation of man is so high, and his natural rate of reproduction so low, that not a great deal of margin is left for selection… it becomes perfectly evident that the present number of children per couple cannot be great enough to allow selection to keep pace with a mutation rate of 0.1..if, to make matters worse, u should be anything like as high as 0.5…, our present reproductive practices would be utterly out of line with human requirements." Hermann Muller quoted by John Sanford; Appendix 1, Genetic Entropy No Matter What Type Of Selection, Mutations Deteriorate Genetic Information - article and animation Excerpt: The animation asserts that if harmful mutation rates are high enough, then there exists no form or mechanism of selection which can arrest genetic deterioration. Even if the harmful mutations do not reach population fixation, they can still damage the collective genome.,,, Nobel Prize winner HJ Muller (of Muller’s ratchet fame) suggested that the human race can’t even cope with a harmful rate of 0.1 (mutations) per new born. The actual rate has been speculated to be on the order of 100-300. The animation uses a conservative harmful rate of 1 and argues (with some attempts at humor) that deterioration would thus be inevitable even with a harmful rate of 1 per new born. https://uncommondescent.com/evolution/nachmans-paradox-defeats-darwinism-and-dawkins-weasel/ Beyond A 'Speed Limit' On Mutations, Species Risk Extinction Excerpt: Shakhnovich's group found that for most organisms, including viruses and bacteria, an organism's rate of genome mutation must stay below 6 mutations per genome per generation to prevent the accumulation of too many potentially lethal changes in genetic material. http://www.sciencedaily.com/releases/2007/10/071001172753.htm Using Computer Simulation to Understand Mutation Accumulation Dynamics and Genetic Load John Sanford1, John Baumgardner2, Wes Brewer3, Paul Gibson4, and Walter ReMine5 Abstract. Long-standing theoretical concerns about mutation accumulation within the human population can now be addressed with numerical simulation. We apply a biologically realistic forward-time population genetics program to study human mutation accumulation under a wide-range of circumstances. Using realistic estimates for the relevant biological parameters, we investigate the rate of mutation accumulation, the distribution of the fitness effects of the accumulating mutations, and the overall effect on mean genotypic fitness. Our numerical simulations consistently show that deleterious mutations accumulate linearly across a large portion of the relevant parameter space. This appears to be primarily due to the predominance of nearly-neutral mutations. The problem of mutation accumulation becomes severe when mutation rates are high. Numerical simulations strongly support earlier theoretical and mathematical studies indicating that human mutation accumulation is a serious concern. http://bioinformatics.cau.edu.cn/lecture/chinaproof.pdf Genetic Entropy – LATEST DEVELOPMENTS http://www.geneticentropy.org/latest-development
Moreover, I hold Moran's 10% estimate for deleterious mutations, that he used in his calculation in his article, to be far too conservative, and thus the percentage of junk DNA, according to his own calculation, should actually be much higher (much worse) 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.com/2010/12/the-first-rule-of-adaptive-evolution/
Of note, Behe extends this thesis in greater detail in his more recent 2019 book "Darwin Devolves"
Darwin Devolves: The New Science About DNA That Challenges Evolution - 2019 Behe contends that Darwinism actually works by a process of devolution—damaging cells in DNA in order to create something new at the lowest biological levels. This is important, he makes clear, because it shows the Darwinian process cannot explain the creation of life itself. “A process that so easily tears down sophisticated machinery is not one which will build complex, functional systems,” he writes. https://www.amazon.com/Darwin-Devolves-Science-Challenges-Evolution/dp/0062842617
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SA @ 3 -
Bob O’H engaged in some hair-splitting by trying to say, basically, that no evolutionists thought that Junk DNA had “no function”.
False . I wouldn't claim that (because someone might have said that junk DNA had no function, even if there was a different consensus). It's clear that not all junk DNA is necesary, because the amounts change between species, and because it's possible to remove large chunks without affecting the organism. But that wouldn't mean that all junk DNA had no function.
I cited Ohno’s paper (and his comments) and Bob’s response was that he Ohno thought NC DNA had “some function”.
Indeed, and I even cited Ohno's very words - he was most definitely predicting functions.
Bob never accepted (or it seemed) that the evolutionary consensus for at least a couple of decades was that there was virtually no function and it was Junk.
I don't think I took a position on that, other than to say that by the late 80s, as far as I recall, there was a consensus that some junk DNA was probably doing something, even if we didn't know that it was doing.
The Scientific American article you quoted offers this also:
They say that the change occurred in the 90s, so i don't see that as being inconsistent with what I wrote. There was a feeling that most junk DNA was functionless (and an absolute pain if you're trying to sequence a species), but we knew about TEs, and also that they could affect evolution (by moving functional DNA around). But yeah, it was mainly seen as an annoyance: it's why geneticists interested in wheat decided to sequence rice instead.
hat is greatly appreciated because Bob O’H decided to try some historical revisionism and pretend that nobody actually considered Non-coding DNA to be non-functional (genomic garbage).
Err, OK. That is, once more, simply false. Some 'junk DNA' was considered non-functional, but not all of it. You seem to be unable to understand that 'junk DNA' is not a single thing. It's like splitting the world into Australia and Not Australia. There is a lot of Not Australia, but not every part of Not Australia is the same. So if I claim that some parts of Not Australia are dry, that does not mean that all of Not Australia is dry, and it also doesn't mean that people who disagree with me think that all of Not Australia is under water.Bob O'H_{January 9, 2020
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Mission: To sustain DNA based self-replicating life for hundreds of millions of years. ID Prediction: You need some kind of DNA proofreading / repair mechanisms ( actually various types of DNA repair mechanisms, because DNA molecule gets damaged in many ways) Reality: It is there .... all of it ... (direct repair, base excision repair, nucleotide excision repair (NER), double-strand break repair (including homologous recombination and nonhomologous end joining), and crosslink repair ) Some DNA repair mechanisms are backed up, when the 1st fails, the 2nd one will make sure the error gets fixed. DNA proofreading / repair is the ultimate proof of cell design. Undeniable, don't matter what all evolutionary biologists in the world say ... they are all wrong.... so simple as that.... they are all wrong and they know that... P.S. talking about proofreading / repair mechanisms, i would also like to mention DNA replication checkpoint. From Nature.com "The DNA Replication Checkpoint Arrests the Cell Cycle The checkpoints detect various issues found on DNA. Once checkpoint proteins identify these issues, the cell activates signal transduction pathways in order to arrest the progression of the cell cycle and allow adequate time to fix the problems on DNA." "... allow adequate time to fix the problems on DNA."" :)))))))))))))))))))))))) Biologists should see a doctor if they believe that blind unguided natural process or natural selection or random mutations or whatever 'invented' DNA replication checkpoint :))))))))) Are these guys mentally ill ? They are not...not all of them.... these guys are only afraid to speak out.... to admit that the cell / life was created is politically were sensitive... could turn the world upside down. and they have to feed their families....martin_r_{January 9, 2020
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PaV @11: Check this out: https://uncommondescent.com/intelligent-design/larry-moran-doesnt-like-any-of-us-not-sure-why/jawa_{January 9, 2020
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FourFaces @10: I like your interesting analogy of OOP in biological systems.jawa_{January 9, 2020
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Seversky: Larry Moran is fighting a losing battle. The day will soon come when he will have to pack up his tent and leave town. He is learned---and wrong.PaV_{January 8, 2020
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The more correct name for it in software engineering is not “nested coding” but hierarchical coding or object-oriented programming. The hierarchy does not have to be purely nested. Multiple inheritance is allowed. It should also be a class hierarchy where each class or branch can be instantiated (as in protein coding) multiple times if needed, without duplicating the class. If ID is correct, the entire genome is organized like a tree with a trunk, branches and sub-branches. This is the true tree of life, in my opinion, the ID tree of life.FourFaces_{January 8, 2020
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