If even genes are into special creation, what’s left for Darwinism now?

_{Denyse O'Leary

April 16, 2020

Creationism, Genetics, Intelligent Design}

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Properly Darwinian genes would have done what Ohno told them a long time ago but not these ones:

For the half past century or more, most biologists agreed with the conclusions of the geneticist Susumu Ohno in his influential 1970 book Evolution by Gene Duplication. While acknowledging that the first genes had to come from somewhere, he wrote: “Yet, in a strict sense, nothing in evolution is created de novo. Each new gene must have arisen from an existing gene…”
This explanation seemed sound because truly de novo genes would have to emerge through evolution acting on the abundant “nongenic” DNA (often dismissed as junk) between genes. It was hard to imagine how that could happen. Cells’ fitness generally depends on the smooth functioning of networks of genes that have coevolved to work together over millions of years. Genes derived from other genes have a better chance of blending into those networks. In comparison, the fairly random transcripts from nascent de novo genes seem as though they should be, at best, inconsequential —-and more likely harmful to cells’ prospects. “The received wisdom is that random sequences are more likely to mess things up than to make them better,” said Aoife McLysaght, a geneticist at Trinity College Dublin.
But in the past 15 years, evidence for de novo genes has steadily accumulated, so much so that the debate has shifted from whether de novo genes exist to how much they contribute to evolution and adaptation.
Vivian Callier, “ Where Do New Genes Come From?” at Quanta

Hey, wasn’t this the alternative reading at Mass for, you know, Genesis 1, where God speaks and all kinds of life forms pop out of nothing? Hmmm. Give it time.

Comments

ID is the only thing that explains the existence of mathematics, the laws of physics, genesis effect and various species on Earth both past and present.BobRyan_{April 17, 2020
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To demonstrate a true de novo gene, the researchers would have to prove beyond a shadow of a doubt that the DNA segment in question, and similar DNA segments (a few base pairs away perhaps) were never functional in any living thing ever. Because it would be much easier for a supposedly de nove gene to get there by horizontal gene transfer (for example) than to actually pop up de novo. Or for it to have been functional at one time, go dormant, and return to functioning status, as another possibility. Hope these optimistic researchers don't jump the gun and conclude too much...not holding my breath tho.EDTA_{April 17, 2020
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We should change the focus of the debate by asking the following question: "Did the evolution of life over the past billion years require an intelligent agent or not?" This clearly distinguishes ID from any potential naturalistic mechanism or mix of supposed mechanisms. To answer the question and to show that ID is in fact falsifiable, I will rework Darwin's own falsifiability statement as follows: "If it could be demonstrated that many complex organs existed, which could credibly have been formed by numerous, successive, slight modifications, then ID theory would absolutely break down." This approach puts the onus on the other side. Rather than hiding behind possible future theories and vague natural mechanisms, Darwinists should attempt to falsify ID through credible, scientific methods. ID has spent a lot of time demonstrating the limitations and impossibilities of full-up Darwinism (in whatever form), without seeing Darwinists budge an inch. It is time to turn the tables and demand they try to credibly falsify ID - emphasis on the word "credibly".Fasteddious_{April 17, 2020
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@3 AaronS1978 Regarding the 'genetic determinism' thing: If: - we are solely our genes - then 'logical processes' are also determined via genes Meaning: that logic is not immutable, therefore if the underlying genes change, so does the logic. Meaning that logical inferences are not universally valid. Meaning your 'reasoning' is not valid. Meaning 'genetic determinism' is not valid (self-referential absurdity). Meaning: there is more to humans than our genes. Please someone correct me if I am wrong.Truthfreedom_{April 17, 2020
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The issue has always been whether there is a natural mechanism that produces major changes in life forms or not. Darwin’s ideas and the modern synthesis were an attempt at providing a mechanism. They obviously fail. That doesn’t mean there aren’t other natural mechanisms. Stephen Gould observed sudden changes and proposed punctuated equilibrium and Juergen Brosius proposes how this happens with junk DNA as it mutates over long periods of time to form a new DNA sequence that produces a useful protein. He claims they have examples. My guess is that there are a couple trivial examples but they fail to be more than trivial. There are research techniques that would validate or disprove this theory but I haven’t seen them applied in any studies. They just assume it happened this way. Its a natural process but definitely not Darwinian. Everyone focuses on Darwin but he would be abandoned in a second if another theory proved viable. So undercutting Darwin does not make ID a done deal. The value of Darwin is that his ideas are readily understandable to the average person and thus plausible. They are meant to get the average person nodding their head. They are then afraid of questioning it else they appear stupid and found believing in superstition. I have been there trying to have a polite conversation with well meaning, educated and polite friends. Debunking Darwin is beyond their pay grade and you end up appearing as an anti science kook to them. The first accusation thrown at someone doing this is that you are a creationist who believes in looney tunes ideas. The last thing one wants to be thought of is as anti science.jerry_{April 17, 2020
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Along that same line of evidence, Michael Behe, in his book ‘The Edge of Evolution’, noted that the ability of the malaria parasite to develop resistance to chloroquine is a two mutation event with a probability of occurring of 1 in 10^20. He then notes that ‘for humans to achieve a mutation like this by chance, we would have to wait 100 million times 10 million years’ (or 1 quadrillion years)
Waiting Longer for Two Mutations – Michael J. Behe Excerpt: Citing malaria literature sources (White 2004) I had noted that the de novo appearance of chloroquine resistance in Plasmodium falciparum was an event of probability of 1 in 10^20. I then wrote that ‘for humans to achieve a mutation like this by chance, we would have to wait 100 million times 10 million years’ (1 quadrillion years)(Behe 2007) (because that is the extrapolated time that it would take to produce 10^20 humans). http://www.discovery.org/a/9461
Michael Behe then put what he has dubbed 'the edge of evolution' to be at 10^20 times 10^20, which is 10^40. ,,, Behe puts the edge of evolution at 10^40 since, as he states, 'there have likely been fewer than 10^40 cells in the world in the last 4 billion years,'.
“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 (chloroquine complexity cluster), 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
Darwinist simply have no evidence that it is possible for Darwinian processes to create new genes and/or proteins, nor do they have any evidence that it is possible to gradually change existing proteins into new proteins,
"Charles Darwin said (paraphrase), 'If anyone could find anything that could not be had through a number of slight, successive, modifications, my theory would absolutely break down.' Well that condition has been met time and time again. Basically every gene, every protein fold. There is nothing of significance that we can show that can be had in a gradualist way. It's a mirage. None of it happens that way.” - Doug Axe PhD. - 200 Years After Darwin - What Didn't Darwin Know? Part 2 of 2 5:25 minute mark https://youtu.be/VKIgNroTj54?list=PLIHsGlleAKaVlItRRFpJ4fzzKBPvAcJoN&t=325 Right of Reply: Our Response to Jerry Coyne - September 29, 2019 by Günter Bechly, Brian Miller and David Berlinski Excerpt: David Gelernter observed that amino acid sequences that correspond to functional proteins are remarkably rare among the “space” of all possible combinations of amino acid sequences of a given length. Protein scientists call this set of all possible amino acid sequences or combinations “amino acid sequence space” or “combinatorial sequence space.” Gelernter made reference to this concept in his review of Meyer and Berlinski’s books. He also referenced the careful experimental work by Douglas Axe who used a technique known as site-directed mutagenesis to assess the rarity of protein folds in sequence space while he was working at Cambridge University from 1990-2003. Axe showed that the ratio of sequences in sequence space that will produce protein folds to sequences that won’t is prohibitively and vanishingly small. Indeed, in an authoritative paper published in the Journal of Molecular Biology Axe estimated that ratio at 1 in 10^74. From that information about the rarity of protein folds in sequence space, Gelernter—like Axe, Meyer and Berlinski—has drawn the rational conclusion: finding a novel protein fold by a random search is implausible in the extreme. Not so, Coyne argued. Proteins do not evolve from random sequences. They evolve by means of gene duplication. By starting from an established protein structure, protein evolution had a head start. This is not an irrational position, but it is anachronistic. 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/
One final note, it is a shame that Ed George has to rely on deceptive accusations against ID supposedly making false predictions in order to try to prop up Darwinian evolution and to try to discredit ID. And moreover, this, i.e. dishonesty, is a repeated pattern on the part of Darwinists in general. I would like to think that Ed George and other Darwinists would find such dishonesty, especially in science, to be morally reprehensible. Thus the question arises as to what drives them to such morally reprehensible dishonesty? My guess is that, like Thomas Nagel was, Ed George and other Darwinian atheists are primarily driven by a fear of God instead of a love for truth?
“In speaking of the fear of religion, I don’t mean to refer to the entirely reasonable hostility toward certain established religions and religious institutions, in virtue of their objectionable moral doctrines, social policies, and political influence. Nor am I referring to the association of many religious beliefs with superstition and the acceptance of evident empirical falsehoods. I am talking about something much deeper–namely, the fear of religion itself. I speak from experience, being strongly subject to this fear myself: I want atheism to be true and am made uneasy by the fact that some of the most intelligent and well-informed people I know are religious believers. I want atheism to be true and am made uneasy by the fact that some of the most intelligent and well-informed people I know are religious believers. It isn’t just that I don’t believe in God and, naturally, hope that I’m right in my belief. It’s that I hope there is no God! I don’t want there to be a God; I don’t want the universe to be like that.” (”The Last Word” by Thomas Nagel, Oxford University Press: 1997)”
Of note:
Rick Warren: Why God Encourages Christians to 'Fear Not' 365 Times in the Bible Excerpt: God encourages his followers to "fear not" 365 times in the Bible, one for each day of the year, Pastor Rick Warren says, emphasizing that He didn't intend for Christians to spend their days preoccupied with anxiety and worry. https://www.christianpost.com/news/rick-warren-why-god-encourages-christians-to-fear-not-365-times-in-the-bible.html Mark 4: 39-41 He got up, rebuked the wind and said to the waves, “Quiet! Be still!” Then the wind died down and it was completely calm. He said to his disciples, “Why are you so afraid? Do you still have no faith?” They were terrified and asked each other, “Who is this? Even the wind and the waves obey him!”
bornagain77_{April 17, 2020
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Ed George states,
Monday: De novo genes are extremely rare, if not impossible, and not observed, therefore ID. Tuesday: De novo genes are fairly common, therefore ID.
Funny, Ed George is dishonestly trying to accuse ID of, basically, being unfalsifiable since it supposedly changed its prediction concerning ORFan genes in mid-stream to accord with the empirical evidence. Yet being unfalsifiable is the bread and butter of Darwinian evolution, not ID. Shoot, the entire article referenced in the OP from Quanta is itself an exercise in Darwinists changing their predictions to accord with the new findings of the empirical evidence. Moreover, what ID actually predicts, from the empirical evidence itself, is not the absence or prevalence of new ORFan genes/proteins within any given species, but is that it is impossible for Darwinian processes to produce a single new gene and/or protein in the first place, PERIOD, full stop! And that prediction has not been violated one iota. Not one new gene and/or protein has ever been observed to arise from Darwinian processes. As Tawfik and Tóth-Petróczy wrote, “no macromutations ... that gave birth to novel proteins have yet been identified.”
Dan S. Tawfik Group - The New View of Proteins - Tyler Hampton - 2016 Excerpt: Tawfik soberly recognizes the problem. The appearance of early protein families, he has remarked, is “something like close to a miracle.”45,,, “In fact, to our knowledge,” Tawfik and Tóth-Petróczy write, “no macromutations ... that gave birth to novel proteins have yet been identified.”69 http://inference-review.com/article/the-new-view-of-proteins
The odds against Darwinian processes producing a new gene and/or protein are simply staggering,
Yockey and a Calculator Versus Evolutionists - Cornelius Hunter PhD - September 25, 2015 Excerpt: In a 1977 paper published in the Journal of Theoretical Biology, Hubert Yockey used information theory to evaluate the likelihood of the evolution of a relatively simple protein.,,, Yockey found that the probability of evolution finding the cytochrome c protein sequence is about one in 10^64. That is a one followed by 64 zeros—an astronomically large number. He concluded in the peer-reviewed paper that the belief that proteins appeared spontaneously “is based on faith.” Indeed, Yockey’s early findings are in line with, though a bit more conservative than, later findings. A 1990 study of a small, simple protein found that 10^63 attempts would be required for evolution to find the protein. A 2004 study found that 10^64 to 10^77 attempts are required, and a 2006 study concluded that 10^70 attempts would be required. These requirements dwarf the resources evolution has at its disposal. 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.,,, http://darwins-god.blogspot.com/2015/09/yockey-and-calculator-versus.html Quantum criticality in a wide range of important biomolecules 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 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 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
Perhaps Ed George would like to be the first Darwinist to ever empirically demonstrate that unguided Darwinian processes can create a new gene and/or protein? And to thus establish Darwinian evolution as a proper and testable science instead of basically being a unfalsifiable religion for atheists? Moreover, even if we granted Ed George and other atheistic Darwinists the existence of a gene and/or protein, Darwinists would still have no evidence that it is possible to change that existing protein, that performed some specific function, into a 'slightly' new protein that performs a new function, Ann Gauger and Doug Axe have found that Darwinian processes would need a trillion trillion years or more—to accomplish the seemingly subtle change in enzyme function that requires just a few mutations.
When Theory and Experiment Collide - Douglas Axe - April 16th, 2011 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://biologicinstitute.org/2011/04/16/when-theory-and-experiment-collide/ “Shared Evolutionary History or Shared Design?” – Ann Gauger – January 1, 2015 Excerpt: 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. http://www.evolutionnews.org/2015/01/happy_new_year092291.html "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_{April 17, 2020
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There’s is a phrase incorrectly attributed to “El Ingenioso hidalgo Don Quixote de La Mancha” but that apparently isn’t in Miguel de Cervantes Saavedra’s classic book. Nevertheless that phrase pops up to my mind when I see some comments here. :)jawa_{April 16, 2020
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The data and digital language of DNA would be considered ID It’s still really close to impossible and still has not been observed, a single gene coming out of a single drop of soup anywhere in the world on its own. Keywords, on its own It is an event that is so rare but so powerful, that once it happens it can cover the entire planet in life Yet it doesn’t seem to happen again and it takes teams of scientists that are incredibly intelligent with near endless amounts of money to still fail to produce this effect, Because it is absolutely true that the parameters, to try to get this to work, are so tight, that it really only seems to happen once I actually quite a bit disagree with this article And I agree with you ED George I noticed that too, thats why I mentioned what I did on the Neanderthal thread, I’ve seen arguments for both I want a definitive position on that But I have also seen exactly the same arguments on the other side from evolutionists Currently I am wrestling with genetic determinism and twin studies, and those that promote it And I’ve noticed they to like to produce the heads I win tails you lose effect All reasons for similarity are genetic all reasons for differences are also genetic Therefore nothing is not genetic I win The same goes for genetics with junk DNA The “we have to have 98% of our DNA to be junk” To “Of course there is vital function, it’s exactly what you would expect from evolution” But I am noticing this a lot from both sides of the coin an ability to describe it in favor of one perspective regardless of the data But if I have to take a side, it’s ID And the thing that pushed me so far away from evolution (I believe it’s part of the grand system, intentional, not blind, not the greatest show on earth) Was the comment of having to convince yourself that what looks like to be design in nature is not That right there is often the comments of an abuser that requires you to rid yourself of your common sense.AaronS1978_{April 16, 2020
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Denyse, Good article. They ain’t seen nothin’ yet. :)jawa_{April 16, 2020
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Monday: De novo genes are extremely rare, if not impossible, and not observed, therefore ID. Tuesday: De novo genes are fairly common, therefore ID.Ed George_{April 16, 2020
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