Chase Nelson at Inference Review: Reconstructing ancestral proteins

Besides the fact that quantum entanglement and/or quantum information, as was mentioned in post 2, now provides us with "very strong empirical evidence suggesting that we do indeed have an eternal soul that is capable of living beyond the death of our material bodies", besides that piece of scientific evidence, we also have another very strong piece of scientific evidence that we can appeal to so as to support the physical reality of the immaterial, and immortal, soul. In the "What is the Soul?" video I listed at post 6, J.P. Moreland stated that, "The soul is an immaterial substance that contains consciousness and animates, and makes living, the body.,,,",,, You have to have a whole that is prior to the parts if you have evidence that the parts function and are what they are in light of that whole."

J. P. Moreland: "The soul is an immaterial substance that contains consciousness and animates, and makes living, the body.,,," Robert Lawrence Kuhn: "If a one cell bacterium or amoeba reacts with its environment, we know it's alive. That it has some kind of soul. Maybe very, very, very, simple compared to our soul." J. P. Moreland: "That's right. It's not conscious. But you can't explain the interaction of its parts mechanistically. You have to have a whole that is prior to the parts if you have evidence that the parts function and aren't what they are in light of that whole." - What is the soul? (J.P. Moreland) – video https://www.closertotruth.com/series/the-soul-immortal#video-2758

And in regards to bacteria, we do indeed have scientific evidence that it has a 'primitive' soul that makes it living. i.e. We have scientific evidence that the 'parts' of the bacterium "function and are what they are in light of that whole (i.e. soul)."

"We have no idea how to put this structure (a simple cell) together.,, So, not only do we not know how to make the basic components, we do not know how to build the structure even if we were given the basic components. So the gedanken (thought) experiment is this. Even if I gave you all the components. Even if I gave you all the amino acids. All the protein structures from those amino acids that you wanted. All the lipids in the purity that you wanted. The DNA. The RNA. Even in the sequence you wanted. I've even given you the code. And all the nucleic acids. So now I say, "Can you now assemble a cell, not in a prebiotic cesspool but in your nice laboratory?". And the answer is a resounding NO! And if anybody claims otherwise they do not know this area (of research).” - James Tour: The Origin of Life Has Not Been Explained - 4:20 minute mark (The more we know, the worse the problem gets for materialists) https://youtu.be/r4sP1E1Jd_Y?t=255 "If I take a sterile test-tube and if I put in a little bit of fluid with just the rights salts, with just the right balance of acidity and alkalinity. Just the right temperature. The perfect solution for a living cell. And I put in it one living cell. This cell is alive. It has everything it needs for life. Now I take a sterile needle and I poke that cell, and all its stuff leaks out into this test-tube. You have this nice little test tube and all the molecules you need for a living cell. Not just the pieces of the molecules but the molecules themselves, and you cannot make a living cell out of them. You can't put Humpty Dumpty back together again." - Punctured cell will never reassemble – Jonathan Wells – 2:40 mark of video https://youtu.be/WKoiivfe_mo?t=165 "But let's, in this thought experiment, say that we already have a functional, working, cell. So everything is in place. But now the cell just dies. Just died a nano-second ago. Just died. What did we just lose and what would we have to do to get it going again because everything is approximately in place? Have we any idea how to get this cell going again?" (To which Stephen Meyer responds), Well, its the Humpty Dumpty problem right. You got all of these pieces but all those pieces does not a living organism make." - The Science & Faith Podcast - James Tour and Stephen Meyer: Life's Origin: Lab + Information = Mind https://youtu.be/x5tUDJ23Kms?t=1038 Extreme Genome Repair - 2009 Excerpt: If its naming had followed, rather than preceded, molecular analyses of its DNA, the extremophile bacterium Deinococcus radiodurans might have been called Lazarus. After shattering of its 3.2 Mb genome into 20–30 kb pieces by desiccation or a high dose of ionizing radiation, D. radiodurans miraculously reassembles its genome such that only 3 hr later fully reconstituted nonrearranged chromosomes are present, and the cells carry on, alive as normal.,,, http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3319128/ In the lab, scientists coax E. coli to resist radiation damage - March 17, 2014 Excerpt: ,,, John R. Battista, a professor of biological sciences at Louisiana State University, showed that E. coli could evolve to resist ionizing radiation by exposing cultures of the bacterium to the highly radioactive isotope cobalt-60. "We blasted the cultures until 99 percent of the bacteria were dead. Then we'd grow up the survivors and blast them again. We did that twenty times," explains Cox. The result were E. coli capable of enduring as much as four orders of magnitude more ionizing radiation, making them similar to Deinococcus radiodurans, a desert-dwelling bacterium found in the 1950s to be remarkably resistant to radiation. That bacterium is capable of surviving more than one thousand times the radiation dose that would kill a human. http://www.news.wisc.edu/22641 Pond scum smashes genome into over 225k parts, then rebuilds it - Sept. 9, 2014 Excerpt: The pond-dwelling, single-celled organism Oxytricha trifallax has the remarkable ability to break its own DNA into nearly a quarter-million pieces and rapidly reassemble those pieces when it’s time to mate, https://uncommondescent.com/intelligent-design/pond-scum-smashes-genome-into-over-225k-parts-then-rebuilds-it/

In other words, we have very strong scientific evidence that it is the 'whole', i.e. the 'primitive soul', of the bacterium that makes the bacterium alive and that dictates how to parts of the bacterium function and get used. It is not, contrary to what Darwinian materialists believe, the parts of the bacterium, i.e. DNA and proteins, that are 'running the show' in life. This same principle of the 'whole', i.e. the soul, 'running the show' is now also shown to be true for multicellular organisms. As Jonathan Wells explains, "I now know as an embryologist,,,Tissues and cells, as they differentiate, modify their DNA to suit their needs. It's the organism controlling the DNA, not the DNA controlling the organism."

Ask an Embryologist: Genomic Mosaicism - Jonathan Wells - February 23, 2015 Excerpt: humans have a "few thousand" different cell types. Here is my simple question: Does the DNA sequence in one cell type differ from the sequence in another cell type in the same person?,,, The simple answer is: We now know that there is considerable variation in DNA sequences among tissues, and even among cells in the same tissue. It's called genomic mosaicism. In the early days of developmental genetics, some people thought that parts of the embryo became different from each other because they acquired different pieces of the DNA from the fertilized egg. That theory was abandoned,,, ,,,(then) "genomic equivalence" -- the idea that all the cells of an organism (with a few exceptions, such as cells of the immune system) contain the same DNA -- became the accepted view. I taught genomic equivalence for many years. A few years ago, however, everything changed. With the development of more sophisticated techniques and the sampling of more tissues and cells, it became clear that genetic mosaicism is common. I now know as an embryologist,,,Tissues and cells, as they differentiate, modify their DNA to suit their needs. It's the organism controlling the DNA, not the DNA controlling the organism. http://www.evolutionnews.org/2015/02/ask_an_embryolo093851.html

Thus in conclusion, besides advances in quantum biology providing us with very strong empirical evidence for the physical reality of the immaterial, and eternal, soul, we also have very strong evidence for a soul in that, as J.P. Moreland stated, (and directly contrary to what Darwinists believe), the parts of the organism "function,, in light of that whole." To repeat, J. P. Moreland: "The soul is an immaterial substance that contains consciousness and animates, and makes living, the body.,,," Verse:

Mark 8:37 Is anything worth more than your soul?

bornagain77

What is the oldest extant species? Wouldn’t that indicate if proteins were different over time?

In 2008, Canadian scientists found a new fossil of a horseshoe crab. This family, the Limulidae, are considered living fossils because they haven't changed much in about 450 million years.

Some others https://www.animalwised.com/the-5-oldest-animals-in-the-world-ancient-extant-species-822.html jerry

@seversky The soul makes choices. The soul is more or less is the totality of all emotions you had in life, and all your personal character. The soul is inherently subjective, as is the agency of a any choice inherently subjective. Subjective meaning that it can only be identified with a chosen opinion. So then it is equally logically valid to say someone does, or doesn't have a soul. But it is a logical error to be forced by evidence to the conclusion someone has, or does not have, a soul. Same as it is equally logically valid to say a painting is beautiful or ugly, in spontaneous expression of emotion with free will, but it provides an invalid personal opinion to be forced to say a painting is beautiful. Consciousness, it refers to the spirit making choices in the universe of mind. I am conscious of the earth, it means I have the earth on my mind. He is conscious, means he is in his universe of mind, making decisions there. He is unconscious, he is not in his universe of mind. Something like that. mohammadnursyamsu

Seversky

Of course, you can say that the matter and energy of which the physical brain is made and, therefore, the emergent property of consciousness came from the overall matter and energy of the Universe and, when the brain dies and decomposes, that matter and energy returns to the neighboring environment, which is part of the Universe.

That's right, but consciousness more than matter and energy - or perhaps not even those things at all. I was just quoting from that excerpt:

But the quantum information, which is in the microtubules, isn’t destroyed.

Matter and energy alone do not give us information (except the physical patterns that we can interpret and gain knowledge from). So I think the assumption that consciousness (which is a part of the soul) comes from the material universe is shaky at best. Information requires an interpreter. That can't come from an unintelligent source. Like tree-rings -- that is information embedded in trees. But it is meaningless without intelligence to interpret the information. (That's a different argument than the question of how the information got there but rather that information exists merely because there are minds to interpret these things and extract meaning from them). Silver Asiatic

Seversky wants to assume, "that consciousness and soul are one and the same thing." Yet, since they are not the same thing, let's not do that.

What is the soul? (J.P. Moreland) - video https://www.closertotruth.com/series/the-soul-immortal#video-2758

bornagain77

Assuming that consciousness and soul are one and the same thing. Assuming that the soul exists, there seems to be a variety of opinions on its nature and purpose, let alone how we might detect it. Of course, you can say that the matter and energy of which the physical brain is made and, therefore, the emergent property of consciousness came from the overall matter and energy of the Universe and, when the brain dies and decomposes, that matter and energy returns to the neighboring environment, which is part of the Universe. Seversky

Leading Scientists Say Consciousness Cannot Die It Goes Back To The Universe

Assuming that consciousness/soul came from the universe. Silver Asiatic

“Were Ancestral Proteins Less Specific?” That's how materialist bias warps the analysis. They need some way to create proteins so they propose that proteins were less specific. But that ignores what could be more likely that ancestral proteins were more specific and just degraded over time. Silver Asiatic

As to, "The deepest questions about the origins of novel gene families remain shrouded in mystery." Hmm, that sounds very similar to what was said in this previous article, "The appearance of early protein families, he has remarked, is “something like close to a miracle.” and “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,,, To the extent that Tawfik’s selection experiments were successful, it is because mutations were localized and contextualized. Mutation had a key but confined role. If evolution proceeded, the prevailing architecture of the active sites and protein shapes nonetheless remains intact. Changes were not to central structures, but to peripheral loops. A great deal of flexibility was discovered. Still, it is hard to see how any of this could build proteins—that is, in the sense of building their fundamental shapes, or scaffolds; and build proteins in terms of explaining the key catalytic strategies of each active site. Even in the impressive demonstration of a transition through nine orders of magnitude, in which a full exchange of a promiscuous activity for the primary activity was seen, the overall geometry of the protein was unchanged, and, although substrates had changed, the fundamental active site strategy stayed the same. ,,, “Modern neo-Darwinism and neutral evolutionary treatments,” remark Leonard Bogarad and Michael Deem, “fail to explain satisfactorily the generation of the diversity of life found on our planet.” It is not that they did not evolve, they say, but that “... most theoretical treatments of evolution consider only the limited point-mutation events that form the basis of these theories.” Their sober conclusion is that “point mutation alone is incapable of evolving systems with substantially new protein folds.”60,,, “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

It is also interesting to note that the honest admission by Darwinists that present day proteins are too 'specific' to evolve into new functions, and that more 'general' ancestral proteins are needed in order to have a feasible explanation for protein evolution, then that pretty much undercuts their entire argument that present day organisms have the capacity within themselves to evolve. As Ann Gauger, (via her work with Doug Axe), explained, "If (present day) enzymes can't be recruited to genuinely new functions by unguided means, no matter how similar they are, the evolutionary story is false.,,, 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."

"Enzyme Families -- Shared Evolutionary History or Shared Design?" - Ann Gauger - December 4, 2014 Excerpt: If (present day) 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

i.e. the fact that present day proteins are highly 'specific' and can't evolve into new proteins with new functions and shapes falsifies Darwinian evolution! To repeat, "If (present day) enzymes can't be recruited to genuinely new functions by unguided means, no matter how similar they are, the evolutionary story is false.,,," But alas, the inability of present day proteins to evolve into new proteins is apparently just another fatal flaw, (of many fatal flaws), within the evolutionary narrative that is acknowledged by Darwinists and then subsequently, and immediately, ignored by them since for them to admit the truth of the situation is to 'allow a Divine Foot in the door' (Lewontin, 1997). As to Tawfik's observation that, "The appearance of early protein families,,, is “something like close to a miracle.” Well, to move the origin of protein families from being just “something like close to a miracle” to being a 'full fledged miracle', I will appeal to recent advances in molecular biology that have established that proteins belong to the world of quantum mechanics, and that proteins do not belong to the world of classical mechanics, as is presupposed within the reductive materialistic framework of Darwinian thought. 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

To drive this point further home, this follow up 2018 article stated that “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)

And while 'no obvious evolutionary reason why a protein should evolve toward a quantum-critical state' is certainly bad enough for Darwinists, 'quantum proteins', due to quantum 'non-locality', actually falsify the entire reductive materialistic framework of Darwinists. What is so devastating to the reductive materialistic presuppositions of Darwinists with the finding pervasive quantum coherence and/or quantum entanglement within molecular biology, is that quantum coherence and/or quantum entanglement is a non-local, beyond space and time, effect that requires a beyond space and time cause in order to explain its existence. As the following paper entitled “Looking beyond space and time to cope with quantum theory” stated, “Our result gives weight to the idea that quantum correlations somehow arise from outside spacetime, in the sense that no story in space and time can describe them,”

Looking beyond space and time to cope with quantum theory – 29 October 2012 Excerpt: “Our result gives weight to the idea that quantum correlations somehow arise from outside spacetime, in the sense that no story in space and time can describe them,” http://www.quantumlah.org/highlight/121029_hidden_influences.php

Moreover, as the following study found, the greater the number of particles in a quantum hypergraph state, (which is exactly the type of quantum coherence that we have with protein and DNA molecules), the more strongly it violates local realism, with the strength increasing exponentially with the number of particles.

Physicists find extreme violation of local realism in quantum hypergraph states - Lisa Zyga - March 4, 2016 Excerpt: Many quantum technologies rely on quantum states that violate local realism, which means that they either violate locality (such as when entangled particles influence each other from far away) or realism (the assumption that quantum states have well-defined properties, independent of measurement), or possibly both. Violation of local realism is one of the many counterintuitive, yet experimentally supported, characteristics of the quantum world. Determining whether or not multiparticle quantum states violate local realism can be challenging. Now in a new paper, physicists have shown that a large family of multiparticle quantum states called hypergraph states violates local realism in many ways. The results suggest that these states may serve as useful resources for quantum technologies, such as quantum computers and detecting gravitational waves.,,, The physicists also showed that the greater the number of particles in a quantum hypergraph state, the more strongly it violates local realism, with the strength increasing exponentially with the number of particles. In addition, even if a quantum hypergraph state loses one of its particles, it continues to violate local realism. This robustness to particle loss is in stark contrast to other types of quantum states, which no longer violate local realism if they lose a particle. This property is particularly appealing for applications, since it might allow for more noise in experiments. - per physorg

In other words, the problem of 'spooky action at a distance', (as Einstein termed quantum non-locality), is actually exponentially worse for Darwinists than it ever was for physicists who were 'merely' working with two entangled' particles and/or photons at a time. Darwinists, with their reductive materialistic framework, (and especially with the falsification of 'hidden variables'), simply have no beyond space and time cause that they can appeal so as to be able to explain the non-local quantum coherence and/or entanglement that is now found to be ubiquitous within biology.

“hidden variables don’t exist. If you have proved them come back with PROOF and a Nobel Prize. John Bell theorized that maybe the particles can signal faster than the speed of light. This is what he advocated in his interview in “The Ghost in the Atom.” But the violation of Leggett’s inequality in 2007 takes away that possibility and rules out all non-local hidden variables. Observation instantly defines what properties a particle has and if you assume they had properties before we measured them, then you need evidence, because right now there is none which is why realism is dead, and materialism dies with it. How does the particle know what we are going to pick so it can conform to that?” per Jimfit https://uncommondescent.com/philosophy/quantum-physicist-david-bohm-on-why-there-cannot-be-a-theory-of-everything/#comment-662358

Whereas Christians readily do have a beyond space and time cause that they can appeal to so as to explain the 'non-locality' of quantum entanglement. As Colossians 1:17 states, “He is before all things, and in him all things hold together.”

Colossians 1:17 He is before all things, and in him all things hold together.

And as John 1:1-4 states,

John 1:1-4 In the beginning was the Word, and the Word was with God, and the Word was God. He was with God in the beginning. Through him all things were made; without him nothing was made that has been made. In him was life, and that life was the light of all mankind.

It is also important to realize that quantum information, besides being 'non-local', is also conserved. As the following article states, In the classical world, information can be copied and deleted at will. In the quantum world, however, the conservation of quantum information means that information cannot be created nor destroyed.

Quantum no-hiding theorem experimentally confirmed for first time - 2011 Excerpt: In the classical world, information can be copied and deleted at will. In the quantum world, however, the conservation of quantum information means that information cannot be created nor destroyed. This concept stems from two fundamental theorems of quantum mechanics: the no-cloning theorem and the no-deleting theorem. A third and related theorem, called the no-hiding theorem, addresses information loss in the quantum world. According to the no-hiding theorem, if information is missing from one system (which may happen when the system interacts with the environment), then the information is simply residing somewhere else in the Universe; in other words, the missing information cannot be hidden in the correlations between a system and its environment. - per physorg

The implication of finding 'non-local', beyond space and time, and ‘conserved’, cannot be created nor destroyed, quantum information in molecular biology on such a massive scale, in every important biomolecule in our bodies, is fairly, and pleasantly, obvious. That pleasant implication, of course, being the fact that we now have very strong empirical evidence suggesting that we do indeed have an eternal soul that is capable of living beyond the death of our material bodies. As Stuart Hameroff states in the following article, “the quantum information,,, isn’t destroyed. It can’t be destroyed.,,, it's possible that this quantum information can exist outside the body. Perhaps indefinitely as a soul.”

Leading Scientists Say Consciousness Cannot Die It Goes Back To The Universe - Oct. 19, 2017 - Spiritual Excerpt: “Let’s say the heart stops beating. The blood stops flowing. The microtubules lose their quantum state. But the quantum information, which is in the microtubules, isn’t destroyed. It can’t be destroyed. It just distributes and dissipates to the universe at large. If a patient is resuscitated, revived, this quantum information can go back into the microtubules and the patient says, “I had a near death experience. I saw a white light. I saw a tunnel. I saw my dead relatives.,,” Now if they’re not revived and the patient dies, then it's possible that this quantum information can exist outside the body. Perhaps indefinitely as a soul.” - Stuart Hameroff - Quantum Entangled Consciousness - Life After Death - video (5:00 minute mark) (of note, this video is no longer available for public viewing) https://radaronline.com/exclusives/2012/10/life-after-death-soul-science-morgan-freeman/

Verse:

Mark 8:37 Is anything worth more than your soul?

bornagain77

From the OP, "The deepest questions about the origins of novel gene families remain shrouded in mystery." In other words, they still have no evidence to support evolution. Everything about evolution is shrouded in mystery. Perhaps the reason is that evolution, something lacking a witness, is little more than fiction. BobRyan