Uncommon Descent Serving The Intelligent Design Community

At Evolution News: Did Life First Arise by Purely Natural Means?

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Walter Bradley and Casey Luskin write:

Major scientific magazines and journals often feature articles on the “Biggest Unsolved Mysteries in Science”1 — and the origin of life is almost always on that list, sometimes as the number one mystery.2 In this and coming posts we will explore key challenges to a natural, chemical origin of life. We’ll examine the formation of the essential functional polymers of life — proteins, DNA (deoxyribonucleic acid), and RNA (ribonucleic acid). How might these extraordinarily complex molecules have formed in oceans, lakes, or ponds from simple, naturally occurring molecular building blocks like sugars and amino acids? What is life? How does it operate? Could life originate by strictly natural means?

Three Scientific Discoveries

Darwin’s theory of evolution and the development of the second law of thermodynamics by Boltzmann and Gibbs are two of the three major scientific discoveries of the 19th century. Maxwell’s field equations for electricity and magnetism are the third. The second law of thermodynamics has had a unifying effect in the physical sciences much like the theory of evolution has had in the life sciences. What is intriguing is that the predictions of one seem to contradict the predictions of the other. The grand story of evolution teaches that living systems have generally moved from simpler to more complex over time.3 The second law of thermodynamics teaches just the opposite, a progression from order to disorder, from complexity to simplicity in the physical universe. Your garden and your house, left to themselves, go from order to disorder. But you can restore the order if you do the necessary work. In the winter, when it is cold, the interior of your house will gradually drop in temperature toward the outside temperature. But a gas heater can reverse this process by converting the chemical energy in natural gas into thermal energy in the house. 

True Everywhere in Life

This simple analogy illustrates what is true of all living systems: they can only live by having access to energy and a means of converting this energy into the alternative forms of energy or work required to oppose the pull toward thermodynamic equilibrium, from complexity to simplicity. Living systems are much more complex than nonliving systems. Like a lawnmower with gasoline as a source of energy and an engine to convert that energy into movement of a blade to cut the grass, living systems must have access to sources of energy and systems to convert the energy into the needs of plants and animals.

Nonliving objects in nature exist without any complex functional systems or any energy flow requirements. They are generally made of simple crystalline or amorphous materials.

The second law of thermodynamics is a law of nature (like gravity, everyone is subject to it). Living plants and animals can survive only with energy flowing through their systems. Nonliving objects such as mountains, rocks, sand, rivers, and soil have no need for energy flow, nor do they have the complexity to utilize energy toward some goal. 

To Utilize and Store Energy

To summarize, plants can utilize solar energy to levitate above thermodynamic equilibrium. Nonliving objects such as mountains, oceans, rocks, sand, and soil have no need for such complexity; they do not store chemical energy like plants do; nor can they process solar or other forms of energy. Living matter is much more complex (e.g., RNA, DNA, protein, etc.), needing as it does to be able to utilize and store available energy from the sun or from the consumption of plants and animals. 

Notes

  1. See for example Ronak Gupta, “The 7 biggest unsolved mysteries in science,” Digit (May 26, 2015), https://www.digit.in/features/general/7-greatest-unsolved-problems-in-science-26132.html (accessed November 18, 2020).
  2. See for example Philip Ball, “10 Unsolved Mysteries in Chemistry,” Scientific American (October 2011), https://www.scientificamerican.com/article/10-unsolved-mysteries/ (accessed November 18, 2020).
  3. Technically the official line from neo-Darwinian evolutionists is that evolution knows nothing of “progress” and does not necessarily move from “simple to more complex.” Nonetheless, it is also true that the grand arc of the evolutionary story moves from simpler organisms toward more complex ones. In this evolutionary story, biological and organic systems began with a single self-replicating molecule and ended up at us. Evolutionary theorists sometimes try to trivialize this clear progression by calling it “bouncing off the lower wall of complexity,” but it cannot be denied that their story entails a march towards greater complexity. See for example Stephen Jay Gould, Full House: The Spread of Excellence from Plato to Darwin (New York: Three Rivers, 1996). 

Full article at Evolution News.

Comments
Jerry at 95, There is no such thing as Artificial Intelligence. What is called Artificial Intelligence is a combination of advanced programs that can assist human beings with complex tasks. That's all. It cannot duplicate human level intelligence. But it's made to sound like it can, today. False. There is another term called "deep learning" which is little understood. It involves algorithms and neural networks. From a 2020 article on another site: "In the soon to be published book titled “Deep Learning” co-authored with Ian Goodfellow and Aaron Courville, they define deep learning in terms of the depth of the architecture of the models. 'The hierarchy of concepts allows the computer to learn complicated concepts by building them out of simpler ones. If we draw a graph showing how these concepts are built on top of each other, the graph is deep, with many layers. For this reason, we call this approach to AI deep learning.'" So, data is manipulated and the goal is to manipulate more data faster. Why? To make money. In areas like computer vision and automated speech recognition, and image and object recognition. Even in cancer detection. No, we're not talking about Terminator level intelligence but screening data for desired information without using human beings. "multiple design events"? Based on what?relatd
September 23, 2022
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So the alternative to universal common descent is some number (how many) of special creation events – true?
Not true! There could be multiple origin events. All of which could be natural. Aside: I personally believe there were multiple design events and no natural origin events. Call them creation events if you want. In the future it’s possible for some humans to cause a new origin event. Maybe an AI will do it.jerry
September 23, 2022
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So the alternative to universal common descent is some number (how many) of special creation events - true?Viola Lee
September 23, 2022
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Jerry at 90, It's a lot simpler than not getting terms and definitions right. The whole point of UD is to show that both sides can't be right. The evolution side is wrong. Ignore all evidence that shows they're wrong. And ignore all posts that show they're wrong. Their only job here is to promote Evolution. Period. Evidence doesn't matter showing they're wrong. They've been deployed here to promote a discredited idea - evolution. And will do this forever. Maybe longer. Propaganda is propaganda.relatd
September 23, 2022
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Jerry, it likely helps to distinguish limited common descent from universal common descent, even as it helps to distinguish small scale adaptation within a body plan [microevolution] from origin of body plan level macroevolution from universal macroevolution from yet wider grand evolution hydrogen to humans (involving cosmological, chemical, biological, human, maybe more). KFkairosfocus
September 23, 2022
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GRAND FAIR COMMENT: It is hard to avoid the conclusion, given years to have learned better, that with AF, we are dealing with willful trollish misconduct, likely driven by crooked yardstick thinking that demands that what is straight and upright conform to a preferred brand of crooked thinking. KF PS, In this context we would be well advised to heed the Lewontin cat out of the bag moment:
[Lewontin:] . . . to put a correct [--> Just who here presume to cornering the market on truth and so demand authority to impose?] view of the universe into people's heads
[==> as in, "we" the radically secularist elites have cornered the market on truth, warrant and knowledge, making "our" "consensus" the yardstick of truth . . . where of course "view" is patently short for WORLDVIEW . . . and linked cultural agenda . . . ]
we must first get an incorrect view out [--> as in, if you disagree with "us" of the secularist elite you are wrong, irrational and so dangerous you must be stopped, even at the price of manipulative indoctrination of hoi polloi] . . . the problem is to get them [= hoi polloi] to reject irrational and supernatural explanations of the world [--> "explanations of the world" is yet another synonym for WORLDVIEWS; the despised "demon[ic]" "supernatural" being of course an index of animus towards ethical theism and particularly the Judaeo-Christian faith tradition], the demons that exist only in their imaginations,
[ --> as in, to think in terms of ethical theism is to be delusional, justifying "our" elitist and establishment-controlling interventions of power to "fix" the widespread mental disease]
and to accept a social and intellectual apparatus, Science, as the only begetter of truth
[--> NB: this is a knowledge claim about knowledge and its possible sources, i.e. it is a claim in philosophy not science; it is thus self-refuting]
. . . . To Sagan, as to all but a few other scientists [--> "we" are the dominant elites], it is self-evident
[--> actually, science and its knowledge claims are plainly not immediately and necessarily true on pain of absurdity, to one who understands them; this is another logical error, begging the question , confused for real self-evidence; whereby a claim shows itself not just true but true on pain of patent absurdity if one tries to deny it . . . and in fact it is evolutionary materialism that is readily shown to be self-refuting]
that the practices of science provide the surest method of putting us in contact with physical reality [--> = all of reality to the evolutionary materialist], and that, in contrast, the demon-haunted world rests on a set of beliefs and behaviors that fail every reasonable test [--> i.e. an assertion that tellingly reveals a hostile mindset, not a warranted claim] . . . . It is not that the methods and institutions of science somehow compel us [= the evo-mat establishment] to accept a material explanation of the phenomenal world, but, on the contrary, that we are forced by our a priori adherence to material causes [--> another major begging of the question . . . ] to create an apparatus of investigation and a set of concepts that produce material explanations, no matter how counter-intuitive, no matter how mystifying to the uninitiated. Moreover, that materialism is absolute [--> i.e. here we see the fallacious, indoctrinated, ideological, closed mind . . . ], for we cannot allow a Divine Foot in the door . . . [--> irreconcilable hostility to ethical theism, already caricatured as believing delusionally in imaginary demons]. [Lewontin, Billions and billions of Demons, NYRB Jan 1997,cf. here. And, if you imagine this is "quote-mined" I invite you to read the fuller annotated citation here.]
kairosfocus
September 23, 2022
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if there is not common descent, then special creation is the only alternative idea that I know of
People should decide what they mean before using a term. There can be many separate origins of life. Hence theoretically, there could be many first ancestors. Hence, many lines of descent. And if special creation starts a life form, then why are not all descendants of this life form not common descent? Terms are not used in any consistent way in Evolution discussions. This leads to people talking past each other constantly. I assume this is the objective. jerry
September 23, 2022
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PPS, finally, slandering a decent, dead man now unable to defend himself; who won hundreds of debates by compiling and citing accurate evidence on the dominant pattern of systematic, papered over gaps in the fossil record. Indeed, given context of the debates, books and clear patterns in the actual fossils, the accusatory term is itself part of the papering over the problem issue, compounded by belittling, slander and demonisation. For shame!kairosfocus
September 23, 2022
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AF, the oh you are quote mining stunt gets old, esp coming from you, proved to evade, pick and twist. In short, the telling evidence is you are confessing by projecting. KF Let's outline: A: Refusal to acknowledge that it is a commonplace starting with Crick, to recognise that the genetic code is a code used to algorithmically assemble AA protein chains, including trying to pretend to know it is not a code. B: Refusing to acknowledge that a few lines below writing DNA is like a code, Crick wrote DNA is a code, underscoring the is. C: Evading cites from Lehninger's heirs, Alberts et al etc on the code. D: Pretending Lehninger was dismissible as dubious, by belittling reference. E: Pretending that ellipsis was evidence of quote mining, i.e. mis quoting or misleading selective citation WITHOUT evidence F: Refusing to take back such unwarranted accusation when confronted with the full quote and more. G: Deliberately, repeatedly conflating the templating used to copy strands DNA > DNA or to create RNA, with coded sequencing of proteins carried by tRNAs on a CCA tool tip. H: Doubling down and now trying similar stunts on someone else. CONCLUSION, FOR CAUSE: Confession by projection.kairosfocus
September 23, 2022
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Good grief, BA77, as I said, I usually scroll over your long posts of highly selected (heh) quotes. Taking a look, 70, 71 and 72 are a veritable Gish gallop of questionable claims. It's the weekend and social events call. I'll see if I can find time to respond. Richard Buggs deserves a closer look, definitely.Alan Fox
September 23, 2022
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You got much bigger problems than just Buggs AF, it is the empirical evidence itself that is contradicting you. And contradicting you on many different levels. And in science it is the empirical evidence itself that has final say. (no matter how much Darwinists may try to ignore what the empirical evidence itself says) But be that as it may, and seeing that honesty towards the evidence is apparently in very short supply on AF's part, I'll let my posts at 70, 71, and 72 stand as stated. I have much better things to do today than chase a Darwinian troll's tail around in a circle.bornagain77
September 23, 2022
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Now I come to think of it, there was a thread at TSZ with both Dennis Venema and Richard Buggs participating. I may have overlooked the subtext. If anyone is interested, I could try and find the exchange.Alan Fox
September 23, 2022
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Jerry Coyne says I'm wrong. https://whyevolutionistrue.com/2021/03/08/a-creationist-professor-of-evolutionary-biology-in-england/Alan Fox
September 23, 2022
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@ BA77 You mean Richard Buggs, professor of evolutionary genomics at Queen Mary College, University if London, I guess. Are you saying Professor Buggs disputes common descent? I've had some brief exchanges with Richard Buggs in the past that would lead me to question that claim.Alan Fox
September 23, 2022
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AF falsely claims, "All evidence is consistent with a single branching tree of descent from the last universal common ancestor." To rephrase Buggs's response to Dawkins's falsely claiming the same thing that AF is now claiming, “AF's statement is simply wrong. Gloriously and utterly wrong.”bornagain77
September 23, 2022
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Ba77, If God did indeed work in His Creation - and He did -, then He created creatures that would survive under one Earth gravity, be able to breathe our air (which is mostly Nitrogen by the way) and metabolize food (plant or animal), then I think viewing land creatures from an engineering standpoint would be helpful. Reusing body plans for locomotion would have been a very efficient approach. Two arms and two legs or four legs. This body plan goes back to the dinosaurs. So, using skeletons as the starting point, and a 3-D rendering program to visualize it (for us here), the Creator would just need to add length and thickness codes, as appropriate, to build any land creature. Birds would get wings of course. A tail, or equivalent, might be added as appropriate. Insects would get modified body plans. This is Intelligent Engineering, or Intelligent Design. God, in His wisdom, created. It's important to add the Biblical account about Adam. Adam was created from "the dust of the Earth." Eve was, in a sense, even more special. She was literally created from Adam's side by God. The connection between Jesus and Adam is explicit, and with His mother, Mary, with Eve. 1 Corinthians 15:44 "It is sown a natural body; it is raised a spiritual body. If there is a natural body, there is also a spiritual body." 15:55 'Thus it is written, “The first man Adam became a living being”; the last Adam became a life-giving spirit.' 15:56 "But it is not the spiritual that is first but the natural, and then the spiritual." 15:67 "The first man was from the earth, a man of dust; the second man is from heaven." "CATHOLIC: When we give this high honor (in Greek called hyperdulia) to Mary, we do no more than Paul did. In Galatians 4:4–5 Paul says, “When the time had fully come, God sent forth his Son, born of woman, born under the law, to redeem those who were under the law, so that we might receive adoption as sons.” Why would Paul think it necessary to emphasize that God’s Son was “born of woman”? On a purely physical level, it is obvious that any man is born from a woman. But Paul is saying something deeper. By speaking of the woman, he is alluding to Genesis 3:15, which says, “I will put enmity between you [the serpent] and the woman, and between your seed and her seed; he shall bruise your head, and you shall bruise his heel.” The woman in Genesis 3:15 is clearly Eve, and Paul is drawing a parallel between Eve and the woman from whom God’s Son was born."relatd
September 23, 2022
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@Viola Hard for me to say. I tend to scroll over BA's long comments containing random quotes. I sometimes read and occasionally respond to shorter comments in his own words that seem relevant. I'm sure he thinks humans are/were separately created. I assume if you believe you are created in the image of God, being told you share ancestry with other living organisms might be interpreted as insulting.Alan Fox
September 23, 2022
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Re 78: So there's an overlap in these two discussions: if there is not common descent, then special creation is the only alternative idea that I know of. Is this what BA thinks has happened?Viola Lee
September 23, 2022
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AF’s false claim about genetic similarity being proof that humans evolved from some ape-like creature. (see post 50).
Not proof, Phil. Science doesn't deal in proof. All evidence is consistent with a single branching tree of descent from the last universal common ancestor. There may be better explanations for our observations but nobody here or elsewhere can tell us what that might be.Alan Fox
September 23, 2022
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I apologize, BA. I haven't been paying attention to that part of this thread.Viola Lee
September 23, 2022
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Always happy to oblige, KF.Alan Fox
September 23, 2022
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I wasn't addressing your claims about Catholicism Viola Lee, but was, primarily, addressing AF's false claim about genetic similarity being proof that humans evolved from some ape-like creature. (see post 50).bornagain77
September 23, 2022
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AF, you are making my point for me, thank you. KFkairosfocus
September 23, 2022
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1. I am not a "Darwinist" 2. I have not been arguing for common descent for humans. I have been arguing that believing in such is acceptable to Catholic theology, and has been recognized by the Pope as a possible alternative to special creation. Sorry to wast your time by triggering you down a path irrelevant to the discussion.Viola Lee
September 23, 2022
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And as if all that was not already bad enough for Darwinists, Darwinists simply have no real-time empirical evidence that it is even possible to change one creature into a brand new creature by mutating DNA alone. As Jonathan Wells states in the following article, “Studies using saturation mutagenesis in the embryos of fruit flies, roundworms, zebrafish and mice also provide evidence against the idea that DNA specifies the basic form of an organism. Biologists can mutate (and indeed have mutated) a fruit fly embryo in every possible way, and they have invariably observed only three possible outcomes: a normal fruit fly, a defective fruit fly, or a dead fruit fly.”
Jonathan Wells: Far from being all-powerful, DNA does not wholly determine biological form – March 31, 2014 Excerpt: Studies using saturation mutagenesis in the embryos of fruit flies, roundworms, zebrafish and mice also provide evidence against the idea that DNA specifies the basic form of an organism. Biologists can mutate (and indeed have mutated) a fruit fly embryo in every possible way, and they have invariably observed only three possible outcomes: a normal fruit fly, a defective fruit fly, or a dead fruit fly. https://uncommondescent.com/intelligent-design/jonathan-wells-far-from-being-all-powerful-dna-does-not-wholly-determine-biological-form/ Response to John Wise – October 2010 Excerpt: But there are solid empirical grounds for arguing that changes in DNA alone cannot produce new organs or body plans. A technique called “saturation mutagenesis”1,2 has been used to produce every possible developmental mutation in fruit flies (Drosophila melanogaster),3,4,5 roundworms (Caenorhabditis elegans),6,7 and zebrafish (Danio rerio),8,9,10 and the same technique is now being applied to mice (Mus musculus).11,12. None of the evidence from these and numerous other studies of developmental mutations supports the neo-Darwinian dogma that DNA mutations can lead to new organs or body plans–,,, (As Jonathan Wells states),,, We can modify the DNA of a fruit fly embryo in any way we want, and there are only three possible outcomes: A normal fruit fly; A defective fruit fly; or A dead fruit fly. http://www.evolutionnews.org/2010/10/response_to_john_wise038811.html
Moreover, starting around the 15:00 minute mark of the following video, Dr. Wells reveals that the central dogma of Darwinian evolution, (i.e. 'genetic reductionism', which simply stated is “DNA makes RNA makes protein makes us”), has now been experimentally shown to be incorrect at every step.
Design Beyond DNA: A Conversation with Dr. Jonathan Wells – video (14:36 minute mark) – January 2017 https://youtu.be/ASAaANVBoiE?t=876 Dr. Jonathan Wells: Biology’s Quiet Revolution – podcast – April 15, 2016 On this episode of ID the Future, Dr. Jonathan Wells discusses a popular claim, which he describes as “DNA makes RNA makes protein makes us”—or, every organism contains a program for itself in its DNA. Though this view fits neatly with the perspective of Darwinian evolution, it has been shown to be incorrect at every step. Listen in as Dr. Wells explains. https://www.discovery.org/multimedia/audio/idtf/2016/04/dr-jonathan-wells-biologys-quiet-revolution/
Darwinists simply have no evidence that morphology, and/or biological form, is reducible to DNA as is presupposed within their 'genetic reductionism' model. As the following 2020 article states, “biological form, was eventually excluded from the conceptual framework of the Modern Synthesis, (neo-Darwinism) as irrelevant.,,, At present, the problem of biological form remains unsolved.”
On the problem of biological form – Marta Linde-Medina (2020) Excerpt: Embryonic development, which inspired the first theories of biological form, was eventually excluded from the conceptual framework of the Modern Synthesis, (neo-Darwinism) as irrelevant.,,, At present, the problem of biological form remains unsolved. https://link.springer.com/article/10.1007/s12064-020-00317-3
Much more could be added that falsifies the Darwinian claim that humans evolved from some ape-like creature, but I will it here for now So in conclusion, although Darwinists will often try to claim that genetic evidence proves that humans evolved from some ape-like ancestor, we instead find, when scrutinizing the details of that claim, that the empirical evidence from genetics actually falsifies those Darwinian claims. And, when considering alternative splicing patterns, falsifies those Darwinian claims in a 'hard manner' by multiple orders of magnitude. If Darwinists were the least bit concerned about their personal intellectual integrity, this 'hard falsification' of their theory should concern them very, very, much. But alas, for whatever severely misguided reason, Darwinists would apparently much rather cling to their religion of nihilistic atheism, rather than to what the empirical evidence itself is actually saying.
Genesis 1:26-27 And God said, Let us make man in our image, after our likeness: and let them have dominion over the fish of the sea, and over the fowl of the air, and over the cattle, and over all the earth, and over every creeping thing that creepeth upon the earth. So God created man in his own image, in the image of God created he him; male and female created he them.
bornagain77
September 23, 2022
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In fact, Dolphins, Kangaroos, frogs, etc.. etc… although being very different morphologically from humans, are, (very unexpectedly), found to have very similar DNA sequences to humans.
Richard Sternberg PhD – podcast – On Human Origins: Is Our Genome Full of Junk DNA? Part 2 5:30 minute mark quote: “Basically the dolphin genome is almost wholly identical to the human genome,, yet no one would argue that bottle-nose dolphins are our sister species”,,, http://www.discovery.org/multimedia/audio/2014/11/on-human-origins-is-our-genome-full-of-junk-dna-pt-2/ Dolphin DNA very close to human, – 2010 Excerpt: They’re closer to us than cows, horses, or pigs, despite the fact that they live in the water.,,, “The extent of the genetic similarity came as a real surprise to us,” ,,, “Dolphins are marine mammals that swim in the ocean and it was astonishing to learn that we had more in common with the dolphin than with land mammals,” says geneticist Horst Hameister.,,, “We started looking at these and it became very obvious to us that every human chromosome had a corollary chromosome in the dolphin,” Busbee said. “We’ve found that the dolphin genome and the human genome basically are the same. It’s just that there’s a few chromosomal rearrangements that have changed the way the genetic material is put together.” http://www.reefrelieffounders.com/science/2010/10/21/articlesafari-dolphin-dna-very-close-to-human/ Kangaroo genes close to humans – 2008 Excerpt: Australia’s kangaroos are genetically similar to humans,,, “There are a few differences, we have a few more of this, a few less of that, but they are the same genes and a lot of them are in the same order,” ,,,”We thought they’d be completely scrambled, but they’re not. There is great chunks of the human genome which is sitting right there in the kangaroo genome,” http://www.reuters.com/article/science%20News/idUSTRE4AH1P020081118 First Decoded Marsupial Genome Reveals “Junk DNA” Surprise – 2007 Excerpt: In particular, the study highlights the genetic differences between marsupials such as opossums and kangaroos and placental mammals like humans, mice, and dogs. ,,, The researchers were surprised to find that placental and marsupial mammals have largely the same set of genes for making proteins. Instead, much of the difference lies in the controls that turn genes on and off. http://news.nationalgeographic.com/news/2007/05/070510-opossum-dna.html Frogs and humans are kissing cousins – 2010 Excerpt: What’s the difference between a frog, a chicken, a mouse and a human? Not as much as you’d think, according to an analysis of the first sequenced amphibian genome. The genome of the western clawed frog, Xenopus tropicalis, has now been analysed by an international consortium of scientists from 24 institutions, and joins a list of sequenced model organisms including the mouse, zebrafish, nematode and fruit fly. What’s most surprising, researchers say, is how closely the amphibian’s genome resembles that of the mouse and the human, with large swathes of frog DNA on several chromosomes having genes arranged in the same order as in these mammals. The results of the analysis are published in Science this week1. “There are megabases of sequence where gene order has changed very little,,,” – per nature
Genetic similarity simply does not line up with morphological similarity as was presupposed within the Darwinian model of 'genetic reductionism'. Moreover, where differences are greatest between chimps and humans, (and between all other creatures), are not in the genetic sequences per se, but are instead found in the alternative splicing patterns of those genetic sequences. As the following paper states, “A major question in vertebrate evolutionary biology is “how do physical and behavioral differences arise if we have a very similar set of genes to that of the mouse, chicken, or frog?”,,, the papers show that most alternative splicing events differ widely between even closely related species. “The alternative splicing patterns are very different even between humans and chimpanzees,”
Evolution by Splicing – Comparing gene transcripts from different species reveals surprising splicing diversity. – Ruth Williams – December 20, 2012 Excerpt: A major question in vertebrate evolutionary biology is “how do physical and behavioral differences arise if we have a very similar set of genes to that of the mouse, chicken, or frog?”,,, A commonly discussed mechanism was variable levels of gene expression, but both Blencowe and Chris Burge,,, found that gene expression is relatively conserved among species. On the other hand, the papers show that most alternative splicing events differ widely between even closely related species. “The alternative splicing patterns are very different even between humans and chimpanzees,” said Blencowe.,,, http://www.the-scientist.com/?articles.view%2FarticleNo%2F33782%2Ftitle%2FEvolution-by-Splicing%2F
In fact, due to alternative splicing, “Alternatively spliced isoforms,,, appear to behave as if encoded by distinct genes rather than as minor variants of each other.,,,” and “As many as 100,000 distinct isoform transcripts could be produced from the 20,000 human protein-coding genes (Pan et al., 2008), collectively leading to perhaps over a million distinct polypeptides obtained by post-translational modification of products of all possible transcript isoforms,,”
Widespread Expansion of Protein Interaction Capabilities by Alternative Splicing – 2016 In Brief Alternatively spliced isoforms of proteins exhibit strikingly different interaction profiles and thus, in the context of global interactome networks, appear to behave as if encoded by distinct genes rather than as minor variants of each other.,,, Page 806 excerpt: As many as 100,000 distinct isoform transcripts could be produced from the 20,000 human protein-coding genes (Pan et al., 2008), collectively leading to perhaps over a million distinct polypeptides obtained by post-translational modification of products of all possible transcript isoforms (Smith and Kelleher, 2013). http://iakouchevalab.ucsd.edu/publications/Yang_Cell_OMIM_2016.pdf
This finding of “perhaps a million distinct polypeptides obtained by post-translational modification” is simply completely devastating to the ‘bottom up’ reductive materialistic explanations of Darwinists, (i.e. to 'genetic reductionism'). As Stephen Meyer stated in the following interview, “it has become increasingly clear that the non-coding regions, the crucial operating systems in effect, of the chimp and human genomes are species specific. That is, they are strikingly different in the two species.,,, I see nothing from a genetic point of view that challenges the idea that humans originated independently from primates,”
An Interview with Stephen C. Meyer TT: Is the idea of an original human couple (Adam and Eve) in conflict with science? Does DNA tell us anything about the existence of Adam and Eve? SM: Readers have probably heard that the 98 percent similarity of human DNA to chimp DNA establishes that humans and chimps had a common ancestor. Recent studies show that number dropping significantly. More important, it turns out that previous measures of human and chimp genetic similarity were based upon an analysis of only 2 to 3 percent of the genome, the small portion that codes for proteins. This limited comparison was justified based upon the assumption that the rest of the genome was non-functional “junk.” Since the publication of the results of something called the “Encode Project,” however, it has become clear that the noncoding regions of the genome perform many important functions and that, overall, the non-coding regions of the genome function much like an operating system in a computer by regulating the timing and expression of the information stored in the “data files” or coding regions of the genome. Significantly, it has become increasingly clear that the non-coding regions, the crucial operating systems in effect, of the chimp and human genomes are species specific. That is, they are strikingly different in the two species. Yet, if alleged genetic similarity suggests common ancestry, then, by the same logic, this new evidence of significant genetic disparity suggests independent separate origins. For this reason, I see nothing from a genetic point of view that challenges the idea that humans originated independently from primates, http://www.ligonier.org/learn/articles/scripture-and-science-in-conflict/
The evidence from genetics, when scrutinized in detail, and directly contrary to what Darwinists claim, simply does not support the Darwinian ‘narrative’ that humans evolved from apes. In fact, the empirical evidence actually falsifies their claim in a 'hard' fashion. Moreover, even if the genetic similarity were as close as Darwinists have falsely claimed it to be for years (98.5%), (and even if the ‘operating systems’ were not ‘species specific’), population genetics has now shown that Natural Selection would be grossly inadequate to explain even that 1.5% genetic difference.
The waiting time problem in a model hominin population – 2015 Sep 17 John Sanford, Wesley Brewer, Franzine Smith, and John Baumgardner Excerpt: The program Mendel’s Accountant realistically simulates the mutation/selection process,,, Given optimal settings, what is the longest nucleotide string that can arise within a reasonable waiting time within a hominin population of 10,000? Arguably, the waiting time for the fixation of a “string-of-one” is by itself problematic (Table 2). Waiting a minimum of 1.5 million years (realistically, much longer), for a single point mutation is not timely adaptation in the face of any type of pressing evolutionary challenge. This is especially problematic when we consider that it is estimated that it only took six million years for the chimp and human genomes to diverge by over 5 % [1]. This represents at least 75 million nucleotide changes in the human lineage, many of which must encode new information. While fixing one point mutation is problematic, our simulations show that the fixation of two co-dependent mutations is extremely problematic – requiring at least 84 million years (Table 2). This is ten-fold longer than the estimated time required for ape-to-man evolution. In this light, we suggest that a string of two specific mutations is a reasonable upper limit, in terms of the longest string length that is likely to evolve within a hominin population (at least in a way that is either timely or meaningful). Certainly the creation and fixation of a string of three (requiring at least 380 million years) would be extremely untimely (and trivial in effect), in terms of the evolution of modern man. It is widely thought that a larger population size can eliminate the waiting time problem. If that were true, then the waiting time problem would only be meaningful within small populations. While our simulations show that larger populations do help reduce waiting time, we see that the benefit of larger population size produces rapidly diminishing returns (Table 4 and Fig. 4). When we increase the hominin population from 10,000 to 1 million (our current upper limit for these types of experiments), the waiting time for creating a string of five is only reduced from two billion to 482 million years. http://www.ncbi.nlm.nih.gov/pmc/articles/PMC4573302/
bornagain77
September 23, 2022
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Darwinists in this thread have tried to suggest that there is scientific evidence, particularly genetic evidence, that proves that humans evolved from some ape-like ancestor. Yet, as with everything else within Darwin's theory, we find that the supposed genetic evidence that humans evolved from some ape-like ancestor evaporates upon close scrutiny. First off, when we look at the 'big picture' of genetic evidence across all species, (instead of just looking at human and ape genetic evidence), the ‘big picture’ genetic evidence across all species simply does not line up with what Darwinists predicted of a gradually branching tree. As the following article explains, “In 1965 one of the most important scientists of the last century, Linus Pauling, and biologist Emil Zuckerkandl, considered by some as the father of molecular biology, suggested a way that macroevolution could be tested and proved: If the comparison of anatomical and DNA sequences led to the same family tree of organisms, this would be strong evidence for macroevolution.7 According to them, only evolution would explain the convergence of these two independent chains of evidence. By implication, the opposite finding would count against macroevolution.“ So what were the results? Over the past twenty-eight years, experimental evidence has revealed that family trees based on anatomical features contradict family trees based on molecular similarities, and at many points. They do not converge.”
Jonathan Witt: Why Is Common Descent A Better Explanation For The History Of Life Than Common Design? Excerpt: “In 1965 one of the most important scientists of the last century, Linus Pauling, and biologist Emil Zuckerkandl, considered by some as the father of molecular biology, suggested a way that macroevolution could be tested and proved: If the comparison of anatomical and DNA sequences led to the same family tree of organisms, this would be strong evidence for macroevolution.7 According to them, only evolution would explain the convergence of these two independent chains of evidence. By implication, the opposite finding would count against macroevolution.“ So what were the results? Over the past twenty-eight years, experimental evidence has revealed that family trees based on anatomical features contradict family trees based on molecular similarities, and at many points. They do not converge. Just as troubling for the idea of macroevolution, family trees based on different molecules yield conflicting and contradictory family trees. As a 2012 paper published in Biological Reviews of the Cambridge Philosophical Society reported, “Incongruence between phylogenies derived from morphological versus molecular analyses, and between trees based on different subsets of molecular sequences has become pervasive as datasets have expanded rapidly in both characters and species” (emphasis in original).8 Another paper, published the following year in the journal Nature, highlighted the extent of the problem.9 The authors compared 1,070 genes in twenty different yeasts and got 1,070 different trees.10 https://uncommondescent.com/evolution/jonathan-witt-why-is-common-descent-a-better-explanation-for-the-history-of-life-than-common-design/
The genetic evidence simply does not fall into a ‘tree-like’ pattern like Darwinists predicted. As Richard Buggs, (an evolutionary biologist who specializes in analyzing DNA sequences), states, "The lay-person reading this, or watching the (Richard Dawkins) video above, is given the clear impression that every gene or pseudogene in every living organism gives essentially the same phylogenetic tree, when analysed with its homologs from other species. This is simply not true.,,, Dawkins’ statements are simply wrong. Gloriously and utterly wrong."
"The lay-person reading this, or watching the (Richard Dawkins) video above, is given the clear impression that every gene or pseudogene in every living organism gives essentially the same phylogenetic tree, when analysed with its homologs from other species. This is simply not true. If this were true, then phylogeny building in the genomic era would be a walk in the park. But, as many of my readers will know from personal experience, it is not. If this were true, terms like horizontal gene transfer, incomplete lineage sorting, introgression, and molecular convergence would be rare curiosities in the genomic literature. But they are common (click on the links in the previous sentence to see searched for these terms on Google Scholar). If this were true, commonly-used phylogenetic software like ASTRAL, ASTRID and BUCKy, designed to deal with gene tree incongruence, would be seldom used. But they are used often. I hardly need to labour my point to the present audience. Dawkins’ statements are simply wrong. Gloriously and utterly wrong." - Richard Buggs, “Obsolete Dawkinsian evidence for evolution” at Nature: Ecology & Evolution - 2021 https://uncommondescent.com/intelligent-design/dawkinss-claim-every-gene-delivers-approximately-the-same-tree-of-life-contested-at-nature-journal/
And this falsification of Darwinian expectations, (i.e. expectations for how the genetic evidence should line up in a tree like pattern), as Winston Ewert has now shown, has been a ‘hard falsification’ of Darwinian expectations that has falsified Darwinian expectations by multiple orders of magnitude, and by no means is it to be considered simply a ‘soft falsification’ of Darwinian expectations with only minor anomalies in the genetic evidence at the periphery of Darwin's theory. As Dr. Cornelius Hunter (PhD Biophysics) explained, when looking at "a total of nine massive genetic databases", "Darwin could never have dreamt of the sheer magnitude of the failure of his theory". The intelligent design model falsified the Darwinian common descent model by 10,064, 40,967 and 515,450 bits respectfully, and this is where 6.6 bits is considered to provide “decisive” evidence for a model.
New Paper by Winston Ewert Demonstrates Superiority of Design Model – Cornelius Hunter – July 20, 2018 Excerpt: Ewert amassed a total of nine massive genetic databases. In every single one, without exception, the dependency graph (intelligent design) model surpassed common descent. Darwin could never have even dreamt of a test on such a massive scale. Darwin also could never have dreamt of the sheer magnitude of the failure of his theory. Because you see, Ewert’s results do not reveal two competitive models with one model edging out the other. We are not talking about a few decimal points difference. For one of the data sets (HomoloGene), the dependency graph model was superior to common descent by a factor of 10,064. The comparison of the two models yielded a preference for the dependency graph model of greater than ten thousand.,,, But It Gets Worse The problem with all of this is that the Bayes factor of 10,064 bits for the HomoloGene data set is the very best case for common descent. For the other eight data sets, the Bayes factors range from 40,967 to 515,450. In other words, while 6.6 bits would be considered to provide “decisive” evidence for the dependency graph model, the actual, real, biological data provide Bayes factors of 10,064 on up to 515,450. We have known for a long time that common descent has failed hard. In Ewert’s new paper, we now have detailed, quantitative results demonstrating this. And Ewert provides a new model, with a far superior fit to the data. https://evolutionnews.org/2018/07/new-paper-by-winston-ewert-demonstrates-superiority-of-design-model/
Thus, given the fact that the ‘big picture’ genetic evidence across all species has, rather dramatically, falsified Darwinian expectations of a tree like pattern, we have more than sufficient reason to be more than a little skeptical of Darwinian claims that the ‘small picture’ genetic evidence between apes and humans somehow establishes human evolution as an undeniable fact. And indeed, when we zoom-in on the ‘small picture’ genetic evidence we find much reason to be very skeptical of Darwinian claims. For instance, according to a Darwinist who studied the methodology of how one of the original 98.5% Chimp-Human DNA similarity comparisons was derived, (and because of the sheer shoddiness of the study), stated that the 98.5% comparison “needs to be treated like nuclear waste: bury it safely and forget about it for a million years”,,,
The Rise and Fall of DNA Hybridization – Jonathan Marks – 2011 Excerpt: the technique of DNA hybridization had devolved into being doubly “tricky” – but more significantly, the outstanding charge of data falsification was there in black-and-white in the leading science journal in America. It seemed as though nothing more needed to be said for the “wheels of justice” to begin turning. Yet they didn’t. In 1993, I was asked by The Journal of Human Evolution to review Jared Diamond’s book, The Third Chimpanzee. Noting that the book’s “hook” was based on the Sibley-Ahlquist work, which Diamond was still touting uncritically, I said: Perhaps you recall Sibley and Ahlquist. In a nutshell, their results were: (1) chimp-gorilla DNA hybrids were more thermally stable than chimp-human hybrids; (2) the differences were insignificant; and (3) reciprocity was very poor when human DNA was used as a tracer. Unfortunately, the conclusions they reported were: (1) chimp-human was more thermally stable than chimp-gorilla; (2) differences were significant; and (3) reciprocity was near-perfect. And they got from point A to point B by (1) switching experimental controls; (2) making inconsistent adjustments for variation in DNA length, which was apparently not even measured; (3) moving correlated points into a regression line; and (4) not letting anyone know. The rationale for (4) should be obvious; and if (1), (2) and (3) are science, I’m the Princess of Wales. This work needs to be treated like nuclear waste: bury it safely and forget about it for a million years.31 31Marks, J. (1993) Review of The Third Chimpanzee by Jared Diamond. Journal of Human Evolution, 24:69-73. http://webpages.uncc.edu/~jmarks/dnahyb/Sibley%20revisited.pdf
To further highlight the shoddy methodology of Darwinists, (and in a stunning display of confirmation bias), Darwinists previously had used the human genome as a ‘scaffold' and/or 'reference’ to assemble the chimp genome before comparing the genomes to one another in order to arrive at their highly misleading, and similar, percentage figures from genetic comparisons. Yet when when the genetic comparisons were done without using the human genome as a 'scaffold' to align the chimp genome to the human genome, the percentage figure for similarity dropped all the way to 80%
New Chimp Genome Confirms Creationist Research BY JEFFREY P. TOMKINS, PH.D. * | FRIDAY, SEPTEMBER 28, 2018 Excerpt: The first time they constructed a chimp genome and compared it to humans, they claimed 98.5% DNA similarity based on cherry-picked regions that were highly similar to human. However, an extensive DNA comparison study I published in 2016 revealed two major flaws in their construction of the chimp genome.1 First, many chimp DNA data sets were likely contaminated with human DNA, especially those produced in the first half of the chimpanzee genome project from 2002 to 2005. Second, the chimpanzee genome was deliberately constructed to be more human-like than it really is.2 Scientists assembled the small snippets of chimp DNA onto the human genome, using it as a scaffold or reference. It’s much like putting together a jigsaw puzzle by looking at the picture on the box as a guide. Since many chimpanzee data sets likely suffered from human DNA contamination, the level of humanness was amplified. I studied the 2005–2010 data sets that showed less human DNA data contamination and found they were only 85% similar to human at best.1 Just this year, scientists published a new version of the chimpanzee genome.3 This new version incorporated an advanced type of DNA sequencing technology that produces much longer snippets of DNA sequence than earlier technologies. It also involved better protocols that greatly reduce human DNA contamination. And most importantly, the authors report that the DNA sequences have been assembled without using the human genome as a scaffold. They also acknowledged the flawed nature of previous versions of the chimp genome: The higher-quality human genome assemblies have often been used to guide the final stages of nonhuman genome projects, including the order and orientation of sequence contigs and, perhaps more importantly, the annotation of genes. This bias has effectively “humanized” other ape genome assemblies.3 This confirms what many creationists have been pointing out for years. Curiously, the authors of the new chimp genome paper said very little about the overall DNA similarity between humans and chimpanzees. However, the University of London’s specialist in evolutionary genomics, Dr. Richard Buggs, evaluated the results of an analysis that compared this new chimp version to the human genome and discovered some shocking anti-evolutionary findings. Dr. Buggs reported on his website that “the percentage of nucleotides in the human genome that had one-to-one exact matches in the chimpanzee genome was 84.38%” and “4.06% had no alignment to the chimp assembly.”4 Assuming the chimpanzee and human genomes are about the same size, this translates to an overall similarity of only about 80%! This outcome is way outside the nearly identical level of 98 to 99% similarity required for human evolution to seem plausible. http://www.icr.org/article/new-chimp-genome-confirms-creationist-research
Moreover, although some Darwinists may try to argue that 80% genetic similarity is still a pretty high degree of genetic similarity, it turns out, directly contrary to Darwinian thought, that genetic similarity has very little, if anything, to do with overall morphological similarity. As James Le Fanu explains, “Contrary to all expectations, many DNA sequences involved in embryo development are remarkably similar across the vast spectrum of organismic complexity, from a millimeter-long worm to ourselves.7 There is, in short, nothing in the genomes of fly and man to explain why the fly should have six legs, a pair of wings, and a dot-sized brain and we should have two arms, two legs, and a mind capable of comprehending that overarching history of our universe.”
Between Sapientia and Scientia — Michael Aeschliman’s Profound Interpretation -James Le Fanu – September 9, 2019 Excerpt: The ability to spell out the full sequence of genes should reveal, it was reasonable to assume, the distinctive genetic instructions that determine the diverse forms of the millions of species, so readily distinguishable one from the other. Biologists were thus understandably disconcerted to discover precisely the reverse to be the case. Contrary to all expectations, many DNA sequences involved in embryo development are remarkably similar across the vast spectrum of organismic complexity, from a millimeter-long worm to ourselves.7 There is, in short, nothing in the genomes of fly and man to explain why the fly should have six legs, a pair of wings, and a dot-sized brain and we should have two arms, two legs, and a mind capable of comprehending that overarching history of our universe. So we have moved in the very recent past from supposing we might know the principles of genetic inheritance to recognizing we have no realistic conception of what they might be. As Phillip Gell, professor of genetics at the University of Birmingham, observed, “This gap in our knowledge is not merely unbridged, but in principle unbridgeable and our ignorance will remain ineluctable.”8 https://evolutionnews.org/2019/09/between-sapientia-and-scientia-michael-aeschlimans-profound-interpretation/ 7. James Randerson, “Fewer Genes, Better Health,” New Scientist, July 13, 2002, 19. 8. Philip Gell, “Destiny and the Genes: Genetic Pathology and the Individual,” The Encyclopaedia of Medical Ignorance, ed.s R. Duncan and M. Weston-Smith (Kidlington: Pergamon, 1984), 179–87.
bornagain77
September 23, 2022
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Well done, Jerry. I was wrong to suspect the Szostak lab of not using the phrase "chemical evolution". From the article you found. Our view of what such a chemical system would look like centers on a model of a primitive cell, or protocell, that consists of two main components: a self-replicating genetic polymer and a self-replicating membrane boundary. They seem to be describing what I would call biological evolution.Alan Fox
September 23, 2022
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We are interested in the chemical and physical processes that facilitated the transition from chemical evolution to biological evolution on the early earth The Szostak Lab
https://molbio.mgh.harvard.edu/szostakweb/     Such fools we are jerry
September 23, 2022
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More can be said.
Go on then. Frinstance tell me how replication and selection work prior to self-sustaining self-replicators.Alan Fox
September 23, 2022
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