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THE ATHEIST'S MAGICAL, MIRACULOUS FAITH BELIEF IN LIFE FROM NONLIFE The more I reflect on the origin of life, the more I realize that abiogenesis (life from nonlife) is no less "magical" or "miraculous" than belief that a dead body can come back to life. The same basic degradative processes are at work. This is backed by a tremendous amount of empirical data (like the "Asphalt Paradox" for example). Take for example the "simplest" cell, or an even simpler hypothetical 'minimal life' cell with say 100 genes and 100 proteins, and thousands of copies of each of those 100 proteins for ~1 million molecules total crammed into an approximately ~1 cubic micrometer space (roughly the size of a bacterium or smaller). If we kill that cell by say puncturing the cell membrane, no one expects the cell to come back to life despite the fact that it still has all the necessary parts (and even if we provide enough energy, and all the right conditions, and a controlled environment, and all the time in the world). We can predict empirically time and time again that nothing will happen, and can predict the inevitable decomposition of the cell back into its component parts. It would be "magic" and a miracle for the cell to come back to life. And yet for some reason many think that if we start with far less than our 100 genes, 100 proteins, and ~1 million total molecules enclosed in a lipid membrane... that if we start with only a small handful of amino acids, and sugars, and fatty acids (a few "nails" and "boards," so to speak, as opposed to an entire "house" that we've knocked out a wall of) that these will spontaneously assemble themselves into a living cell. And this despite the fact that this is simply the working assumption in science. An unproven assumption that has not only not been empirically demonstrated, but that the weight of empirical evidence is against, and that we don't know how it could happen even in theory on paper... And lest you think this is just the opinion of a non expert, even experts like origin of life researcher Pier Luisi have said as much that we "don't have the slightest idea how life originated from non-life"; and that "we do not have a conceivable theoretical scheme on paper, on how the origin of life may have come about"; and that even the popular "RNA World" hypothesis for the origin of life is "equivalent to invok[ing] a miracle, and then there are other theories based on miracles, which are much more accredited" (See, Dr. Luisi's "The Prebiotic Experiment"). Many agnostics and atheists will often deride, mock, and ridicule theists for their "irrational" beliefs, and invoking "magic" and miracles and silly beliefs like a dead man coming back to life. They have somehow convinced themselves that they hold a "rational," "respectable," "superior" position. And yet I see little difference between the two. Atheism has to appeal to "magic" and miracles, too. Invoking a supernatural agent to originate life is no less magical or miraculous than the atheist's magical, miraculous faith belief that life can spontaneously emerge from non-life.

Are ID/YECs right about anything?

If there isn't a reason for evolution to begin in a purely materialistic manner without outside intervention, why do people think it did? If hope only suggests it did, how is that different from saying, "God did it?" What happened = Life Reality has to be involved in what happened; therefore, whatever we believe took place in what happened needs to be possible, and if we suggest something that isn't, it should be rejected out of hand.

The Clergy Letter - from American Christian Clergy – An Open Letter Concerning Religion and Science Clic aquí para leer la carta en españolCliquer ici pour la version francaiseClique aqui para ler a carta em português Within the community of Christian believers there are areas of dispute and disagreement, including the proper way to interpret Holy Scripture. While virtually all Christians take the Bible seriously and hold it to be authoritative in matters of faith and practice, the overwhelming majority do not read the Bible literally, as they would a science textbook. Many of the beloved stories found in the Bible – the Creation, Adam and Eve, Noah and the ark – convey timeless truths about God, human beings, and the proper relationship between Creator and creation expressed in the only form capable of transmitting these truths from generation to generation. Religious truth is of a different order from scientific truth. Its purpose is not to convey scientific information but to transform hearts. We the undersigned, Christian clergy from many different traditions, believe that the timeless truths of the Bible and the discoveries of modern science may comfortably coexist. We believe that the theory of evolution is a foundational scientific truth, one that has stood up to rigorous scrutiny and upon which much of human knowledge and achievement rests. To reject this truth or to treat it as “one theory among others” is to deliberately embrace scientific ignorance and transmit such ignorance to our children. We believe that among God’s good gifts are human minds capable of critical thought and that the failure to fully employ this gift is a rejection of the will of our Creator. To argue that God’s loving plan of salvation for humanity precludes the full employment of the God-given faculty of reason is to attempt to limit God, an act of hubris. We urge school board members to preserve the integrity of the science curriculum by affirming the teaching of the theory of evolution as a core component of human knowledge. We ask that science remain science and that religion remain religion, two very different, but complementary, forms of truth. https://www.theclergyletterproject.org/Christian_Clergy/ChrClergyLtr.htm

Large scale genetic changes (Whole Genome Duplications) may help explain why some species survived extinctions. See here also.

Ground breaking news https://www.news-medical.net/news/20230628/First-programmable-RNA-guided-system-found-in-eukaryotes.aspx

https://scitechdaily.com/mankinds-missing-puzzle-pieces-the-deleted-genes-that-made-us-human/

Is biological sex an objective fact? And if so, does that make transgenderism a delusion (i.e., a false belief about external reality)?

The evidence for the fish-tetrapod transition has continued to increase over the last hundred years as more and more gaps keeps getting filled (See, my OP on "No Transitional Forms" and "No Transitional Fossils Have Been Discovered"), and labs have discovered that changes in a single gene can cause leg bones and muscles to instantly appear in fish fins. The discovery of Tiktaalik is an interesting example-- a missing link with fish and tetrapod traits that have earned it the name "fishapod." What's interesting is how it was discovered. Based on fossil fish lower in the fossil record (380 million years old), and tetrapods higher in the record (365 million years old), scientists predicted that this intermediate should exist and in sediments dated in between. The scientists went looking for this transition and picked research locations based on evolutionary predictions, and lo and behold, found Tiktaalik just as predicted. That is the sign of a good scientific theory: one that makes testable predictions that are then confirmed by the evidence.

(6) What is Information? | Episode 1403 | Closer To Truth - YouTube Very interesting

https://www.newscientist.com/article/2377527-octopuses-edit-their-own-genetic-code-to-adapt-to-colder-water/

https://www.sciencealert.com/tweaking-just-a-few-genes-transforms-scales-into-feathers

The endlessly repeated "there are no transitional forms" mantra of YECs is an interesting study. First, the term "transitional form" is a slippery YEC term that YECs define in such a way as to make it impossible to ever demonstrate (even if we were just talking about human history and your own family tree!). But that aside, what I find interesting is how this YEC mantra persists regardless of how many "transitional" forms are found; which begs the question of how many "transitional" forms will it take to make a YEC happy before they're willing to acknowledge, "Okay, maybe, just maybe, those things might be related to each other"? And the answer, of course, is that no amount of "transitional" forms will ever be enough, because they've already pre-decided (before any evidence) that they are not related, no-way, no-how, no matter what. The example that comes to mind is the origin of tetrapods (incorrectly called the "fish-to-amphibian" transition by YECs). And specifically I recall a picture in YEC Duane Gish's 1970s/1980s book "Evolution: the Fossils Say No!" that criticized the "lack of transitional/intermediate forms" between fish and tetrapods: "THERE ARE NO TRANSITIONAL FORMS!" The Gish picture (figure 1) is still used by YECs today (figure 1 caption) to say "look, fully formed fins & feet with no intermediate transitional forms in between!" Of course, Ichthyostega (discovered in 1932) was already old news, and before the days of the Internet information was harder to find, so perhaps Gish didn't know about Acanthostega (discovered 1952) which had characters intermediate between fish and Ichthyostega. Of course, once that discovery became more well known that still wasn't a good enough transitional form, so the YECs could still shout: 'THERE ARE NO TRANSITIONAL FORMS!" And then, of course, more discoveries were made, but for whatever reason these weren't good enough, or didn't count, or still left large "gaps," so YECs felt they could still confidently shout: "THERE ARE NO TRANSITIONAL FORMS!" And then more discoveries were made... "THERE ARE NO TRANSITIONAL FORMS!" And still more discoveries were made (like the discovery of Tiktaalik in 2006).... "THERE ARE NO TRANSITIONAL FORMS!" *So evolution keeps changing, while young earth creationism stays the same ("THERE ARE NO TRANSITIONAL FORMS!"), and apparently no amount of "transitional forms" will ever be enough to get YECs to acknowledge, "Hey, you know, maybe, just maybe, those things might be related." OR EVEN JUST, "I still disagree, but I can see why everyone else concludes that they're related."

https://phys.org/news/2023-04-evidence-interdomain-horizontal-gene-eye.amp

True or False: the Genome (DNA) of an organism contains all the instructions (the "blueprint") for making that organism?

A recent 2021 study argues that "expected evolutionary transition times likely exceed the lifetime of Earth, perhaps by many orders of magnitude." (See, "The Timing of Evolutionary Transitions Suggests that Intelligent Life is Rare"). Ever since John Maynard Smith & Eors Szathmary published their (1997) book on The Major Transitions in Evolution, the idea of "Major Evolutionary Transitions" (METs) has attracted the attention of biologists and astrobiologists alike. These are major *Major* evolutionary transitions; not normal, repeated macroevolutionary events like speciation for which there is an abundance of evidence and which we can study in real time; but seemingly unique, one-of-a-kind, never again repeated events. These "Major Evolutionary Transitions" (METs) have been variously called "critical steps" or "hard steps" in evolution. Just how many there are depends on one's definition and who you talk to, but the list usually includes things like the following: (1) The origin of life(2) The origin of photosynthesizing bacteria (3) The origin of eukaryotes (4) The origin of sexual reproduction (5) The origin of complex multicellularity with cell tissue differentiation (6) The origin of human symbolic language/intelligence These "hard steps" are thought to be extraordinarily improbable, one-time events in Earth's history. And some, like the origin of life on Earth, seem an impossible occurrence even within the age of the universe. As the researchers note, "it would take >>10^200 times the present age of the universe for a particular folding [of a 300 amino acid long protein] to occur, even assuming a sampling rate of 1 trillion conformational states per molecule per second and a volume of concentrated protein solution the size of Earth's oceans." This problem is compounded by the presence of life so quickly on Earth, essentially as soon as the Earth was habitable (~4.3 Gyr) if reports of biogenic carbon in 4.1 Gyr zircon crystals are accurate. If true, then that means there is an extremely small window of time for the first *two* "hard steps"---the origin of life *and* also complex photosynthesizing bacteria---as the biogenic carbon discovered is indicative of carbon fixation in photosynthesis. If this weren't difficult enough, there are some researchers (e.g., Raup & Valentine (1983), Multiple Origins of Life) who argue that (even if life did originate abiotically) the probability of life surviving is low unless there were multiple origins of life (they estimate 10 independent origins for one to survive). The researchers note, "The transition to eukaryotic life also involves similar “chicken and egg” difficulties [as the origin of life], with uncertainty on how an archaeon acquired a proto-mitochondrion, since endocytosis requires complex machinery only present in eukaryotes. A second potential hurdle for eukaryogenesis was the survival of the first prokaryotic host with a bacterial symbiont. Without the protection of spliceosomes and a nucleus, the prokaryotic host would be disrupted by extensive intron transfer from the lysis of its symbionts, resulting in few functional proteins. The chimera cell would need to evolve these complex defenses faster than the mutation ratchet effect driving the (already tiny) population to extinction, which could have also required a rare specific outcome among a vast combinatorial space." The researchers considered four "hard steps": the origin of life, origin of eukaryotes, origin of sexual reproduction, and the origin of human symbolic language in light of recent evidence that suggests there is only ~1 billion years left before the earth becomes uninhabitable due to the sun's increasing luminosity (vs. the 4 billion years once thought). This shorter window of time (~5 billion yrs) to achieve these evolutionary "hard steps" for an earth-like planet; combined with the fact that our sun is not a common type of star, and that planets orbiting red dwarfs (the most common type of star) do not seem habitable for life (which effectively rules out 75% of the Milky Way Galaxy); the researchers conclude that intelligent life must be rare in the universe. Importantly, the investigators indicate predictions of their model and what it would take to overturn their conclusions.

This topic arose in the Notes section of the forum, so I'm starting a post on it here, where the topic can be adequately addressed. "Natural Genetic Engineering" (NGE) is a phrase coined by Chicago University microbiologist/evolutionary biologist Dr. James Shapiro Wikipedia provides a summary of the idea. Based on volumes of evidence from microbiology and genomic studies over the past three or so decades, Shapiro concludes that: Shapiro has a book on the subject And numerous peer reviewed published science journal articles on the topic, some of which I have frequently referenced: "Living Organisms Author Their Read-Write Genomes in Evolution" (2017) " Nothing Makes Sense in Evolution Except in Light of Genomics: Read-Write Genome Evolution as an Active Biological Process" (2016) "Biological Action in Read-Write Genome Evolution" (2017) "How life changes itself: the Read-Write (RW) genome" (2013) "Why the Third Way of Evolution is Necessary" (2021) "What prevents mainstream evolutionists teaching the whole truth about how genomes evolve?" (2021) "What we have learned about evolutionary genome change in the past 7 decades" (2022) .... "Mobile DNA and evolution in the 21st century" (2010) "The basic concept of the read-write genome: Mini-review on cell-mediated DNA modification" (2016) "Genome system architecture and natural genetic engineering in evolution" (1999)

The focal point of most creation-evolution debates centers on the ability (or not) of random mutation and natural selection to account for life's diversity. This is understandable because it is still what is emphasized and receives the most attention in introductory biology courses. So people on both sides of the debate find it surprising and at odds with what they've learned and perhaps even unbelievable when I say evolutionary biology today recognizes that life's diversity cannot be explained by mutation-selection only, that there is much more in addition to this, and a plurality of mechanisms involved. I have then talked about the Extended Evolutionary Synthesis, given examples, and posted links articles like microbiologist James Shapiro's "Nothing in Evolution Makes Sense Except in Light of Genomics. Reactions to this range from continued denial/rejection of what I say to possible acceptance on the basis of my word, but still without really understanding why. At least that's my perception, and I've realized (after recent discussions with @MindWalk and @stephen_33 on this topic) that I need to do a better job connecting the dots for people. It is my intent to do that very thing with this new thread: to better connect the dots for people as to how evolutionary biology has evolved beyond the standard Neo-Darwinian view (i.e., the Modern Synthesis) of mutation-selectionism, and most importantly *why*, so that people understand the underlying reasons instead of just taking me at my word. To this end, I have selected an article (that I don't think I've posted on before) that does an excellent job explaining these changes and how advances (especially in genomics) have revolutionized our understanding of evolutionary biology. The article is over ten years old but still relevant for the discussion, and methodically goes through the issues in a historical, chronological manner that I think people will find especially helpful (so my plan is to similarly follow this approach with a step-by-step walk through this article). Here's the article link and abstract: "Darwinian Evolution in the Light of Genomics" (2009) by Koonin Abstract-Comparative genomics and systems biology offer unprecedented opportunities for testing central tenets of evolutionary biology formulated by Darwin in the Origin of Species in 1859 and expanded in the Modern Synthesis 100 years later. Evolutionary-genomic studies show that natural selection is only one of the forces that shape genome evolution and is not quantitatively dominant, whereas non-adaptive processes are much more prominent than previously suspected. Major contributions of horizontal gene transfer and diverse selfish genetic elements to genome evolution undermine the Tree of Life concept. An adequate depiction of evolution requires the more complex concept of a network or ‘forest’ of life. There is no consistent tendency of evolution towards increased genomic complexity, and when complexity increases, this appears to be a non-adaptive consequence of evolution under weak purifying selection rather than an adaptation. Several universals of genome evolution were discovered including the invariant distributions of evolutionary rates among orthologous genes from diverse genomes and of paralogous gene family sizes, and the negative correlation between gene expression level and sequence evolution rate. Simple, non-adaptive models of evolution explain some of these universals, suggesting that a new synthesis of evolutionary biology might become feasible in a not so remote future. *To start with, I have highlighted three key ideas in the abstract: (1) Natural selection is only one evolutionary force and not the (quantitatively) dominant one. (2) The popular conception of evolution as an "increasing [trend in] complexity" is a myth. (3) The new evidence from genomics indicates that a paradigm shift may be in order (*this article predates and anticipates the Extended Evolutionary Synthesis). ***OK, but why? For those interested, we will walk through the article and see.