TRUTHFUL ORIGINS EVO

“There is for me powerful evidence that there is something going on behind it all … it seems as though somebody has fine-tuned nature’s numbers to make the universe. The impression of design is overwhelming.” ~ Paul Davies, physicist, agnostic Introduction People who argue against evolution and especially for creationism of course are overwhelmingly coming from religious views. However, two arguments for a creator tend to be very attractive to the non-religious, including many in the fast growing “nones” category. These are the two main design conclusions which appear on the surface to be very intuitive and logical, sometimes due to a limited knowledge of nature. First, the biological design view is seen in the arguments for Intelligent Design (ID). This occurs probably often due to ignorance of all the unintelligent adaptations that can only be rationally explained by natural selection. It is very difficult to defend a wise Great Engineer and Grand Architect designing for example men having breast tissue that leads to breast cancer in 3,000 American men per year, the crazy Recurrent Laryngeal Nerve route, the poorly designed vertebrate eye, baleen whales that grow teeth as a fetus, or why humans would have dead genes for making egg yolk. Rather, an honest view of nature without cherry picking reveals instead very often clumsy natural selection producing adaptations due to limitations and restraints. Copious examples mostly just for humans have been detailed in a blog and short video presentation. The appeal of intelligent design for the religious is often a result of motivated reasoning and confirmation bias, whereas for the non-religious it tends to be erroneous intuition due to a lack of adequate biological knowledge and testing for falsifiability. It is intuitive but wrong that we exist on a flat immobile planet at the center of our solar system when in fact we are spinning on a sphere at 1,000 mph and going around the sun at 67,000 mph. So also it is counter-initiative that the biological complexity and diversity we see now and in the fossil record is not the result of a Great Design but rather the result of evolution, leaving the theist and creationist only theistic evolution or evolutionary creationism as a viable species origin narrative. The second design view involves cosmology and is called Fine Tuning . Like Intelligent Design for biology, this also seems correct initiatively and is a very common argument for believing in some kind of entity behind our universe existing. Many people who reject religion still find this argument compelling. In this case, instead of biology people will turn to physics and cosmology to argue that certain parameters that we find in our universe are so finely tuned that they could not be present without a design or purpose. The Fine Tuning Argument Inherent in the Fine Tuning argument for cosmology is the question fine tuned for what ? The answer is life, our planet’s life - us. What is claimed to be fine tuned? Our universe or even aspects of our planet. We could not be here unless the universe was found to have exact, inflexible parameters it is asserted. They could not have occurred by chance. Collins writes: “The chance that all of these constants would take on the values necessary to result in a stable universe capable of sustaining complex life-forms is almost infinitesimal. And yet those are exactly the parameters that we observe. In sum, our universe is wildly improbable.” ~ Francis Collins, The Language of God… 2006. p. 74. What are these constraints or parameters? The number varies by author but several are most commonly listed. The claim is that if any are changed even in the slightest, our universe could not support life or the evolution of life, or even be present. These values are thus delicately balanced and must be so exact that our universe must be designed to allow life, and any change in the slightest to any of then would make life impossible. This argument has been called the best argument against atheism by both atheistic philosophers and physicists, and of course theists. In my experience it is also very attractive to agnostics and persons holding to non-religious but spiritual views. Along with ID, the Fine Tuning argument is often the only two assertions left standing in debates after other arguments for a creator or design have been countered or dismissed. The physicists Barrow and Tipler outlined in 1986 a detailed discussion mathematically of the notion of a fine-tuned universe for humanity in their “ The Anthropic Cosmological Principle ”. There are two basic forms of the anthropic principle, called weak and strong. Anthropic refers to the existence of human life and in terms of cosmology refers to constraints on our universe. Other physicists such as Dicke, Hoyle, and Davies are all scientists who have written that the universe seems fine turned for life (2). Theists who are strong proponents include the Christian apologists Hugh Ross of Reasons To Believe , Francis Collins who founded Biologos , the prodigious philosophical debater William Lane Craig and the theologian Richard Swinburne. Cosmological Parameters often discussed These parameters are observed and claimed that any deviation beyond a certain maximum value would either prevent our universe from existing or would make any form of life impossible. Some have listed more than 30 (1, 3). These appear to be more minor and include the earth’s axis, earth’s unique moon and it’s beneficial effects, Jupiter protecting earth from asteroids, and more. The ones below seem to be the major parameters most often mentioned by physicists and cosmologists. Ratio of Electrons to Protons 1/10^37 Ratio of Electromagnetic Force to Gravity 1/10^40 Expansion Rate of Universe 1/10^55 Mass Density of Universe 1/10^59 Cosmological Constant 1/10^120 Stenger addressed the above five parameters specifically in his book (1). A. Electron/Proton ratio (chapter 10) - The number of electrons (-) and protons (+) should be the same because of charge observation as the total electric charge of the universe is neutral. This is a result that must be unchanged when you change reference frames or points of view. If physics “ models are to be objective, that is, independent of any particular view, then they are required to have point-of-view invariance… physicists have no choice in the matter, or else their models will be subjective, that is, will give uselessly different results for every point of view” (pg. 82). His conclusion: there is no fine-tuning; the parameter is fixed by established physics and cosmology. B. Electromagnetism/Gravity ratio (chapters 7, 13) - If the ratio were larger, no stars would form. If smaller no large stars would form and then no heavy metal production through explosions. Stenger ran a program where he could vary the electromagnetic force, electron mass, and proton mass and then observe the results. “ In disagreement with the claims of fine-tuners everywhere, I find that when the parameters are varied by two orders of magnitude, 37 per cent of the universes simulated have the features needed for life similar to ours to evolve, where strict conditions were applied. ” His conclusion: there is no fine-tuning; the parameter is in the range expected from established physics… This example also illustrates a major mistake made by most fine-tuning proponents.They hold all the parameters constant and just vary the one of interest. A proper analysis must vary all parameters at once, since a change on one can often compensate for a change in another." (Pg 280). C. Expansion rate of the universe (chapter 11) - if it were larger there would be no galaxy formation. If it were smaller the universe would have collapsed before stars could form. This fine tuning argument is often cited from Hawking: “If the rate of expansion one second after the Big Bang had been smaller by even one part in a hundred thousand million million, the universe would have collapsed before it ever reached its present size”. However, both Craig and D’Souza quote mined and failed to note what Hawking wrote 7 pages later for why no fine tuning was necessary - “The rate of expansion of the universe would automatically become very close to the critical rate determined by the energy density of the universe. This could then explain why the rate of expansion is still so close to the critical rate, without having to assume that the initial rate of expansion of the universe was very carefully chosen” (A Brief History of Time, pg. 121) Stenger’s conclusion: there is no fine-tuning. The parameter is fixed by established physics and cosmology. D. Universe mass density (chapter 11) - if it were larger, there would be too much deuterium and stars would burn too rapidly. If smaller, there would be too little helium and too few heavy elements would form. However, the critical value we now measure was a prediction from inflation before it was actually measured. Conclusion: there is no fine-tuning. The parameter is fixed by established physics and the accepted inflationary cosmology that is a well established part of the standard model of cosmology. E. Cosmological Constant (chapter 12) - according to Stenger the calculation producing the maximum number is wrong but the LHC should be able to confirm this. Evidently physicists have not reached a consensus on the question of this parameter. Stenger’s conclusion: “ The standard calculation of this parameter is grossly wrong and should be ignored. Viable possibilities exist for explaining its value [ghost solutions of relativistic quantum field theory and holographic universe] , and until these are ruled out, no fine-tuning can be claimed.” Other objections to fine-tuning 1. Why fine-tuning arguments don’t work (8 min.) Dr. Sean Carroll, theoretical physicist at Cal Tech; Debate with William Lane Craig. https://www.youtube.com/watch?v=zR79HDEf9k8 1. We don’t really know that the universe is tuned specifically for life, since we don’t know the conditions under which life is possible. 2. Fine-tuning for life would only potentially be relevant if we already accepted naturalism; God could create life under arbitrary physical conditions. 3. Apparent fine-tunings may be explained by dynamical mechanisms or improved notions of probability. 4. The multiverse is a perfectly viable naturalistic explanation. 5. If God had finely-tuned the universe for life, it would look very different indeed. This part is perhaps his best part as he compares predictions of theism vs. naturalism. Post debate comments by Dr. Carroll: https://www.preposterousuniverse.com/blog/2014/02/24/post-debate-reflections/ Full debate: https://www.youtube.com/watch?v=07QUPuZg05I&t=1s (2hrs, 45min.) Carroll’s response starts at 30:30. To Craig’s premise #1, if the universe began to exist, it had a transcendent cause. Carroll states the correct way to ask this question in cosmology is can I build a model of the universe that had a beginning and no transcendent cause? Yes, it has been done . Worse for this claim it appears there is good evidence that our universe may indeed be infinite. See Big Bang including a fantastic 10 min video. 2. The universe is not fine-tuned for life. The universe is about as inhospitable to life as one could imagine. Is it fine-tuned so life could exist? Then that’s a tremendous waste of space and volume as pointed out in the movie “Contact”. As one physicist has remarked if the universe has any purpose it is to make black holes. If anything the universe is configured for death and is overwhelmingly hostile to life which would make any creator malevolent or indifferent.  The universe on average contains only 1 proton per cubic meter. Dr. Neil deGrasse Tyson discusses briefly in this FB reel why the universe and much of the earth are actually deadly to life. It's a fallacy of thinking that nature if made for life and us. https://www.facebook.com/reel/3974704276180764 3. Life, Personal Observation & Reality. A universe in which life exists to wonder why the universe is suitable for life will be suitable for life. That can happen in either a fine tuned or non-fined tuned one. 4. The Multiverse. This idea is not something atheistic scientists made up to make theists angry and frustrated. It actually just falls right out of the equations for inflation which is well established for the Big Bang. Some theoretical physicists say it’s actually inevitable. See Part B in this blog. Probably a 10 minute read. If the multiverse turns out to be true, than there would be an infinite number of universe with different parameters and different forms of life could exist that would not need our specifics. It’s highly probable that some universes just by the shear number produced could support life. 5. Fine tuning may be an illusion. "The tuning required for some of these physical parameters to give rise to life turns out to be less precise than the tuning needed to capture a station on your radio, according to new calculations," says Miriam Frankel, who authored the FQXi report, which was produced with support from the John Templeton Foundation. "If true, the apparent fine tuning may be an illusion," Frankel adds… The report then outlines arguments that fine-tuning is an illusion, noting that life may take a very different form than naively imagined, and that if multiple physical parameters are considered to vary simultaneously, it could alleviate any apparent fine-tuning problems. This suggests that the universe may not be so finely tuned; it may be able to produce life under a much wider range of circumstances than first thought… But the equations of stellar structure may have more solutions than most people realize. "Stars can continue to operate with substantial variations in the fundamental constants," says Adams, whose work is featured in the report. "Moreover, if a particular astrophysical process becomes inoperable, then (often) another process can take its place to help provide energy for the universe.” (5) 6. Fine-Tuning implies an evil or incompetent God. As a believer, Halvorson submits similar to Carroll above that arguing that our universe is improbable would “disconfirm God’s existence”. Because " a benevolent God would want to create physical laws so that life-conductive universes would be overwhelmingly likely.” As Carroll noted in the short video above, listing all the attributes of nature near the end of his video clip soundly points to naturalism, not theism. “An analogy here might be apt. Suppose that you’re captured by an alien race whose intentions are unclear, and they make you play Russian roulette. Then suppose that you win, and survive the game. If you are convinced by the fine-tuning argument, then you might be tempted to conclude that your captors wanted you to live. But imagine that you discover the revolver had five of six chambers loaded, and you just happened to pull the trigger on the one empty chamber. The discovery of this second fact doesn’t confirm the benevolence of your captors. It disconfirms it. The most rational conclusion is that your captors were hostile, but you got lucky.” (7). 8. Probability. There is a quote by Collins at the beginning of this article stating that the parameters we measure together that allow life are so improbable that he believes it can only be explained by having a designer, God, putting it all together. But what if we calculate the probability of our own existence? What’s the probability of a certain egg of the thousands and a specific sperm from 300 million getting together? That those specific adults would meet? That the zygote won’t break down due to genetic problems? That the embryo won’t implant? That the fetus won’t miscarry? That before modern medicine you would not die at childbirth? That before modern medicine you would not be the 50% of children born that died before age 5? It would probably produce an even smaller number than the fact of our universe or planet supporting life. Actually Collins, you, and I are proof that low probability events happen all the time. Your chance of winning a multi-million dollar lottery may be infinitesimally small, but the probability that someone will win it after several runs is nearly 100%. Once a low probability event happens their probability becomes 100%. Conclusion The fine-tuning argument is one of two major design arguments for a creator, and rests on cosmological and physics observations. Like it’s cousin intelligent design for biology it has great initial appeal as it is at first very intuitive. It is even attractive to the non-religious. Intelligent Design has utterly failed in the biological sciences because it has been shown to be a religiously driven movement and it only takes some additional education in biology to see all the unintelligent designs that can only be rationally explained by evolution without the need of a creator. Evolution is an emergent property of the structure of life. In addition we now have fantastic evidence that shared DNA findings rise to the level of proof for macroevolution with more than sufficient naturalistic mechanisms only. For the simplist example see shared DNA breaks and unique repairs . There appears in life, in our DNA, and in the history of life in the rocks and fossils no ultimate goals or purpose to life. No personal Creator, Designer, or Engineer behind the origin of species. Likewise, design assertions from cosmological observations also fail. The major parameters most often listed as so improbable that our universe must have been created for life by a super intelligent being can be shown however to be fixed by established physics and cosmology. On the contrary, a creator making the parameters so narrow that a universe is so improbable for life makes an all wise and loving creator evil or incompetent. The parameters are not so narrow as originally thought and if more than one is allowed to change at one time, often compensation from the others can take place. It appears that the multiverse is inevitable from inflation and an infinite number of universes means ours was certain to happen with the parameters it has and that life markedly different from ours could be in another universe. Lastly, our universe is not designed for life. It is an incredible inhospitable place of certain death for life anywhere in the vastness of the universe except in some minuscule areas. The incredible overwhelming volume of the universe contains mostly huge expanses that are death sentences for any life. All design arguments when examined objectively and closely succumb to critical examination whether they be biological claims or cosmological ones. Citations And References 1. Stenger, Victor. 2011. The Fallacy of Fine-Tuning: Why The Universe Is Not Designed For Us. Prometheus Books, Amherst, NY. 345pp. 2. Fine-tuned Universe. Wikipedia. https://en.wikipedia.org/wiki/Fine-tuned_universe 3. Fine-tuning argument. Religions Wiki. https://religions.wiki/index.php/Fine-tuning_argument 4. What is Wrong with the argument for fine-tuning? Reddit Debate thread. https://www.reddit.com/r/DebateAnAntheist/comments/3ur8oy/what_is_wrong_with_the_argument_from_finetuning/?rdt=56343 5. Is the ‘fine-tuned universe’ an illusion? https://phys.org/news/2022-02-fine-tuned-universe-illusion.html 6. The Fine-Tuning Argument. Manson, Neil A. University of Mississippi. Philosophy Compass 4/1 (2009); 271-286. https://home.olemiss.edu/~namanson/Fine%20tuning%20argument.pdf 7. Fine-Tuning Does Not Imply a Fine Tuner. Some think that fine-tuning is evidence for God, but in fact the opposite is true. Halvorson, Hans. 2017. https://nautil.us/fine-tuning-does-not-imply-a-fine-tuner-236373/

"Scientists long assumed that evolution made new genes from old ones - by copying them in error, or by fusing together or breaking apart existing ones. Now, more and more examples are emerging of genes being created 'de novo', from barren non-coding portions of the genome." ~ Adam Levy, Genes From The Junkyard Introduction  The theory of evolution explains why we see the fossil record going from simple to complex over about 15,000 ft of sedimentary rock with scores of transitional fossils and no mixing over 500 million years. It explains the endemic biota of the Hawaiian Islands via biogeography and it’s geology including the Emperor Seamounts through a Pacific hot spot and plate tectonics. It explains why pterodactyls are only found in one layer and never with human remains or more ancient life forms. It explains crazy anatomical features like the recurrent laryngeal nerve in vertebrate necks, the inverted and poorly designed vertebrate eye with at least four workarounds by natural selection, and the finding of thousands of pseudogenes we share with other species - genes deactivated by mutations - including three for making egg yolk even though we don’t lay eggs. These and more examples are discussed in the blog on why intelligent design is only credible if one chooses to cherry pick nature, conflating complexity with design, and ignoring all the biology that tells us we are the product of evolution and not intelligent design. See blog on ID here. For significantly new species to form it would take the ability of nature to produce new genes, new products that various selection forces could identify as important in survival and reproduction, and then promote them to spread in successive populations. Natural selection diminishes variation. Thus, this is a foundational need, and all “macroevolution” claims would fail if new genetic information, new genes could not arise. Gain of function is needed. Gain of information, however one wants to define “information”, genetically is especially required.  Setting the stage - the issue For anti-evolutionists, the mantra that nature can’t produce new genes that make new information for evolution is a major assertion. As in the false claim proclaimed by many creationists that there are no transitional fossils - because to them there can’t be - they must claim there can never be new genes and no new information formed. Variation is limited to speciation from “kinds” because macroevolution is assumed impossible. It’s a presupposition that macroevolution has never happened despite   DNA findings that essentially prove it .The variety in life to them originates like an orchard and not like a bush. Most creationists claim diversity and variety arises not from new genes but from the originally created genomes that supposedly carry enough diversity to only form similar species within limits; for example dog kind, cat kind, and humans were specially created without ape ancestors. This results in microevolution of “kinds” only - no evolution between major groups and certainly not human evolution from shared ancestors with the other great apes (but we now have the DNA findings to prove human evolution is true). See The Demise of Evolution Objections . This is the opposite of accepted evolution, and indeed Michael Behe in his book “Darwin Devolves”  discusses example after example of genes that are turned off and disabled so new phenotypic changes can come about. His central point is that only previously present genes are disrupted to see the changes we observe, for example with polar bears degrading genes to match its diet and white fur. Behe writes in his third book, “Darwinian evolution proceeds mainly by damaging or breaking genes, which, counterintuitively, sometimes helps survival. In other words, the mechanism is powerfully devolutionary. It promotes the rapid loss of genetic information”(1). There is little to no room for the formation of new genes, new information for natural selection to work on in the anti-evolutionist world of species origins. Several scientists pointed out how wrong Behe is again. But is that true? Are there no examples of new genes forming? Have evolutionary biologists been fooled, or worse in denial? (17). Methods for acquiring new genes On the genetic level mutations are changes in the DNA letters of the genome. They can be beneficial or deleterious. Many people are under the impression that point mutations, changing a single letter of the ATCG letters in DNA, is the primary way mutations are proposed to occur and add new information to genomes but this is not the case. In the Origins of New Genes and Pseudogenes several ways new genes form are discussed (2). 1. Gene Duplication Most evolutionary biologists would probably point out that new genes predominantly arise through gene duplications. Duplications are very common. Even today in our present human population, we have what are called copy variants  between people. Finlay notes that genomic analysis has identified 11,700 variable locations in the human genome where any two people differ at about 1,100 of these DNA areas that are copied but not equally present in different people. Any two people vary by the number of olfactory receptor genes, and in a few taste receptor genes. It is true that people can taste and smell differently at least in part due simply to the number of receptor genes they have. We have little cellular factories for making proteins called ribosomes and people have from 35 to 175 copies of the rRNA genes. People vary by the number of salivary amylase genes they have, with European and Japanese populations having the higher number of AMY1 genes. The more salivary amylase you have the better at breaking down starches starting in your mouth and this will lessen the chance of developing diabetes (3). The idea is that when genes are duplicated, most copies develop disabling mutations because the original gene is still present and the duplicated gene is not under strong selection to conserve it. Many would then become pseudogenised. But rarely, mutations develop that allow the copied gene to acquire the ability to make new products that can have new functions. Gene duplication rates are actually very high (2). The platypus has venom in its spurs that includes three peptides similar to a compound it uses in its immune system with antimicrobial properties. It evolved from gene duplications (4). Opsin genes for color detection evolved from duplications (5). In one experiment, scientists disabled a gene in Salmonella enterica that makes tryptophan. Another gene with a different function had a weak ability to do some of the original gene’s work. The bacteria duplicated the second over-worked gene and the copies acquired random mutations that eventually led to a second new different gene that evolved a new function making tryptophan again. This occurred in just a year and 3,000 generations (6).  A gene that codes a receptor for sialic acids underwent gene duplication to produce a new gene and the story has been revealed by scientific sleuths. “The SIGLEC11 gene was duplicated in an ancestor of humans and chimps…the duplicated copy was pseudogenised and part of the pseudogene subsequently pasted back into the parent SIGLEC11 gene… A subsequent gene conversation went the other way, generating a revivified allele of the pseudogene. The… process generated two novel genes existing only in humans. The novel SIGLEC11 gene encodes a protein with novel sialic acid-binding properties, and is expressed by microglial cells in the brain. It is also active in the ovary… and, when abnormally expressed, to a uniquely human disease (polycystic ovarian syndrome)”  (3). Work by Nathan Lents and students discovered that some microRNA genes found on human chromosome 21 were not found in the other great apes. These in the past might be considered orphan genes and antievolutionists have touted them as evidence against evolution since they appear not to have precursors in other species. Further evaluation revealed this area of the chromosome had undergone extensive genomic rearrangements not present in other apes. The 8 different human only microRNA genes in that area were embedded within an array of ribosomal RNA genes and these microRNA genes resemble parts of the rRNA genes. It appears that as the rRNA genes underwent segmental duplications that a part of them broke off and formed the smaller microRNA genes. This would be the first evidence of de novo  new gene formation through genomic rearrangements. (7). Researchers in Finland have also shown how new microRNA genes have arisen out of DNA copying mistakes by looking at their signature palindromes (7a). Scientists knocked out the flagella regulatory gene fleQ  for the proper function of a bacterial flagellum. They then put the bacteria under strong selection to regain mobility. The bacteria used  two independent random mutations to regain the lost flagella in 4 days. They did this by diverting a related regulator gene to switch from controlling nitrogen uptake to instead control flagella biosynthesis. The bacteria co-opted a regular gene normally not involved in flagella formation (11). In terms of gene duplications, it’s hard to beat plants. They often completely duplicate their entire genomes and sometimes several times over. This is called polyploidy. This frees up many parts of their genomes to develop new genes and new functions. Scientists studying the specialized carnivorous Asian pitcher plant, or Nepenthes, found it had a decapod genome in its diploid state, a complex structure almost unprecedented in flower plants that reflected a five whole-genome multiples. One of the subdomains was dominant, but the others were free to evolve new functions. The enzymes that help Nepenthes break down insects’ hard exoskeletons, for example, were repurposed from those that originally shielded plants from being eaten by those animals. (8). Three new genes were produced by a copy and paste duplication error involving the NOTCH gene, called the NOTCH 2NL group. They created new proteins that in the human fetus helped human brains to enlarge from the original NOTCH gene (10). In addition, thousands of random segmental duplications that include genes have been identified and noted to be shared often by other species. If we find the same random segmental duplications shared between species this is near proof of common descent. This is discussed in the blog on duplications and evolution . 2. Horizontal or Lateral Gene Transfer This happens mostly in prokaryotes like bacteria. New genes are acquired by bacteria exchanging DNA, often mediated by viruses called phages that pick up DNA from an infection in one cell before transferring it to another cell after budding off. Mitochondrial DNA (which are cellular organelles that have their own DNA - see blog and how we know mitochondria were former bacteria  and can have some of their DNA transferred to the host nuclear DNA through a DNA repair process. See how shared DNA repairs  between species proves evolution (2). Since this type of obtaining new genes is not a significant method for multicellular life little more will be discussed.  3. Gene Fusion and Fission Genes can also fuse or undergo fission thereby forming new genes. “Interestingly, it has been observed that chimeric fusion genes sometimes involve two copies of the same gene (e.g., the alcohol dehydrogenase gene in Drosophila), and when that happens, the resulting genes undergo parallel evolution in which they shift away from the functions of their parental genes.” (2) 4. Transposable Element Protein Domestication TEs are segments of DNA that have the ability to copy themselves and randomly jump around in the genome. They increase the genome size but usually do not code proteins. A genome can acquire new genes by recruiting transposable element proteins and using them as cellular proteins. It is estimated that about 45% of the human genome is derived from retroviral infections and their viral derivatives (retrotransposons for example). Many TE domesticated proteins have been identified and some play a role in vertebrate immune system and light sensing in plants (2). In addition, various TEs - “jumping genes” - have been identified in human genomes. We have found the same random jumping genes shared by other species in the same homologous locations. Because they jump randomly, if we find the same TE in the same location between species often with the same mutations the only conclusion is common ancestry; common design as an explanation becomes intellectually impossible. This is discussed further in the bog on how  shared TEs prove evolution . Possible Objection - the anti-evolutionist could claim that these new genes with new applications and “information” still had to come from pre-existing genes that were changed. At a minimum these examples disprove the idea of no new genes and information; they do indeed introduce new genes and new information into the genome. Speciation and phenotypic changes occur not just from disabling existing original genes. What if the new genes from duplications themselves are duplicated and produce further new genes, resulting in a steady or even exponential incremental increase in information and complexity - exactly what we see in the fossil record? Evolutionary compound interest? If this new information and products influence other parts of the genome what inhibits incremental coordinated phenotypic changes to better serve a changing environment? Disabling genes at the same time new genes were being produced would seem to be a method for how evolution could be driven at the molecular level let alone if drift accelerates or influences the entire process. What many are interested in however are genes that arose de novo . This is something usually anti-evolutionists claim can’t happen. De novo  genes would answer the creationist claims that orphan genes (ones that don’t have known other similar genes in evolutionary related species) disprove evolution. Actually they support it by demonstrating why they are unique - they arose de novo.  Instead of being a problem for evolution, they support it while explaining where new information comes from to supply raw material for natural selection to change species. Mic drop. This is similar to creationist discussions that certain structures in the vertebrate eye are designed when in truth the four aspects of the vertebrate eye that they think are wonderful eye designs only exist because solutions are needed to patch up the consequences of having an inverted retina that compromises vision. See section  1h   in the blog on unintelligent design  for a discussion and visual diagrams of the four workarounds provided by natural selection to attenuate the poor design of the vertebrate eye. Those four structures speak to poor design in the vertebrate eye necessitating natural selection work arounds rather than a great “design”. Duct tape over a broken car tail light is not a great original engineering design.  De Novo Gene Formation A classic story of new gene formation involves Ice Fish antifreeze proteins and will be discussed below in a separate section. Caroline Weisman published a paper in the Journal of Molecular Evolution in 2022 entitled “The Origins and Functions of De Novo Genes: Against All Odds?”  A de novo gene was one that “evolved from previously non-genic DNA”, something thought to be rare as it would be unlikely that random sequence would produce a functional gene. (9) She listed her criteria for a true de novo  gene: “First, I require positive evidence of the gene’s absence from outgroup species. For RNA genes [non coding genes], there must be evidence that the orthologous sequence is not transcribed, or that it produces a substantially different transcript, in outgroups. For protein-coding genes, there must be evidence that the orthologous sequence is not translated, or that the ORF [open reading frame] is substantially different, in outgroups. Note that the failure of, e.g., BLAST to detect homologs in outgroups, a common methodology, does not constitute such evidence. Second, I require at least two outgroups for which the above is true. This is the minimum number required to make de novo  gene gain likelier than the alternative of gene loss in outgroups, assuming (generously) that these events are equally likely. Finally, I require data suggesting that the gene has a biological effect, in the form of an observable phenotype when it is knocked out or down. For protein-coding genes, there must be some evidence that this phenotype is due to the novel protein rather than the transcript. (As others have noted, the word “function,” especially for de novo genes, is fraught (Keeling 2019 ); when I use it here, it is as shorthand for this criterion of “producing a biological effect,” and does not imply other frequently associated concepts like having been evolutionarily selected.)” Wiseman then goes on to list some of the protein and non-protein (RNA) coding genes that have been identified as true de novo genes according to her strict criteria 1. Saccharomyces cerevisiae MDF1 Originated de novo within the last few million years. Represses expression of genes in the mating pathway. 2. Sacchromyces cerevisiae  BSC4  First de novo gene subjected to experimental structural characterization 3. Homo sapiens PBOV1 Found in an intron of the conserved gene BIG3, on the opposite strand. Originated de novo in humans or hominid primates. Over expressed in various cancers. 4. Homo sapiens  NYCM Overlaps the well known oncogene MYCN. Likely emerged either uniquely to humans or prior to the split with chimpanzees. It is arguably the best experimentally characterized of all the de novo genes. Contributes to oncogenesis.  5. Homo sapiens  MYEOV Role in cancers.  6. Homo sapiens  ELFN1-AS1 RNA gene unique to humans, in the intron for conserved gene ELFN1 Promotes various cancers by increasing cell proliferation.  7.  Mus musculus Poldi Noncoding RNA in several Mus  species likely emerged around 3 million years ago. It is expressed in the post meiotic round spermatids. She goes on to note: Much of the noncoding DNA is subject to a low rate of reading, called pervasive and promiscuous transcription and translation. Some of these random sequences do actually produce products that have surprisingly similar structural features shared by known proteins. Related work has often found intergenic open reading frames which can provide raw material for de novo  genes to arise. A “transmembrane-first” model is the first proposed cell biological mechanism for de novo  gene birth. Two genes, MYEOV and MDDF1 act as transcription factors by dimerizing with conserved transcription factors that under different conditions have different binding partners. They then drive expression of the same promoters but under different conditions. (9)  This is considered by some to be a program primarily used in development which is then reactivated in cancer, allowing mature tissues to aberrantly migrate and metastasize. Others of these genes aberrantly activate other pathways used elsewhere in normal physiology, like TGF-B signaling… New proteins may generally find it easy to flip all kinds of cellular switches; cancer may often be the result she notes (9). Cancer and Evolution Note that many of the new genes Weisman lists above are associated with cancer. The role evolution plays as a model for cancer can’t be under appreciated. It would be interesting if there are  any anti-evolutionists who study cancer at the molecular level. The word cancer comes from a transliteration of the Greek word for crab in Latin. It is a term used since Hippocrates to denote types of tumors that show abnormal growth in the shape of a crab. Today we also have the words carcinogen and carcinoma. In astrology it is the fourth sign of the Zodiac and it also refers to a constellation. The study of cancer can give us great insights into evolution since cancer begins from a few mutations in a single normal behaving cell and then begins to develop more mutations in a nested series that adds new genes (A, A+B, A+B+C,…) and functions to a mass of cells that goes rogue, growing according to principles of natural selection (some mutated cells are better at surviving and reproducing than others). It leaves a record of the mutations that resemble evolutionary trees in biology and researchers can work backwards to know when in the tumor growth for example a mutation occurred and spread.  It is not evolution per se, but rather a model of what happens on a species population level as new genes form and can be selected. A cancer that begins as a cell disobeying its host constraints, must develop new genes and functions to avoid the body’s immune system, often the ability to move to other parts to invade (metastasize), and the ability to outcompete normal cells for nutrients and other cells and tissues. It did not have these functions before mutating them. Yes, random mutations can generate new genes with new functions. “Evolutionary theory “makes sense” of cancer, giving us critical insight into how it works. This has become particularly clear in recent years. Now, we can sequence all the genes in a patient’s cancer, and see how they change over time as cancer evolves. Cancer evolves with the same evolutionary mechanisms that drive the evolution of new species. Like breadcrumbs marking a path through a forest, cancer evolution leaves information in cellular genomes that evolutionary theory can decode. Going the other direction, cancer makes sense of evolution too. Cancer itself is not evolution at the species level. However, it validates the mathematical framework underlying modern evolutionary theory. Cancer cells evolve multiple new functions in an evolutionary process, creating precise genetic signatures of common descent. At both a genetic and functional level, cancer follows patterns explained by evolutionary theory…In cancer… we can directly verify that evolutionary theory correctly reconstructs a cancer’s history, including its ancestry. We see all the same patterns in cancer evolution that we do in the evolution of species: neutral drift, nested clades, novel functions, and positive selection. The same math, software, and theory that is used to study the evolution of species works for cancer too. From a biological point of view, it is now clear that cancer is an evolutionary disease. Cancer biologists use evolutionary theory because it is useful and accurate, not because they are pushing an “evolutionary agenda.” In cancer, cells evolve a set of new functions. These functions are beneficial to the cancer cell, but ultimately lethal to their host. And cancer must do much more than just grow quickly.  Nonetheless, in all cases, more than just rapid growth is required for cancer to develop. Several new functions are required. Ultimately, many cancers will acquire more than ten beneficial (to the cancer cell) mutations that enable these new functions. Evolution, it turns out, is a much more useful framework for understanding cancer. From the cell’s point of view, cancer is evolving new functions in the environment of the host’s body. It evolves these functions in an evolutionary process. Cancer exists only because biological systems, including humans, have the intrinsic ability to evolve.”  ~ Joshua Swamidass, MS, MD, PhD. Associate Professor of Laboratory and Genomic Medicine, the Washington University School of  Medicine in St. Louis. From the blog, this site :  Evolutionary Medicine. Is it important? A Tale of Two Fishes*  No discussion of new genes and new functions arising naturally would be complete without talking about the anti-freeze adaptation found in some fishes. And yes, in science when talking about more than one species of fish, it’s fishes.  Notothenoid fishes (Southern Ocean) It has been known for many years that some fish species in the arctic and antarctic regions survive subfreezing temperatures through the use of anti-freeze like glycoproteins ( afgp s). These proteins bond with any ice forming in the fishes and stop the crystals from connecting to other ice crystals by lowering the freezing point of body fluids. One of the first groups studied were the predominate group of notothenoid fishes of the antarctic (southern) ocean. In 1997 Chen et. al. worked out the evolution of these afgp s. “We have found that the antifreeze glycoproteins (AFGPs) of the predominant Antarctic fish taxon, the notothenioids, evolved from a pancreatic trypsinogen… The primordial AFGP gene apparently arose through recruitment of the 5′ and 3′ ends of an ancestral trypsinogen gene, which provided the secretory signal and the 3′ untranslated region, respectively, plus de novo amplification of a 9-nt Thr-Ala-Ala coding element from the trypsinogen progenitor to create a new protein coding region for the repetitive tripeptide backbone of the antifreeze protein.” (12). Note that this is mostly the typical gene duplication method of producing a new product from a previous gene discussed earlier. In this case the original gene was specialized as a pancreatic enzyme.  Sequence divergence between the ancestral pancreatic trypsinogen gene and the afgp s according to the researchers indicated an origin of the antifreeze gene of around 5 - 14 million years ago. A much more recent 2023 paper by Bista et. al. looking at 24 species of the Notothenioidei fish group allowed them to narrow the radiation of this group to 10.7 million years ago origin. Genomic evaluation of the afgp  expansion revealed a very complete reconstruction of the radiation of these fish species by comparing the antifreeze glycoprotein gene families (13). This period corresponds to paleoclimatic changes appearing at that time. Global cooling and polar icecap formation was occurring due to the separation of the Antarctic continent from surrounding land masses and the subsequent establishment of the Antarctic Circumpolar Current (ACC) (13). Note that this is another way evolutionary theory reconstructs the past well, combining plate tectonics, continental drift, paleoclimatic changes, and species radiation through the understanding in this case by using comparative genomics of antifreeze proteins in a group of fishes! Codfishes (Arctic Ocean) In studying the Atlantic codfish’s evolved antifreeze protein researchers were surprised to find that instead of its origin being in gene duplications from existing genes as in the notothenioids, “this protein had seemingly been built from scratch, from desolate stretches of the genome that do not code for functional molecules.” This species, Gadus morhua , had an antifreeze protein that was produced from a de novo  gene. (15). Baalsrud et. al. determined that the afp  in Codfish was de novo  and not from duplications by several findings (14): First, they performed a BLAST and did not get any hits against any part of the afgp  in genes or ORFs (open reading frame) in high quality codfish genomes. Neither did they get hits in Uniport, the Ensembl genomes, or Genbank. The gene is an orphan gene.  Secondly, de novo genes are more likely to arise in GC-rich genomic regions as these regions are more active in transcription and more likely to obtain an ORF because of stop codons that are AT-rich. GC content in the afgp copies was as high as 76% vs. 56% on average for all genes in the G. morhua  genome assembly. Third, they calculated codon usage and there was a significant bias for the amino acids in the repeats across all the afgp s in the codfish species being investigated. “This finding, together with the afgps on a single linkage group with well conserved synteny between the G. morgue and M. aegllefinus strongly suggests common origin of codfish afgps, with subsequent gene duplications.” Fourth, a protein translated from non-coding DNA is intrinsically more disordered. They used a program to determine intrinsic structure disorder (ISD) for all four functional afgps  in G. morhua. The values for disorder (.68 and .75) were much higher than the average mean ISD for all the annotated genes in the G. morhua genome of .36. Summary: Antifreeze fishes Research has shown that the antifreeze proteins found in the antarctic fish Notothenioidei evolved mostly by gene duplications, although even in this gene there is a  de novo  amplification of a 9-nt Thr-Ala-Ala coding element from the trypsinogen progenitor. Conversely, in the northern arctic areas codfish antifreeze proteins evolved by de novo gene formation followed by gene duplications. The evolution of these proteins allowed various species of fish in sea regions that were now experiencing freezing temperatures to remain as continental movements and changing paleoclimate forced other tropical species to move out, leaving open niches for the remaining fish species to fill who could succeed in a harsh environment. The evolution of afp s coincided with paleoclimatic changes that produced ice and glaciers near the poles millions of years ago. In the past 10 years researchers have found numerous newly minted de novo  genes including in fruit flies, mice, humans and important crop plants so de novo gene evolution may not be as rare as researchers thought in the past. (15). “De novo gene origin has recently become more widely recognized as a regular source of new genes (Tautz and Domazet-Lošo 2011; Wu et al. 2011; McLysaght and Guerzoni 2015; Schlötterer 2015; McLysaght and Hurst 2016), which often encode novel functions representing lineage specific adaptations to the environment (Khalturin et al. 2009; Tautz and Domazet-Lošo 2011)." (14) Rives, et. al. (Sept. 2024)  analyzed were able to expose how how fish antifreeze proteins evolved through de novo production and duplication. " Diverse Origins of Near-Identical Antifreeze Proteins in Unrelated Fish Lineages Provide Insights Into Evolutionary Mechanisms of New Gene Birth and Protein Sequence Convergence. " https://academic.oup.com/mbe/article/41/9/msae182/7746024?login=false They note: " Each lineage independently evolved a de novo coding region for the novel ice-binding protein while repurposing fragments from their respective ancestors into potential regulatory regions, representing partial de novo origination - a process that bridges de novo gene formation and the neofunctionalization of duplicated genes. The study supports existing models of new gene origination and introduces new ones: the innovation-amplification-divergence model, where novel changes precede gene duplication; the newly proposed duplication-degeneration-divergence model, which describes new functions arising from degenerated pseudogenes; and the duplication-degeneration-divergence gene fission model, where each new sibling gene differentially degenerates and renovates distinct functional domains from their parental gene." *Note   - the evolution of antifreeze proteins has actually occurred in many species, and not just fish. “… the evolution of the antifreeze proteins (AFPs), which have evolved independently in bacteria, plants (≥ four times), fungi, insects (≥ two times), and teleost fish (≥ seven times) (Cheng 1998; Ewart et al. 1999; Harding et al. 2003; Bildanova et al. 2013; Gupta and Deswal 2014) (14). Many of you may have noticed that anti-freeze proteins are a fantastic example of convergent evolution across many varied species. My apologies to Charles Dickens for attempting to have some increased credibility bestowed upon this humble author by indirectly, and hopefully not inappropriately, associating the story of ice fish evolution with a famous book.  Proto-Genes Ideally, if genes were forming de novo  it would be nice to see early steps and transitions: pre-genic DNA coming together in the forms of proto-genes. This has been noted in the E. coli  Long-Term Evolution Experiment (LTEE). Researchers noted how proto-genes originated by starting in one of two acquisitions. They wrote, "... we identified instances of proto-gene emergence in which a previously unexpressed sequence was transcribed after formation of an upstream promoter. Tracing the origin of the causative mutations, we discovered that most occurred early in the history of the LTEE, often within the first 20,000 generations, and became fixed soon after emergence. Our findings show that proto-genes emerge frequently and within evolving populations, persist stably, and can serve as potential substrates for new gene formation. " (16) This is shown graphically below: From: Genes From The Junkyard. Adam Levy. Nature, vol 574, Oct. 17, 2019.Fair use attribution. For educational purposes only. (15) Conclusion Even the most fundamentalist anti-evolutionist who believes the entire human population at one time along with all the terrestrial animals were wiped out and then rebooted from only a few pairs of “kinds" on a boat a few thousands of years ago understands that natural selection is intuitive. Various pressures on populations of animals and plants will result in the most fit for survival and reproduction leaving more offspring to the next generation on average and populations will thus evolve to fit the present circumstances of that species. If shifts occur in the environment for example, the species can adapt.  Unless those shifts are too sudden and strong (asteroids), or the species does not have the variations needed, or perhaps the species became too specialized and runs out of options, the species can evolve to meet the changes. This has been called “microevolution” and no one rejects this who understands it. Evolution has been defined since at least the 1940s as the change in gene frequencies or alleles in a population over time. See Evolution, this site . We see that every day in the lab, field and in medicine. Even those few “kinds” coming off a boat at one time had to evolve into the millions of flora and faunal species we see today in only a few hundred years (never mind that this is impossible rationally).  What about large scale changes like we see in the fossil record, a nearly 15,000 ft collection of sedimentary rock showing changes from simple to complex as in layers of a massive tall cake with no mixing and lots of transitional fossils? That faunal succession would need new information, new genes to produce very different phenotypes, structures, and biochemical pathways. If “macroevolution” is true then where did the new genes come from to make those new adaptations? Scientists have identified five major methods for new genes to arise: duplications and then new functions off the copied genes, lateral gene transfer from outside the organism, gene fusions and fissions,  co-option of transposons, and with some surprise, de novo  genes. The last category is important because it negates the criticism that is often brought forward by creationists and anti-evolutionists that the others only operate from pre-existing genes. This article has shown that nature can and does generate functional genes from non-gene, non-coding raw DNA material. It is thus a false statement to say new genes, new information for various selection forces can’t arise through natural means only. This final objection to evolution attempting to negate variation sources for natural selection and other mechanisms to push “macroevolution” changes can be dismissed. Together with the newer DNA findings that rise to the level of proof of human evolution and macroevolution, there are no intellectually honest viable objections to evolution remaining. Random mutational activity is demonstrated to produce the raw material for evolution. Random changes to our genomes that are shared by other species rises to the level of proof that macroevolution, human evolution is a fact. See The Demise of Evolution Objections.  The theory of Evolution, that which explains the origin of species, has passed every challenge and test to it for 150 years and grows stronger with passing time. For human interests, how we got here, when, from what and from where goes a long way to explaining the “why’s” of life and its many existential questions.  Notwithstanding, discovering perhaps the most amazing true, and fascinating story  ever revealed has value in its own right. Literature cited  1. Behe, Michael J. 2019. Darwin Devolves . HarperCollins, New York, NY 10007. Paperback, 2020. 342 pp.  2.  On the Origin of New Genes and Pseudogenes.  https://www.nature.com/scitable/topicpage/origins-of-new-genes-and-pseudogenes-835/ 3. Finlay, Graeme. 2021 (paperback). Human Evolution: Genes, Genealogies and Phylogenies.  Cambridge University Press. University Printing House, UK. 359 pp.  4. Venom evolution through gene duplications.  https://www.sciencedirect.com/science/article/abs/pii/S0378111912000388 5. Gene Genesis: Scientists Observe New Genes Evolving From Mutated Copies.  https://www.scientificamerican.com/article/gene-genesis-scientists/ 6. Real-Time Evolution of New Genes by Innovation, Amplification, and Divergence. https://www.science.org/doi/abs/10.1126/science.1226521 7. Witnessing the Birth of human-specific genes https://thehumanevolutionblog.com/2023/01/26/witnessing-the-birth-of-human-specific-genes/ https://onlinelibrary.wiley.com/doi/abs/10.1002/ajpa.24504 7a . New genes found that can arise "from nothing" https://phys.org/news/2023-12-genes.html?fbclid=IwAR3auKKirGzwBN0VHc4xC1-ZZQPs2XR_wNoELyAvS4tiX6nTOkDhucS12X4https://phys.org/news/2023-12-genes.html?fbclid=IwAR3auKKirGzwBN0VHc4xC1-ZZQPs2XR_wNoELyAvS4tiX6nTOkDhucS12X4 8. Genomic study sheds light on how carnivorous Asian pitcher plants acquired signature insect trap. https://www.buffalo.edu/news/releases/2023/11/how-carnivorous-Asian-pitcher-plants-acquired-signature-insect-traps.html 9. The Origins and Functions of De Novo Genes: Against All Odds? https://link.springer.com/article/10.1007/s00239-022-10055-3 10. Genetic error led humans to evolve bigger more vulnerable brains https://projects.research-and-innovation.ec.europa.eu/en/horizon-magazine/genetic-error-led-humans-evolve-bigger-more-vulnerable-brains 11. Two step mutations to rewire a regulatory network via natural selection https://www.science.org/doi/10.1126/science.1259145 https://www.the-scientist.com/evolutionary-rewiring-35878 12. Evolution of antifreeze glycoprotein gene from a trypsinogen gene in Antarctic notothenioid fish. https://www.pnas.org/doi/full/10.1073/pnas.94.8.3811 13. Genomics of cold adaptations in the Antarctic notothenioid fish radiation. https://www.nature.com/articles/s41467-023-38567-6 14. De Novo  Gene Evolution of Antifreeze Glycoproteins in Codfishes Revealed by Whole Genome Sequence Data.  https://academic.oup.com/mbe/article/35/3/593/4693805 15. Genes From the Junkyard. Levy, Adam https://www.nature.com/articles/d41586-019-03061-x.epdf?no_publisher_access=1&r3_referer=nature https://www.nature.com/articles/d41586-019-03061-x#correction-0 16. Promoter capture drives the emergence of proto-genes in  Escherichia coli https:// www.biorxiv.org/content/10.1101/2023.11.15.567300v1.full 17. The End of Evolution? A biochemist's crusade to overturn evolution misrepresents theory and ignores evidence. https://www.science.org/doi/10.1126/science.aaw4056

"The current understanding of science holds that spacetime began to exist when the universe began to exist. It is meaningless to ask what came before the Big Bang, in the same sense that it is meaningless to ask what is south of the South Pole." ~ Dave Muscato “More than half of our neighbors believe that the entire universe was created six thousand years ago. This is, incidentally, about a thousand years after the Sumerians invented glue.” ~ Sam Harris [less than half by now] This discussion will briefly address why anti-evolutionists are so excited about the Big Bang as evidence for a Designer and why they often believe that the multiverse concept is just an attempt by many scientists to avoid the contention that the Big Bang logically points to a Designer. A disclaimer - I have no educational background in cosmology but have been following this aspect of cosmology for many years and hope that I at least understand the main issues. A. The Big Bang Most physicists and cosmologists in the 19th and 20th centuries, including Einstein, viewed the universe in a static state or steady state condition. Although it had been observed since 1912 that galaxies (at that time called nebula because telescopes were not strong enough to reveal they were really galaxies and not globs of gas/dust) were receding from earth, the importance of this observation was not appreciated. In 1924 Hubble observed that these nebula were actually other galaxies outside our own and by 1927 he had formulated a law to describe how fast they were moving away from us. A Belgian Roman Catholic priest and physicist, Georges Lemaître, working with mathematical equations showed that the universe was actually expanding. Fred Hoyle, who was a proponent of the steady state model, described during a BBC interview in 1949 this expansion theory as “The Big Bang” and the name stuck. Gradually over the decades observations such as the Cosmic Microwave Background Radiation (CMB) in 1964 , galaxy formations, and mathematical models supporting the Big Bang all coalesced into convincing support for the theory. It is now accepted that the Big Bang occurred 13.8 billion years ago. A major advancement was the development of inflation by Guth from theoretical mathematics that solved some problems with the Big Bang Theory(1). There are several major misconceptions about the Big Bang. First, it was not an explosion like we experience explosions on earth. Rather, the observable universe is expanding and carrying galaxies with it. This very brief expansion period is known as inflation and is integral to the Big Bang Theory but also as we will see is critical to the Multiverse idea. This is also why the galaxies are not only moving away from us but counterintuitively, accelerating. Another misconception is that the Big Bang explains the origin of the universe. However, it does not explain the origin of energy, space and time. Current calculations place the observable universe with a diameter of 93 billion light years and age of 13.8 billion years. Note this is not what we can observe but rather what is the physical limit the speed of light produces for the theory (2). The reason many love the Big Bang is they think it points to a beginning, not an infinite state, and that this confirms many views. This expectation is summarized in the Cosmological Argument but more specifically the Kalam Cosmological Argument where since everything is said to have a cause the universe must have been caused. My simplified rendition: Things are always caused by something The Universe began at the Big Bang The Universe was thus caused by something The best explanation must be an Intelligent Agent But as I will now show, it’s not at all clear that the Big Bang was the start of the universe. An infinite universe is also possible. Questions then arise. What is the universe expanding into ? Furthermore, what caused inflation? Well, it turns out that it is entirely possible that our universe could be infinite and the Cosmological Arguments must now be suspended. “Our current cosmological model does an excellent job describing the universe down to the first fraction of a second. It is only a tiny fraction of a second where our theoretical models break down: physics becomes very different from anything we could build an experiment for here on earth and we also struggle to look back this far since our view is obscured by things like the Cosmic Microwave Background. But just because a tiny fraction of a second seems small on a human timescale that doesn't mean there isn't a lot of room for a lot to have happened back then that we don't yet know about: maybe our universe started from nothing, maybe it bounced back from a previous universe or started from within another. We don't even know if our universe is a finite size or infinite. All we are pretty confident about so far is that our universe has been expanding for many billions of years. When we extrapolate backward the entire part of the universe that we can observe today was converged to a single point around 14 billion years ago. Time is a concept that works great in our daily life but there are limits to it… So when we say before the big bang, we can not just assume that something like "a second before the big bang happened" has to make sense. For example, the future can be infinite, a clock ticking forever, I don't need to imagine anything beyond that. In the same way in the early universe density diverges and the concept of time can stop existing as we reach time zero, there does not have to be a before.” (4) From Karen Masters: “ We can define the universe as everything there is, so in that case there is nothing outside of it. We also say that space and time both started at the Big Bang and therefore there was nothing before it. Another definition for the universe is the observable universe - which is the part of it that we can technically see. We cannot know what is outside of that (since we can't observe it), but we think that physics works the same everywhere and so we think that it should be very similar to the observable universe. We actually think that the universe might be infinite in extent, and so goes on forever, even though we can only see a finite part of it. We can speculate in meta-physics or in religion about what was before the Big Bang, but again, we cannot use science to tell anything about it as physics as we understand it breaks down at that point.” (5). As Pandian writes, things in theoretical physics can become very strange and as the video below by Physics Girl also explains: “ As to where everything came from, there is no conclusive opinion. One idea was that the Universe was created from vacuum. This is because according to quantum theory, the apparently quiescent vacuum is not really empty at all… Such [quantum] vacuum fluctuations cannot be observed directly as they typically last for only about 10-21 seconds and the separation between the electron and positron is typically no longer than 10-10 cm. However, through indirect measurements, physicists are convinced that these fluctuations are real… In 1982, Alexander Vilenkin proposed an extension of Tyron's idea and suggested that the Universe was created by quantum processes starting from "literally nothing", meaning not only the absence of matter, but the absence of space and time as well.” “Another idea is from Stephen Hawking and James Hartle. Hawking proposed a description of the Universe in its entirety, viewed as a self-contained entity, with no reference to anything that might have come before it. The description is timeless, in the sense that one set of equations delineates the Universe for all time… In Hawking's words, the Universe "would neither be created nor destroyed. It would just BE”… So, the origin of mass in the Universe and the Universe itself is quite speculative at this point.” (6) Important short fun 10 min. video to update us on cosmological understandings - and misunderstandings. Please watch! And you may never look at raisin bread the same way again. https://www.youtube.com/watch?v=I9q-7GPQr1Y Very probably no singularity - https://bigthink.com/starts-with-a-bang/big-bang-beginning-universe/ The start of our universe - 2 interpretations Either the Big Bang was the start of the universe or it was not but was preceded by a period of inflation. It turns out there is a way to test which origin explanation is true. "As you can clearly see, there can be no doubt that there truly are super-horizon fluctuations within the Universe, as the significance of this signal is overwhelming. The fact that we see super-horizon fluctuations, and that we see them not merely from reionization but as they are predicted to exist from inflation, is a slam dunk: the non-inflationary, singular Big Bang model does not match up with the Universe we observe. Instead, we learn that we can only extrapolate the Universe back to a certain cutoff point in the context of the hot Big Bang, and that prior to that, an inflationary state must have preceded the hot Big Bang." https://bigthink.com/starts-with-a-bang/evidence-universe-before-big-bang/ There was a universe before the Big Bang. And has been noted above, an infinite universe cannot be ruled out. The Cosmological Argument for God thus rests on an unproven premise and should be discarded at this time. Ethan Siegel - What is our universe expanding into? https://bigthink.com/starts-with-a-bang/what-universe-expanding-into/ "John Lennox always uses the argument that because science supports Genesis 1:1 with there being a beginning of the universe. That’s a terrible argument because: 1. Correlation does not imply causation: Even if science confirms the universe had a beginning, it doesn't necessarily validate the Genesis account. Other natural explanations, like the multiverse hypothesis or quantum fluctuations, could be responsible. 2. Genesis 1:1 is too vague: The verse "In the beginning, God created the heavens and the earth" is too broad to be considered a scientifically accurate description of the universe's origin. 3. Scientific and biblical timelines contradict: The Genesis account suggests a young Earth, while scientific evidence indicates an approximately 13.8 billion-year-old universe. 4. Lack of empirical evidence: There's no empirical evidence to support the supernatural claims made in Genesis, unlike scientific theories, which are testable and falsifiable. 5. Cherry-picking: Lennox selectively uses scientific findings to support his religious agenda while ignoring contradictory evidence and the broader scientific consensus. 6. Misinterpretation: He misinterprets the Genesis account as a scientific text, rather than a theological or mythological one, which is its intended context. 7. God of the gaps: Lennox invokes God to explain the universe's origin, but this is a classic "God of the gaps" fallacy, where divine intervention is used to fill gaps in scientific knowledge. 8. Unfalsifiable claims: Religious claims, like those in Genesis, are unfalsifiable and untestable, unlike scientific theories, which are open to revision or rejection based on new evidence. Lennox's argument and demonstrate that the origins of the universe are still best explained by scientific inquiry, rather than religious doctrine. In other words, Lennox doesn’t know what he’s talking about when it comes to the beginning of the universe." ~ David Eugene Fitzgerald, FB post, July 27, 2024. How vs. What and Einstein? Scientist : Einstein's theory of general relativity has been validated and corroborated by evidence. Critic : Einstein's theory of relativity cannot be valid until you explain the origin of space-time. Scientist : Listen, there is evidence for this theory, let's talk about that. Critic : If you cannot explain the origin of space-time, your theory is false, because where did the space-time needed by general relativity come from ? It's a religion because you can't explain the origin of space-time ~Adeleke Emmanuel Oluwasegun Brian Cox Explains that the universe can be eternal.  He then discusses his confusion how this upsets some people: https://www.facebook.com/reel/1272367077542530 Summary My point is that we don’t know if the universe is finite or infinite. We don’t know what came before the Big Bang other than inflation and neither do the theologians nor philosophers. And to suggest that it must be an Intelligent Designer is just another example of a God of the Gaps Argument (logical fallacy) which has a terrible track record with science, forever shrinking in the face of ongoing scientific research and discoveries. Anti-evolutionists are no longer justified in making this inference. If they were honest the Cosmological Argument and it’s offspring the Kalam Cosmological Argument should be put in a box to be discussed later if an infinite universe is someday ruled out. If it is finite there still may be natural explanations. Citations for section A 1. Big Bang. https://en.wikipedia.org/wiki/Big_Bang#cite_note-penzias-78 2. Misconceptions. https://en.wikipedia.org/wiki/Observable_universe 3. What was there before the Big Bang? http://curious.astro.cornell.edu/the-universe/cosmology-and-the-big-bang/101-the-universe/cosmology-and-the-big-bang/general-questions/1098-but-seriously-what-was-there-before-the-big-bang-beginner 4. What was there before the Big Bang? http://curious.astro.cornell.edu/the-universe/cosmology-and-the-big-bang/101-the-universe/cosmology-and-the-big-bang/general-questions/585-what-was-there-before-the-big-bang-and-what-is-there-outside-of-our-universe-beginner 5. Where did the universe come from? http://curious.astro.cornell.edu/the-universe/cosmology-and-the-big-bang/101-the-universe/cosmology-and-the-big-bang/general-questions/572-where-did-the-universe-come-from-intermediate 6. How small was the universe at the start of the Big Bang? [never was a singularity] https://www.forbes.com/sites/startswithabang/2021/08/25/how-small-was-the-universe-at-the-start-of-the-big-bang/?sh=35a8618e5f79 7. Yes, the universe is really 100% reductionist in nature. https://bigthink.com/starts-with-a-bang/universe-reductionist/#Echobox=1690577002 B. The Multiverse The anti-evolutionists I have interacted with often think that scientists desire to never admit the possibility of a universe beginning and that the multiverse is a way for science to deny that the universe had a beginning; the multiverse then amounts to an excuse for scientists to supposedly move past the Cosmological Argument. Never mind that in America at least, a significant percentage of scientists are theists. My limited reading however is that the multiverse falls out of equations for inflation, which was briefly detailed in part A of this posting, and is supported and integral to the Big Bang Theory. It is not just something science imagined to avoid the Big Bang as an origin to the universe. As Ethan Siegel writes : “ One of the most successful theories of 20th century science is cosmic inflation, which preceded and set up the hot Big Bang. We also know how quantum fields generally work, and if inflation is a quantum field (which we strongly suspect it is), then there will always be more "still-inflating" space out there. Whenever and wherever inflation ends, you get a hot Big Bang. If inflation and quantum field theory are both correct, a Multiverse is a must.” “That’s what the multiverse is, and why scientists accept its existence as the default position. We have overwhelming evidence for the hot Big Bang, and also that the Big Bang began with a set of conditions that don’t come with a de facto explanation. If we add in an explanation for it — cosmic inflation — then that inflating spacetime that set up and gave rise to the Big Bang makes its own set of novel predictions. Many of those predictions are borne out by observation, but other predictions also arise as consequences of inflation.” (7) “ This picture, of huge Universes, far bigger than the meager part that's observable to us, constantly being created across this exponentially inflating space, is what the Multiverse is all about. It's important to recognize that the Multiverse is not a scientific theory on its own. It makes no predictions for any observable phenomena that we can access from within our own pocket of existence. Rather, the Multiverse is a theoretical prediction that comes out of the laws of physics as they’re best understood today. It’s perhaps even an inevitable consequence of those laws: if you have an inflationary Universe governed by quantum physics, this is something you’re pretty much destined to wind up with.” “It's possible that our understanding of the state before the hot Big Bang is incorrect, and that our ideas about inflation are completely wrong for this application. If that's the case, then the existence of a Multiverse isn't a foregone conclusion. But the prediction of an eternally inflating state, where an uncountably large number of pocket Universes are continuously born and driven inextricably apart from one another, is a direct consequence of our best current theories, if they're correct.” (8) Brian Cox discusses the Big Bang and the Multiverse concept here: Conclusion Our universe may indeed by infinite or finite. If infinite, the Cosmological Argument fails. The Big Bang is strongly supported by science but says nothing about what came before or why it started. These unknowns negate alternative arguments through logical inferences because the premises are not established as claimed, or are falsified. The Big Bang does not by default support only a universe that had a beginning. If the Multiverse is true, then again the Big Bang Theory may indicate infinite universes. An important observation from Sabine Hossenfelder is that the Multiverse is not a scientific theory and it’s also not even a scientific hypothesis because to date there is no way to test it. It is a theoretical prediction from inflation where inflation is integral to the Big Bang Theory. It is beyond irony that some embrace the Big Bang which depends on inflation while trying to diminish the multiverse idea which is a direct consequence of that same inflation. Citations for section B 7. Why the multiverse is suspected https://bigthink.com/starts-with-a-bang/physicists-multiverse-exists/ 8. The Multiverse is Inevitable https://www.forbes.com/sites/startswithabang/2017/10/12/the-multiverse-is-inevitable-and-were-living-in-it/?sh=55fc36f016c9

"To conclude: our genome contains thousands of disabled genes... When multiple species share one of these mutations, it is only because they have inherited it from the reproductive cell in which the unique mutation occurred. The burgeoning scientific field of pseudogenealogy establishes the concept of common descent in a way that would have been inconceivable before the DNA sequencing revolution. Humans and the other apes have common ancestry". ~ Graeme Finlay Biological Plagiarisms as a model I had a friend who used to work for Intel, the giant chip maker. He (B.D.) related to me that the company purposely put some error codes in their chips. Why? Because if a competitor copied their chip and claimed that they did not copy Intel’s chips but developed the same approaches separately due to common design constraints, the competitor would need to explain why they had the same exact errors in their chips in the same locations. Claiming “common design”, that they just happened to arrive at the same solution and code would not explain the same exact unique errors. Textbook publishers sometimes purposely put in errors for the same reason. To prove that a competitor copied their work and did not arrive at the same “design” independently. Rather, it was “common ancestry” - in this case the competitor’s work was derived and copied from the original. A last example is a teacher teaching an online course involving students from all over the world. If the teacher is grading papers and two papers come in from students who claimed they did not communicate with each other, but there are large sections of the exact same sentences and paragraphs in their papers, the teacher knows the students derived their papers from the same online source. The two papers were not derived independently; they shared the same origin and had a common literary ancestor because they contained the exact same errors. Those papers were not original to the students. It was not “common design” but rather “common ancestry or descent” - in this case the Internet. And if those two papers even had the same errors that were missed in the on-line source, then there is no question they used the same source. The use of errors in original work to expose competitor’s copying has been upheld in court. When it comes to shared errors, common design as an explanation for similar DNA characteristics between species utterly fails. It must be common ancestry, common descent. If you have read this web site, you will see that this same principle holds true with shared ERVs that insert randomly and are found in the exact same locations between species, or with shared DNA breaks & repairs (because the patches are unique). Since the retroviruses insert randomly and that’s been demonstrated, when we find identical 200,000 ERVs (mostly as LTRs) in the exact same positions in the DNA between two different species, we can be sure that the resultant ERVs formed because the retroviruses inserted before the species split. See ERVs, this site. There is no other rational explanation. Likewise, the finding of shared DNA scars between two species that involve random DNA damage and random emergency patching leaves one with only one rational explanation - common descent, or evolution. There is yet a third area of DNA findings that provides solid robust evidence of evolution, human evolution and macroevolution, and those are pseudogenes. What are pseudogenes? The human genome contains about 3 billion base pairs, the ATCG nucleotide "letters". Only 1.5% of those are protein coding genes, and they number about only 20,000. Scientists studying our genomes have discovered about 20,000 genes that are also disabled, corrupted and no longer function or perform their original functions. They have been deactivated by various mutations such as stop mutations (codons), deletions and insertions, frameshift destruction, and the loss of regulatory sites. These are called pseudogenes. Some are the original genes but most are copies. Some are functional or partially functional, as they can be partially transcribed. Some have even been able to take on new functions. There are three main types of pseudogenes, but the vast majority fall into only two categories. One type is called duplicated pseudogenes . They result when large parts of DNA are duplicated producing segmental duplications and within the large sections a gene is also swept up and caught and duplicated. Large duplications are not uncommon; many of these segmental duplications lead to genes that become cancerous. In some plants the entire genome was duplicated in the past. Since it’s a duplicate, a pseudogene is often not needed by the host and is not maintained but decays to the point where it no longer can produce a product from the original parental gene. Less likely in evolution, some duplicated genes can undergo changes and even develop new functions. The second major type are called a processed pseudogene. These are derived from parental genes by an RNA intermediate. Note that this is similar to how transposable elements (TE) jump around the genome. They arise because TE-encoded enzymes randomly select RNA transcripts of genes and copy them, convert them to DNA, and insert them back into the genome (1). These RNA copies are at least partially processed (for example by having their introns cut out; exons are the parts left over that go on to code for proteins). Nearly all of the pseudogenes are evenly distributed between these two types. The third type is not nearly as common and are called unitary pseudogenes . Unlike the other two types that involve damage to copied genes, this is where a single gene, the original, is damaged. Confusion in the Literature Pseudogenes may develop new functions “... but they are defined by their loss of the original parent gene function and not whether they have functions or not currently.” (Finlay, 1). Confusion arises when people assume that pseudogenes can’t have functions (2, 8). Indeed, a few pseudogenes have been noted to exhibit gain of function as noncoding RNAs (3). If one only includes pseudogenes that have no known function some will claim there are only about 12,000 pseudogenes but as Finlay and Moran point out, that is not how pseudogenes are defined. We know some pseudogenes have gained new functions or are partially transcribed because the gene has only been partially disabled. That however, does not negate the fact they have lost their original function : they are pseudogenes. Moran makes these points in his blog: “The idea that most duplicated genes will become pseudogenes is consistent with a ton of data and fits well with our understanding of mutation rates and genome evolution. This is an important point. We don't arbitrarily assign the word "pseudogene" to any old DNA sequence. The designation is based on the fact that the duplicated region is no longer transcribed, or it is no longer correctly spliced, or that it carries mutations rendering the product nonfunctional. (In the case of protein-coding genes it could be that the reading frame is disrupted.) It's also important to understand that the frequency these inactivating mutations and the rate of fixation of the resulting allele is perfectly consistent with everything we know about molecular evolution. There are some examples of DNA sequences that appear to be pseudogenes but they also have functional regions. The best examples are duplicates that contain small RNA genes within their introns or genes that contain other functional regions like SARs and origins of replication. In those cases, the inactivated gene is still a pseudogene but the other functional regions are best characterized as something else. There are also quite a few examples of pseudogenes that have secondarily acquired a distinct new function such as producing a small RNA that might have a regulatory function. The review by Cheetham et al. contains several examples of such pseudogenes. They are still pseudogenes but the region may now specify a new lncRNA gene or some other gene such as an siRNA gene.” (4) Pseudogenes: molecular fossils If we look around at various species we find all kinds of damaged and dead genes that once produced viable products or are suppressed because their regulatory genes are damaged. Chickens still have the genes for making teeth and a tail (5,6). Baleen whales per my Part 1 whale evolution video make teeth buds as a fetus and have pseudogenes for making teeth enamel. Of course adult baleen whales do not have teeth. We know however from paleontology that they evolved from toothed whale ancestors and are not surprised that they still make teeth during fetal development. Placental animals without teeth such as anteaters, tree sloths and armadillos still have the pseudogenes for making teeth enamel. Under the right conditions, snakes can grow legs and cavefish can grow eyes their ancestors had (6). Sperm whales grow atavistic hind legs in about 1:5000 births (15). The DNA is there, but the genes or regulatory sequences are damaged or turned off. Sometimes it can be exposed. It makes no sense unless evolution is true that species would have the DNA instructions to make ancestral structures (atavisms) that they will never use or supposedly never had in the first place. Humans have about 850 genes that code for olfactory receptors. Over half are knocked out and disabled (14). Although all primates have several hundred functioning olfactory genes, dolphins and whales have very few. They share a distant ancestor with the hippopotamus and it also has very few functioning genes, consistent again with a shared ancestry with whales and dolphins (1). See whale evolution videos . Humans make a yolk sac that is visible in the normal 5 week embryo. It has important functions presently, but if it was originally for holding yolk due to our ancestors laying eggs we should find decayed genes, pseudogenes, for making egg-yolk which is normally only found in egg laying species. This is why the Theory of Evolution is science; it makes testable predictions. Recall that vestigial can mean without function or without the original function. The yolk sac is vestigial. At first scientists had trouble finding the predicted egg-yolk pseudogenes because they were so degraded. But they did eventually by using the clever trick of looking for preserved genes flanking where the pseudogenes should be. And not surprisingly for evolution, they are at the same homologous chromosomal positions as in chickens (7). See Figure 1. See my blog on Intelligent Design where this example and many more observations in nature point definitively to common ancestry and not intelligent design. Figure 1. Egg yolk human pseudogenes. From: https://biologos.org/articles/vitellogenin-and-common-ancestry Fair use attribution. VIT 1,2,3 are yolk producing genes. In 2022 researchers discovered that many species with little hair still had the genes for making hair to cover their bodies. They studied 62 species and compared the hairy ones to several that had little hair. These included genes and regulatory sequences for elephants, rhinos, the naked mole rat, human, pig, armadillo, walrus, manatee, dolphin and orca along with 52 hairy species (9,10). Many of the genes involved in hair production were damaged and pseudogenes, but more had disabling mutations instead in the non-coding/regulatory DNA. In other words, the DNA areas that controlled if a gene turned on or off was damaged but not significantly the genes for hair itself. Humans have a pseudogene that is not shared by other primates. The MYH16 gene at one of the codons suffered a loss of the two bases (AC). Instead of ACC, the deletion produced - - C. We know this because the ACC codon is present in all apes and many monkeys but not humans. This deletion resulted in a gene destroying frame shift mutation.(1) A frame shift mutation is devastating to a gene because like reading a sentence it shifts all the letters over. The big dog ate... > The gdo gat... Yet another example is where chimps and humans but not other apes share the same mutation in the ACYL13 gene - a point mutation in a codon changed a TGG to a TGA, which is a stop codon (TGA) and thus disabled the gene. (1: pg. 155) The discussion of shared pseudogenes would not be complete without mentioning the GULO pseudogene since this has generated a significant amount of anti-evolution articles. Vitamin C, or ascorbic acid, is made by most mammals in which case it is not a vitamin for them. It is produced in a four enzyme series from glucose. The final step is catalyzed by the last enzyme, L-gulono-y-lactone oxidase, or GULO. The gene is non-functional and located on chromosome 8 at p21 (12). "Human GULO is a severely degenerated copy of the gene as only 5 of the original 12 exons remain, the locus has been bombarded by with retrotransposons and those parts of the gene that are identifiable are riddled with mutations... The GULO pseudogene contains multiple indel and stop mutations. The oldest appears to be a stop mutation, shared by representatives of all simian primate groups - apes, Old world Monkeys and New World Monkeys... Subsequently, exons 2 and 3 were lost from the genomes of apes and OWMs by a DNA deletion event that eliminated approximately 2,500 bases from the genome. A representative stop mutation is shared by OWMs. A codon specifying the amino acid arginine (possibly CGA) has ended up as a gene-truncating TGA codon." (1). Below is a view of the GULO gene sequence in Figure 2. Notice that there are two large exon deletions shared by all humans, chimps and macaques. It is estimated based on neutral substitution rate analysis that the gene was disabled about 61 mya (12). Other species such as the guinea pig and some bats have also inherited GULO pseudogenes but their mutations are different from those shared by selected apes and monkeys. Figure 2. GULO pseudogene showing identical deletions shared by humans, chimps, macaques but not galagos (bush babies). From Sandwalk, 2017. Fair use and educational use applied. https://sandwalk.blogspot.com/2017/10/creationists-questioning-pseudogenes_28.html Dr. Michael Behe at the creationist Discovery Institute , of intelligent design fame, and father of irreducible complexity (both of course are not true) nevertheless knows from his studies that human evolution is true. Not only for the GULO pseudogene but he notes another example: “When two lineages share what appears to be an arbitrary genetic accident, the case for common descent becomes compelling, just as the case for plagiarism becomes overpowering when one writer makes the same unusual misspellings of another, within a copy of the same words. That sort of evidence is seen in the genomes of humans and chimpanzees. For examples, both humans and chimps have a broken copy of a gene that in other mammals helps make vitamin C As a result, neither humans nor chimps can make their own vitamin C. Of an ancestor of the two species originally sustained the mutation and then passed to both descendant species, that would neatly explain the situation. “More compelling evidence of the shared ancestry of humans and other primates comes from their hemoglobin - not just their working haemoglobin, but a broken haemoglobin gene, too. In one region of our genomes humans have five genes for proteins that act at various stages of development (from embryo through adults) as the second (betalike) chain of haemoglobin. This includes the gene for the beta chain itself, two almost identical copies of a gamma chain (which occurs in fetal haemoglobin), and several others. Chimpanzees have the very same genes in the very same order. In the region between the two gamma genes and a gene that works after birth, human DNA contains a broken gene (called a "pseudogene") that closely resembles a working genre for a beta chain, but has features in its sequence that preclude it from coding successfully for a protein.   “Chimp DNA has a very similar pseudogene at the same position. The beginning of the human pseudogene has two particular changes in two nucleotide letters that seem to deactivate the gene. The chimp pseudogene has the exact shame changes A bit further down in the human pseudogene is a deletion mutation, where one particular letter is missing. For technical reasons, the deletion irrevocably messes up the gene's coding. The very same letter is missing in the chump gene. Towards the end of the human pseudogene another letter is missing. The chimp pseudogene is missing it too.   “The same mistakes in the same gene in the same positions of both human and chimp DNA. If a common ancestor first sustained the mutational mistakes band subsequently gave rise to these two modern species, that would very readily account for both why both species have them how. It's hard to imagine how there could be stronger evidence for common ancestry of chimps and humans.   “That strong evidence from the pseudogene points well beyond the ancestry of humans. Despite some remaining puzzles, there's no reason to doubt that Darwin had this point right, that all creatures on earth are biological relatives.” Behe M The Edge of Evolution: The Search for the Limits of Darwinism (2007: Free Press) p 71-72 Recall there are and estimated 20,000 human pseudogenes and as we find them, we can compare them in different species. Some are only found in humans, some only in humans and chimps, and still others across several apes species. The ABCC13 pseudogene and the glucocerebrosidase pseudogene show identical mutations and are found only human, chimp and gorilla species because the mutation occurred in a shared ancestor of those three species (1:pg. 158). See Figure 3. Figure 3. ABCC13 pseudogene (top). Glucocerebrosidase pseudogene (bottom). Bases in bold are identical in species. See text. From: Finlay, Graeme. 2013. Human Evolution: Genes, Genealogies and Phylogenies . p 158. Figure 3.8. Cambridge University Press. 2021 ed. Social sharing and Fair dealing applied per publisher's web instructions. In contrast the urate oxidase pseudogene was damaged because a C was mutated to a T producing a stop codon and this unique mutation is found only in four species of apes: human, chimp, gorilla, and orangutan (1: pg. 161) See Figure 4. Figure 4. The urate oxidase pseudogene shared by the great apes. See text. From: Finlay, Graeme. 2013. Human Evolution: Genes, Genealogies and Phylogenies . p 161. Figure 3.10. Cambridge University Press. 2021 ed.Social sharing and Fair dealing applied per publisher's web instructions. Do you see what is forming? Thousands of pseudogenes can be found in humans and we can look for them in other species. They produce a pattern where some species have them and if they have identical mutations the only rational explanation is shared ancestry. If we group the raw observations an evolutionary tree is produced. And a specific pseudogene tree matches the paleontology trees, the ERV trees , the LTR trees , and the DNA repair trees . It’s how we can be assured that we have the evolutionary story correct because evidence from independent lines of DNA findings confirms macroevolution in apes and monkeys. If all these damaged genes happened at one time, a nested hierarchy of data and observations that shows evolution would not be possible. See Figure 5. Figure 5. Nested hierarchy of various pseudogenes showing times they appeared during evolution. Specific pseudogenes in boxes. Numbers refer to additional unitary pseudogenes. See text. From: Finlay, Graeme. 2013. Human Evolution: genes, genealogies and phylogenies . p 172. Figure 3.18. Cambridge University Press. 2021 ed. Social sharing and Fair dealing applied per publisher's web instructions. We can even show an evolutionary tree with a single pseudogene. How? Because some pseudogenes are very old and have accumulated different mutations of the gene in different species. These can also be nested into an evolutionary tree. One gene that demonstrates this is the ARG pseudogene. " Multiple mutations are shared by humans, chimps, macaques (representing OW monkeys) and marmosets (a NW monkey). All simian species studied shared one stop, three splice-site, three frameshift and two TE insertion mutations. In addition, apes and OWMs share mutations that are absent in NWMs, and apes share a splice-site mutation that is absent in OWMs and NWMs.” (1: pg. 169). This one pseudogene provides a nested evolutionary tree by itself! Another example of different mutations occurring over time to a single shared pseudogene that produces an evolutionary nested tree is the TRPC2 pseudogene. See Figure 6. Figure 6. Mutations in the TRPC2 pseudogene of apes and Old World Monkeys. Mutations (S) are stop mutations, (ind) indels - insertions or deletions, and (Rv) reversions. See text. From: Finlay, Graeme. 2013. Human Evolution: genes, genealogies and phylogenies . p 174. Figure 3.19. 2021 ed. Cambridge University Press. Social sharing and Fair dealing applied per publisher's web instructions. Processed Pseudogenes Recall that unlike unitary pseudogenes that were knocked out by mutations and have no copies of themselves, many pseudogenes represent disabled copies from the original gene. One type results from a “copy and paste” method. In this case a type of “jumping gene” known as a LINE-1 retrotransposon grabs a gene as it copies and then the gene disengages from the LINE-1, inserting randomly back into the DNA. Because it left behind associated regulatory sequences it can no longer be transcribed and is termed DOA - 'dead on arrival'. This happens in Duchenne muscular dystrophy where a fragment of a non-coding RNA from chromosome 11 was inserted into exon 67 of the dystrophin gene located on the X chromosome (1). The human genome contains over 5,000+ processed pseudogenes alone. One particular gene, NANOG, is a master regulator of gene expression and 11 pseudogenes are known from it, 10 being of the processed type. Nine of these are also present in the chimp genome. One of these, NANOGP4, has developed several gene killing mutations. Humans have four stop mutations and three deletions. Three of the stop mutations are shared by chimps, and chimps also share two of the deletions with humans. The NANOGP8 acts as an oncogene and is probably responsible for our increased tendency to develop cancers compared to other primates (1, 11). Studies of various ape and monkey genomes have shown 48 processed pseudogenes in humans only, 94 shared in humans and chimps only, and 337 in the genomes of all three great ape species (humans, chimps, gorillas) but not in macaques. As you should be able to guess by now this will produce an evolutionary phylogenic tree that matches the other trees (1). Please note that all three types of pseudogenes produce independent phylogenetic trees separately that match those produced by ERVs and DNA repairs discussed elsewhere on this web site. This DNA evidence for evolution, macroevolution and human evolution, is confirming and overwhelming. About 800 retrotransposed pseudogenes produced from transfer RNA and hY RNA genes have been discovered in the human genome. The four hY RNA genes we have have been copied by retrotransposons and inserted into our DNA as 966 pseudogenes; 95% are identical to those shared with chimps (1). The vast majority thus must have occurred before the human-chimp ancestor split. Common Objections 1. The most frequent objection is a straw man characterization that pseudogenes can't have functions. As pointed out above, both Finlay and Moran note some can and some can even have gain of function with new functions. Many that show functions are only partially transcribed. But as in the definition of vestigial, pseudogenes are not defined by the presence or absence of function. Again, Finlay writes: "The progressive changes in base sequence provide the history of a pseudogene, and this history defines evolutionary relationships of those species that share the pseudogene. Current functionality is irrelevant to the value of pseudogenes as evolutionary markers." [my emphasis in the underlined only] (1) Most anti-evolutionary attacks seem to fall into trotting out a few functional pseudogenes as if that is a knock-out blow to evolution. It is not. Recall there are 20,000 pseudogenes and the independent evolutionary trees for three types of pseudogenes are solid evidence for evolution and discount a supposed appeal to a one time introduction of zapped disease and suffering into the world which would not produce nested evolutionary trees. The vast number of pseudogenes are non functional. Evolutionary trees rule out any species narratives that do not include macroevolution and disprove a one time event that damaged most or all of the DNA, introducing disease and death. 2. The GULO pseudogene is a very common target for anti-evolutionists. Articles have been written extensively by anti-evolutionists against GULO as a pseudogene and include Tomkins, Truman, Terborg (Borger?), RTB, and others. Their objections have been addressed and countered. See Moran (12), Venema (13) just for a few examples. 3. Most creationists are anti-evolutionists (ICR/AIG/CMI/RTB) and will deny macroevolution at every turn. For example the denial of transitional fossils occurs despite scores of found and predicted transitional fossils because in their origin narratives and presuppositions there can never be transitional fossils. In whales alone over 200 fossil species have been found, some showing the gradual movement of the blow hole up the skull and the gradual shrinking of hind limbs as the fossils for example. Likewise there is no room for pseudogenes in their a priori views - ever. Thousands of pseudogenes have been found and hundreds can be nested in evolutionary trees that anti-evolutionists cannot accommodate in their species origin narratives. Conclusion Our genome contains up to 20,000 pseudogenes. Most are copies either through gene duplications or "copy and paste" mechanisms with retrotransposons after they are processed and inserted randomly back into a new site in the DNA. The third type is mutations to genes that have no back up copy, called unitary pseudogenes. All three types produce nested evolutionary hierarchal trees independently that rise to the level of proof of macroevolution. The denial of DNA present in genomes to make structures that anti-evolutionists claim as impossible is telling. Atavisms abound to negate evolution denial. Chickens carry genes for making teeth and tails, tails in humans have been seen in about 100 cases, whales and dolphins are occasionally born with hind legs that attach to a vestigial pelvis (recall the proper definition of vestigial), and baleen whales carry pseudogenes for making teeth enamel. All of these are explained well by evolution but cause mortal damage to origin species narratives that deny macroevolution. Or they are poorly rationalized by anti-evolutionists sometimes to absurd lengths. If these species were formed separately none of these findings would be possible or expected. Most creationists (ICR/AIG/CMI/RTB) will deny macroevolution at every turn. For example the denial of transitional fossils occurs despite scores of found and predicted transitional fossils because in their origin narrative and presuppositions there can never be transitional fossils. In whales alone over 200 fossil species have been found, some showing the gradual movement of the blow hole up the skull through time, and the gradual shrinking of hind limbs for example. Likewise there is no room for pseudogenes in their a priori views - ever. Thousands of pseudogenes have been found and hundreds can be nested in evolutionary trees that anti-evolutionists cannot accommodate or discount effectively. Pseudogenes and nested pseudogenes are fantastic evidence for macroevolution and join human chromosome 2 fusion , shared ERVs , shared segemental duplications and shared DNA identical repairs as amazing evidence for macroevolution for those without ant-evolution commitments. With these DNA findings constituting a "second fossil record", one can wonder if traditional fossils are still the best evidence for evolution. Well, we need those also but I assert that the DNA findings are great at showing macroevolution is true with perhaps fewer interpretations needed. Literature Cited and References 1. Finlay, Graeme. 2013. Human Evolution: Genes, Genealogies and Phylogenies . Cambridge University Press. 283 pp. not including References and Index. Paperback edition 2021 - ISBN 978-1-009-00525-8 2. https://www.nature.com/articles/s41576-019-0196-1 3. https://onlinelibrary.wiley.com/doi/abs/10.1002/9780470015902.a0020836.pub2 4. https://sandwalk.blogspot.com/2020/01/are-pseudogenes-reallypseudogenes.htmlfbclid=IwAR2bgaNWkTxU5RzoJ_M7LXWzXZkUjJcsvNvx3FJsIzfxUWNuGol8ne-q5yo Also: https://sandwalk.blogspot.com/2015/08/how-do-intelligent-design-creationists.html?showComment=1440535786147#c8524274909861681663 5. https://www.livescience.com/7051-surprise-chickens-grow-teeth.html 6. https://www.npr.org/templates/story/story.php?storyId=5230538 7. https://journals.plos.org/plosbiology/article?id=10.1371/journal.pbio.0060063 8. https://genomebiology.biomedcentral.com/articles/10.1186/s13059-022-02802-y 9. https://elifesciences.org/articles/76911 10. https://www.popularmechanics.com/science/health/a42638271/humans-can-still-grow-full-coat-fur/ 11. Evolution of the NANOG pseudogene family in the human and chimpanzee genomes. Fairbanks, Daniel J. and Maugan, Peter J. 2006. BMC Evolutionary Biology. https://www.ncbi.nlm.nih.gov/pmc/articles/PMC1457002/ Feb 9. doi: 10.1186/1471-2148-6-12 Also: https://bmcecolevol.biomedcentral.com/counter/pdf/10.1186/1471-2148-6-12.pdf 12. https://sandwalk.blogspot.com/2017/10/creationists-questioning-pseudogenes_28.html Also: https://sandwalk.blogspot.com/2015/08/how-do-intelligent-design-creationists.html?showComment=1440535786147#c8524274909861681663 13. https://biologos.org/series/genetics-and-the-historical-adam-responses-to-popular-arguments/articles/adam-eve-and-human-population-genetics#common-ancestry-nested-hierarchies-and-parsimony 14. https://www.pnas.org/doi/full/10.1073/pnas.0535697100 15. Limbs in whales and limblessness in other vertebrates https://www.researchgate.net/publication/6162489_Limbs_in_whales_and_limblessness_in_other_vertebrates_Mechanisms_of_evolutionary_and_developmental_transformation_and_loss https://onlinelibrary.wiley.com/doi/abs/10.1046/j.1525-142X.2002.02033.x

“Although I am fully convinced of the truth of the views given in the volume, I by no means expect to convince experienced naturalists whose minds are stocked with a multitude of facts all viewed, during a long course of years, from a point of view directly opposite of mine. It is so easy to hide our ignorance under such expressions as “plan of creation,” “unity of design,” etc., and to think that we give an explanation when we only restate a fact. Any one whose disposition leads him to attach more weight to unexplained difficulties than to the explanation of a certain number of facts will certainly reject the theory.” ~ C. Darwin, On the Origin of Species. Chapter XIV "I think of a little child in east Africa with a worm burrowing through his eyeball. The worm cannot live in any other way, except by burrowing through eyeballs. I find that hard to reconcile with a notion of a divine and benevolent creator". ~ Sir David Attenborough [ Loa loa , African Eye Worm] Life seems so amazing and intricate, why does it not point to intelligent design, with the implication of a designer? There are several critical reasons in my opinion. Some examples of unintelligent design best explained by evolution will be discussed, in addition to why ID (intelligent design) is not science. 1. There is too much "unintelligent design" in life that can only be explained by evolution. People have noticed this and there are several books that have even been written detailing all the workarounds by natural selection. First, ID supporters are in general equating complexity with design; it is very, very complex to the point of being mind blowing. A logical fallacy that is common is confirmation bias - looking at only items that support your views rather than the entire picture. To the anti-evolutionist, function is everywhere and since in their view evolution (“macroevolution”) cannot have occurred there should be a function for just about everything. Anti-evolutionists will retort that design doesn’t mean optimal design necessarily. Here are some examples of adaptations that are best or only explained by evolution. a. The recurrent laryngeal nerve . There are four nerves that come off the vagus nerves (one of the cranial nerves) that innervate the larynx or voice box, two on top (superior) and two on the bottom (inferior). The two superior laryngeal nerves branch off and go directly to the voice box. But the two lower nerves instead go all the way down to the heart area, wrap around and then come back. It’s like driving in America from San Francisco to Seattle through New Jersey first. This occurs in all tetrapods. Look at the giraffe. Think what a wasteful design this would be in a dinosaur. From: Wikipedia commons (top) From: kilpartz.com (top) From: Presumed course of RLN in Sauropods From: zoology-ubc-ca. Bio 336 Lectures Why would any engineer bypass where the nerve needs to go (the inferior side of the voice box) and then come back to it? Anti-evolutionists will claim that it is needed for normal functions - either it supplies branches off the long course for example to the cardiac areas, is a developmental constraint of the organism or thirdly that it even serves as an early warning system for neck cancer! A fourth excuse is that even if it's an imperfect design it's still a design. No attempt to test which if any are valid. Any one will suffice. But science coalesces around truths by ruling out possibilities (hypotheses). How can you test these rationalizations? What would invalidate this “must be” anatomy? How about people born without recurrent laryngeal nerves and they do just fine? Google it! All swans are white until you find a black one. It's not a developmental constraint. It's not an early warning system because that's a teleological excuse since any long nerve like the ones that go down the leg also would incidentally do the same thing. Claiming it's still a design but just not perfect does not address the fact that anti-evolutionists are claiming "Intelligent" design. It's not. So, what is the evolutionary explanation? It goes back to what would be our fish ancestors. Fish don’t have necks but when amphibians evolved and moved onto land the inferior laryngeal nerves were trapped between certain gill arches and natural selection can only work with what it has. The nerve does take a direct route in fish. Hence a workaround for later tetrapods. Here we see the fossil record and human anatomy coming together to support evolution. The recurrent laryngeal (inferior) nerves’ journey is not a constraint for development or function. It’s a result of our past evolution. A medical student studying anatomy can’t truly understand their subject without evolution (see my blog on evolutionary medicine ). It’s a constraint alright - an evolutionary historical one but not developmental. And excellent book and series is Neil Shubin's "Your Inner Fish" . I highly recommend it. b. The outer part of our ears , the auricles, are held to the head by vestigial ear muscles rather than other attachments such as connective tissue. Look at your cat, deer or other mammals as they move away from you. They can rotate their ears nearly 180 degrees to listen behind them. Since we evolved from distant ancestors that had that function it makes sense we’d still have vestigial muscles there. If we were designed from the beginning, no reason for useless muscles. Yes you can wiggle your ears slightly, but nothing like what other mammals can do. Below are the vestigial auricle muscles. They now can somewhat add to facial expression. But recall in my whale presentations vestigial can mean loss of function or loss of original function . And yes, it’s always had that definition. c. Human males and breast cancer. Men not only have breasts with nipples, but they have breast tissue for producing milk. At the time of this writing, just under 3,000 men in America are diagnosed with breast cancer yearly and it is as deadly as in women. If you were a designer, would you give men tissue for making milk they would never use? Also, it’s not uncommon for people to have vestigial nipples (supernumerary) on their upper abdomen. Once you point it out to them, they agree that they are not like the other “moles” they have. And these nipples always form along the “nipple line” in humans. I have had a patient who had to have an armpit (axillary) developing breast removed from her left armpit. The nipple line is best explained by our evolutionary past. From: DermNet, New Zealand. R. Suhonen From : Wikipedia: Mammary Ridge Common use permitted free use. d. The Kiwi bird - has vestigial flight wings. Yes, they can be used for secondary uses but why have stubs of vestigial wings that indicate they once performed flight? The original function has been lost, satisfying the definition of a vestigial structure. e. Many beetles with wings under fused elytra (coverings) over their thorax. And under these fused elytra some have no wings but some have wings that they can never use to fly . In Cyclotrachelus for example, the wings are present but reduced (brachypterous). This occurs in many beetle species. Why would a designer make beetles with wings they will never use? f1. Humans have genes for making egg yolk that are mutated into non-functional pseudogenes. But we still produce the yolk sac during embryonic development. From: https://www.slideserve.com/mirby/placenta-powerpoint-ppt-presentation Fair use attribution. The empty sac acts as an early embryonic blood supply, nutritional and gas exchange, and is eventually absorbed into the gut of the embryo. It has functions temporarily, but it’s not the original function because we know there are dead genes (ancestral vitellogenin-encoding genes) we have for producing egg yolk that we no longer use. Our yolk producing three pseudogenes (VIT1, VIT2, and VIT3) were so degraded they had to be found by looking for functioning genes around them that were known from the chicken. The human pseudogenes were located at the same "DNA address" as in the chicken. From: https://biologos.org/articles/vitellogenin-and-common-ancestry Fair use attribution. The yolk sac is very important in confirming a healthy pregnancy as it can be seen on ultrasound as early as five weeks post fertilization and evaluated for normal morphology. If you watched my whale evolution video Part 1 recall that vestigial can mean without function or loss of original function and this definition has been in use since at least the 1960s. The anti-evolutionist cry of functions is appropriately applied only to the yolk sac as a vestigial organ, best understood through evolution. Chickens - Studies have found that chickens have the pseudogenes for making tails and also for making teeth and a stronger jaw. Because birds evolved from ancestors that had tails and teeth. Indeed, scientists have found a way to reactivate those genes to have the chickens produce rudimentary teeth https://pubmed.ncbi.nlm.nih.gov/3232853/ https://www.livescience.com/7051-surprise-chickens-grow-teeth.html The vast majority of male birds don't have a penis for reproduction. But just discovered is that a rudimentary penis is formed during development and then disappears later. https://www.smithsonianmag.com/science-nature/scientists-discover-the-genetic-reason-why-birds-dont-have-penises-94130874/#ixzz2VSNRg46z These are all explained well by evolution and poorly if not at all be anti-evolution attempts. f2. Recently, a study was published in 2023 detailing the finding of mutated pseudogenes that humans have for producing a full coat of hair/fur. The best explanation is evolution. A Designer who created humans without evolution would not put in dead genes for making a full coat of body hair if we never were covered with such. https://www.sciencedaily.com/releases/2023/01/230104135604.htm https://www.yahoo.com/entertainment/disturbing-humans-still-grow-full-185700595.html?soc_src=social-sh&soc_trk=tw&tsrc=twtr f3. TP53 Gene - Some animals live long lives relative to others their size. This includes Bowhead whales, naked mole rats and elephants. In the case of naked mole rats they secrete hyaluronan, a substance between cells that prevents mutated cells from reproducing. Humans make it also, but a different variety and in lower amounts so we are not as protected. Bowhead whales have genetic mutations that protect them from cancer, although the specifics are unknown. Elephants have 20 copies of the tumor suppressor gene TP53 which produces the protein p53. Humans only have one copy. This protein guides the cell with damaged DNA either to repair the damage or stop the cell from dividing and to undergo self destruction (apoptosis). Evolution is the best explanation. https://medlineplus.gov/genetics/gene/tp53/ https://www.worldatlas.com/articles/animals-that-do-not-get-cancer.html g. Goose bumps are created when a small muscle pulls at the base of a hair raising the hair and producing a small dimple ( arrector pili muscle ). In mammals with fur it can help with defense to make an animal look bigger (your cat arching its back and raising its fur; when you sense danger or are cold the “hair on the back of your neck stands up” is the saying). Likewise birds use the same mechanism to fluff up their feathers to trap air to help with warming. In humans the goose bumps are vestigial activations but still might help slightly with increased sensation. They sure don’t make you warmer or bigger looking. h. The vertebrate eye is poorly "engineered". The retina is inverted due to evolution compared to eyes that are not inverted. Notice the diagrams below. The vertebrate eye on the left has the light sensing cells not only pointing away from the incoming light but light needs to go through multiple layers of tissue before it even reaches the photoreceptors (see eye comparison diagrams below). This would be like placing a radio antenna or TV dish in front of a dense forest, degrading the signals before they reach the antenna or even then pointing the dish away from the signal! There's a reason we put antennas on roofs with unobstructed views of the sky. The octopus eye on the right does not have this limitation; the rods and cones are logically placed so they receive light directly and don't produce a blind spot the brain must create an estimated image of. "In vertebrate eyes (left), the nerve fibers route before the retina , blocking some light and creating a blind spot where the fibers pass through the retina. In cephalopod eyes (right; no blind spot), the nerve fibers route behind the retina , and do not block light or disrupt the retina. 1 is the retina and 2 the nerve fibers. 3 is the optic nerve. 4 is the vertebrate blind spot." From: Wikimedia Commons: From Wikimedia Commons: Caerbannog - Own Work, based on Image: Evolution_eye.png created by Jerry Crimson Mann 07:07, 2 August 2005 UTC (itself under GFDL). From: https://www.brainkart.com/article/Retina_26069/ Fair Use Attribution Notice that the photoreceptors in the above diagram are not only on the far side pointing away from light entering the eye but there is a tremendous number of support cells and wiring that the light must pass through to reach its final destination, the photoreceptors. Only nerves are shown; there is also a dense network of blood vessels and support cells that interfere with light transmission. This is not present in the cephalopod eye structure which evolved separately from the vertebrate eye. Objections The photoreceptors need nutrients and have a high metabolism so they need to be in close proximity to the retinal pigment layer (RPE - #10) that has all those blood vessels. The RPE can also act as a cooling mechanism. If the photoreceptors were like the octopus eye, the RPE would be directly in front of the light entering, causing a severe obstruction. Answer: Recall with the RLN example (1a in the section above) that the crazy route of this nerve was not due to some purposeful "design" or "developmental constraint" but because of evolution. It's a constraint alright, an evolutionary constraint . The nerve was trapped in the evolving neck and natural selection had to do a "work-around" resulting in an amazing compromise (see dinosaur diagram). So here also, the extra blood vessels in the RPE (#10 above diagram) and in the layers in front of the photoreceptors was what natural selection had to do because of the inverted nature of the rods and cones. How do we know? Because the cephalopods don't have this problem and don't create a blind spot with their better arrangement. Furthermore, another vertebrate eye with this same problem has a solution and work-around that is even better than the one in humans. In all birds they have an organ called the pecten oculi ( conus papillaris in reptiles) that satisfies the nutrient needs and does not need an RPE. This organ acts like a giant radiator, pushing nutrients into the vitreous for the cells, and reducing the blood vessels and other obscuring support cells in front of the photoreceptors. It is there as a solution to a problem and bad design created by having an inverted vertebrate eye. This reduces the blood vessels and support cells in front of the bird photoreceptors, providing one reason why birds have better vision than we do. Humans evolved the RPE; birds have a pecten oculi . Both are to solve a design problem of the inverted retina. From: Jfbleak. 2008. Updated 2013. Fair use attribution. Bird eye. https://www.wikiwand.com/en/Pecten_oculi#Media/File:Birdeye.jpg In Michael Behe's book, Darwin Devolves, he mentions that the human eye is beautifully designed because it also has some cells that act as a "fiber-optic cable system" to channel light to the photoreceptors of the cell that are deep in the retina from the surface of the retina receiving light. That the retina has this is rather proof that there is a problem to be addressed. There is significant obstruction going on and natural selection has another work-around demonstrated here to get past the problem. Rather than a "neat" design, this is another example of a poor adaptation (inverted photoreceptors buried in the retina and pointing in the wrong direction) that needs help. Still another solution to the inverted eye problems and loss of light is found in the tapetum lucidum . Nocturnal animals have an even worse problem at night if light is degraded before it reaches the photoreceptors as it is with the present vertebrate eye. So these animals have a reflective layer behind the retina to amplify light coming in. This is why cats, dogs, and deer for example have eyes that shine at night if we put light on them from cars or flashlights. Humans being diurnal do not need this adaptation 'patch'. A not uncommon anti-evolutionist response to counter the claim of the vertebrate eye being a poor design is to cite the 2022 article by Baden in Nilsson where they note in the evolution of both the vertebrate eye and cephalopod eye they both work very well. The authors note advantages to the inverted retina. In the 7th paragraph after Figure 4 the authors write and the anti-evolutionist will sometimes produce this quote: " In terms of performance, vertebrate eyes come close to perfect." But just above this sentence which is never quoted is "So, in general, the apparent challenges with an inverted retina seem to have been practically abolished by persistent evolutionary tweaking. In addition, opportunities that come with the inverted retina have been efficiently seized." Thus, the authors are not only saying that the vertebrate eye evolved and functions well but they confirm this author's thesis that the vertebrate eye only performs well because of evolutionary "tweaking" or workarounds that make it perform well and not due to the original inverted retina 'design'. They also note that some species of fish, reptiles and bird cell bodies contain oil droplets to improve color vision and to help focus light. Thus, we see an example of dishonest quote mining and also additional fixes to the vertebrate eye necessary for improved vision not needed with the cephalopod eye. https://www.cell.com/current-biology/fulltext/S0960-9822(22)00335-9?fbclid=IwY2xjawFdhVxleHRuA2FlbQIxMAABHQuYeEIeRXxsmtDRGALfODvoNOcYoizdIrh2xNvH9GgXLxkmgjZHGj2SSw_aem_tb7aKF4RhXFQVceV-F31ew In July of 2023 Nathan Lents wrote on his blog about the tapeta found in various species and that all indications point to attempts at minimizing the degradation of light in the vertebrate eye (4). A confirmation of this occurs in jumping spiders who have two types of eyes. The primary eyes have cephalopod like retinas but the smaller secondary eyes are wired like vertebrate eyes. Sure enough, the secondary eyes only do have a tapedum lucidum to improve light sensitivity! From: Wikimedia Commons. Lukas Jonaitis Thus, the pecten oculi   in birds, the conus papillaris  in reptiles, the " fiber-optic cables ", the RPE  , the tapetum lucidum   in many nocturnal animals, and oil droplets  in the ocular cell bodies of some animals are all different workarounds or tweaks by natural selection in the vertebrate eye to solve problems of reduced light caused by an inverted retina instead of what cephalopods have. All of these point to a vertebrate eye evolutionary constraint , solving problems by natural selection, and hardly point to intelligent design. It's just the opposite. If we had eyes designed with everted retinas we would not see all these work-arounds by natural selection in various animal species. Why then did the vertebrate eye evolve like this? One reason could be that early eyes were in a water environment and an inverted retina has space saving advantages. Kroger and Biehlmaier discuss how studies support this view: https://www.sciencedirect.com/science/article/pii/S0042698909003162#fig2 Addendum : A key protein needed for vertebrate eye function has been found to be of bacterial origin, acquired by horizontal gene transfer in the distant past. At least 50% of our genome is derived from viruses or duplicated viral products and genes. All of this is consistent with evolutionary explanations and best explained through evolution. "Here, we describe the essential contribution of bacteria to the evolution of the vertebrate eye, via interdomain horizontal gene transfer (iHGT), of a bacterial gene that gave rise to the vertebrate-specific interphotoreceptor retinoid-binding protein (IRBP). We demonstrate that IRBP, a highly conserved and essential retinoid shuttling protein, arose from a bacterial gene that was acquired, duplicated, and neofunctionalized coincident with the development of the vertebrate-type eye >500 Mya." https://www.pnas.org/doi/10.1073/pnas.2214815120 [paper] https://phys.org/news/2023-04-evidence-interdomain-horizontal-gene-eye.html [additional discussion and explanation] 2. The ID movement is another religious attempt to force a specific supernatural belief into science. Who says? Actually, they do and so has the scientific community and even the courts. For example, the origin of the modern ID movement is the Wedge Document (1) with its 5 and 20 year plan to “destroy” evolution and Darwin that was the founding document for the ID movement and the Discovery Institute, the main proponent of ID. This was leaked online in the late 1990s and specifically outlines the motivation and how their goals would hopefully succeed. Here is look at the exact text of the Wedge Document: https://ncse.ngo/wedge-work Intelligent Design has failed an important court case. Update - the attempt to make Intelligent Design an academic discipline with respect in the biological sciences appears to be failing. The Discovery Institute has shut down its " Biologic Institute ". May, 2021: https://pandasthumb.org/archives/2021/05/biologic-institute-closes.html January, 2023: https://whyevolutionistrue.com/2023/01/08/intelligent-design-nearly-down-the-drain/ Of course, for many people who look at the complexity of life even without a religious context, ID appears to be intuitive. Those persons I posit are not aware of all the evidence from biology that life is actually a product of natural processes and certainly not an Intelligent force given all the unintelligent work arounds by natural selection. 3. Attempts by ID proponents to find examples of life that cannot be explained, or never will be explained by natural processes alone have failed. Examples include the flagellum and the clotting cascade. When these were addressed by biologists, the ID proponents moved on to other attempted examples. This of course results in a never ending wack-a-mole regression and reveals the true religious motivations of the ID advocates and their rationalizations. What is even more interesting is that at least one of the major proponents of ID, Michael Behe of the Discovery Institute, even admits evolution, “macroevolution”, is true but attempts to show that natural selection is insufficient to drive it. ID is a big tent approach, but inside the tent anti-evolutionists often hold mutually exclusive approaches to origins but rarely expose these differences and their fights to outside audiences. Everyone who is considering ID should definitely watch the documentary of the 2005 Dover Trial, when ID proponents tried to get their textbook and teaching into a school system (2). The judge was a conservative Republican and wrote a scathing report denouncing ID in science courses. A nice summary of why the main points in ID fail. https://barryhisblog.blogspot.com/p/intelligent-designer-spotting.html 4. Calls to “teach the controversy” are hollow appeals because there is no controversy in science about evolution ; it is settled science (biology, geology, paleontology, biogeography, developmental biology, geochronology, plate tectonics/continental drift, evolutionary psychology, etc) . The Theory of Evolution is overwhelmingly supported by multiple independent fields of science. It is in the same category as Gravity, Cell, Germ and Relativity scientific theories; all are both fact and also theories that will never be overthrown although they can be modified. It has withstood testing for more than 150 years. It makes predictions that have come true. We talk about the fact of gravity and also Gravitational Theory. Yes, for many it’s not intuitive. But the false impression that the earth is flat, stationary, and that the sun goes around us needed strong evidence for many people to realize the opposite is true, even though initially counter-intuitive. Pilots when undergoing instrument training must learn to trust their instruments and not their false “gut” feelings since it is easy to be fooled. Science is basically a method not to be fooled. Evolution is counter-intuitive for most but our scientific “instruments” tell us it is true. We don’t teach astrology in astronomy nor alchemy in chemistry for the same reasons we don’t teach ID, creationism, or “scientific creationism” in biology, geology or paleontology. Conclusion There are many reasons why ID is not science and just a new iteration of a particular religion. ID proponents have failed to prove their points in a court of law and have failed to provide evidence that can’t be explained with natural process or future research. Their founding document is a religious manifesto against well established science and they have failed to produce any useful research. Finally, there are just too many examples of “ unintelligent ” design better explained by evolution. Meyer for example is still beating the same drums - that the universe had a beginning and therefore a Designer, and the Cambrian Explosion. Newer views indicate that the universe could be infinite after all . We have found many fossils in the layer before the Cambrian so the Cambrian fossils did not get zapped into existence without precursors. Meyer ignores all the incredible DNA evidence for evolution including shared ERVs, human chromosome 2 fusion , that our genome is made up of at least 50% old parasitic viruses (strange way to create), and the thousands of dead genes called pseudogenes that we share with the other great apes. These are all slam dunk evidence for evolution to an objective searcher. Dr. Moran in a 2023 post about ID, How Intelligent Design Creationists try to deal with the similarity between human and chimp genomes , writes that: " But in addition to being mere speculation based on the presumption of a designer, there's one other problem with this model. The differences between genomes aren't just due to specific modifications that create distinct species as the designer model predicts. Instead, the evidence shows that they are mostly concentrated in parts of the genome that are not under strong selection. What this means is that most of the mutations are effectively neutral and thus the affected DNA should be evolving at the neutral rate, which, according to population genetics, is equivalent to the mutation rate. This prediction turned out to be correct and changes at the neutral rate are what gives rise to the approximate molecular clock.1 (See Calculating time of divergence using genome sequences and mutation rates (humans vs other apes) .) What this means is that our current understanding of evolution has enormous explanatory power. It satisfactorily accounts for the data on genome differences in a way that no competing model can. If Intelligent Design Creationists expect to be taken seriously as scientists then they have to do more than come up with hand-waving arguments about the possible motives of the designer. Instead, they have to explain why those differences just happen to fall in line with known mutation rates, which then give times of divergence from common ancestors that just happen to correlate with the fossil record." Collinsworth writes: “… ID offers no descriptions of the design process or the designer. In fact, proponents do not even agree among themselves as to which biological phenomena were designed and which were not. Ultimately, this “theory” amounts to nothing more than pointing to [supposed] holes in evolution and responding with a one-word, unceasingly repeated mantra: “design.” But unless ID advocates fill in the details, there is no way to scientifically test intelligent design or make predictions from it for future research. In short, it is not valid science.” (3) I strongly urge you to read some source material exposing ID as another manifestation of fundamentalist religion and is not scientific. Some sources are listed under References. Citations https://ncse.ngo/wedge-document Judgement Day: Intelligent Design On Trail (NOVA) The Flaws in Intelligent Design Is Nocturnal Eye Shine an Adaptation for the Backwards Retina? July 11, 2023. The Human Evolution Blog. Nathan Lents, PhD. References Only A Theory: Evolution and the Battle for America’s Soul. 2008. Kenneth R. Miller. Penguin Books. 244pp. [author is a Christian and was a witness at the Dover trial] Human Errors: A Panorama of Glitches, From Pointless Bones to Broken Genes . 2019. Nathan H. Lents. First Mariner Books. 233pp. The Not-So-Intelligent Designer: Why Evolution Explains the Human Body and Intelligent Design Does Not. 2015. Abby Hafer. Cascade Books. 229 pp. Why Darwin Matters: the case against Intelligent Design . 2006. Michael Shermer. Owl Books. 199pp. The Big Tent and the Camel’s nose. 2001. Eugenie C. Scott. Executive Director of the National Center for Science Eduction (NCSE). [ID is not testable] Bipedalism and other human oddities. 2022. Pievani, Telmo https://thereader.mitpress.mit.edu/bipedalism-and-other-evolutionary-oddities/ Adapted from his book - Imperfection: A Natural History . 2022. Pievani, Telmo. MIT Press. 176pp. 7. The Discovery Institute Exposed: Part 1. https://www.youtube.com/watch?v=HRxq1Vrf_Js Part 2. https://www.youtube.com/watch?v=Akv0TZI985U A simple challenge to the DI: 8. Evolution Gone Wrong: The Curious Reasons Why Our Bodies Work (Or Don' t). Bezzerides, Alex. 2021. Hanover Square Press. 384 pp. Professor of biology at Lewis-Clark State College in Idaho, where he teaches a wide range of biology classes, from human anatomy and physiology to entomology. He has a bachelor’s degree in biology and a PhD in neurobiology and behavior.

Updated: Sep 5 Modern whales and dolphins are mammals (giving their young milk) and mammals are four limbed (tetrapods) and usually terrestrial (land dwelling). "The “problem”, of course, is that modern whales are emphatically not terrestrial, nor do they have four limbs–they have two front flippers and a tail, with no hind limbs in sight. Yet they are mammals, which forces evolution’s hand as it were. Evolution thus is dragged, under protest, to the prediction that modern whales, as mammals, are descended, with modification, from ancestral terrestrial, tetrapod ancestors... And yet, these difficulties are the stuff of science. If indeed our “educated guess” of terrestrial, tetrapod ancestry for whales is correct, the evidence will show that these transitions, challenging though they may seem, did indeed occur on the road to becoming “truly cetacean.” ~ Venema, Dennis. Whale Evolution: theory, predication and converging lines of evidence. 2017. Biologos Part 1: Living (Extant) Whales Part 2: Whale Fossils (Extinct Whales) Part 3: DNA and Whale Evolution What About Objections? Most objections seem to fall into just a few categories. Many unfortunately contain so many errors and misunderstandings about evolution and biology that it would be very difficult to begin to address the writings without attempting to correct all the misunderstandings first. Many quotes against whale evolution are decades old and disproven or taken out of context. Most in my experience will basically list all the adaptations and appeal to the reader with, “how could all this have happened?” without addressing the evidence we DO have. Mechanisms of “how” are important but can’t negate the evidence of “what” we have. In addition, we do know in many cases how it happened by studying their genomes. Please see the blog about "How vs. What" , this site. See also some of the applicable articles in the References section below. The evidence for whale evolution is truly overwhelming as is the various scientific fields that all contribute to this huge body of supporting evidence: 1. Paleontological evidence 2. Morphological evidence 3. Molecular biological evidence 4. Vestigial evidence 5. Embryological evidence 6. Geochemical evidence 7. Paleoenvironmental evidence 8. Paleobiogeographic evidence 9. Chronological evidence (see: https://ncse.ngo/origin-whales-and-power-independent-evidence ) See also other sources listed in the Reference section. To dismiss the mountain peaks of whale evidence amounts to dismissing a mountain range of robust and sound evidence. To deny whale evolution from what has been scientifically discovered is now perverse. For example, whales have many dead genes for smelling on land: " The macroevolutionary transition of whales (cetaceans) from a terrestrial quadruped to an obligate aquatic form involved major changes in sensory abilities. Compared to terrestrial mammals, the olfactory system of baleen whales is dramatically reduced, and in toothed whales is completely absent. We sampled the olfactory receptor (OR) subgenomes of eight cetacean species from four families. A multigene tree of 115 newly characterized OR sequences from these eight species and published data for Bos taurus revealed a diverse array of class II OR paralogues in Cetacea... Phylogenetic analyses of OR pseudogenes using both gene-tree reconciliation and supermatrix methods yielded fully resolved, consistently supported relationships among members of four delphinid subfamilies." https://pubmed.ncbi.nlm.nih.gov/18686195/ To dismiss the mountain peaks of whale evidence amounts to dismissing a mountain range of robust and sound evidence. To deny whale evolution from what has been scientifically discovered is now perverse. An analogy is someone traveling to their vacation home only to find it completely destroyed. Pieces in front of them are on the ground, or more accurately what remains in this example. But what if we don’t know or are unsure how it was destroyed? Fire, hurricane, earthquake, tornado, angry neighbor, or gas leak? The fact of the event is independent of the “how” or mechanism. Would we really deny the fact of the home destruction until we knew exactly how it occurred, to our satisfaction, while dismissing the input from experts and the observations before our very eyes? So it is with whale evolution. We know it occurred because of the overwhelming evidence. It’s a great example of evolution and indeed “macroevolution”. One does not need to “be there”. One does not need to have every step worked out. Our courts certainly operate on the “what” even if the “how” is incomplete or even unknown. See “The Teacher’s Pet” case. When it comes to evolution we even have an idea of the hows. I write here why putting "how" before the "what" is wrong and an avoidance mechanism so as to not address the evidence for whale evolution. https://biologos.org/articles/whale-evolution-theory-prediction-and-converging-lines-of-evidence Why would a deer like creature venture into the water? https://bigthink.com/surprising-science/ancient-deer-like-creatures-returned-to-the-ocean-to-become-whales-paleontologists-say/ Nice summary of whale evolution - podcast. If interested in just the main fossil discussion, start at 1:00:00. https://www.youtube.com/watch?v=wR_FnKu-VPA&list=PLfdiT8Klm_YPa0lNVa9ygwAjy_1Lpz9_S Why whale origins pose an incredible problem for Young Earth Creationism when viewing geology and paleontology: https://thenaturalhistorian.com/2017/10/05/walking-whales-on-board-noahs-ark-the-inevitable-end-point-of-creationists-post-flood-hyper-speciation-belief/ Summary I assert that the evidence for whale evolution is so broad and numerous that any person not committed to a previous position against it would agree that whales evolved as science has discovered. The evidence comes from at least three broad areas. Other evidence such as continental drift and the late Tethys Sea that was present at the time all impact on why whale evolution occurred when it did; it’s an amazing true story that brings in many areas of science and history all to a single conclusion. Objections rarely if ever address the copious evidence but instead attempt to throw doubt by appealing to intuition and mechanisms as the sole arbitrators regarding whale origins. From: Ancient Archeology Secret Resources What is the Evidence for Evolution? https://www.youtube.com/watch?v=lIEoO5KdPvg Whale Evolution https://www.proof-of-evolution.com/whale-evolution.html Prothero, Donald. 2017. Evolution: what the fossils say and why it matters. 2nd ed. Columbia University Press. When Whales Walked. PBS Eons https://www.YouTube.com/watch?v=_OSRKtT_9vw The Evolution of Whales https://evolution.berkeley.edu/what-are-evograms/the-evolution-of-whales/ Whale Evolution: Theory, Prediction and Converging Lines of Evidence https://biologos.org/articles/whale-evolution-theory-prediction-and-converging-lines-of-evidence The Origin of Whales and The Power of Independent Evidence https://ncse.ngo/origin-whales-and-power-independent-evidence The Evolution of Whales From Land to Sea https://knowablemagazine.org/article/living-world/2022/evolution-whales-land-to-sea#aoh=16695035475710&csi=0&referrer=https%3A%2F%2Fwww.google.com&_tf=From%20%251%24s How Whale Genes Evolved to Produce Huge Sized Whale bodies https://www.nature.com/articles/s41598-022-24529-3 How Whales Evolved From Land to Water, Gene by Gene [85 pseudogenes] https://www.sciencefriday.com/segments/whale-evolution-genetics/ How Paleontologists Pieced Together the Strange Story of Whale Evolution https://science.thewire.in/the-sciences/whale-evolution-india-pakistan-fossils-indohyus-pakicetus-remingtonocetus-basilosaurus/ The Origin and Early Evolution of Whales: Macroevolution Documented on the Indian Subcontinent. 2009. Bajpai, S., JGM Thewissen, and A.. Sahni. J. Biosci. 34(5). Indian Academy of Sciences. 678-686. Ancient Whales Were the Biggest and Smallest of Their Kind to Ever Roam the Oceans. New discoveries show how whale diversity exploded after the dinosaurs disappeared. 2023. The Smithsonian. https://www.smithsonianmag.com/science-nature/the-first-whales-to-rule-the-seas-were-giganticand-tiny-180983202/

“The evolution of life, and the evolutionary origin of mankind, are scientifically established as firmly and completely as any historical event not witnessed by human observers. Any concession to anti-evolutionists, suggesting that there are scientific reasons to doubt the facticity of evolution, would be propagating a plain untruth.” ~ Theodosius Dobzhansky (Christian) "Whilst on board the Beagle I was quite orthodox, and I remember being heartily laughed at by several of the officers (though themselves orthodox) for quoting the Bible as an unanswerable authority on some point of morality... But I had gradually come by this time, i.e., 1836 to 1839, to see that the Old Testament was no more to be trusted than the sacred book of the Hindoos..." ~ Charles Darwin. From Charles Darwin: His Life Told in an Autobiographical Chapter, and in a Selected Series of his Published Letters (1902), edited by his son Francis Darwin. Secondary source: Tom Siegfried in Sciencenews.org January 31, 2009 "Darwin's natural selection redefined the idea of design”. The Theory of Evolution is the foundation for biology and many other scientific and medical fields. As the famous biologist Dobzhansky, a Christian, wrote in 1973, “ Nothing in Biology makes sense except in the light of evolution. ” Like the scientific theories of Gravity, Cell, Germ, and Relativity, Evolution is both fact and theory and will not be going away. It is that well supported by overwhelming evidence. Even modern medicine is based on it. When I began medical school after teaching biology at the college level, I was surprised that the professors often referred to evolution more often than my biology textbooks! Why would several of the best medical schools in the world use a famous fish paleontologist (Shubin: Your Inner Fish. University of Chicago) and a cetacean paleontologist (Thewissen - Duke, Northeast Ohio Medical University) to teach human anatomy to medical students? Because we can’t fully understand human anatomy, genetics, disease, and physiology without evolution. Examples of human clues to our evolutionary past include our recurrent laryngeal nerve that is positioned because we have fish ancestors. We have numerous vestigial ear muscles to hold our pinna - our outer ears - to our heads (see post on unintelligent design, this site) We have thousands of olfactory pseudogenes left over from our much better smelling ancestors. We inherited some of our immune genes from Neanderthals. Tibetans are adapted for high altitude living in part because of a gene called EPAS1 that their ancestors inherited from interbreeding with Denisovans. So much of what makes a human can’t be understood without evolution (including psychology) that books have been authored detailing it. Our unintelligent designs only make sense under the lens of evolution. For example see books by Lents, Lieberman, Shubin, and Hafer. Of course, that’s just detailing with one species - us. All other animals, plants and fungi also have their evolutionary stories to tell. The evidence for evolution comes from so many areas of science it would take a small book just to list and discuss all the contributory fields to this grand scientific theory. Instead, I chose to ask what would be my top two best examples for someone that was interested, had limited time, and perhaps little to no biology background. This section will discuss in detail those two examples; whale evolution and shared ERVs among the great apes, which includes us. First, there needs to be some definitional discussion regarding several important terms. What is Evolution? The most common definition since the 1940s when Darwin’s idea and genetics merged to form Neo-Darwinism is a change in gene frequency (alleles) in a population over time. Notice that individuals don’t evolve, populations do and if occurring over long periods a new species may arise. Let’s say for example that genes for lighter skin color were advantageous for people living in cold and dark regions (vitamin D is made in our skin from sunlight). Those people who just happen to have lighter skin would do better and have more successful offspring. They would pass their genes on to the next generation at a higher percentage than others. If we were measuring skin color through many generations, the population would develop lighter skinned individuals as a percentage of the population. Forrest Valkai of Internet fame defines evolution simply as a change in heritable characteristics of a population through successive generations . That leaves out the reference to alleles, which of course are what is changing to produce the heritable characteristics. But it's an excellent definition. The individuals who just happened to inherit better genes for this particular environment would be more “fit” if they produced more successful offspring. Notice that there is no planning - what if the environment happens to change? Then the population characteristics would be under different selection pressures. But what is really changing through generations is the gene frequencies in the population that are producing the physical or behavioral characteristics of individuals. Of course there could be pressures for darker skin also depending on the amount of sunlight or other factors in this example. People who oppose evolution accept that this can be shown in the lab and in the field but claim these changes are limited. One mouse species evolving into another mouse species is “ microevolution ” in most lay literature. They are the same “kind” and we never see “ macroevolution ” they claim - a reptile evolving into a mammal or a fish evolving into an amphibian for example. I am using the terms here as they are commonly used in public discussions and not necessarily how they are actually defined in biology. Macroevolution is mostly a forensic or historical science, involving changes above the species level. We can accumulate so much evidence in science regarding a conclusion that to deny it would be perverse even if it was not directly observed. Science rarely proves; that’s for some areas of philosophy or mathematics. A good tracker can tell from prints what the species was, which direction it was moving, maybe it’s sex by weight and age, if it was injured, how fast it was moving, when it passed by, etc. without ever seeing the animal. The same occurs in court cases where a person can be convicted even if the murder weapon (the “how”) is not found. The “what” is not in question. See why that is important: How vs. What . With evolution, we can know it happened without necessarily seeing all the macro changes. The evidence for evolution is now so overwhelming that to not accept it is perverse. Macroevolution involves more than micro over large time scales. It includes many independent scientific fields and also must include contingencies and random processes (like a rock coming from outer space and ending the reign of the dinosaurs). Macroevolution is the history of life. Laurence Moran has written about his views on micro/macro evolution in his biochemist Sandwalk Blog: https://sandwalk.blogspot.com/2022/10/macroevolution.html "... evolution is a theory. It is also a fact. And facts and theories are different things, not rungs in a hierarchy of increasing certainty. Facts are the world's data. Theories are structures of ideas that explain and interpret facts. Facts don't go away when scientists debate rival theories to explain them. Einstein's theory of gravitation replaced Newton's in this century, but apples didn't suspend themselves in midair, pending the outcome. And humans evolved from ape-like ancestors whether they did so by Darwin's proposed mechanism or by some other yet to be discovered" ~ Stephen Jay Gould in Discover Magazine, May 1981. An interesting study in marine snails that went from reproducing using eggs to live births has shown that the genes involved indicated gradual steps as Darwin proposed:  " Scientists were able to identify 50 genes that are perfectly associated with reproductive mode, as well as estimate the time of their origin. The results showed they accumulated gradually, spreading at different times in the past. This demonstrates that innovation can evolve progressively, rather than in a single evolutionary step." https://scitechdaily.com/there-is-no-monster-mutation-biologists-uncover-the-secrets-of-evolutionary-change/?fbclid=IwAR0LA2XDm11hjiac3VjlCsbLfZFY351Q0MFBXxYnfCMiuzQTR5M8tTK1y0g Also - what is the difference between scientific facts, theories, laws and hypotheses in the context of evolution? https://evolution-outreach.biomedcentral.com/articles/10.1007/s12052-007-0001-z What is Natural Selection? This has commonly been defined as the differential reproductive success of individuals within a population. We can demonstrate NS in the lab and in the field. Bacteria developing antibiotic resistance is an example. A bacterial population changing to be more resistant is due to the antibiotic killing off most but leaving some behind to reproduce that just happened to be resistant. In future generations more and more bacteria in this strain will be resistant to that antibiotic. The change in the bacterial population over time is evolution. Again, Forrest Valkai defines natural selection as simply the nonrandom selection of random mutations . Opponents of evolution by NS claim that NS is not powerful enough no matter how much time to produce significant changes in populations. For example they agree again to microevolution but deny that this mechanism is powerful enough to drive the changes from a shared chimp ancestor to us. Note that NS is just one mechanism - there are others such as genetic drift, horizontal gene transfer and endosymbiosis. For NS to work it needs variation in the population and anti-evolutionists reject known methods to produce significant variation. Notice that they are arguing against the “how” and not the “what” - the observations and facts that are only explained well by evolution. Mechanisms for evolution are debated all the time in science; the fact of evolution is not. If your house is destroyed and this is not witnessed, one can argue if it was by hurricane, tornado, earthquake, fire, or an angry neighbor but the fact that your house is destroyed is not open to debate. We have so much evidence for evolution that its occurrence is no longer up for debate. There is no controversy about the fact of evolution in science now, just about other issues related to it such as mechanisms (how), abiogenesis, rates, etc. How We Found That Evolution Is True. Darwin was not the first person to figure out that evolution explained the rich diversity of species, both in the present and past. Many before him had the idea but could not figure out how it may have happened. Watch this short presentation as the idea of evolution unfolded. https://www.youtube.com/watch?v=18YwBwIK_no Darwin and Wallace In 1837, a year after Darwin returned from his five year voyage on the Beagle, he drew his famous stick figure “ I think - transmutation diagram ” in his Notebook B that species were not fixed. Darwin had read Lyell’s book about a better way to understand geology while on his voyage (Darwin was primarily trained in geology) and in 1838 read Malthus’s ideas about population growth and why species don’t overpopulate. The parts for his theory had now all come together. He already knew by then that species could and had changed over time, explaining why many were extinct, fossils and why we see so many that appear related. Mostly because of his wanting to write a book that would be so well documented for his proposed mechanism that his theory could not be dismissed and probably fears about religious backlash, he did not publish his natural selection idea for 20 years but kept doing research. Before marrying Emma in 1839, who was religious, he wrote to her about what his theory would mean: “As soon you realize that one species could evolve into another, the whole structure [foundations of a society established on the some religious beliefs] wobbles and collapses” . Later in 1844 Darwin would write to Hooker regarding his ideas, “ I have read heaps of agricultural & horticultural books, & have never ceased collecting facts— At last gleams of light have come, & I am almost convinced (quite contrary to opinion I started with) that species are not (it is like confessing a murder) immutable.” “At last gleams of light have come, & I am almost convinced (quite contrary to opinion I started with) that species are not (it is like confessing a murder) immutable.” ~ Charles Darwin Darwin’s reasons for delaying publishing his theory of natural selection are debated to this day but his delay was challenged when another scientist, Wallace, discovered natural selection also decades later and shook Darwin to his core when Wallace sent him a draft of natural selection to review for possible publication. Darwin thought he had been “scooped” since he had yet to publish. Wallace had sent a draft in 1858 to Darwin to review and true to Darwin’s good character instead of demanding that he had the idea long before Wallace - which was true and documented - it was decided that both would present the concept of natural selection together. The joint presentation to the Linnean Society in London of their papers occurred on July 1, 1858. Now Darwin could wait no longer to publish his book, but there was not enough time to write all that he wanted so instead he quickly wrote an “abstract”, what we know as “On The Origin of Species by Natural Selection, or the Preservation of Favored Races in the Struggle for Life” and published it in 1859. See two excellent movie titles about his life in the section Resources. In Victorian times “races” did not mean what we associate that word with now. Note from the title Darwin’s idea is not about the origin of life and it’s also really not about evolution directly but a mechanism, natural selection, to explain how life unfolded in the past and how to account for the species we see today. At its core only natural processes could explain nature. Of course many religious people including Francis Collins, and the Pope who speaks for over a billion Catholics, have accepted evolution through adopting theistic evolution or evolutionary creationism. Denying evolution is not rational with all the overwhelming experimental and observational evidence available. Two Examples of Evolution, Including "Macroevolution" I would like to offer only two examples as evidence of evolution. And both of these should satisfy the desire for “macroevolution” evidence. The second is an example of both human evolution and macroevolution. There is overwhelming evidence for evolution from many scientific fields, but let’s just concentrate on these two and drill down on specifics when needed. If you wish to look at some of the many other independent scientific areas that together provide overwhelming evidence for evolution, the University of Berkley has a nice, easy introduction on their site: Lines of Evidence. Part 1: Whale evolution - The first is whale evolution , because evolving over about 15 million years from an ancestor the size of a raccoon walking around to a toothless baleen blue whale should satisfy as “macroevolution”. If you’ve wondered how scientists know whales evolved I don’t want to tell you, I want to show you the overwhelming evidence so you can see for yourself. The slides usually have citations included so if desired you can go to the original sources. I’ve compiled the material by producing a 3 part series that looks at modern cetaceans, fossil whale ancestors, and DNA evidence with each about 25 minutes in length. Take a look. It will be 90 minutes well spent for all three parts. If you disagree after watching all 3 parts that whales evolved, please write to me as to why. In the comments section of Part 3 I’ve also linked some objections to whale evolution. In most cases critics fail to address the evidence presented but instead put forward a focus only on how all the adaptations arose - how could this have happened? Or what about this instead of addressing the overwhelming evidence we do have. See the discussion on why "what" comes before "how" and how is not necessarily critical to the fact of an occurrence. Part 2: Shared ERVs - shared ERVs is the best evidence for evolution I’ve seen in decades. It’s more technical to explain but well worth your time. I hope you will examine this topic. Others have noticed how powerful it is also and I will be linking sites and short videos for you to evaluate. Also I’ll discuss the common objections put forward and why in my opinion they fail. Conclusion If I can convince you that whale evolution must be true (no matter how it happened) then accepting other evolutionary changes should not be overly difficult to accept. If you can understand that 200,000 broken down, randomly inserted retroviral remnants that are found in the exact same locations between chimps and humans can only be explained rationally by a common ancestor then we’ve got our human evolution, and macroevolution evidence in another example. “Seen in the light of evolution, biology is, perhaps, intellectually the most satisfying and inspiring science. Without that light it becomes a pile of sundry facts -- some of them interesting or curious but making no meaningful picture as a whole.” ― Theodosius Grigorievich Dobzhansky References The Human Story https://www.sciencenews.org/century/human-evolution-origins-fossils-paleoanthropology#seeking-our-origins Genetics Provide Powerful Evidence of evolution https://thelogicofscience.com/2017/02/28/genetics-provide-powerful-evidence-of-evolution/ Whales and Viruses: The Light of Evolution - Episode 1 https://www.youtube.com/watch?v=1GMBXc4ocss

“There is grandeur in this view of life, with its several powers, having been originally breathed into a few forms or into one; and that, whilst this planet has gone cycling on according to the fixed law of gravity, from so simple a beginning endless forms most beautiful and most wonderful have been, and are being, evolved.” ~ Charles Darwin. On The Origin of Species A. How to use this section When interacting in dialog about evolution, there are major topics which deserve significant discussion. Many other topics are minor however and can probably be addressed with a short entry. This section is for those; a collection of items that often still make an appearance in debates by anti-evolutionists but can be addressed without needing a lengthy explanation. Many even are asked not to be used by a major Young Earth Creationist site. The best way to use this section is to just enter a topic of interest into the   Search Function  in the upper right. There is no particular order to the entries. B. Index By Title  11. Atheism & Communism       Cambrian Explosion (see blog here )  6. Coelacanth Fish       De Novo Genes  2. Dinosaur blood and soft tissue fossils 19. Earth at the center of the universe by cosmology? 18. Edward Blyth       ENCODE (see blog here ) 10. Evolution - just a theory 20. Evolution - not a religion 12. Evolution - atheistic 19. Genesis 1:1 - "In the beginning..." translated correctly?  9. Genomic Entropy 14. Incomplete Linkage Sorting      Junk DNA (see blog here ) 13. Love Explained Naturally? 17. Human-Chimp DNA Similarities  4. Human & Apes?  5. Humans Did Not Evolve From Monkeys     Orphan Genes (see blog here )      New Genes, New Information (see blog here )  8. Polonium Haloes 16. "Polystrate" Fossil Trees  7. Punctuated Equilibrium  1. Second Law of Thermodynamics 15. Stegosaurus carving?  3. Transitional Fossils C. Topics to Avoid   From the Young Earth Creationist   organization Answers In Genesis , is a page where they have determined that some topics should no longer be used by those advocating against evolution. https://answersingenesis.org/creationism/arguments-to-avoid/ Second Law of Thermodynamics The Fall Darwin’s Supposed Conversion If Humans evolved from apes, why do apes exist today? Have NASA computers proved Joshua’s long day? Was there no rain before the Flood?  God created things to “look old”. Didn’t Darwin call the evolution of the eye absurd? Didn’t a fishing boat find a dead plesiosaur? Women have more ribs than men Darwin’s deathbed conversion - a legend? Were giant skeletons found in the desert? That boat-shaped rock…is it Noah’s Ark? The “moondust” argument D. Anti-evolutionary Musings It is expected that this section may keep growing as more minor topics become aware to the site's author (often ones that were refuted years ago), where the main blogs and entries once written will not be significantly changed in the future. 1.  The Second Law of Thermodynamics. Claim:   The 2nd Law describes increasing disorder & entropy at every energy exchange. Evolution is fundamentally an increase in order and complexity. Thus it violates the Second Law. Response:  The 2nd Law of thermodynamics only applies to a closed system. The earth is not closed but is bathed in energy from the sun. For the same reason that a developing fetus is not violating the 2nd Law as it increases from a single celled zygote to a complex organism with trillions of specialized cells. The net energy/heat must be evaluated and evolution in no way violates that. Eventually the sun will die out and then evolution will stop on earth (yes, I know there won’t be an earth because of the way our star will die). If there could be a planet here after our sun’s death, the ultimate satisfaction of the 2nd Law and entropy increase will happen at this location. https://biologos.org/common-questions/does-thermodynamics-disprove-evolution 2. Dinosaur blood Claim:  Soft tissue has been found in dinosaur fossils supposedly 60+ millions of years old. It is impossible that soft tissue would be preserved for that long, thus dinosaur fossils must only be a few thousands of years old. Response:  Scientists never imagined that any organic material could last millions of years in fossil specimens. One researcher decided to test that in 2005 and Mary Schweitzer shocked the scientific world with the finding of collagen in an intact T. rex specimen she reported in 2006. Fourteen years later scientists finally revealed what probably was occurring. An iron oxyhydroxide mineral was probably cross linking with the proteins producing a very stable organic compound which was protected by the dense mineralized bone around it. Evolution is not threatened at all by this finding. https://www.vox.com/2015/6/9/8748035/dinosaur-fossil-blood-proteins   https://www.nature.com/articles/nature.2012.11637   A 2023 published study looked at the two major hypotheses that explain how soft tissue could be fossilized for millions of years and determines that rather than being exclusionary, they both are probably part of the same process: " This review posits a chemical framework describing the persistence of biological “soft" tissues into deep time. The prior iron-mediated radical crosslinking and AGE/ALE mechanisms are re-described in context of established chemistry from a diversity of scientific fields. Significantly, this framework demonstrates the hypotheses presented by Schweitzer et al. (2014)  and Wiemann et al. (2018)  are, in many cases, subsequent steps of a single, unified reaction mechanism, and not separate hypotheses. Knowledge of the chemical mechanisms underlying vertebrate soft tissue preservation has direct implications for molecular archaeology and paleontology, including efforts at molecular sequence recovery within the ancient DNA and palaeoproteomic communities." A chemical framework for the preservation of fossil vertebrate cells and soft tissues. https://www.sciencedirect.com/science/article/pii/S0012825223000569?via%3Dihub Dinosaur blood and so much more! 2019. Buchanan, Scott. More: Mary Schweitzer, PhD on creation. Radiometric dating. Great Review. https://letterstocreationists.wordpress.com/dinosaur-soft-tissue/?fbclid=IwAR2r9A1n8DpdwXJXOWqYooCiDRYGOaR7rKiFww-MbgPMAW_KXeZtvOf0J3A Why radiocarbon gives erroneous dates on dinosaur bones https://online.ucpress.edu/abt/article-abstract/84/6/336/189896/Radiocarbon-in-Dinosaur-Bones-RevisitedProblems?redirectedFrom=fulltext More troubling is when a leading anti-evolutionist and apologist makes what should be a very embarrassing video about the discovery. Please watch : https://www.youtube.com/watch?v=R9bo9tyTmC8   3. Transitional Fossils Claim:  There are no transitional fossils. Because to an anti-evolutionist evolution cannot be true and thus there can’t be any. Response: There are scores of transitional fossils. Some like Tiktaalik  were first predicted and then found by looking in the appropriate aged rocks. These fossils show an intermediate state and characteristics between an ancestral trait and those of its later descendants. Indeed the 200+ whale fossil species can all be considered transitional. See part 2 of the evolution of the whale and fossils   presented here that actually shows hind limbs shrinking, blow holes migrating, intermediate whale fossils with teeth and baleen, etc. It is simply not true that there are no transitional fossils. There are plenty. Transitional Fossils: http://www.fossilmuseum.net/Evolution/transitionalfossils.htm   Transitional Fossils: https://en.wikipedia.org/wiki/Category:Transitional_fossils   Darwin's fear of an incomplete fossil record was unjustified: "Now, a team of sedimentologists and stratigraphers from the Netherlands and the UK have examined how this incompleteness influences the reconstruction of evolutionary history . To their surprise, they found that the incompleteness itself is actually not such a big issue... The regularity of the gaps, rather than the incompleteness itself, is what determines the reconstruction of evolutionary history," explains Niklas Hohmann of Utrecht University's Faculty of Geosciences, who led the study. "If a lot of data is missing, but the gaps are regular, we could still reconstruct evolutionary history without major problems, but if the gaps get too long and irregular, results are strongly biased." https://phys.org/news/2024-08-darwin-unjustified-fossil-gaps-major.html "A common misconception of evolutionary biology is that it involves a search for “missing links” in the history of life. Relying on this misconception, antievolutionists present the supposed absence of transitional forms from the fossil record as evidence against evolution. Students of biology need to understand that evolution is a branching process, paleontologists do not expect to find “missing links,” and evolutionary research uses independent lines of evidence to test hypotheses and make conclusions about the history of life." https://evolution-outreach.biomedcentral.com/articles/10.1007/s12052-009-0126-3 4. Humans & Apes Claim : Humans are not apes. Response : Sure they are. We are not plants, rocks or fungi; we are animals. And when looking at comparative DNA, anatomy, and physiology we resemble the great apes and are placed with them in taxonomy and classification. K. Animalia>:P. Chordata>C. Mammalia>O. Primates>F. Hominidae (Gorillas, Orangutans, Chimps & Bonobos, and Humans). This generally has been the classification used in some form by science as early as 1758 by Linnaeus and especially by Gray in 1825. https://en.wikipedia.org/wiki/Human_taxonomy   5. Humans did not evolve from Monkeys Claim : We did not evolve from monkeys. If we did, why are there still monkeys? Response : Correct. We did not evolve from present day monkeys, but rather from a shared ancestor with them. The last ancestor we shared with chimps was about 6 million years ago as determined by DNA molecular clocks and fossils, although no fossil of this species has been found to date. The tropics rarely produce good fossilization due to the warm temperatures and degradation. In addition, we have human chromosome 2 fusion  which shows why we have 46 chromosomes and the other great apes 48. We were derived from Adam who was created from dust? Why is there still dust?  Matthew Bonnan, Malcomb Il. Middle school student evolution contestant. Florida. http://www.flascience.org/ss2010top10.html   6. Coelacanth fish Claim : Science claimed that this fish was extinct. It has been found and now is called a "living fossil". It did not evolve, which disproves evolution Response:   The coelacanth's deep sea habitat has been stable over millions of years, there was little predation and there probably were few evolutionary pressures to change. Scientists thought it was extinct since until that time only fossils had been found. In 2013 it was announced that its genome had been sequenced and it was indeed evolving, although slowly. https://www.nature.com/articles/nature12027   https://phys.org/news/2021-02-fossil-coelacanth-evolved-dozens-genes.html?fbclid=IwAR2OOyDf5-A6kZPw6IRawCHNfsZ79cEGBo27uXrAyvOjog4aIHOwYJTLTHk   7. Punctuated Equilibrium Claim:   There are large gaps in the fossil record. Two famous paleontologists coined the term to describe this because the gaps are persisting. The gaps are there because evolution is not true. Response: In 1972 Eldridge and Gould suggested that the pattern often in the fossil record was not gradual change but long periods of stasis followed by relatively quick evolution, producing more of a step pattern and happening so quickly in geological time that gaps were normal. Since their publication many transitional fossils have been found. Most change in the fossil record is a mixture of stasis and gradualism. PE does not negate evolution at all. Even Darwin noted that rates of change would not be constant and probably varied between species. PE coexists with gradualism. https://www.quora.com/Is-punctuated-equilibrium-the-most-widely-accepted-plausible-theory-of-evolution   Hancock discusses why punctured equilibrium was eventually abandoned as a mechanism for explaining fossil record stasis. " Few concepts in the history of evolutionary biology are as misunderstood and misapplied as Gould and Eldredge's theory of punctuated equilibrium. In this video, I explain what it meant originally, the claims that it made, and ultimately why it's rejected today." 8. Polonium Haloes Claim:  Discolorations sometimes occur in rocks due to radioactive decay of alpha particles producing a dark radioactive halo looking like tiny bathtub rings on cross section. Robert Gentry spent years studying them and since polonium decays with a short half life (1380 days), these decay haloes are evidence of a young earth that was created only thousands of years ago and the basement layer is Precambrian. Response:  Although it may still be incompletely explained, enough is known that Gentry's hypothesis of a young earth creation has been refuted by Thomas A Baillieul, and others. It's basically a God of the Gaps argument. "Gentry’s polonium halo hypothesis for a young earth fails, or is inconclusive for all tests. His samples are not from “primordial” pieces of the earth’s original crust, but from rocks which have been extensively reworked. He is unable to demonstrate that concentric halos in mica are caused uniquely by alpha particles resulting from the decay of polonium isotopes. Finally, his hypothesis cannot contend with the many alternative lines of evidence that demonstrate a great age for the earth. In the end, Gentry’s young-earth proposal, based on years of measuring discoloration halos, fails to generate a scientific model that is either internally consistent or consistent with generally accepted scientific understanding of geophysical processes and earth history."  [Polonium Haloes Refuted] http://www.csun.edu/~vcgeo005/baillieul.pdf   "First of all, the samples of biotite that contain Gentry's polonium halos came from pegmatite dikes and calcite vein dikes which cross-cut metamorphosed volcanic, sedimentary, and igneous rock units. The dikes are clearly the last to have formed, not the first. Second, these dikes are not the vast, extensive granite gneisses which Gentry claims are the backbone of the mountains and continents; they are relatively small features. Third, two of Gentry's sites are not even granites but calcite vein dikes, most likely of hydrothermal origin. The biotite was formed in the solid matrix by metamorphosis. And fourth, crystal size in igneous, vein, and metamorphic rocks ranges from microscopic to very large, is primarily due to cooling rates, and cannot be used to identify "created" rocks. So, the "basement rocks" in which Gentry found his halos turn out not to be "basement rocks" at all. In fact, they appear in rocks that formed much later than Earth's oldest rocks. This fact alone tells us that the rocks bearing Gentry's halos, even if instantly created, have no bearing on the origin and age of Earth.... Still, we must give Gentry his due. Nothing in geology fully explains the apparent occurrence of the polonium halos as described by Gentry. They do remain a minor mystery in the field of physics. But this does not mean that no explanations are possible or that it is time to throw in the towel and invoke the "god of the gaps." [Gentry's Tiny Mystery Unsupported by Geology] https://ncse.ngo/gentrys-tiny-mystery-unsupported-geology   9. "Genomic Entropy" . This is an argument developed by the creationist John C. Sanford PhD, a retired plant geneticist from Cornell University. A former atheist, he moved through Theistic Evolution to Old World Creationism eventually landing on Young Earth Creationism, a belief that rests on absurd claims like the universe and earth are less than 100,000 years old (his words), there was a global Noachian flood, an ark, a historical Adam/Eve and a "Fall", etc. He is a strong advocate of Intelligent Design, which is basically a religion and has been debunked, and even I list some examples in one of my blogs; Why not Intelligent Design?  . I think it fair to see what other beliefs people hold also. What other views accompany certain assertions that they make and how does this not impact on our ability to trust their claims? Disclaimer: I have not read his book, newest edition in 2014 at the time of this writing. The critical comments on Amazon regarding his book are telling. His basic argument is derived from population genetics modeling which is actually not his area of expertise. His background is in plant genetics as an applied geneticist, an inventor, and a good one. His basic premise is that the human genome collects so many mutations that are not removed by natural selection that if evolution were true we and other species would have degenerated into extinction long ago. He asserts that there have been no new functional genes since Adam and The Fall. Like Behe, he claims only degeneration in life in terms of structures and genomes. He dismisses beneficial mutations because they are too rare. He cites Kimera's Curve as a prediction for his conclusions. But Kimera himself disagrees with Sanford, claiming that any beneficial mutations would have a greater  effect rather than none ( Kimera, 1979 ). I don't know if Sanford is just looking at point mutations (it seems so) rather than segmental duplications and gene duplications which is how new genes are produced and has been documented - pointed out in this blog  - to the level that they basically prove evolution. Population geneticists working in the field don't find Sanford's claims or other similar creationist writings for genetic entropy convincing at all. For example: "If we, as a species, were simply constantly accumulating new mutations, then one would predict the gradual degradation of every aspect of fitness over time, not just intelligence. Indeed, life could simply not be sustained over evolutionary time in the face of such genetic entropy. Fortunately (for the species, although not for all individual members), natural selection is an attentive minder. Analyses of whole-genome sequences from large numbers of individuals demonstrate an ‘excess’ of rare or very rare mutations. That is, mutations that might otherwise be expected to be at higher frequency are observed only at low frequency. The strong inference is that selection is acting, extremely efficiently, on many mutations in the population to keep them at a very low frequency. One of the key misconceptions in the Crabtree articles is that mutations happen to ‘us’, as a species. His back-of-the-envelope calculations lead him to the following conclusions: ‘Every 20–50 generations we should sustain a mutation in one copy of one of our many ID [intellectual deficiency] genes. In the past 3000 years then (∼120 generations), each of us should have accumulated at the very least 2.5–6 mutations in ID genes’. The loose phrasing of these sentences reveals a fundamental underlying fallacy. ‘We’ have not sustained mutations in ‘our’ intellectual deficiency (ID) genes, and ‘each of us’ has not accumulated anything over the past 3000 years, having only existed for a fraction of that time. Mutations arise in individuals, not populations. Neither does it matter that there are many thousands of genes involved in the developmental systems that generate a well-functioning human brain; selection can very effectively act, in individuals, on new mutations that impair these systems." https://www.cell.com/trends/genetics/fulltext/S0168-9525(12)00194-1   It also appears that if there is a lot of junk DNA in our genome, the mathematical modeling he uses breaks down if that is true. How we know our genome is mostly Junk DNA  is discussed here. To fully evaluate his assertions one needs to know about nearly neutral theory  and how it can avoid purifying natural selection to fix genes in a population via genetic drift. This approach emerges from molecular population genetics and mathematical modeling. Needless to say, we know evolution is true because of all the DNA evidence we have (see the blogs on this site). Since we and large animals have not all gone extinct, his modeling must be producing conclusions in error. No, the universe and earth are not 6,000 to 100,000 years old and there was no ark or global Flood a few thousand years ago. Women don't die every 2 minutes in childbirth around the world due to a curse brought on by a single woman eating a forbidden fruit offered by a talking snake plucked from a magical tree planted in a middle of a fantasy garden so she would not miss it a few thousand years ago. They die and suffer because of the evolution of bipedalism and a delayed developmental process especially in infants. Genetic Entropy is a real concept in population genetics and it's unfortunate that those writing opposing creationist claims conflate it with the 2nd Law of Thermodynamics and entropy as used in physics. Unfortunately many biologists may not be knowledgeable in nearly neutral theory in population genetics. I certainly am not qualified to discuss it. What we need is an evolutionary molecular geneticist who can actually speak to Sanford's book and this highly mathematically and specialized topic. And there is one on the Internet. No, evolution is in no way threatened by genetic entropy. It is just another creationist fail, but this one is more complicated than most and is much more "sciencey". Genetic Entropy (Again) . Mutational load paradox and more. https://www.youtube.com/watch?v=WFoVOXeuBzg   The Fatal Flaws of Genetic Entropy . Comment section instructive. https://www.youtube.com/watch?v=P2o_KC7sc98&t=1032s   10. Evolution is just a theory. When one reads this there are at least two issues. The first is that the person does not know what a scientific theory is and secondly there is an emphasis by the claimant of "just". Evolution is defined as the change in heritable characteristics (alleles at the DNA level) of a population through successive generations. This definition has been used in many branches of biology since the 1940s. Of course this is true - we can see it in lab experiments and also in the field directly. Evolution as it is used and studied by scientists and medical researchers is a fact. Yes,  evolutionary theory is critical to modern medicine. Secondly, the  Theory of Evolution  is just as well supported as the scientific theories of Germ, Cell, Gravity and Relativity. We speak of the fact of gravity and also Gravitational Theory. A scientific theory is a coherent group of tested general propositions and facts shown to be correct that can be used as principles of explanation and predictions for a class of observations. It explains "how"  we know the observations of evolution are true - the facts of evolution. Evolution has withstood 150 years of testing and  predictions. It can be falsified. In contrast, a scientific hypothesis is an educated guess  that needs testing. If we were to see smoke coming out of a internal combustion car, we could guess that it was a water leak (head gasket?) and not an oil leak by the color. Looking for the problem will confirm or rule out our  educated (we know something about car engines) guess. Saying I have "theory" about the cause is not using the term as scientists use "theory", a scientific theory. At best guessing the problem causing thick smoke to come out of a car is equivalent to a hypothesis and not a theory, even though that is how we may speak commonly. Who says evolution is both fact and a scientific theory?  Lots of qualified people! "Well evolution is a theory. It is also a fact. And facts and theories are different things, not rungs in a hierarchy of increasing certainty. Facts are the world's data. Theories are structures of ideas that explain and interpret facts. Facts don't go away when scientists debate rival theories to explain them. Einstein's theory of gravitation replaced Newton's in this century, but apples didn't suspend themselves in midair, pending the outcome. And humans evolved from ape-like ancestors whether they did so by Darwin's proposed mechanism or by some other yet to be discovered." ~ Stephen J. Gould, "Evolution as Fact and Theory"; Discover, May 1981   " Let me try to make crystal clear what is established beyond reasonable doubt, and what needs further study, about evolution. Evolution as a process that has always gone on in the history of the earth can be doubted only by those who are ignorant of the evidence or are resistant to evidence, owing to emotional blocks or to plain bigotry. By contrast, the mechanisms that bring evolution about certainly need study and clarification. There are no alternatives to evolution as history that can withstand critical examination. Yet we are constantly learning new and important facts about evolutionary mechanisms." ~ Theodosius Dobzhansky. Nothing in biology makes sense except in the light of evolution. American Biology , 1983. " Today, nearly all biologists acknowledge that evolution is a fact. The term theory is no longer appropriate except when referring to the various models that attempt to explain how life evolves... it is important to understand that the current questions about how life evolves in no way implies any disagreement over the fact of evolution." ~ Campbell, Biology  2nd ed. 1990. " A few words need to be said about the "theory of evolution," which most people take to mean the proposition that organisms have evolved from common ancestors. In everyday speech, "theory" often means a hypothesis or even a mere speculation. But in science, "theory" means "a statement of what are held to be the general laws, principles, or causes of something known or observed." as the Oxford English Dictionary defines it. The theory of evolution is a body of interconnected statements about natural selection and the other processes that are thought to cause evolution, just as the atomic theory of chemistry and the Newtonian theory of mechanics are bodies of statements that describe causes of chemical and physical phenomena. In contrast, the statement that organisms have descended with modifications from common ancestors--the historical reality of evolution--is not a theory. It is a fact, as fully as the fact of the earth's revolution about the sun." ~ Futuyma, Evolutionary Biology , 2nd Ed. 1986. Also - what is the difference between scientific facts, theories, laws and hypotheses in the context of evolution? https://evolution-outreach.biomedcentral.com/articles/10.1007/s12052-007-0001-z The Theory of Evolution is not "just" a theory . It is arguably the most important discovery made by humans. I argue for that assertion here because it affects so much of our lives - The Greatest Discovery. 11.  Atheism and Communism Claim: The official position of communist countries about religion is state sponsored atheism. Their ideology is inherently evil and thus atheism is evil and produces immoral and dysfunctional societies. Response: There are multiple errors with this claim. First, correlation does not equal causation. It's true that in communistic countries state sponsored atheism is often supported. That however is often a means of the communistic leaders to control religious beliefs and all other aspects of its citizen's lives. Because Hitler wore a certain type of mustache, does every man who wears a mustache believe as Hitler did? Secondly, the problem with communistic countries is not atheism but rather communism. Many of its leaders are despots and have a history of torture and killing (Stalin, Pol Pot). They did not kill in the name of atheism but rather for communism and themselves. They erected statues of themselves and basically forced worship of their leaders - which resembles a religion more than a secular society. There are no parades showing large "A" flags, no statures erected for Atheism alone. Thirdly, this confuses atheism with a worldview. It is not. Nor is it a religion. How do we know? Because different atheists have different worldviews. If atheism was a worldview that would not be possible. Atheism is the lack of a belief in God due to a lack of convincing evidence for the claim. It is not the belief that there is no God; that is a positive statement. A lack of belief can't be a belief. Compare the life of a compassionate scientist like Sagan and the evil immoral Stalin and Pol Pot. All are atheists. Does one really want to say they have the same worldview? Some atheists even have founded charities to help in disasters. Fourth, we can test the least religious and most atheistic societies in terms of human well being and flourishing. What do we see? The best places to live year after year are the most atheistic societies, countries and in America the least religious states. See the evidence here.  If one wished to compare a religious worldview with atheism, we need apples to apples and the worldview most adopted by atheists is secular humanism; that far outperforms religious worldviews - we have the evidence for that conclusion. Atheism is just the lack of a belief in theistic claims (God) due to a lack of good evidence for God assertions. It is provisional and subject to change if sound evidence is ever provided. A lack of belief can't be a belief no more than bald a hair color. 12. Evolution is atheistic Claim: If you accept evolution, macroevolution, that means you are an atheist. Evolution always leads to atheism. Response: Absolutely not. Evolution is a fact and theory that explains the origin of species. It makes no direct assertions about religions. In fact evolution is accepted by many believers. And this includes the Catholic Church and the Pope, leader of 1.2 billion Christians. Christian apologist evangelicals and scientists like Dennis Venema, Francis Collins, Joshua Swamidass, Denis Lamoureux and many, many others accept evolution because they realize how overwhelming the evidence is. This is called theistic evolution or evolutionary creationism (TE/EC). It is true that some religions and creationisms make assertions to history, science and reality that conflicts with evolution. For those working in cancer research, evolution for these believers is necessary for their oncology work . The main issue here in my opinion is that evolution appears to be naturalistic and materialistic. There appears to be no goals or planning. Natural selection sacrifices incredible numbers of offspring to get just a few replacement individuals into the next generation. Mutations to produce new genes are random. There have been 5 huge mass extinctions and over 99.9% of all species that have existed have gone extinct, some by rocks from space. Truthfully, what major creationist organizations attack is the apparent conclusion of many people looking at evolution, macroevolution, that it is all naturalistic and materialistic. No room for God. In addition, a close look at biology without cherry picking reveals no intelligent design . 13. What about love? Claim : Science can't explain love Response: Not only can science explain and study it, but also marvel in the joy of it and not diminish it. "Understanding how chocolate tastes good doesn't diminish how good it tastes." https://www.facebook.com/reel/1747651992368587 14. Incomplete Linkage Sorting (ILS) It turns out that when comparing genomes there are many exceptions to the clustering of random DNA changes from ERVs , segmental duplications , DNA repairs , transposon elements  (TEs) and pseudogenes . Normally thousands of these random DNA changes fit nicely into predicted phylogenetic evolutionary trees. As an example, TEs have been found to be inserted into gorillas and humans but not chimps. Doesn’t this invalidate using these markers for evolution? Not at all. What is going on is called  incomplete linkage sorting (ILS). Our genomes are made up of many different alleles, which are possible genes at a given location or locus. As an example, with the major blood group ABO, one can be OO, AO, BO, AB, AA or BB. Because we normally get one chromosome from each parent there are only two possible places for these specific multiple alleles. With the immune system for example there is an MHC complex where hundreds of possible alleles for a gene are available. Genes that have multiple possible alleles are called polymorphic. If speciation occurs rapidly relative to the time required for it to become fixed in a population (where all members have it), a new species may randomly lose particular genes just by chance and genetic drift when it splits off from the ancestor species. Anti-evolutionists made a big deal in 2012   after the gorilla genome was sequenced and it was found that up to 30% of the chimp, human and gorilla genomes showed incomplete linkage sorting (5). Considering that a particular critic of evolution is perhaps the leading creationist geneticist the attempt at obscuration and misrepresenting the findings was breathtaking. We’ve met Dr. Tomkins before in several other blogs on this site. See human chromosome 2 fusion   , pseudogenes , and especially comments by Dr. Zach Hancock.   Dr. Tomkins is arguably the most prolific Young Earth Creationist writer in terms of genetics. It seems lost on anti-evolutionists that ILS is expected, noted and actually was predicted from population genetics by Kingman in 1982 (*). Instead of bad news for evolution this apparent anomaly in phylogenetic analysis actually supports evolution due to calculations, and the real apparent problem is why a top creationist apologist in genetics seems to have left his PhD back at his granting institution. For an explanation of ISL - it’s not easy to understand - see an article at The Panda’s Thumb  and Freethought Blogs   (7). One of the best insights possible into erroneous anti-evolution claims is drilling down on their arguments to expose fallacies, often committed by omission. * - see also discussion here:   Understanding Incomplete Linkage Sorting. https://www.reddit.com/r/evolution/comments/2w42at/understanding_incomplete_lineage_sorting/# 15 . A Stegosaurus carving? Young Earth Creationist claim. "Atheists say that Christian's are the ones who deny evidence. But time and time again, atheists will deny this excellent and absolutely solid piece of evidence against their dogmatic religion of atheism. They have to have millions of years because without it, their worldview will collapse. They don't want the Bible to be true, so they go with humans and dinosaurs being separate by millions of years. However, we have this archeological discovery where ancient people carved a Stegosaurus. Don't tell me how the anatomy is wrong, because what if it's just the artist's interpretation?" FB: Evolution and Creationism Open Debate. 11/29/2023 "This time it’s the silly “ Stegosaurus at Ta Prohm ” rumor. This myth has been popularized by young earth creationists*, who’ve argued that one particular small carving on a doorway at Ta Prohm depicts a Stegosaurus. Never mind that the entire temple is covered with carvings of fantastic and mythical creatures, this one carving is evidence that humans and dinosaurs co-existed. The carving is found within a series of other carvings depicting non-mythological creatures, such as monkeys, deer, birds, and water buffalo, and other scenes... So, what we would have in this doorway is a series of carvings of wild animals (with the exception of a domesticated water buffalo) that are frequently found in the forests of Cambodia. Maybe it’s a lizard, or a rhino, or a pangolin. But it is not a dinosaur." https://alisonincambodia.wordpress.com/2014/10/14/that-is-not-a-stegosaurus/?fbclid=IwAR3PvW-XKJl4S-0oxcJYI7j92gqiqkGjreiLDSfGxmwTHwQHtxcEgZQnZW0   More like the local rhinos with added decorations. This confirmation bias and motivated reasoning overload is common among YECs. 16. "Polystrate" Trees To the anti-evolutionist, this is a "gotcha" for evolution. Fossil trees that supposedly span millions of years, thus completely disproving evolution in their view. Note that this is an argument put forward mainly by Young Earth Creationists. A simple Google of "polystrate" trees will show how popular these are in YEC circles, and YouTubes will demonstrate how gleeful they are that these findings supposedly are perfectly explained by a global flood and supposedly disprove evolution. Ancient in situ   lycopsid , probably Sigillaria , with attached stigmarian roots . Specimen is from the Joggins Formation ( Pennsylvanian ), Cumberland Basin, Nova Scotia. From: Michael C. Rygel via Wikimedia Commons These fossil upright trees have been found in several places around the world. The term polystrate is not a recognized term in geology; it's a term coined by Young Earth Creationists. They explain them as a product of a global catastrophic Flood that occurred about 4,000 years ago. What is the truth about them, and more importantly how do we know? What are the creationist PhDs not telling us? Lying by omission is still lying. These are actually formed by rare and infrequent localized flooding. The fact that they only occur in certain areas is a clue to what really happened. An 11 minute video by Erika details the main points that disprove this creationist claim. Below is her summary. 1. Polystrate is not an accepted geological term  because they don't span millions of years of strata 2. The fossils show root growth  after partial burial. Impossible for the creationist explanation in seawater but perfectly understandable by geology 3. Some of the upright fossil trees show regenerative growth  - they were growing after their partial repeated burials as the trees tried to recover 4. We can see this type of repeated local flooding and partial burial of trees today  in certain areas. The areas in the fossils and today show repeated sedimentary flooding partially burying the trees. The trees respond by growth until the next flooding and that continues through cycles. 5. Thus, when examining ALL the applicable evidence, these upright tree fossils actually disprove young earth creationism and are wonderfully explained by evolution and geology. Please watch this 11 minute video because she SHOWS the evidence that fits evolution and actually disproves them supporting a global flood. And she's entertaining! Perhaps the best 11 minutes you could spend today. A good summary from Wikipedia: https://en.wikipedia.org/wiki/Polystrate_fossil 17 . Human and chimp genomic similarities How similar are chimp and human genomes? Well, it depends on what one is comparing. Recall that we have 25,000 genes. The protein coding genes make up 20,000 and there are another 5,000 genes that code for RNA products that have functions with regulation for example but do not directly produce protein products. Enzymes that control just about everything are the main proteins produced. These genes that don’t produce proteins are called “non-coding”. Our genome contains about 3 billion  pairs of ATCG letters but only a few million of those compose genes. For example, when a gene sequence is read to make a messenger RNA, many areas of the initial mRNA sections are cut out and thrown away and the active parts of the mRNA are then fused together for the final instructions to go to the protein ribosomal “factories”. The initial mRNA needs to be processed and refined before being sent to the ribosomes. The active areas in the mRNA are called  exons and the sections that are nearly always thrown away and degraded are called introns . About 30% of our genome is made up of these introns which are a type of junk DNA.  So, what we include in our chimp - human comparison matters. Do we just include the active genes which tend to be conserved in evolution (little changed over time and between species) or do we include introns or even parts of the chromosomes that have been inserted and deleted, called indels ?  It turns out that if we compare those 20,000 protein coding genes between humans and chimps the ATCG exact base sequences are 99% identical to every letter between us and chimps. If we include all the insertions and deletions, changes in the genome due to movements of genetic material, we are still 96% exactly the same as chimpanzees (1, 2). What then makes us different from chimps? We think it’s largely how and when those genes are turned on and off. And those regulatory genes are in the other parts of the genome. In other words, if you want to make a bigger more complex brain, you keep those genes active in embryological and fetal development turned on longer. That is an oversimplification but that is the general idea of how we can have 99% the same exact protein coding genes and yet have important phenotypic differences between humans and chimps. Anti-evolutionist attacks on the percentages Since these similarities are best explained by evolution and evolution deniers presuppose and assert that humans were created separately from all the other great apes, there has been a concerted effort to lower the observed DNA similarity percentages between us and chimps/bonobos. For example, Tomkins in 2013 wrote an article claiming that the real similarity between chimps and humans was only 70%; all the other scientists except his small fringe group that thinks the universe is only about 6,000 years old are purposely misleading with the findings (3). Notice that Tomkins did not publish in an established peer reviewed scientific journal where his assumptions could be evaluated. Novella showed in 2015 that Tomkins’ attempt was not credible: " So how does Tomkins come up with 70% . Well, he is not comparing point mutations of aligned segments. He is comparing chromosomes to see how many segments line up to some arbitrary amount.  As many others have already pointed out , this result is not wrong, it’s just irrelevant. Well, it might also be wrong. Others have found it  difficult to reproduce his results . But even if his analysis is accurate, it is simply the wrong analysis to apply to dating the last common ancestor.  To explain the problem further, he is applying mutation rates for point mutations (changing a single base pair) to other types of mutations, like gene duplications or insertions, that might change thousands or millions of base pairs with a single mutation. He is essentially treating a single mutation that results in the insertion of 10,000 base pairs into the genome as if it were 10,000 separate mutations of single base pairs.” (4) Another creationist article cited Luskin in an attempt to throw doubts on the figures scientists have produced and confirmed. They also attempt to mock scientific findings that show common descent and human evolution (5). Humans and chimps are 99% or 96% exactly the same depending on which parts of the genome are compared. These figures are sound, confirmed and most consistent with evolution.  Literature Cited. 1. https://www.genome.gov/15515096/2005-release-new-genome-comparison-finds-chimps-humans-very-similar-at-dna-level 2.   https://www.nature.com/articles/nature11128 3.  https://digitalcommons.cedarville.edu/icc_proceedings/vol7/iss1/33/ 4. https://theness.com/neurologicablog/chimp-and-human-dna/ 5.   https://breakpoint.org/of-primates-and-percentages-no-humans-arent-99-chimp/ 18. What about Edward Blyth? "One of the tactics that creationists use to cast doubt on evolution is to suggest that Darwin undeservedly received the credit for the theory of natural selection and misappropriated the idea from the work of other scientists (see for example http://www.uncommondescent.com/intelligent-design/was-blyth-the-true-scientist-and-darwin-merely-a-plagiarist-and-charlatan/ ). This claim is as false as the “science” of creationism itself.As  any student of science and history knows, new discoveries in science seldom emerge from a single source. Many of the advancements of science occur when new knowledge, derived from a variety of sources, is blended together to form new theories. Credit for scientific discovery is often a messy business and this was certainly the case with Darwin. Contrary to Looy’s claim, natural selection was first described not by Blyth (or Darwin for that matter), but by the ancient Greek philosophers Empedocles and Aristotle in the third and fourth centuries BCE. Many scientists and philosophers in the centuries that followed contributed to the understanding of the adaptation of species due to environmental and competition pressures: al-Jahith, Harvey, Paley, Linnaeus, Buffon, Mathus, Lamarck, and Darwin’s grandfather, Erasmus Darwin, to name a few (see http://evolution.berkeley.edu/evolibrary/article/0_0_0/history_index_01 ). Blyth contributed to the pool of knowledge with his insightful observations of bird species (specifically the birds of India) and his analysis of selective breeding practices of domesticated animals in a series of articles in The Magazine of Natural History  from 1835 to 1837." https://ncse.ngo/edward-blyth-creationist-or-just-another-misinterpreted-scientist Even the biologist and creationist Dr. Todd Wood notes in his article that Darwin did not plagiarize natural selection. There is no Darwin Conspiracy: https://answersresearchjournal.org/no-darwin-conspiracy/ 19. Is Earth really at the Center of the Universe? Claim: Cosmological observations (Cosmic Background Radiation, for example) indicates we are at the center of the universe. This supports a Biblical worldview of Genesis 1:1 Response : First, yes it does appear that way. But it’s an illusion because anywhere in the universe will look to an observer that they are the center of the universe. Most creationists who think they have a Genesis gotcha appeal to two sources. The most common referenced quote is from Lawrence Krauss in 2006: “That is, we live in one universe, so we're a sample of one. With a sample of one, you have what is called a large sample variance. And maybe this just means we're lucky, that we just happen to live in a universe where the number's smaller than you'd predict. But when you look at CMB map, you also see that the structure that is observed, is in fact, in a weird way, correlated with the plane of the earth around the sun. Is this Copernicus coming back to haunt us? That's crazy. We're looking out at the whole universe. There's no way there should be a correlation of structure with our motion of the earth around the sun — the plane of the earth around the sun — the ecliptic. That would say we are truly the center of the universe. The new results are either telling us that all of science is wrong and we're the center of the universe, or maybe the data is imply incorrect, or maybe it's telling us there's something weird about the microwave background results and that maybe, maybe there's something wrong with our theories on the larger scales. And of course as a theorist I'm certainly hoping it's the latter, because I want theory to be wrong, not right, because if it's wrong there's still work left for the rest of us.” The Energy of Empty Space That is Not Zero Another quote often put forward is from Hubble in his 1937 book: “…Such a condition would imply that we occupy a unique position in the universe, analogous, in a sense, to the ancient conception of a central Earth.…This hypothesis cannot be disproved, but it is unwelcome and would only be accepted as a last resort in order to save the phenomena. Therefore we disregard this possibility…the unwelcome position Here of a favored location must be avoided at all costs… such a favored position is intolerable…. Therefore, in order to restore homogeneity, and to escape the horror of a unique position…must be compensated by spatial curvature. There seems to be no other escape.” No, we are not the center of the universe. There are many sources that will clarify that the creationist is not understanding what the science is nor what the context of their quotes are. A quick Google search will turn up many: “ This does not mean, however, that we are at the centre of the Universe; it just means that we are at the centre of our observable Universe. A fundamental principle in our understanding of the Universe itself, called the Cosmological Principle, states that the Universe is homogeneous and isotropic on the largest scales. That means that on the whole, the Universe as seen from any vantage point (even one that is 15 billion light-years away from us!) will measure a spherical observable Universe with a radius of 15 billion light-years.” https://www.reddit.com/r/DebateAnAtheist/comments/z8ukqg/the_earth_appears_to_be_the_center_of_the_universe/ And: “In summary, the data received by WMAP and Planck shows that we are the center of the universe. However, there is no evidence to suggest that we are literally at the center of the universe. Multiple other stellar systems and galaxies are seen to be aligned around us, but there is no apparent pattern that suggests we are at the center.”“We are the exact center of the OBSERVABLE universe. That's purely because we observe things with light, we can see in all directions at most 13.6 billion years because time started then and light didn't exist before it. So we exist in one location, what does one location extruded in all directions the same distance produce? A perfect sphere with the original point at the center. It makes no difference what's beyond that, you are by definition the center of the observable universe because observation in local.” https://www.physicsforums.com/threads/is-the-cmb-data-showing-that-we-are-the-center-of-the-universe.829178/ Krauss has also made comments about how his quotes have been taken out of context and used in a film promoting of all things - geocentrism!: https://slate.com/technology/2014/04/lawrence-krauss-on-ending-up-in-the-geocentrism-documentary-the-principle.html In summary to the first point, the creationists are quoting these scientists out of context. Of course they don’t believe there is any evidence that we are at the center of the universe. Just like it appears that the earth is flat, immobile and the sun is rotating around us is not true. It  only appears that way. This link also has a good short discussion of how to property interpret the CMB findings instead of projecting a religious presupposition onto the data: https://www.quora.com/Since-we-have-the-distance-in-light-years-to-the-CMB-can-we-find-the-center-of-the-universe No, Genesis 1:1 does not say the universe was created from nothing Now to the second point. The Hebrew interpretation of Genesis 1:1 has been most commonly translated: “In the beginning God created the heavens and the earth” . This would indicate an ex nihilo creation from nothing at a single point in time. But Hebrew scholars the past decades have noted that Gen 1:1 can’t be taken by itself but must be understood in the context of all three first verses, and if properly interpreted Genesis is not talking about creation out of nothing. “First, as many modern Hebraists have noted, Genesis 1:1 opens with a temporal clause. The precise meaning of its first word, bere’shît, is literally “in the beginning of.” This is a complex grammatical topic, but simplified, the way in which the first word has come to be vocalized, indeed the first letter, bet, implies that grammatically the word is in the construct state, that is a noun which is followed by another noun. A literal translation is “in the beginning of.” And this is exactly what we find as the proper understanding of bere’shît when this same word appears elsewhere in the Hebrew Bible. So, for example, the Hebrew of Jeremiah 27:1, bere’shît mamelekhet yihôyaqim, is properly rendered: “In the beginning of the kingdom of Jehoiakim.” But the grammatical problem in Genesis 1:1 is that bere’shît is not followed by a noun but rather a verb-subject pair: bere’shît bara’ ’elohîm. Thus a literal rendering of the first three words of Genesis 1:1 is impossible: “In the beginning of God created.” Thus many modern translations have sought to capture the temporal aspect in the opening word of the book of Genesis by rendering the Hebrew: “In the beginning of God’s creating…” or “In the beginning when God created…” or even “When God began to create…” “Despite strong traditional and often authoritative interpretative claims that were formed centuries after this ancient text was written and devoid of knowledge about its historical and literary context, the opening of Genesis 1 does not depict a creatio ex nihilo, that is a creation out of nothing. The Hebrew text is clear on this point… Rather, what the text of Genesis 1:2 informs us is that when God began to create, earth in some manner of speaking already existed as a desolate, formless, empty waste—tohû wabohû in Hebrew, literally “desolation and waste”—in the midst of a dark surging watery abyss (tehôm). https://contradictionsinthebible.com/genesis-1-not-a-creatio-ex-nihilo/ A Hebrew Scholar in this 10 min video demonstrates the best interpretation: https://fb.watch/rSAGA6fC9s/ 20. No, Evolution is not a Religion First, what do we mean most of the time by religion ?  One can apply a literary device of the term that may be clever but loses it’s main meaning, such as saying golf or football are someone’s “religion”. But that is not how people view what it means to be religious most of the time.  Some definitions of religion include: “the belief in and worship of a superhuman power or powers, especially a God or gods. "ideas about the relationship between science and religion”.  ~ Oxford Dictionary “a personal set or institutionalized system of religious attitudes, beliefs, and practices” “the service and worship of God or the supernatural” “commitment or devotion to religious faith or observance” ~ Merriam-Webster "By religion, then, I understand a propitiation or conciliation of powers superior to man which are believed to direct and control the course of nature and of human life"    ~ James George Frazer, (The Golden Bough). "[Religion is] the belief in Spiritual Beings"  (Edward B Tylor, Primitive Culture) Secondly, what do scientists mean when they use the term evolution, especially since the 1940s?  It is the change in allele (gene) frequencies in a population through generations. As mutations occur and natural selection and other mechanisms filter out some genes over others, in successive populations the proportion of certain genes in successive populations will change. This is discussed in more detail  here: evolution  . We thus see evolution every day - in the field, the lab, and even in the hospital through for example antibiotic resistance in bacterial populations. Third and perhaps most important because it falsifies this claim that evolution can be a religion is the fact that evolution is accepted by thousands of scientists who do  have different religious views. There are Christian, Muslim, Hindu, agnostic, and atheist scientists who accept evolution due to the overwhelming evidence for it. Most have mutually exclusive religious beliefs or they lack belief. Lastly, religion forms the foundation of many worldviews. One way to know evolution is neither a religion nor a worldview is to note how easy it is to find scientists with totally opposed worldviews who share an affirmation that evolution is true. From the Pope to Richard Dawkins. To the evangelical debater and philosopher William Lane Craig to the late Christopher Hitchens or Sam Harris. For example the atheists Stalin and Pol Pot killed and murdered for the ideology of communism (see more # 11 this blog page) and not atheism. There are many atheists that are kind and compassionate, even some that have founded charities to help those struggling in life. Evolution is just the finding of how, from where, what and when species arose on our planet. It can’t be a religion because it is the study of the natural, not the supernatural and people who have mutually exclusive religious beliefs can agree,. accept, and work together with this grand scientific theory.  23. Shapiro, Noble Show That Darwinism Is In Deep Trouble? Claim:  Many secular biologists are showing that Darwinian evolution is in trouble. There was a meeting and symposium in England even that was held to detail many of the problems and inadequacies. Response: No, Neo-Darwinism is alive and well. First, note that Shapiro, Noble and few others are supporters of evolution fully. They don't think the mechanism of Dawin is sufficient. Please understand that the Theory of Evolution is not Darwinism. Darwin proposed a mechanism for evolution per his book title: "On The Origin of Species by Natural Selection..."  Are there other mechanisms? Sure, such as Lateral Gene Transfer, Endosymbiosis, Genetic Drift and Nearly Neutral Theory especially important at the DNA level. Natural Selection is alive and well and stronger than ever but even IF it was discarded we'd still have all the overwhelming evidence for evolution. Evolution is a fact (see above number 10). Now what is telling is despite these Third Way scientists', as they call themselves, books and publications no scientists besides themselves, creationists and Intelligent Design believers take them seriously. For those who think the scientists of the Third Way are onto something special about evolutionary theory, to be fair they must read critical specific reviews about their assertions from well respected evolutionary biologists and biochemists also. A. Denis Noble: The illusions of Denis Noble https://sandwalk.blogspot.com/2021/04/the-illusions-of-denis-noble.html?fbclid=IwZXh0bgNhZW0CMTAAAR1n5lUWCDxhcjXhdunxkPd00OHHplhFpmNqk3-fnoG70G2OAsW2wtdhMVA_aem_h7EYdHJgdVkPvNEdZrAGNg Famous physiologist embarasses himself https://whyevolutionistrue.com/2013/08/25/famous-physiologist-embarrasses-himself-by-claiming-that-the-modern-theory-of-evolution-is-in-tatters/?fbclid=IwZXh0bgNhZW0CMTAAAR0749R_AtsJChC3tOmrWAKbjnaxIVGmpabpBHSzG_7lPFozQYWiQxbptDk_aem_V-HrJYgyeRtKZoLCVbFrfg B. James Shapiro The illusions of James Shapiro https://sandwalk.blogspot.com/2021/04/the-illusions-of-james-shapiro.html?fbclid=IwZXh0bgNhZW0CMTAAAR2mjYVDrIfZuSE7-9aYmLSG89z3avMwDMiHElLJtxp_wb73NYMHTDH01AA_aem_ZSgjawGNKJuDZCL3Liky3Q James Shapiro gets evolution wrong again https://whyevolutionistrue.com/2012/12/02/james-shapiro-gets-evolution-wrong-again/?fbclid=IwZXh0bgNhZW0CMTAAAR37uFPAekLxKjM9ngQh0cU-RqyPXAzUunHxBO0bg6GrGknoZ7ZPWVx8Yns_aem_LcZnEvtBdWUYYvQNGYD8MA C. The illusions of both https://sandwalk.blogspot.com/2021/05/more-illusionsdelusions-of-james.html?fbclid=IwZXh0bgNhZW0CMTAAAR2HpeS39tTNc7E7POdZvBpFxV-M-mFQoEcO5CbxCMmGz4ZvhTPHh-TKQKE_aem_SWf7Vsj28SqO5WLBv4eIVQ " " The title [of the book Moran is reviewing] is ridiculous since no respectable scientist ever equated selfish DNA with junk DNA... The Modern Synthesis (MS) was not based on a "gene-centric" view. For the past 50 years, no respectable scientist, and no knowledgeable expert in molecular evolution, has restricted the definition of "gene" to just protein-coding genes. For the past 50 years, no expert in molecular evolution has ever thought that the genome is just a collection of protein-coding genes. For the past 50 years, experts in molecular biology have known about transposons and have considered the view that some of them might be "controlling elements." They have concluded that most transposon-related sequences are just fragments of defective transposons with no biological function. Nobody cares whether mobile genetic elements fit within the narrow confines of the Modern Synthesis as described by Huxley and other in the 1940s because no expert in molecular evolution has believed in that view of evolution since the late 1960s. The Britten and Kohne paper established that the genomes of most multicellular eukaryotes contain large amounts of repetitive DNA. This was an attempt to resolve the C-value paradox. Britten and Kohne didn't like the idea that this could be junk DNA so they offered some speculation about function. However, further data established that most of this repetitive DNA is, indeed, junk and Britten and Kohn's speculations have been discredited. Britten and Kohn were attempting to interpret their result within the context of the adaptationist views that characterized the the Modern Synthesis back then. The correct interpretation of their results came with the overthrow of the Modern Synthesis and the adoption of a new view of evolutionary theory that focused on Neutral Theory, Nearly-Neural Theory, and the importance of random genetic drift. Shapiro and Noble missed that revolution so they continue to attack an old-fashioned strawman version of evolutionary theory." To be continued, most likely as I become familiar with further popular anti-evolutionist arguments.

"Dear Francis [Crick], I am sure that you realize how frightfully angry a lot of people will be if you say that much of the DNA is junk. The geneticists will be angry because they think that DNA is sacred. The Darwinian evolutionists will be outraged because they believe every change in DNA that is accepted in evolution is necessarily an adaptive change. To suggest anything else is an insult to the sacred memory of Darwin." ~ Thomas Jukes, 1979 Introduction Does our genome contain a lot of junk DNA, none, or only some? Or, is it mostly junk? To the anti-evolutionist, there must be little to no junk DNA because a creator would not create us that way. So the "there is no junk DNA" becomes another assertion that must be defended in their religious or intelligent design views at any cost. I assert that our genome is mostly junk and we know why and how that happened. This denial of junk DNA/RNA becomes another statement from a mostly religious presupposition to join claims that there are no transitional fossils, that human evolution did not happen, and that there must be a historical Adam & Eve to found the human race. All are demonstrably wrong by scientific findings and other arguments. In this case however, the voices crying "no junk DNA" on religious grounds are joined by much of the scientific community who agrees with the anti-evolutionists. The topic of junk DNA is indeed controversial, unlike evolution. In part 1 of this 2 part blog, I will attempt to summarize the history of the controversy and the components of our genome. In Part 2 I will write about the publications in 2012 that appeared to show we had little genomic DNA/RNA and why those were wrong. Both parts are primarily based on Laurence Moran's 2023 book. DNA/RNA - we need to discuss some basic biology. This is important Just about everyone has heard of DNA. Another related molecule is RNA, which stands for ribonucleic acid. RNA can be thought of as one side of a ladder whereas DNA is a ladder that has been twisted along its central axis. Besides being a double helix compared to the single stranded RNA, DNA has one less oxygen, hence it’s name of deoxy ribonucleic acid. The four bases that make up the steps to the twisted ladder are A,T,C,G. Due to structural constraints and bonding, A bonds with T and C bonds with G to make up the “steps” for each “steps” of the “ladder”. Additionally in RNA uracil (U) replaces thymine (T). In human cells the amount of DNA if present (RBCs don’t have any, for space) is about 3.2 billion base pairs. Human DNA is normally packaged like luggage when it’s time to divide, into 46 chromosomes. Moran notes that Chromosome 20 for example, one of the smaller chromosomes, has 60 million base pairs. If we unwind DNA we get a sequence of bases and the opposite side will have the pairs that bond as discussed above. For example a sequence might be …ATCGGATTC… The other side would read …TAGCCTAAG… and thus the sides are said to be complimentary. The sides of the ladder, the backbones, run in opposite directions. This was worked out by Watson and Crick and published in 1953 especially after they saw an X-ray photograph of DNA by Rosland Franklin. By convention, biologists and biochemists write the code in one direction, from what is called the 5’ end to the 3’ but that is not important for our purposes. Not all of your DNA is in the nucleus. In most of your cells there are hundreds of mitochondria and since they are derived from ancient bacteria (see mitochondria and your mom blog) that set up a symbiotic relationship with us millions of years ago; they have their own DNA. Their DNA is not included when we talk about the DNA in an organism. Most plants have the same situation with chloroplasts that were derived millions of years ago from cyanobacteria. History As early as the 1950s scientists knew from staining DNA how much was present and then it was an easy calculation to find the number of base pairs - 3.2 billion. By 1991, scientists had worked out the approximate amount of human DNA in each chromosome and the total amount in females was 3.23 Gb and in males 3.17 Gb; the Y chromosome is very small compared to the X. (1). Much of the genome consists of highly repetitive DNA which is difficult to sequence. This is why the first announcements that scientists had sequenced the human genome were really very good drafts and in general did not include the highly repetitive DNA. This is especially common in the ends of chromosomes called telomeres, and chromosome areas called centromeres where spindle fibers attach when duplicated chromosomes are pulled apart during the production of new daughter cells. Although the sequencing of the human genome was announced to great fanfare in 2003, it really wasn’t fully sequenced until 2022. DNA Makes Various RNAs When the cell needs to make products, it unwinds some of the double helical DNA and on one side the four bases are “read” to make a complimentary single strand of RNA. If the RNA is destined to code for a protein, it is called messenger RNA (mRNA) and goes to a factory to assemble a protein from amino acids. Those little factories are called ribosomes and are made up of ribosomal RNA (rRNA). Amino acids that will make up proteins are brought to the ribosomes by other RNAs called transfer RNAs (tRNA). There are exceptions for the direction of DNA to RNA. For example a type of virus that infects animals is called a retrovirus because it’s instructions are in RNA and not DNA. To infect a victim for example it must take its RNA and convert it to DNA before it parasitizes animals and inserts its DNA into the host DNA. HIV is an example of a retrovirus (goes from RNA to DNA rather than the more common route). Since retroviruses insert randomly into DNA, when we find thousands of identical ones in the exact same locations between us and the other great apes especially chimps for example, they are great proof of human evolution. See the section on ERVs. There are other RNAs that do not make proteins also. These we don’t generally need to know their functions but they are also non-coding RNAs and include a gene called 7SL RNA that gave rise to ALUs which we will discuss later, snRNAs, snoRNAs, miRNAs, siRNAs, piRNAs and especially important in the discussion of junk DNA are the lncRNAs. All the non coding RNA genes however add up to only about 5,000 genes in the genome. Gene The reading of DNA to produce RNA is called transcription and this is a huge issue with the controversy surrounding junk DNA, especially with the ENCODE researchers which will be discussed in Part 2. To start transcription the cell needs a section that tells an enzyme to start reading the DNA. This binding site is called a promoter. Transcription involves initiation, elongation, and termination. The promoter site is not part of the gene. Sites that control transcription initiation are together called regulatory sequences and can also enhance or inhibit transcription. This will also become important when we discuss the controversy around junk DNA. At the ribosome, the factory can read the mRNA sequences and an AUG means start making the protein and several codes mean stop assembling the amino acids into the protein (UAA, UAG or UGA). What is a gene? Believe it or not biologists unfortunately use different definitions, which has caused all kinds of problems, as we shall see. The best definition and the one used by biochemists for decades is a DNA sequence that is transcribed to produce a functional product . There are two types of genes. One type codes mRNA to make proteins . Recall that DNA can also make other RNAs and the genes that produce these are called non-coding genes because they don’t code for proteins. In humans about 20% of genes produce functional RNAs and about 80% of our genes produce proteins (1). Gene processing One more aspect needs to be mentioned and that is called RNA processing. It turns out that the transcript that is produced for eukaryotic genes (non-bacteria; us for example) are much larger than the finished product. There are sections in the genes called exons and introns. After transcription is completed the introns are removed and discarded and the exons are spliced together before going to the ribosomes. "Intron sequences account for about 30% of the genome. Most of these sequences qualify as junk and are littered with defective transposable elements.” (2) Early observations Over 50 years ago scientists were comparing genome sizes between various species and groups of related organisms when they were confronted with facts that were counterintuitive to the idea that more complexity should equal a larger genome and more genes. As species became more complex surely genomes would track with a size increase. It turned out that genome size did not reflect the number of genes however (1). For example the genome of the lungfish turned out to be one of the largest vertebrate genomes ever measured at 133 billion base pairs (133 Gb) - nearly 40 times larger than the 3.2 of ours. What was it doing with all that DNA? And this non-correlation with apparent complexity held up within groups also. The leaping frog Xenopus sp. has a genome about the same size as ours, but another called the green frog Rana sp. has a genome size of 10 Gb. How can it be that one frog has a genome 3X the size of another? It is hard to believe that the Rana sp . frog is so much more complex than another frog. This was called the C-Value Paradox ; there was no correlation between genome size and complexity.(1) Beginning in the late 1960s results studying mammalian genomes showed that they consisted of highly repetitive DNA (about 10%), a lot of moderately repetitive DNA (about 40%) and the rest unique sequence DNA (about 50%). Larger genomes just had more repetitive DNA and mRNA hybridization studies showed that in eukaryotic cells only a few percent were typically involved in protein coding genes. These studies established that large eukaryotic genomes contained a great deal of repetitive DNA and that there were fewer than 30,000 genes (1). It became apparent by the late 1960s that the C-Value Paradox could be resolved by assuming that much of the genome is composed of non functional repetitive DNA - junk DNA (1). Thus, all mammals have pretty much the same genes, 10,000 ’house keeping genes’, and the differences in species is in developmental constraints of when genes are turned on and off and not in large numbers of unique genes for more complex species (1). In 1972 the geneticist Ohno coined the term Junk DNA. Notice that it is not garbage that you put at the curb for pick-up but rather refers to some of the used stuff we have in our garages, attics and that ubiquitous junk drawer often in our kitchens that are not being used or are broken. Ryan Gregory has termed the Onion Test for those who want to say genome size is correlated with function and complexity. "The onion test is a simple reality check for anyone who thinks they have come up with a universal function for non-coding DNA. Whatever your proposed function, ask yourself this question: Can I explain why an onion needs about five times more non-coding DNA for this function than a human?" (3) He notes that some non-coding DNA like the RNAs discussed earlier is functional. But that’s only 5% of the genome and does not rescue all the other non-coding DNA. He notes also that members of the onion genus Allium have genome sizes in the range of 7pg to 31.5pg. Can one onion species really make do with only one fifth as much instructions if it’s all functional? It should also be strongly noted that all the early biologists working in genomics knew that not all the non-coding DNA was junk; the regulatory sequences including promoters and RNA genes were known to be scattered in the non-coding DNA. No one ever said, despite the current false narrative, that it was all junk. A Wikipedia article on junk DNA offers a short and apparently accurate overview of the history of the junk DNA controversy (4). In 2024 the genome of the African lungfish was fully sequenced and found to have 90 billion base pairs to our 3 billion. Perhaps the Onion Test should be renamed. (5) Genes, Genes, and Genes Recall that about a half century ago geneticists predicted that humans would be found to have about 30,000 genes. Today we know the total is closer to 25,000 with 20,000 protein producing genes and about 5,000 non-coding genes (RNAs mainly, including regulatory genes). About the same number as the worm Caenorhabitis elegans. Thus, the earlier scientistic predictions were remarkably close. When the first draft of the human genome was announced in 2003 the media proclaimed that science was shocked that humans had so few genes compared to other species given especially our complex brains. Not true. It was predicted decades before. The bruised egos for many humans was not a problem for many of the scientists studying genomes; it was just what nature was presenting. The protein producing genes (coding genes) thus only make up about 1% of the human genome and the total percent of the genome of all genes is no more than 2%. In the protein coding genes 37% of those genes are introns, mostly junk DNA. Of the non-coding genes 6% are made up of introns, mostly junk (1). “The total amount of the genome devoted to genes is close to 45%. Of this total, less than 2% is functional, and the rest is junk DNA in introns” (1). What does it mean to be functional? Moran defines it as any stretch of DNA that cannot be deleted from the genome without reducing the fitness of the individual. Basically, functional DNA is constrained by purifying selection. A good way to determine function is to check to see if the gene exists in other species and is being transcribed. If it does this is called sequence conservation and is perhaps the strongest method of inferring function. Not Genes (from Moran) 1. Pseudogenes - make up about 5%. These are broken genes that resemble functional genes but have too many mutations to work. However a tiny number can take on new functions. See blog on pseudogenes this site and how they can be used to essentially prove human evolution. 2. Regulatory sequences. About 1.8%. Promoters and DNA sequences that bind various transcription factors. These have been known since the 1960s. 3. Centromeres . About 6%. Consists of millions of base pairs that is repetitive DNA for spindle attachment to pull chromosomes apart during cell reproduction. Much of it is non essential since some people have 2% and others 10%. To be very conservative, assume 1% and the rest is redundant. 4. Telomeres . Only 0.1% 5. Scaffold Attachment Regions . 0.3%. DNA wraps around proteins called histones to package the DNA when not being “read”. DNA sequences called SARs function to maintain the organization. 6. Viruses. About 9%. Defective viruses that invaded our ancestral line but are now non functional (good for us!). We have co-opted many for our own use however. 7. Transposons . About 47%. Includes SINEs (ALUs mostly - 13%), LINEs (21%), LTRs (9%), DNA transposons (4%). Table 1. Functional and junk DNA in the human genome according to Moran, 2023. From: Moran, Laurence A. 2023. What’s In Your Genome?: 90% of your genome is junk . Aevo UTP. University of Toronto Press. 372pp. Page 133. Table 5.1. See text for explanations of terms. Fair use attribution. For educational purposes only. Thus, the real amount of junk DNA in our genomes is probably closer to 90% according to Moran. The missing 7% in the table could be either functional DNA or junk, or a combination of the two. Although these figures may change some in the coming years Moran notes that it won’t be enough to change from that 10:90 ratio. I have read that other scientists like Shubin have claimed 75% junk and still others 50%. In Figure 1 shows some of these categories in pie form. Note that these figures are from 2013 and have been revised some but the overall ratios and relationships are similar. Even in 2013 about 45 - 50% of the human genome was felt to be junk by these textbook authors. Figure 1. From Reece et al. 2013. Campbell’s Biology . No copyright infringement intended. Fair use permitted. [Exons are the coding parts of DNA. Although Introns are non-coding they rarely have functions. Moran lists introns as 30% of the coding genome before splicing out. Transposons and repetitive DNA are often functionless and much is junk left over from evolution.] Will "Dark Matter" DNA reveal in the future that most of the non coding DNA is functional? (2024). " Tom Cech  won a Nobel Prize for discovering one example of a catalytic RNA. He recently published an article in the New York Times extolling the virtues of RNA and non-coding genes [ The Long-Overlooked Molecule That Will Define a Generation of Science ]. There's a fair amount of hype in the article but the main point is quite valid—over the past fifty years we have learned about dozens of important non-coding RNAs that we didn't know about at the beginning of molecular biology [see: Non-coding RNA , Non-coding DNA ]. The main issue in this field concerns the number of non-coding genes in the human genome. I cover the available data in my book  and conclude that there are fewer than 1000 (p.214). Those scientists who promote the importance of RNA (e.g. Tom Cech) would like you to believe that there are many more non-coding genes; indeed, most of those scientists believe that there are more non-coding genes than coding genes (i.e. > 20,000). They rarely present evidence for such a claim beyond noting that much of our genome is transcribed.Let's dissect this to see where the bias lies. The first thing you note is the use of the term "dark matter" to make it sound like there's a lot of mysterious DNA in our genome. This is not true. We know a heck of a lot about our genome, including the fact that it's full of junk DNA. Only 10% of the genome is under purifying selection and assumed to be functional. The rest is full of introns, pseudogenes, and various classes of repetitive sequences made up mostly of degraded transposons and viruses. The entire genome has been sequenced—there's not much mystery there. I don't know why anyone refers to this as "dark matter" unless they have a hidden agenda. The second thing you notice is the statement that 75% of the genome is transcribed at some time or another and, according to Tom Cech, these transcripts have an unknown function. That's strange since protein-coding genes take up roughly 40% of our genome and we know a great deal about coding DNA, UTRs, and introns. If you add in the known examples of non-coding genes, this accounts for an additional 2-3% of the genome.1 Almost all the rest of the transcripts come from non-conserved DNA and those transcripts are present at less than one copy per cell. As the ENCODE researchers noted in 2014, they are likely to be junk RNA resulting from spurious transcription. I'd say we know a great deal about the fraction of the genome that's transcribed and there's not much indication that it's hiding a plethora of undiscovered functional RNAs." https://sandwalk.blogspot.com/2024/06/tom-cech-writes-about-dark-matter-of.html?m=0 Is this Hancock video from 2024 the best explanation and defense for junk DNA?   Intro to why this video: Discovery Institute, functional definition Junk DNA - A complete history 3:37 The Ecology of Parasites 15:50 The History of the Junk DNA Hypothesis 39:24 Mutational Load, functional genes 42:40 - 44:45 CoT Analysis 44:55 - 46:37 Junk DNA term, introns, nearly neutral theory, transposons 48:23 - 59:35 ENCODE 59.55 (conclusion to date); 1:00:50 (why it is being fought) Closing thoughts 1:24:40 Summary, Part 1 The point is that anti-evolutionists that claim there can’t be any junk DNA because a Creator would not create genomes with junk are wrong. Certain researchers initially claiming 80% function in the human genome in 2012 were wrong as will be discussed in Part 2. Many other scientists who may not be religious but continue to claim that nearly all or all non-coding DNA must be functional are certainly wrong. Many scientists appear to be unable to accept that most of the human genome is junk, the result of millions of years of duplications, deletions, insertions, and transposons jumping around the genome. Certainly creationists and other anti-evolutionists cannot face the genomic facts due to their religious allegiances. Others may be afflicted with human exceptionalism ego deflation; many of us just can’t admit that our genome is filled with that much junk DNA. We’re the "top species and too complex" to have a genome smaller than some worms and many plants, and about the same functional genes as other mammals. Each of those two sides pin much of their hopes on future discoveries for function. A large set of studies that were published in 2012 still have today the majority of scientists and creationists believing that the human genome contains little to no junk DNA. Of course the anti-evolutionists celebrate that the majority of main stream science appears to reject that we have lots of junk DNA in our genome. That research came mainly from ENCODE, which will be discussed in Part 2. .. Obviously this blog is based primarily on Dr. Moran's book. Please get a copy of it for yourself and see what you think about his thesis. In March, 2024 Dr. Moran wrote a 9 part blog analysis of a 2024 paper by Niles Walter, PhD Professor of Chemistry at the University of Michigan who supports the view that there is little junk DNA in the human genome. This will help focus the discussion to the various issues that repeatedly arise in the controversy over junk DNA. https://sandwalk.blogspot.com/2024/03/nils-walter-disputes-junk-dna-9.html?fbclid=IwAR1KtPMKrm67N1dCwZdZBD2yTqA3QK8q7otie9Lb2R0t4aMI4D3VgV7CaUE Citations 1. Moran, Laurence A. 2023. What’s In Your Genome?; 90% of your genome is junk . Aevo UTP. University of Toronto Press. 372pp. 2. What’s in Your Genome? May 08, 2011. Sandwalk. Strolling with a skeptical biochemist. https://sandwalk.blogspot.com/2011/05/whats-in-your-genome.html 3. The onion test. April 25, 2007. Genomicron. Exploring genomic diversity and evolution. https://www.genomicron.evolverzone.com/2007/04/onion-test.html 4. https://en.wikipedia.org/wiki/Junk_DNA 5. https://arstechnica.com/science/2024/08/the-fish-with-the-genome-30-times-larger-than-ours-gets-sequenced/

“Yes, evolution by descent from a common ancestor is clearly true. If there was any lingering doubt about the evidence from the fossil record, the study of DNA provides the strongest possible proof of our relatedness to all other living things” ~ Francis Collins, 4/6/2007, CNN "The new DNA evidence has a very important role beyond illuminating the process of evolution. It could be decisive in the ongoing struggle over the teaching of evolution in schools and the acceptance of evolution in society at large. It is beyond ironic to ask juries to rely on human genetic variation and DNA evidence in determining the life and liberty of suspects, but to neglect or to undermine the teaching of the basic principles upon which such evidence, and all of biology, is founded." ~ Sean Carroll, "The Making Of The Fittest: DNA And The Ultimate Forensic Record of Evolution". 2006. What are these ERVs? The abbreviation stands for E ndogenous R etro Vi ruses. Let’s take each word separately starting from the right. A virus is a very small entity that must use a host cell to reproduce. They must hijack a cell and can’t reproduce by themselves. They are basically tiny infectious parasites; thousands can fit inside of a cell. They use genetic material, either DNA or RNA, that they inject into host cells to use the host resources to make more of themselves. The DNA or RNA is carried from cell to cell by a protein capsule. Because they can’t replicate without hijacking a cell and have no significant structures compared to cells biologists still don’t know whether to call them living or not. Retro refers to some viruses that use RNA instead of DNA as their genetic material and must do a conversion to DNA to use the host machinery. The host cell’s primary instructions are DNA, so this category of virus needs to convert its RNA to DNA before it can be inserted into host DNA to trick the host cell into making viral products instead of normal cell substances. Normally, RNA comes from DNA. Thus this is “retro” going backwards from RNA to DNA. Most viruses just use the cellular machinery outside the nucleus to make more viruses without inserting into the cell’s DNA. Viruses then bud off having their genetic material inside their protein and lipid capsules to infect other cells. But these viruses, called retroviruses, directly infect the host DNA in the nucleus. Often, the infection kills the cell. Also, the body can detect the infection and the immune system attacks the cell or the cell realizing it is infected, commits suicide, a process called apoptosis. Many retroviruses cause cancer and disease. If a cell is infected successfully by a retrovirus the body can fight it off but often the genetic instructions can be left behind or become silent, called being latent to awaken later - thus passing them along to offspring if the retrovirus infects a sperm or egg cell (gametes). Over time these spread throughout the population and because they pick up mutations they eventually are genetic fossils of past infections. Since they now pass onto all the offspring in the population each generation, the old degraded retroviruses are now endogenized ; they now become part of the genome although originally they came from outside their ancestors. If the ERV is only found in humans, it’s called a HERV. Retroviral lifecycle and components. We need to get into some details here, but it’s very important. It will be important to evaluate anti-evolution objections especially in the light of how scientists know what ERVs are and what they mean to evolution. Please take 5 minutes and watch a short video of a retroviral life cycle below after reading this section. In this case the prestigious Howard Hughes Medical Institute is looking at HIV, but all retroviruses have the same life cycle and the same basic genetic components. Notice that the retroviral genome is spliced into the host DNA by cutting it in using an enzyme called integrase and then sealing the ends of the retroviral and host DNA. The viral RNA has been converted to DNA by another enzyme the virus brought with it called reverse transcriptase . This produces two cut ends on either side called Target Site Duplications (TSDs). Think of these as knots on each end of a section of rope if you were splicing it in. The cut ends can be identified in the example below by the DNA sequence - ATTAT. Also note that the retroviral lifecycle is complex, which will be an important issue when looking at objections put forward to the ERV evidence. The end result of the retroviral genome insertion is this sequence of genes, shown in orange in the diagram below: LTR-gag-pro-pol-env-LTR In order to get the provirus read, the virus uses a host enzyme called RNA polymerase II . This enzyme is normally used to transcribe mRNA for use into later translation of peptides (making proteins, especially enzymes to make other products), so although it uses a promoter to start transcription, since the promoters don’t code for amino acids that make up proteins, the host enzyme doesn’t transcribe them. Promoters are needed to start copying the DNA. With only one set of promoters in the provirus, the copied provirus would have no promoters at all for the next generation of virions and they would not be able to activate after being inserted into another cell. The retrovirus “solves” this problem by polymerizing lots of promoters during reverse transcription. Due to the copying system it turns out that these promoter copies all must be identical. These are called Long Terminal Repeats , or LTRs . These promoter copies are in the hundreds in LTRs and will be critical to our discussion shortly. Note: the host cell already has it's own promoters. The LTRs are a collection of promoters from the virus so it can continue to infect other cells when copied. The LTRs are not original to the cell line but have been passed down after the original infection. Retroviral Lifecycle: HIV as an example The gag genes code for capsid proteins, the pol for reverse transcriptase and other enzymes, and env into molecules for the envelope. As noted, ERVs are dead old retroviral insertions and are mutated to the point of being non-functional. However, the host cells have been able to use some of the viral genes for themselves. The most famous is probably the placental formation in mammals that is dependent on an old proviral env gene. Another is the ARC gene used by nerve cells for communication that was once a gag ERV gene. So although there are no functional ERVs, parts can be used by the cells. The process whereby cells use old retroviral genes for their own use is called exaptation or co-option. Summary. Retroviruses are different from most other viruses in that they have RNA that must be converted to DNA so they can insert their DNA into host chromosomes/DNA to trick the cell into making viral products instead of host products. They are DNA parasites. This process of producing a DNA copy of their RNA is done by one of their enzymes they bring with them called reverse transcriptase . Another enzyme the virus also brings in, integrase, is used to cut the host DNA to finish the insertion. We know this occurs because both ends that are sealed back together with the viral DNA between them leave marks called TSDs on each end. The virus then uses a host enzyme to read it’s three genes ( gag-pol-env ) to make viral proteins. But this enzyme, host RNA polymerase II usually reads mRNA to make RNA products and will not read a promoter needed to start the copying, so the virus’ “offspring” upon infecting another cell will have no way to start reading its DNA. To get around this problem the retrovirus makes a bunch of promoters and puts them on either side of the provirion genes. These are called LTRs because the promoters are copied many times over. Importantly, unlike reverse transcriptase, the copying of the LTRs is very exact and all the LTRs for that particular insertion have no errors or mutations. The end result is TSD-LTR-gag-pol-env-LTR-TSD. Some authors include an additional coding domain called “pro” that codes for protease before the “pol” coding domain. ERVs - function, and anti-evolution confusion The parts of the ERV that cells especially love to co-opt for their own use are the LTRs because they are rich in promoters. The LTRs are central in the attempts to discredit this evidence for human evolution which I will discuss shortly. It turns out that about 8% of the human genome is made up of ERVs. That’s 8% of about 3 billion nucleotide pairs in the DNA “rungs of the ladder”; a huge part of human genomes. Most of these by far are single LTRs since the other viral genes have degraded so much over time. There are however, some fully sequenced ERVs with all the genes present. When reading the literature, it is often written that ERVs have functions, but note that they are talking about only LTRs nearly all the time. A fully functional ERV is not present because if it was it would be called a provirus; an active retrovirus in the host DNA. And ERVs are dead retroviruses by definition that have been endogenized. Most of the 8% are LTR-retrotransposons. These can no longer make new infectious retroviruses and have the sequence LTR-gag-pol-LTR . As you can see they lack the env genes. But they can jump around in and out of the host genome and are a type of transposon. Thus, when an article notes that an ERV has function, they are usually referring to only a LTR component, a part left over from an ERV, and not the entire ERV. Same with co-opted env or gag genes. Stop - Let Me Up For Air! Let’s summarize some points so far. 1. When a retrovirus infects a cell it inserts its genome into the cell’s DNA to parasitize the cell, hijacking the cell’s machinery to make new viruses. We can see that happening today. 2. These retroviral genomes are identified as LTR-gag-pol-env-LTR DNA sequences. We know the lifecycle of retroviruses and know where and how these components are made. There are retroviral infections right now that we can see and study in humans like HIV and even currently in a retroviral epidemic in Koala bears; this current retrovirus has not become fully endogenized. When we find ERVs throughout a population or just their LTRs we know sometime in the past the species had a retroviral infection in the sex cells. 3. Where the retrovirus inserted its genes into the host DNA there are two spliced areas on each end as a result, called TSDs or Target Site Duplications. The ERVs, mostly LTRs, are not original to the host DNA. They were cut in. 4. Many ERVs are just remnants of the original provirus. Most are mutated and degraded down to their LTRs only. Some gag and env genes are left, still functional, and are used and co-opted by the host cell - turning the tables on the virus. This is called exaptation. Similar to you using a wrench as a hammer if needed. Not the original function, but a new function that can work. The irony of turning a parasite’s corpse to good use should not be lost. LTRs are rich in promoters and cells love to use them for their own functions. Scientists are finding functional parts for some ERVs all the time but so far it represents a very small percentage of the total. 5. ERVs are old retroviral infections. Their genomes, when intact, match retroviral genomes (called proviruses) that make new retroviral particles to infect new cells. Their DNA is not original to the host DNA. In the literature, ERVs are often mentioned as functional but what the authors are referring to most often are the left over LTRs alone. 6. Recall from your biology courses that mRNA reads the DNA, and it in turn is read by tRNAs that have certain amino acids attached. As the string of amino acids grows in length to becomes a peptide and they can become large enough to be called proteins. The four bases (ATCG) are actually read in 3s which are called codons. There are thus 64 possible combinations of three bases to specify a codon. Some of the codons specify STOP and not an amino acid. But since life tends to use only 20 amino acids, there is a lot of duplication and this is called Codon Degeneration. Note in the table below for example the amino acid Serine can be specified by tRNAs using UCU, UCC, UCA, or UCG. Why is this being discussed here? Because different living species often have a codon bias for using different codons. One way we know ERVs are not native is that they have a different bias from native host DNA when specifying amino acids. For example in humans Cystine is specified by UGC but in a yeast species ( S. cerevisiae ) it is UGU. Glutamine is GAG in humans but GAA in this yeast (Wikipedia). It's like you can tell an English accent from different parts of the world - England, Scotland, Ireland, Australia, or America (also Boston vs southern accents). If the ERVs were native to our DNA they should have the same codon bias. They don't. From: University of Leicester. Fair use attribution So - What’s the big deal? Well, here’s the big deal. First, it turns out that when a retrovirus inserts its genome into the host DNA it does so randomly. There are preferred areas that pick up more than others such as chromosome 19, and they often insert into transposons called LINEs. But the actual insertion is random to locus (like a specific address) . A locus (loci, plural) is the exact DNA location looking at the A,T,C,G sequence. Secondly, after the human genome was sequenced it was noted that a huge percentage of our DNA is made up of ERVs - 8%. What do you do if you’re a scientist? You sequence other great ape genomes, like chimp, gorilla and orangutan and compare them. What did they find? Turns out that 200,000 ERVs are shared by chimps and humans alone. Remember, these are the result of random insertions down to the genetic code level. They are in the exact homologous locations between chimps and humans despite that we know they insert randomly to DNA sequence (but some broad genetic areas can be preferred, just like some intersections tend to have more accidents but do not involve the same vehicles and the exact same areas within the intersections). We can know this by looking at the DNA sequences and nearby DNA sections. Many have the exact same mutations. It’s like two students writing papers on the same topic thousands of miles apart and claiming that they shared nothing between them, no communication, etc. But when you look at their papers written at different schools with different authors and in different states, what do you do if the papers have the same exact sentences? You know what happened. They both went on the Internet and copied from the same source material. They were not independent but share the same source material. They were not produced independently of one another. It is mathematically impossible that 200,000 randomly inserted retroviruses happen to be in the exact same locations between two different species. There is only one rational conclusion - those retroviruses had to have inserted in a common ancestor before they split to become different species. This is solid proof of a shared ancestry between chimp and humans and we know we split from a shared ancestor with chimps about 6 million years ago. We did not evolve from modern chimps but with a shared primate ancestor in the distant past. The only rational explanation, for example, for finding 200,000 shared ERVs between chimps and humans that insert randomly and are found in the same locations between species, often with the same mutations, is that the ERVs must have been inserted before the species split. That is the summary for this entire evolution section on ERVs, or to be exact, shared ERVs. It rules out common design and rises to the level of proof for common ancestry. Human evolution and most would argue macroevolution is true based on shared ERVs in the great apes alone. Paleontologists long ago constructed phylogenetic trees showing that humans and chimps shared a common ancestor at one time, about 6 million years ago due to the fossil evidence. The DNA in our own cells when compared to chimps and the other great apes shows evolution and confirms the fossil evidence. The only rational explanation, for example, for finding 200,000 shared ERVs between chimps and humans that insert randomly and are found in the same locations between species, often with the same mutations, is that the ERVs must have been inserted before the species split. Phylogenic Trees; their importance to species' origin debates If you recall I mentioned that scientists also sequenced other great ape’s genomes and compared them for ERVs. As expected, as one moved away evolutionarily from humans and chimps the number of shared ERVs decreased between the species. Also, because ERVs had inserted over many millions of years the ones more distantly related had fewer and fewer ERVs that were the same in terms of mutations. Evolutionary trees can be constructed just looking at ERVs and LTRs that confirm the fossil record for great ape evolution produced by paleontologists. Below is an ERV that was found in three species. Notice the TSDs on either side. Top: ERV insertion - ERV-K105 Bottom: ERV insertion ERV-K18/K110 From: Finlay, G. 2021. Human Evolution: genes, genealogies and phylogenies. Paperback ed. Page 39. Cambridge University Press. 283 pg. without Ref and Index. Fair Use Attribution The next diagram below shows many ERVs that were identified. Some are shared by nearly all, some only found in fewer species. They nest in a hierarchy that produces a phylogenic tree confirming evolution and common ancestry. Recall there have been hundreds of ERVs discovered and finding the exact same ones in different species that can be nested like this is only explained by evolution. Also remember that phylogenic trees can be produced independently by many areas of origin research including fossils, gene sequences (see DNA evidence in whales), DNA repair, pseudogenes, etc. This coming together of multiple independent evolutionary lines of confirmation is known as consilience. ERVs that entered the primate germ line, from their presence or absence in the genomes of primate species. OWM= old world monkeys; NWM - new… Notice that some ERVs like ERV-KC4 are found in most species tested whereas others such as ERV K-18 are found in fewer species. White and black boxes refer to two different sources. From: Finlay, G. 2021. Human Evolution: genes, genealogies and phylogenies. Paperback ed. Page 36. Cambridge University Press. 283 pg. without Ref and Index. Fair Use Attribution Lastly, below is a phylogenic tree using ERVs that were found just from one family of ERVs, ERV-K. Notice again that some are shared by some groups and not others. If evolution were not true, this nested grouping would be impossible. For example, 30 were found just in humans, whereas 10 were found in all groups except New World Monkeys. Recall these insertions are random and represent hits to DNA that can only be explained if the retroviruses inserted before the species split off. Full length ERV-K (HML-2) inserts in the human genome showing the number arising (ovals) at each branch leading to humans. Data for solo LTRs are from chromosomes 7, 19, and 21. From: Finlay, G. 2021. Human Evolution: genes, genealogies and phylogenies. Paperback ed. Page 40. Cambridge University Press. 283 pg. without Ref and Index. Fair Use Attribution If you recall I mentioned that the scientists also sequenced other great ape’s genomes and compared them for ERVs. As expected, as one moved away evolutionarily from humans and chimps the number of shared ERVs decreased between the species. Also, because ERVs had inserted over many millions of years the ones more distantly related had fewer and fewer ERVs that were the same in terms of mutations. Evolutionary trees can be constructed just looking at ERVs and LTRs that confirm the fossil record for great ape evolution produced by paleontologists. The site immediately below details them if you’d like to see what they look like and how they were produced. A great site if you want to drill down on details. If LTRs were original and indicated common design, we would not be able to compare them between ape species and produce an evolutionary phylogenic tree based on mutations for example. https://evolutionarymodel.com/ervs.htm Many others have noted this incredible evidence for human evolution and macroevolution. Graeme Finlay wrote the definitive book on DNA findings rising to the level of proof of human evolution (6). It's an amazing book for the lay person. Jon Perry and Stated Clearly produced a video about it. Barry Desborough has dedicated an entire web site to it and has a FAQ section that covers just about every question or objection. Actually, Perry’s entire Stated Clearly series detailing other science and evolution topics is excellent. Please watch his short video below on shared ERVs; it may also help to crystalize my presentation here in video form. So, it’s not about ERVs actually, its about shared ERVs that insert randomly and are found in the same locations between species. It’s not about functions, because no fully ERVs have functions; just parts do and they are co-opted functions. Again, Barry’s site as a great resource for all your shared ERV questions: https://barryhisblog.blogspot.com/p/endogenous-retroviruses-frequently.html A creationist PhD reverses his opinion  about ERVs as evidence for human evolution. Jonathan McLatchie is a Fellow at the Intelligent Design Discovery Institute  in Seattle. Previously, he was an assistant professor at Sattler College, Boston, where he lectured in biology for four years. He holds a Bachelor’s degree (with Honors) in Forensic Biology, a Masters (M.Res) degree in Evolutionary Biology, a second Master’s degree in Medical and Molecular Bioscience, and a PhD in Evolutionary Biology. In early writings about ERVs he pushed back about them being excellent evidence for human evolution. However, even he can't avoid the conclusion of common ancestry from ERVs. " Primates are thought to have been on the scene for 50-55 million years. During that history, they have undergone many infections by retroviruses (RNA viruses that can reverse transcribe their RNA into DNA and integrate themselves into the genome of their host). Sometimes, those retroviruses infect the germ cells (those cells that are passed on to an organism’s progeny). When this happens, the retroviruses can be vertically inherited from one generation to the next, becoming permanent relics of past viral infections. These relics are referred to in the technical lingo as endogenous retroviruses (ERVs). There are literally hundreds of thousands of those endogenous retroviruses in the human genome. What evolutionary biologists have noticed is that the distribution of those retroviral sequences across the genomes of different primates forms a nested hierarchy, resembling a family tree — exactly what you would expect to observe on the hypothesis of common descent. [24] " Furthermore, in addition to the placement of ERV sequences in orthologous loci (and its pertinent nested hierarchical pattern), we must also take into consideration the shared mutations among orthologous ERVs which also fall into very similar nested hierarchies. [25] Since mutation and ERV placement are independent factors, this is again best explained by the hypothesis of descent. Moreover, the comparative degrees of divergence between the long terminal repeat sequences on both termini of the retroviral sequence (which serve as retroviral promoters) among orthologous ERVs are also implicative of the common descent model. The long-terminal-repeat (LTR) sequences, on either end of the retroviral sequence, must be identical upon insertion. Since LTRs are identical upon reverse transcription and integration, greater mutational divergence (assuming common ancestry to be true) ought to correlate with an older insertion. This is precisely what we observe. [26] Thus, this three-tiered evidence is quite surprising on the hypothesis of separate creation but not surprising at all given the truth of the scenario of common descent." He details the two most common creationist objections - functions and target site preferences which he appropriately dismisses from the evidence. He ends by admitting human evolution from the shared random ERVs is the best conclusion but appeals to his incredulity ( a logical fallacy ) that it could have happened without God guiding it. " To  recap, we have seen that, while the evidence indicates that a transition from a chimp-like ancestor to humans is unlikely to have occurred by an unguided evolutionary process, there is nonetheless genomic evidence confirmatory of common descent of primates that cannot be ignored. I do not believe evolutionists have adequately responded to the former evidence, and I do not believe creationists have adequately responded to the latter evidence." https://jonathanmclatchie.com/the-search-for-adam-and-eve-human-origins-according-to-scripture-and-science/ Common Objections If you’re satisfied with the above reasons why shared ERVs among the great apes is slam dunk evidence for human evolution and macroevolution you can probably skip this part. But anti-evolutionists, often religious creationists, will still try to find something wrong with the science and conclusions here because in their minds evolution can’t be true no matter how solid the evidence. For that, read on my intrepid follower. Remember, Barry’s site (an Englishman living in France) has just about any objection that can be made answered on his site. In my experience, below are the most common objections put forward for shared ERVs and evolution. 1. An early one was that the ERVs don’t insert randomly . There are areas that are generally preferred but not exact locations. Yes they do - by locus. 2. ERVs have functions . No they don’t, but parts ( gag, env ) do, especially the LTRs as detailed above. 3. The VIGE myth. The latest an perhaps the last objection is that ERVs are not old retroviral insertions . They have functions (referring probably to the LTRs only). The reason they are in the same spots between species is because of common design and that the great apes are very similar. They are original to the DNA. Nope. We have research and present day retroviral examples showing how they insert and cause disease. The retroviral proviral genomes match exactly the ERV genomes, including the LTRs. We have the TSDs at each end where they were spliced into the host DNA. They are not original to the host DNA. Scientists have reconstituted a retrovirus from a family of HERVs and it produced infective parasitic retroviruses, not host DNA functions. This resistance to shared ERVs proclaiming loudly human evolution and evolution in general eventually leads to the manufactured idea of the " VIGE", so called"variation-inducing genetic elements". These are like unicorns and leprechauns; VIGEs don't exist except in the minds of anti-evolutionists and are ad hoc imaginary DNA sections. In their view all the ERVs have functions and that's why they are shared across so many species' lines. This attempt of salvaging common design fails. Why? Because of phylogenetic trees. ERVs nest in a way that proves evolution. If ERVs were originally native to the host and later became defective , they could not be put in a diagram that shows evolution. The broken down gene sequences and mutations in LTRs would not show a pattern of common ancestry. In addition, we are told over and over that evolution can't produce new genes and new information (not true) and yet if these ERVs were original and then became parasites and retroviruses later, that means complex new life cycles and viral entities had to form, thus violating the anti-evolutionist claims about new forms never evolving, or "de-evolving". Before today, they jumped around but did not cause disease by breaking genes like they often do now? Where and how did the retrovirus get integrase and reverse transcriptase from? You can’t have your retrovirus/ERV cake and eat it too. They are forcing a theological concept (VIGE mythology really masquerades for science) into a science discussion, because they have no real science to back up their last attempt to salvage common design, which with nested ERVs and phylogenetic trees is disproven. Barry Desborough writes concerning how "VIGEs" don't help anti-evolutionists https://barryhisblog.blogspot.com/p/could-you-have-this-backwards.html?m=1 Modern humans evolved about 300,000 years ago and the population never went below 10,000. https://socratic.org/questions/what-is-the-lowest-number-of-human-population-in-history "In other words, yes, it is a theoretical possibility that quite a bit of human genetic variation was created in a primordial couple, but the genetic evidence does not look that way. Instead, it looks very much like all of our variants come from mutation. And as we noted earlier, if the variation represents accumulated mutation, that accumulation has been going on for a very long time, on the order of a million years." "In other words, the answer to our original question is no: genetic data does not provide evidence that our ancestral population ever consisted of a single couple. A straightforward interpretation of that data is that our ancestors were part of a population in the thousands as far back as we can see... Every indication we currently have from this kind of analysis, then, is that genetic data do in fact rule out a single pair of ancestors within the last 500,000 years. Such a date would put Adam and Eve well before the appearance of Homo sapiens, making them members of an earlier Homo species... What are Christians to do with Adam and Eve, then, given this evidence? That is not really something for me to say: I study genetics, not theology. For those of us who never thought Adam and Eve were recent historical figures and also our sole genetic ancestors, these findings don’t matter much". https://biologos.org/articles/what-genetics-say-about-adam-and-eve "While this quantitative data is not as easy to appreciate as other sorts of evidence we have examined, it nonetheless is compelling: humans, chimpanzees, and gorillas have, within their genomes, the exact pattern of incomplete lineage sorting predicted by (a) relatedness as evidenced by all other lines of genomic evidence (such as shared mutations in individual genes) and (b) large ancestral population sizes throughout the speciation process... The actual result is about 30%, suggesting a population of about 62,000 individuals. This result adds further support to the prior evidence that the common ancestral population of humans and chimpanzees was large." https://biologos.org/series/genetics-and-the-historical-adam-responses-to-popular-arguments/articles/adam-eve-and-human-population-genetics 4. Perhaps you are thinking that one way to test these two competing ideas that ERVs are old retroviral infections vs. they were originally part of the genome would be to resurrect an old HERV and see what it did. If it made retroviruses that went on to infect other cells would not that be great evidence to the objective reader that ERVs are old retroviral infections? I think anti-evolutionists are focusing on LTRs and not the 10% of ERVs that have the entire genome sequence or all the retrotransposons that have all the genes and LTRs except the env gene. I don’t see how their VIGE idea fits because of these exceptions to their “model”. That’s what the scientists did. It turns out trying to repair a single human ERV was not feasible, but knowing that a certain family of HERVs had evolved from an ancestor HERV as it jumped around and mutated they could by overlapping and comparing several, work backwards to reconstruct what the original ancestor HERV was. Guess what? It produced viable retroviruses that went on to infect other mammalian cells. And of course, if evolution were not true, they would not have been able to reconstruct the ancestral retrovirus from its evolved downstream ERVs. They called this ancestral retroviral progenitor that became an active retrovirus " Phoenix " . Conclusion: ERVs including their LTRs are not original to the host genomes. https://www.scientificamerican.com/article/how-to-resurrect-an-extin/ https://www.nature.com/news/2006/061030/full/news061030-4.html Here is the actual publication: https://www.ncbi.nlm.nih.gov/pmc/articles/PMC1665638/ Interestingly, a PhD student also resurrected a functional retrovirus [ Derivation of HERV-KCON ] from a family of ERVs, and published his dissertation in 2010. " Here, a HERV-K provirus whose sequence resembles that of an ancestral human-specific HERV-K(HML-2) was constructed. All viral proteins encoded by this provirus were demonstrated to be capable of functioning in the context of a retroviral replication cycle. While some recent studies have reconstituted “live” viruses from synthetic DNA (Cello et al., 2002; Tumpey et al., 2005), this and a similar study of HERV-K published nearly simultaneously (Dewannieux et al., 2006) are the first examples in which the replication cycle of a virus has been reconstituted using a group of sequences that represent ancient fossils and are demonstrably defective." https://digitalcommons.rockefeller.edu/cgi/viewcontent.cgi?referer=&httpsredir=1&article=1077&context=student_theses_and_dissertations A mouse ERV reverted to a fully functional retrovirus provirus able to produce retroviruses with only 1 mutation. The defect in Emv-3 is caused by a single base substitution in codon 3 of p15gag. https://journals.asm.org/doi/10.1128/jvi.64.5.2245-2249.1990 5. Jon Perry got so much push back against his video on shared ERVs from anti-evolutionists that he made another video to answer their objections and rationalizations. This is a superb video detailing why their objections fail. Other videos Perry made in response to creationist objections can be found here: Anti-evolutionists are angry with Jon Perry: Endogenous Retroviruses - Part 1 https://www.youtube.com/watch?v=B75lH9FeYiM Anti-evolutionists are angry with Jon Perry: Endogenous Retroviruses - Part 2 https://www.youtube.com/watch?v=Ox2-BXTfKss 6. I have not discussed here in detail but one can also look at the LTRs themselves as evidence for common ancestry in the apes (humans are classified in biology appropriately as one of the great apes). This involves what are called discontinuity ratios and nesting trees. If evolution were false, the trees could not be reproduced. Recall that when the LTRs are made by the retrovirus prior to insertion they are all identical. Over time mutations build and these LTRs mutations are independent of ERV placement for evolution evidence. In other words, comparative degrees of mutational divergence between the LTRs of the retroviral sequence also nest in evolutionary trees and indicate another layer of human evolutionary evidence. See the creationist McLatchie's comments immediately above this Objections section. 7. Claim: There are no known examples of germ line retroviral infections. Not true. Retroviruses have been infecting our ancestors using molecular dating for probably 100 million years - plenty of time for thousands of endogenizations. a. We actually can see it happening right now in the Koala retroviral pandemic. "C uriously, 38 koalas have been born in Japanese zoos since the original importation, and 36 of these animals are infected with KoRV. This high rate of infection is a consequence of the fact that KoRV DNA integrates into DNA of koala germ cells. The viral genome is transmitted vertically, from mother to offspring."    https://virology.ws/2009/04/21/a-retrovirus-is-invading-the-koala-genome/ b. "Efficient Insertion of genes into the mouse germ line via retroviral vectors" https://www.ncbi.nlm.nih.gov/pmc/articles/PMC391009/pdf/pnas00358-0132.pdf c. "Spontaneous Germ Line Virus Infection and Retroviral Insertional Mutagenesis in Eighteen Transgentic 'Srev' Lines of Mice". https://www.ncbi.nlm.nih.gov/pmc/articles/PMC362159/pdf/molcellb00049-0193.pdf 8. Usually, nearly all objections will contain some kind of assertion that the ERVs (really fragments; only solo LTRs are left most often. See above) are vital for functions (functions, functions, functions!!!) and that is why chimps and humans (and the other great apes) share them in the same homologous locations. In effect, common design. But not all humans have some LTRs, so that is a difficulty for anti-evolutionists. They must admit SOME of them must have been from retroviruses. In addition, the host already has it's own promoters and enhancers - why also have them from viruses? We can use these observations to evaluate attempts to discount shared ERVs as great evidence for common ancestry in the great apes as is done in this 20 minute video: 9. In June, 2023 a fascinating report was published that detailed a type of cellular survival of the fittest that occurs in every early embryo - "An Ancient Battle Is Playing Out in the DNA of Every Embryo" Millions of years ago, retroviruses invaded the human genome. Today some of these viral remnants threaten the developing embryo while others fight to defend it." https://www.wired.com/story/an-ancient-battle-is-playing-out-in-the-dna-of-every-embryo/ https://journals.plos.org/plosbiology/article?id=10.1371/journal.pbio.3002162 10. In January, 2024 researchers identified a  viral gag gene that produces the viral protein MERVL-gag which is necessary in very early embryonic and modulates our URI gene. https://phys.org/news/2024-01-virus-infected-animals-hundreds-millions.html?fbclid=IwAR1nSSiHo3OicLvrizXna9uQa46GbxvXjQ3mERAiybxvuEXQbvcRwgFZ0OQ What fossil evidence is known that points to the earliest hominid candidate branching from chimps and bonobos 6 - 7 mya? Looking for Mr. Goodlink? - https://pandasthumb.org/archives/2024/07/looking-for-mr-goodlink.html?fbclid=IwZXh0bgNhZW0CMTEAAR1tqB8ZjQYkNc9xiw7Y-JeQu8kHQp-Xv_F4lkb0RGcrO_cTtbgMgHbKVAQ_aem_gSjMcNZ_alEk8DVfk13n3w#more Summary I have chosen shared ERVs between humans and the other great apes because I think that this observation represents some of the best evidence for evolution. That it also satisfies desires for “macroevolution” and human evolution evidence is a special bonus. The concept of shared ERVs is deceptively simple. Let me try another analogy in addition to the plagiarized papers I already gave. Let’s say we have two persons living in different states or countries. They are each instructed to take identical pistols and bullets and fire 100 shots at a paper target 50 yards away. When you compare the two targets all the holes line up. That of course is mathematically impossible. Somehow the targets were copied either from one of them or a third master target - but the targets somehow trace back to the same ultimate origin. The bullets are like the retroviruses targeting the host DNA. The bullet hole edges are ragged like the cut-ins in the host DNA with flanking TSDs at either end. What we know is that these were not independently created. Most importantly, there are 200,000 shared exact homologous “holes” (ERVs) between chimps and humans in their genomes. The ONLY rational explanation is that chimps and humans share the same origin and that these insertions could only have happened before the species split . Are there more examples of evolution from comparative DNA findings in the great apes? Absolutely. Human chromosome 2 is a fusion of two chromosomes and if one lines up chimp chromosomes 12 and 13 end to end to our HC2, they match (called 2a and 2b when comparing all of the chromosomes between us and chimps). See my discussion of HC2 fusion here . After our ancestors split from a common ancestor we shared with chimps, we went from 48 chromosomes to 46. For individuals this only takes two generations in a population. The reason I don’t list this as the best evidence for evolution is that it could still be claimed that a designer just made humans that way after creating the other great apes. To my astonishment however many evolutionists are actually arguing that HC2 is not a fusion. Another DNA finding is similar to shared ERVs. It turns out that we have about 20,000 pseudogenes - old mutated genes that no longer function. And we share many of them in the same locations often with the same mutations as chimps and less so with the other great apes who are more distantly related to us. See pseudogenes here . This also is great evidence that we share a common ancestor with chimps, and evolution explains the similarities in our looks (phenotypes) and at the genetic level (genotypes) while common design is ruled out. Third, it turns out that DNA breaks easily and emergency repairs mean the cell grabs any nearby DNA to make a patch. These patches occur due to random breaks and create unique patches which can be identified. When we find the same breaks and same patches in the same homologous locations between species we know the only rational explanation is that the break and repair must have happened in a shared ancestor. See the blog discussion this . Evolution is demonstrated to a very high level of confidence when looking at our genomes and comparing them to other animals, especially chimps and the other great apes. Anti-evolutionists must stop trying to deny our biological histories. As one person wrote, the newer DNA findings result in a second Galileo moment for anti-evolutionists. The DNA findings cry out common descent, common ancestry. Evolution, “macroevolution” is true not only from the fossils, biogeography, developmental biology, etc. but confirmed by DNA findings. References 1. How the Placenta evolved and why https://whyy.org/segments/the-placenta-went-viral-and-protomammals-were-born/?fbclid=IwAR1xG6y3zP3NOOMWbOKW17ikvBUvgnY9nIOtpjaPxWbRECbdwnfsnzO8myI 2. Endogenous retroviruses - increasing genomic plasticity [functions for parts of ERVs] https://www.ncbi.nlm.nih.gov/pmc/articles/PMC3921067/?fbclid=IwAR0XrbQxLEWbgJ7hG73td8ev-INnOe9Yqdlh_J9GGWpYvGY6KMo0XEE2vm0 3. Essential role of endogenous retroviruses in evolution https://www.youtube.com/watch?v=bTLD6Nki92A 4. The Case For Junk DNA [with comments about ENCODE] https://journals.plos.org/plosgenetics/article?id=10.1371%2Fjournal.pgen.1004351&fbclid=IwAR0Sih-kUTid35xGiASCeg8veWc4u871lPJQCKjXACubtSNHQ7tFe2v0BwQ 5. Three layers of evidence for evolution from ERVs https://evolutionarymodel.com/ervs.htm That site is no longer available. :-( There is a Google Doc copy: https://docs.google.com/document/d/17KaYjZ9zM7e8zkG2y9udqVG-NQJx-QP_Gjz1xzyt5Fk/edit?fbclid=IwAR0OUCVejbJ7Xbqz0Cl0hjRAasAi90sVv8y-ppLAv2e67AVy_ctKlROIHA8&pli=1#heading=h.lb8ebmgum4wx His YouTube explanation: https://www.youtube.com/watch?v=_kfLo4Wd6cc 6. Finlay, G. 2021. Human Evolution: genes, genealogies and phylogenies. Paperback ed. Cambridge University Press. 283 pg. without Ref and Index 7. Origin and Deep Evolution of Human Endogenous Retroviruses in Pan-Primates. 2022, June 23. Viruses. 2022 , 14 (7), 1370; https://doi.org/10.3390/v14071370 8. The Evolution of the HERV-W group. HERV-W Group Evolutionary History in Non-human primates: : characterization of ERV-W orthologs in Catarrhini and related ERV groups in Platyrrhini. 2018. https://link.springer.com/article/10.1186/s12862-018-1125-1 9. Ancient Viruses in Your DNA Fight Off New Viruses https://www.wired.com/2016/03/ancient-viruses-hidden-human-dna-fight-off-new-viruses/   10. Million Year-old viruses help fight cancer, say scientists https://www.bbc.com/news/health-65266256   11. Ancient Viral DNA may help humans fight infections https://www.nih.gov/news-events/nih-research-matters/ancient-viral-dna-may-help-humans-fight-infections#:~:text=Researchers%20found%20that%20stretches%20of,insights%20for%20fighting%20viral%20infections .   12. New study reveals an innate genome response to retroviruses in kolas. https://www.umassmed.edu/news/news-archives/2019/10/new-study-reveals-an-innate-genome-immune-response-to-retroviruses-in-koalas/   13. Evolutionarymodel. Wonderful details about ERVs and evolution https://web.archive.org/web/20230327203649/https://www.evolutionarymodel.com/ervs.htm

With a review first of Creationism Types "Science wants to know the mechanism of the universe, religion the meaning. The two cannot be separated." ~ Charles Townes, Physicist Creationisms Creationism refers to those who believe God had a hand somehow in the formation of species. Of course it also aligns with other topics such as the origin of the universe and the origin of life (see my posts about the https://www.truthfuloriginsevo.info/post/big-bang-multiverse  and also abiogenesis ) which do not directly connect with evolution. If we never discover what came before inflation or how the first cell came about that would still not impact the evidence for evolution. I will argue that with what science has discovered even the creationism that seems to accommodate evolution with God using or guiding it called theistic evolution , or as some prefer to rebrand it evolutionary creationism,  also fails to fully accommodate science. I will refer to this creationism with it’s older, better known term theistic evolution (TE) but acknowledge the advantages of the new term for them. I will also assert that although this is the only creationism that appears to accommodate science, it suffers from other mortal flaws, leaving all forms of creationism ultimately unable to form a foundation for religious and agnostic views. Lastly I will further posit that all forms of creationism will be unable to ever have a viable origin narrative that is both scientifically sound and  also not suffering from other refutations. These will be detailed. Abrahamic believers number about 4.2 billion of the 8 billion humans alive today. I am not addressing the 1.2 billion Hindus and 500 million Buddhists (1) but plan to write about major religious beliefs in the future. The major types of Biblical creationisms today in my opinion are Gap, Day-Age, Figurative, Young Earth (AIG, ICR, CMI organizations), Progressive (RTB organization), and Theistic Evolution (TE) . Young Earth Creationism (YEC) claims the universe and earth are less than 10,000 years old, that there was a global Noachian Flood, an Ark and other literal interpretations of Genesis. All the others are various Old Earth Creationisms (OECs). Gap   creationism proposes that there are billions of years between Genesis 1:1 and 1:2. Day-Age  Creationism suggests that each day of the creation week can be millions or billions of years based on 2 Peter 3:8 (a day to the Lord is as a thousand years). This attempt to accommodate Genesis with science along with Gap addressed mainly the geological findings and radiometric dating but did not adequately deal with evolution well and so are not popular today. A Figurative  approach basically assigns Genesis to metaphor, analogy, hyperbole, or other more liberal interpretations. It is rejected by the conservative Abrahamic religions as sacrificing too much of the scriptures to literature and mythology and so is usually not acceptable to them. Progressive   creationism, championed by Hugh Ross and Reasons to Believe (RTB) , accepts an old universe and earth but further explains the geological column as successive whole extinction events and repeated complete new creations by God. This idea of repeated cycles of mass extinctions by God so unique species could be de novo  created each time without evolution is not new. Thus the denial of transitional fossils existing (for example to prepare the earth for humankind's need for fossil fuels) traces back to Cuvier (d. 1832). He postulated the same solution to explain all the fossils he was identifying. He called these episodic mass extinctions and complete reboots of life "revolutions". Before Cuvier most people rejected fossils and extinctions because that idea did not fit with their concept of Biblical creation, as God declared everything good at the end of the creation week. For them, having millions of species go extinct did not seem consistent with Genesis and all "good" species. Reasons To Believe  also holds tightly to a historical Adam and Eve and denies human evolution. YECs   are the most scientifically radical. In order to hold to this interpretation of Genesis, they must redefine or reject laws of physics (radiometric decay and red shift, for example), redefine geology and anthropology (glaciation, plate tectonics, the geological column, etc.), reject all of evolution and it’s evidence including DNA findings and paleontology, and insert a global year long flood, an Ark, a Tower of Babel to explain languages, belief in a talking snake and donkey, and belief that people once lived to nearly 1,000 years. To them women have extreme pain and sometimes die in childbirth because two people ate fruit suggested by a talking snake from the wrong tree God specifically put in the middle of a special garden so they would not miss it. They reject the evolution of bipedalism and changes to the female pelvis documented in the fossil record that makes giving birth to a large headed primate difficult. They are also prodigious in their publications and probably account for 95% or more of the creationism articles and videos on the Internet. I will be writing in the future about how YECism basically must thus wrap themselves with a cloak of conspiracy thinking at this level of denial and rejection of settled science. The other consideration is that many people construct a personal and unique creationism (and also worldview) of their own, often combining many different aspects of an origin narrative, thus producing a mosaic or mash-up of ideas. This may be very true of the “nones” in America, that although not religious, often are spiritual or agnostic towards theology in some way. So it is vital that when discussing origin narratives, assumptions are not made about what the person believes; ask them for specifics. Unfortunately, many people may not be aware of inconsistencies in their species origin narratives. Their simple answer may just be an insufficient “Goddidit”. Theistic Evolution/Evolutionary Creationism Types I have demonstrated on this site with just two examples - whale evolution and DNA discoveries that rise to the level of proof of human evolution (see ERVs ; also see Human Chromosome 2 fusion , DNA repair patches , pseudogenes  and transposons ) - that evolution is true. Evolution is settled science (see Evolution.   Also see "How We Found Out Evolution Is True,"  a wonderful short TEDx presentation by John van Wyhe ). Mechanisms for how it occurred are still debated but not that it did occur. Given that evolution is no longer debated in science, I assert that all creationisms including TE suffer in some way from rejecting evolution as we find it . If a creationism rejects human evolution considering the overwhelming evidence we have for it, we are more than justified in dismissing it out of hand as a viable explanation for species origins. Figurative creationism is generally rejected by Abrahamic believers themselves since it sacrifices too much in their view of the original scriptural meaning. It makes a mockery of their core beliefs by assigning too much to mythology. That leaves only TE to address. Do any of the various forms of TE/EC really accommodate evolution as science has found it? There appear to be several TE variations. One form especially common among Catholics accepts "molecules to man" but proposes supernatural intervention at various times in history. These TE advocates may feel the need to have God tinker with the evolutionary process at some points. For example, by causing certain mutations or de novo genes to occur at certain stages in evolution despite that fact that in 400 years of intense research science has found no evidence for this. I think Behe of the Discovery Institute uses this type of God directed evolution in his TE beliefs. Adam & Eve are usually just metaphors. A second type of TE accepts scientific evolution but still must have a historical Adam to try and accommodate Genesis.  Recall that genomics has demonstrated that humans never went through a bottleneck of 2, or 8 off a boat; we never went below 3,000 - 10,000 individuals. The evangelical William Lane Craig, one of the most prodigious debaters for conservative Christianity, now publicly accepts human evolution in his writings but has a modern Adam being created by God at the time of Homo heidelbergensis  and then somehow replacing that hominin population with the new, modern guy on the block who is injected into earth's history from above . Joshua Swamidass accepts human evolution but has God creating a garden and Adam 6,000 years ago only to see Adam’s DNA spreading around the world  and completing its journey just in time for Jesus to arrive and save the world 2,000 years ago. All of these variations of TE contain unproven religious presuppositions injected into the theory of evolution, hoping again to save their interpretation of Genesis in the face of robust evidence for evolution, and especially human evolution. They are absurd and are ad hoc even if they can't be disproven. The above variations of TE are not evolution as science has found and described it. Evolution relies on random mutations, brutal natural selection plus other naturalistic mechanisms, and there is no evidence of a historical Adam/Eve. As I've written, genomics indicates the human population never went below 3,000 - 10,000 and certainly not all the way down to 2, or 8 off an ark with a brutal and cruel genocidal reboot by drowning. Nor has science revealed a God reaching down and tinkering with the process of evolution at just the right moments. The "solutions" by Craig and Swamidass indicate desperation to hold onto Genesis at any intellectual cost and stretch credibility to where it breaks. A third type of TE/EC is probably best described by the scientists and academic Christians at Biologos (2), the site founded by Francis Collins in 2007 with a Templeton grant to showcase especially the DNA evidence for evolution. They posit that God used evolution as science has found it to create life on earth. They also interpret Genesis as more mythology or figuratively/symbolically, including the Biblical Flood as a local event for example. They fully argue for an all naturalistic approach to evolution as God's method for the origin of species. YEC literature bemoans the growth of TE in churches but I have not seen that. Perhaps it's in the younger generations and the "nones", and I am just not aware of it. In evangelical circles and other conservative religion writings I have not seen the message of Biologos changing theist minds to any great significance. Why TE Fails "And after millions of years of mutations, mass extinctions, devastating diseases, and violent death, God saw all that He had evolved and behold it was very good!" ~ Dan Lietha (Young Earth Creationist) There are many reasons why TE/EC fails as an attempt to accommodate Genesis with science, evolution. 1. At best, this form of creationism would be superficially consistent only with deism. A personal theistic God that interacts with His creation frequently and answers prayers is not supported. A theist still has a mountain of evidence and logic to provide. 2. I assert that if God used evolution to create or allowed it, then this God is not worth worshipping. He would then be   incompetent, indifferent  to the waste and suffering or malevolent  having enjoyed all the waste, death and suffering. Let me explain by looking at how natural selection and evolution actually work. As I wrote in the Introduction to Evolution ,  evolution is when a population genetically changes from a previous one. Specifically, more individuals happen to inherit certain genes that code for certain characteristics. This occurs because natural selection selected which offspring variants are best fitted for the current conditions and live long enough to produce more viable offspring than other variants in the population. In order for this system to work, nature produces lots of offspring. Given time, adaptations will arise and spread throughout the species. For example, populations tend to be stable from generation to generation. Despite thousands of eggs laid by a fish, only one or two will survive into the next generation to reproduce. Dogs have many puppies and cats kittens but on average if a population is stable, over the life of the parents only two on average in sexual species of all those offspring will survive to reproduce. An oak tree will produce millions of acorns each year and billions over its life only to have one replace itself in a stable forest. What about humans? From the time of fertilization until a child grows to a reproductive age there is nearly an 80% death rate before modern medicine and societies. Many fertilizations don’t implant. Some of those that implant miscarry (a spontaneous abortion in medicine). Some offspring die at birth and more later before reaching reproductive age. Around the world a woman dies every 2 minutes during pregnancy or giving birth. Human parents needed to have many children even a hundred years ago because so many died before adulthood. The waste and suffering is incredible to just get a few offspring into the next generation in nearly all the species that live or have ever lived. In a theistic world, this God either designed this system that includes so much death or allowed it. People want to worship this horrible architect? When we look at the history of life on earth, 99.9% of species that have ever existed have gone extinct. There have been at least five huge mass extinctions. Sometimes it's a rock from space. Another time huge lava flows in Siberia cover the planet for millions of years and poison the air. Some species can’t compete against other species, especially if a new species is introduced. This can happen due to continental drift or a pregnant founder species onto an island for example. A system of creation that depends on evolution is one that is incredibly wasteful. Children die of starvation, infection or cancer by the thousands for example. This is why I assert that although TE/EC appeals to all natural mechanisms it paints this God as incompetent because this method is hardly worth embracing by anyone. One can’t hold up awesome redwoods and beautiful butterflies without also mentioning childhood cancer, malaria, and Ebola. Or, this deity is indifferent to all the waste and suffering and offers nothing better. A “Fall” as an excuse if offered means all those innocent children and animals are just collateral sacrifices? Lastly, perhaps God likes the suffering and waste and is really malevolent. In contrast to this theistic way of looking at nature via a God designed creative evolution, the way we find the world and universe is exactly what we would expect if evolution were true and there was no Engineer and Designer at the wheel of the evolution bus. 3. There is no evidence of God the Tinkerer. Mutations for producing new genes to form new species are overwhelmingly random. Mutations are often neutral or deleterious.   No evidence for any supernatural intervention has been found during intense evolutionary research. 4. Our genome is 80 -90% junk DNA. Please see how we know this by reading the blog on  Junk DNA . It's difficult to imagine worshipping a God that ends up creating humans and other organisms like this. God the DNA junk hoarder? 5. A theist must still argue for a "soul" that persists after death. What kind of entity or force or energy this would be is not specified. Well respected physicists now argue that physics demonstrates that people can't have a "soul" . 6. When we look at the history of life as revealed in the fossil record and in the DNA of species we see no planning or goals . Every theist arguing for TE/EC posits the assumption that God used evolution to evolve humans; we are the end result of a grand plan. But the record of life reveals 99.9% species failures, horrible mass extinctions, and genomes consisting of massive amounts of junk DNA. We are the product of billions of years of evolution and contingencies and not the end goal for evolution. We are fortunate to be here; several times we almost went extinct  and here . This does not speak to some kind of grand plan with evolution as the method; just the opposite.Some like Conway Morris have argued that since we note convergent evolution frequently that there appears to be constraints on evolution. As a challenge to Gould who wrote that if the tape of life was rewound and restarted that the same species would not appear, he counters that they would still originate despite contingencies and what appears to be random events. Thus, teleology still has a place in TE/EC according to these theistic evolutionists (4). However, just focusing on convergent evolution without considering other factors such as junk DNA, massive extinctions, and the waste and suffering baked into evolution just reveals motivated reasoning and confirmation bias. 7. In order to hold to TE/EC huge amounts of the various scriptures need to be interpreted as mythology, literature or rationalized to the point they lose divine meaning. For example, Noah's Flood is local despite Genesis having birds taken on board and the verses specifying  high mountains  were flooded. A bible's supernatural narratives dismissed to accommodate science dismisses its claims to divinity also. The malevolent Designer? Is God Good? "I go into a lab and create a unicellular eukaryotic organism that will kill millions I infect flying insects to serve as the delivery system If I release it, would I be evil? Without exception every theist I asked replied 'yes' I then ask them to explain malaria." ~ Author unknown. Attempting to explain malaria with "The Fall", and absolve God won't work. Who created the very complex parasitic Plasmodium  species? We are told by some creationists that nature can't increase complexity or add new information. If not God, who or what? Did it "de-evolve"? How? Did God then at least allow it? What happened? From what? What are the steps we can reconstruct in its DNA to show this? Thus, if God used or allowed evolution to create, this means He/She/Them/It is not worth worshipping. This is the best He could do? He doesn’t care or can’t do anything about the waste and suffering? TE/EC fails as a viable creation narrative option in my view because it not only sacrifices too much of its scriptures to mythology, but is irrational. Thus, Christians and other theists are left with no choices for an origin narrative that is believable and accommodates science. Origin narratives serve as foundations to our worldviews. In my opinion, theists will never be able to formulate an origin narrative that will stand up to science, not compromise their scriptures with too much mythology, and withstand a rational evaluation. It’s not the fault of science that religion keeps making claims that are falsifiable, and trespassing into areas that science and philosophy study. One of the most comprehensive reviews of the multiple failed attempts by Christian apologists to accommodate Genesis with Evolution and science is the book “Evolving out of Eden”  by Price and Suominen. (3) It should be noted that some atheist/agnostic scientists such as Lents are very willing to support theistic evolution because in their view believers endorsing evolution means at least science will no longer be under ongoing attacks from religious fundamentalists. That is a pragmatic approach to take when considering the long struggle for evolutionary theory acceptance, especially in America. But the form of TE/EC that is being accepted is often not the Theory of Evolution as it is taught and practiced in science. It remains to be seen if short term goals met in this scenario brings only long term confusion and problems later. This may be just kicking the Evolution can down the road. A good collection of articles in favor of theistic evolution defended by Catholic scholars can be found here, especially the article by Austriaco in "The Fittingness of Evolutionary Creation ". However, it fails to address my claims. Evolution is not a  "most efficient way for divine providence" as I detailed above in point number 2.   Using random asteroid strikes for example to open up niches via whole species slaughter rather smacks of planetary near genocide. Calling extinct species just "necessary left-overs from the creative evolutionary process"  and ignoring that at least 80% of our genome is junk DNA is incredibly fanciful. Rather, this speaks of evolution without goals or planning let alone any method a wise, compassionate deity would use to create species. Conclusion Major forms of creationism are reviewed. Most are Old Earth Creationisms which accommodate a universe and earth billions of years old but usually deny evolution and especially human evolution. Young Earth Creationism rejects nearly every significant finding of science in regards to origins; it is the one type that clutches its beliefs mainly through denial. All the major forms of creationism reject large scale evolution, "macroevolution", and human evolution except for Theistic Evolution or its newer name, Evolutionary Creationism. Thus, the agnostic or theist who wishes to ascribe the origin of extinct and living (extant) species to a creator and be consistent with science will often turn to TE/EC as an answer to species origins thinking that this is a viable solution. The problems with TE/EC as a viable option to explain species origins for Abrahamic creationists are numerous and include painting the divine Designer or Engineer with incompetent, indifferent, or malevolent colors and injecting the unsupported goal of producing humans as an ultimate divine plan. That many of the "nones" may be adopting TE without a sound knowledge of how evolution really operates and how TE is thus not a viable option, is troubling. In addition, so much of the theist scriptures need to be compromised with analogy, metaphor and appeals to mythology that the Abrahamic God fades into history to join Norse, Greek, and Roman stories as literature and mythology only. For "nones" this latter problem may not be an issue. "We cannot escape our origins, however hard we try"  ~ James Baldwin Citations 1. https://en.wikipedia.org/wiki/List_of_religious_populations   2. https://biologos.org/ 3. https://www.amazon.com/Evolving-out-Eden-Christian-Responses/dp/0985136243   4. https://capturingchristianity.com/btw-evolution-is-teleological/?fbclid=IwY2xjawEhzeNleHRuA2FlbQIxMAABHTIjFdHGBWoNsV6fhCO5kIVz9lUyH_psuDOXOhLa5tEnwveho_JTE2ezZg_aem_km269S4179FpMrV5Smwj2A

"Thus we have seen that the "Cambrian explosion" is a myth. It is better described as the Cambrian slow fuse. It takes from 600 to 520 million years ago before the typical Cambrian fauna of large shelly organisms (especially trilobites) finally develops." Donald Prothero, Part II. Evolution? The Fossils Say Yes! From:  Evolution - what the fossils say and why it matters.  2nd ed. 2017. The Anti-evolutionist Claim : Complex forms appear suddenly in the Cambrian layer with few or no precursors. This is not predicted by evolution and fits best with a creation event. For most Young Earth Creationists, it represents the basal layer of a Global Flood that occurred about 4,000 years ago. Answers In Genesis gives an exact year: “Using the Bible, well-documented historical events, and some math, we find that the Flood began approximately 4,359 years ago in the year 1656 AM or 2348 BC. Some may look for an exact date (i.e., month and day), but we are not given that sort of precision in Scripture.” (3).    For Progressive Creationism ( Reasons To Believe , an Old Earth Creationism group) it is interpreted as an early creation event millions of years ago to be followed by many cycles of extinctions and new creation events through thousands of feet of sedimentary rock. In addition, anti-evolutionists note many of the Cambrian fossils are unique and do not persist above the Cambrian.  A senior member of the Intelligent Design Discovery Institute , Stephen Meyer, has practically made a career of promoting the Cambrian Explosion as supposedly disproving evolution. Since creationists believe the only alternative to evolution is some type of creationism, many creationists don’t feel the need to propose, discuss, or test a specific and falsifiable alternative to evolution. For Meyer and others, it’s a one and done paleontological rug pulled out from evolution if the Cambrian indicates flora and fauna suddenly appearing. But does complex life suddenly appear in the Cambrian with no evidence of precursors? Introduction The geological record around the Cambrian is noted below. The Cambrian Period is the first and oldest layer of the Paleozoic Era as one ascends towards our time. Logically enough, the Era before the Paleozoic is called the Precambrian and is composed especially for this discussion of a Period immediately before the Cambrian called the Ediacaran.  From: https://www.fossilicious.com/blog/geologic-time-reference-chart/ Used by permission. Fair use educational purpose Persons exposed to anti-evolutionist material about the Cambrian may get the impression that life and certainly complex life just appeared suddenly in the Cambrian. That is not the case. The Cambrian Period spans a period of about 538 mya to 495 mya but fossils are known to science that show life going back to 3.5 billion years in the form of cyanobacteria from the Archaea rocks of western Australia. These are microfossils (1).  So life did not appear in the Cambrian. The oldest rocks on the planet are 3.8 billion years old; the earth is 4.6 billion years old. Life did not wait too long to get started but for about 2 billion years life on earth consisted only of single celled organisms, called prokaryotes. “ There are hundreds of microfossil sites around the world. Everywhere we look in rocks between 3.5 billion years old and about 1.75 billion years old, we see nothing more complicated than prokaryotes and stromatolites. The first fossil cells that are large enough to have been eukaryotes do not appear until 1.75 billion years ago, and multicellular life does not appear until 600 million years ago (2)”. We know we can even trace our eukaryotic lineage into deep time due to our mitochondria, a result of endosymbiosis (see short blog on  mothers and mitochondria ). So life did not first appear in the Cambrian.  The Cambrian is now divided into Early, Middle and Late. Traditionally, the Cambrian was marked by the appearance of the trilobites, but now we know these forms occur at the end of the Early time and other fossils preceded them in the Cambrian. The Cambrian “explosion” was a fast evolutionary diversification event that occurred over about 20 million years in the last part of the Early section of the Cambrian. As will be discussed later, other relatively fast evolution examples have been noted before in the fossil record - times of quick diversification geologically. The Ediacaran Period  This is the time just before the Cambrian and it contains a weird assortment of flora and fauna. Nearly all are soft bodied organisms without skeletons. “ These impressions have reminded some paleontologists of the impressions made by sea jellies, worms, soft corals, and other nonskeletonized organisms. Over 2,000 specimens are known, usually placed in about 30 - 40 genera and about 50 - 70 species, so they were relatively diverse.”  (2). Some are very different from today’s species. Other paleontologists suggest they are unique because they lack modern patterns and may represent early failed experiments in multicellularity. The Ediacaran fossils are known from soft sea floor bottoms only and few important features are present. Thus, where they fit into classifications is controversial. They are definitely multicellular but paleontologists are not sure even what kingdom to place them into or even if they represent a new kingdom (2).  Scientists have calculated molecular clock estimates for the divergence times of the major invertebrate groups and these figures indicate that major branching points go back as far as 800 - 900 million years ago well into the pre-Cambrian times (4, 2). This means that advanced multicellular life (without fossilizable skeletons) were present on the earth 600 million and even 900 million years ago - at least 50 million years before the Cambrian. The Ediacaran fauna represents the next logical stage bridging single celled life to the appearance of soft bodied life.  Early Cambrian Stages The fossil record indicates it took 3 billion years for life to develop the ability to mineralize shells which is what we finally see in the early Cambrian stages. When they did develop mineralization it was calcium phosphate, the mineral that makes up bones, and not calcium carbonate that most of today’s marine invertebrates utilize. Prothero writes about what followed after the Ediacaran: for almost 25 million years many tiny phosphorous fossil shells (a few millimeters only) were abundant in the earliest stages of the Cambrian. The Nemakit-Daldynian and Tommotian stages from 520 - 545 mya. revealed that some looked like coiled mollusks, some like primitive clams, and others like tubular forms or even like miniature jacks. The earliest sponges had already appeared in the Ediacaran, and sponges have always been considered to be the most primitive animals we have today. By the Tommotian stage 530 million years ago larger fossil invertebrates appear such as the brachiopods. Abundant burrowing can now be seen indicating a true internal cavity or coelom. Thus, the earliest Cambrian shows evidence of a gradual increase in diversity from the Vendian, but no “explosion”  (2). Another author notes:  “…the Cambrian explosion does not document the “sudden appearance” of all animal phyla. A significant number of animal phyla are already present prior to the explosion. It is simply that we remain unsure of their exact classification precisely because they are so different from living animals.” (4) Later Cambrian Stages The third stage is known as the Atdabanian stage and there is a significant development of diversity found. Much of it is the genera of trilobites. “Most of the other animal phyla had already appeared by this time (including mollusks, sponges, corals, echinoderms) or would appear later in the Cambrian (vertebrates) or even in the Ordovician Period that followed (e.g., the “moss animals or bryozoans)… Then in the Middle Cambrian we have the extraordinary soft-bodied preservation of fossils…Some are still complete mysteries to zoologists, not fitting into any living phylum. Others are apparently soft-shelled arthropods.” (2) Summary 1. What “exploded” in the Cambrian? When fossils were first found in this period it was mostly just the hard shelled trilobites - lots of them. They and other mineralized fossils seemed to appear suddenly without precursors. They were fairly complex multicellular organisms. But that is an old and early observation. The early Cambrian has 25 million years of small shelled animals before the arrival of the larger forms. The fossils of the Ediacara have since been discovered and it’s obvious that there was a gradual increase in diversity from the Ediacaran stages to and through the Cambrian.  Many feel that the appearance of so many new forms in the Cambrian was more a function of an “End-Ediacaran" mass extinction that happened before the Cambrian. “This implies that the "explosion" did not represent animals "replacing" the incumbent organisms, and pushing them gradually to extinction; rather, the data are more consistent with a radiation of animals to fill in vacant niches, left empty as an extinction cleared out the pre-existing fauna” (8) 2. The Cambrian “Explosion” was just a fast diversification event, an adaptive radiation period. We know that this has happened in other parts of the fossil record such as the 10 - 15 million years of whale evolution, (see the actual overwhelming evidence for whale evolution  in 3 relatively short videos here) and the mere 10 million years from the Cretaceous-Paleocene extinction that produced all our different orders of birds. The “explosion” is basically a myth and hold-over from early observations and catchy titles. As in the Big Bang; it was really not an explosion either.  3. Although the Cambrian diversification event (“explosion”) is normally stated to have occurred over a 10 - 20 million span, if we include the precursors in the Ediacaran to the large shelly organisms in the Tommotian, like the trilobites, we are really looking at 80 million years (2). In addition it follows a series of logical stages from simple and small to larger and more complex mineralized forms. The development of more complex life from 600 to 540 mya is hardly an “explosion”.  “The theory of evolution has no issue with the Cambrian explosion, as the explosion spans such an extraordinary long period of time.” (5) 4. The tiny fossils found in the early stages of the Cambrian and span 25 million years are nicknamed the “little shellies” because they are so small and so abundant. Their shells are calcium phosphate instead of calcium carbonate like our marine invertebrates today. This is not a killer argument against evolution. Some scientists think this could have resulted from an environmental condition such as low oxygen at the time. This is a gap in our knowledge and gaps are by definition lacking information - which is different than finding actual evidence that disproves something. Despite the denial by Intelligent Design advocates, the movement is centered around a well known logical fallacy involving trying to use gaps which by definition are lacking in evidence as evidence. Absence of evidence is not evidence of absence. 5. What about all the Cambrian forms that are extinct? Is not that a problem for evolution since many did not end up being precursors to the later fossils and today’s species? This is probably a misunderstanding of classification. “Many of these ‘extinct phyla’ from the Cambrian were really part of the arthropod phylum. Some are clearly brachiopods, and some were mollusks. Although these animals are anomalous when compared to today's SPECIES, they really are not anomalous when compared to today’s PHYLA.” (6)  6. All major life groups did not appear at the Cambrian. It was not a “creation” event for life on earth.  Biologos notes: “The major animal body plans that appeared in the Cambrian Explosion did not include the appearance of modern animal groups such as: starfish, crabs, insects, fish, lizards, birds and mammals. These animal groups all appeared at various times much later in the fossil record. The forms that appeared in the Cambrian Explosion were more primitive than these later groups, and many of them were soft-bodied organisms. However, they did include the basic features that define the major branches of the tree of life to which later life forms belong. For example, vertebrates are part of the Chordata group. The chordates are characterized by a nerve cord, gill pouches and a support rod called the notochord. In the Cambrian fauna, we first see fossils of soft-bodied creatures with these characteristics. However, the living groups of vertebrates appeared much later. It is also important to realize that many of the Cambrian organisms, although likely near the base of major branches of the tree of life, did not possess all of the defining characteristics of modern animal body plans.” (7) Conclusion Thus, the Cambrian did not represent the sudden appearance of many major groups that are present today. It does not support Young Earth Creationist and Intelligent Design claims that life as we know it appeared suddenly in the Cambrian, but rather a proper examination of what came before, during, and after the Cambrian supports instead evolution. A very thorough evaluation of the amazing discoveries in the Cambrian and pre-Cambrian fossils including challenges in interpreting them can be found in Budd's 2013 review (9). Nothing in the Cambrian discounts evolution at all: "Together with a remarkable growth in knowledge about the environments that these early animals lived in, these discoveries have long exerted a fascination and strong influence on views on the origins of animals, and indeed, the nature of evolution itself. Attention is now shifting to the period of time just before animals become common, at the base of the Cambrian and in the preceding Ediacaran Period. Remarkable though the Burgess Shale deposits have been, a substantial gap still exists in our knowledge of the earliest animals. Nevertheless, the fossils from this most remarkable period of evolutionary history continue to exert a strong influence on many aspects of animal evolution, not least recent theories about developmental evolution." (9) An early simile for Intelligent Design was that finding a watch implied a watchmaker. The Cambrian explosion has been thought by anti-evolutionists as a good example against evolution. However, a close review demonstrates that it instead fully supports evolution albeit with much that remains unknown. As if often the case when discussing anti-evolution claims, it is vital to ask what is being withheld from the conversation. Note below the Cambrian in context. From: https://www.britannica.com/science/Cambrian-explosion .  Cambrian Explosion; paleontology. Fair use claimed; educational purpose. This article is a good brief review of the Cambrian. Research is revealing some of the environmental changes that drove diversification in the Cambrian. Mobility evolved which encouraged predation and defensive evolution. https://www.ed.ac.uk/news/2024/sea-level-changes-shaped-early-life-on-earth-fossi https://rosarubicondior.blogspot.com/2024/08/refuting-creationism-what-caused.html?fbclid=IwY2xjawEbHBBleHRuA2FlbQIxMQABHWGjiZv4SpfzOhyIU1Lyi2t-X7-nBOt_GCkcYZTzrhhdj5FJG-X-C9EWdA_aem_zgCwhlL11DFMFZcuqhq0CA Literature Cited 1.Cyanobacteria Fossil Record. https://ucmp.berkeley.edu/bacteria/cyanofr.html#:~:text=The%20oldest%20known%20fossils%2C%20in,the%20easiest%20microfossils%20to%20recognize . 2. Prothero, Donald R. 2017. Evolution: What The Fossils Say and Why It Matters. Columbia University Press. 2nd ed. New York. 427 pp. 3. Timeline for the Flood https://answersingenesis.org/bible-timeline/timeline-for-the-flood/ 4. Why “Sudden Appearance” Is Not as It Appears https://evolution-outreach.biomedcentral.com/articles/10.1007/s12052-009-0165-9 5. Doesn't the sudden appearance of all the "modern groups" of animals during the Cambrian explosion prove creationism? (Hassan Lahiri)  https://www.quora.com/Doesnt-the-sudden-appearance-of-all-the-modern-groups-of-animals-during-the-Cambrian-explosion-prove-creationism 6. How Would You Explain the Cambrian Explosion? (David Rosen) https://www.quora.com/How-would-you-explain-the-Cambrian-Explosion 7. Does the Cambrian Explosion Pose a Challenge to Evolution? https://biologos.org/common-questions/does-the-cambrian-explosion-pose-a-challenge-to-evolution 8. Doesn’t the sudden appearance of all the “modern groups” of animals during the Cambrian explosion prove creationism? (Paul Lucas) https://www.quora.com/Doesnt-the-sudden-appearance-of-all-the-modern-groups-of-animals-during-the-Cambrian-explosion-prove-creationism 9. At the Origin of Animals: The Revolutionary Cambrian Fossil Record https://www.ncbi.nlm.nih.gov/pmc/articles/PMC3861885/