TRUTHFUL ORIGINS EVO

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/ 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 claim from science: the vertebrate eye is poorly "designed'. Without additional adaptations to the original structure  it would have severe functional limitations Introduction The vertebrate eye  is poorly "engineered". The retina is inverted due to evolution compared to eyes that are not inverted. 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 pointing away from the incoming signals, in the basement with all kinds of obstructions, and needing to run electricity down there because it needs extra support. There's a reason we put antennas on roofs with unobstructed views of the sky and pointed towards a satellite or tall source antenna. The octopus eye on the right does not have this limitation; the rods and cones are logically placed so they receive light (photons) directly and don't produce a blind spot where there are no receptors; all the nerves leave the retina to begin their path to the brain to form an image without producing a blind spot. See Figure 1. Figure 1. "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." 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 In Figure 2, notice that the photoreceptors in the diagram not only are on the far side away  from light entering the eye, but their orientation points away  from the light photons, and there is a tremendous number of support cells and wiring required that the light must  pass through  to reach its final destination, the photoreceptors. Thus there are three major "design" issues from the beginning. Not shown in this figure is a fourth issue; as the nerves gather to exit the eye, that produces a blind spot where there can be no 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. In addition the cephalopod eye has no need for an RPE. Figure 2. From: https://www.brainkart.com/article/Retina_26069/ Fair Use Attribution Various adaptations to lessen the vertebrate eye deficits Comparative anatomy can help us conclude that the vertebrate eye is not only poorly constructed in its original form but that evolution has on numerous occasions applied "fixes" or workarounds to mitigate the deficits inherit to the vertebrate eye. A. Pecten oculi in birds Bird eyes are well known to provide them with better vision than other non-avian vertebrate species. The Retinal Pigment Epithelium  (#10 in Figure 2) in vertebrates is a layer of support cells below the retina that provides nutrition and support to the photoreceptors. Due to their high visual demands birds have an added structure to supplement their vision needs, called the pecten oculi.  It serves at least two functions. First, it provides extra nutrients and oxygen to the eyes and second this allows fewer retinal support vessels that would normally obstruct light passing through to the photoreceptors. This structure is present because it helps a problem with the vertebrate eye and its basic structure. See Figure 3. Figure 3. From: Jfbleak. 2008. Updated 2013. Fair use attribution. Bird eye. https://www.wikiwand.com/en/Pecten_oculi#Media/File:Birdeye.jpg   B. Conus Papillaris in some reptiles Similar to the pecten oculi in birds, reptiles also have a structure to help their eyes function better called the conus papillaris. As in birds it lessens the thickness of the tissues interfering with light traveling to the photoreceptors and also provides extra nutrition and oxygen, supplementing the RPE. See Figure 4. Figure 4. A - Reptile, lizard Conus papillaris. B - Pecten oculi, bird.From: Ringvold, Amund. 2022.  The Function of Pecten Oculi. Conus Papillaris in Reptiles and it's Analog Pectin Oculi in Birds Evolved in Tandem with increasing Uric Acid in Serum . https://www.alliedacademies.org/articles/the-function-of-pecten-oculi-conus-papillaris-in-reptiles-and-its-analogue-pecten-oculi-in-birds-evolved-in-tandem-with-.pdf For educational use only. Fair use attribution. C. Tapetum Lucidum Nocturnal animals are hampered by very low levels of light compared to diurnal animals. Evolution has provided a structure for many of these species to amplify what light that is available for night vision. These species have a structure in the RPE called the tapetum lucidum. When we shine a night light at animals who have this layer, the eyes reflect light back to us and appear iridescent. The light that has passed through the retina is reflected back to the photoreceptors as a secondary stimulation to the photoreceptors. See Figure 5. Figure 5. Tapetum lucidum reflecting light back from under the retinaFrom: https://www.reddit.com/r/Awwducational/comments/100uxki/the_reason_for_your_cats_reflective_eyes_in/ For educational use only. Fair use attribution In July of 2023 Nathan Lents wrote in his blog* about the tapeta found in various species and that all indications point to attempts at minimizing the loss of available light in the vertebrate eyes who have it. 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, only the secondary eyes have the need of a tapetum lucidum to improve light sensitivity! As Lents writes, "tapeta is a compensatory co-adaptation for the sub-optimal nature of the inverted retinas" . I would assert that it is only one such compensatory structure and joins several others as discussed in this blog. From: Wikimedia Commons. Lukas Jonaitis * https://thehumanevolutionblog.com/2023/07/11/is-nocturnal-eye-shine-an-adaptation-for-the-backwards-retina/ D. Fiber Optic Cable System 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. He includes as photograph. Rather, that the retina has this is just more evidence that there are problems to the inverted retina that have been confronted by evolution. There is significant obstruction from all the support structures in front of the photoreceptors (see Figure 2) and natural selection has produced another compensatory work-around. 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 to function efficiently. Anti-evolution objections The attempts to claim that the vertebrate eye is wonderfully designed by most creationists tend to discuss cabling systems, the RPE, etc. as advantages and aspects of good "design". The blind spot is dismissed as not an issue. The RPE is said to supply nutrients and cooling and if we had a retina that was not inverted, the RPE would be in front of the photoreceptors. This is an error because cephalopods don't have or need an RPE. The vertebrate eye has it only because of the evolutionary constraints on the original "design" Similar to the evolutionary constraints of the recurrent laryngeal nerve. See here on this blog 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 often produce this quote: " In terms of performance, vertebrate eyes come close to perfect." However just above this sentence which is usually never quoted is this: " 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." The authors are not only saying that the vertebrate eye evolved and functions well but they confirm that the vertebrate eye only performs well because of evolutionary "tweaking" or workarounds that make it perform better, 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 in their photoreceptors to improve color vision and to help focus light. Thus, this is an example of dishonest or sloppy quote mining by the creationist. There are multiple structural compensations 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 Creationists and the eye; Creationist "Contraductions" on display In 2024 Dan Barker published a small book titled "Contraduction" with the intent to establish a new word for an apologist and creationist error he repeatedly encountered during his debates*. Several well known authors have praised the word and concept: "An ingenious word for an invaluable concept. Sharp, clear, and timely" ~ Steven Pinker, Professor of Psychology, Harvard "Both a delightful read and a penetrating argument: Barker has invented an invaluable new concept, and puts it to work with clarity, wit, and above all conclusiveness." ~ A.C. Grayling, Philosopher "I am completely down with the concept of contraduction. It fills a need. False pattern recognitions pose a real danger to our survival. Well done!" ~ Ann Druyan What Barker had recognized and Druyan labelled are false pattern recognitions that completely and erroneously invert the conclusion to a set of observations. As Barker points out, an example would be if you are sitting in a train and you falsely note for a moment that you are pulling out of the station only to correctly understand a moment later that the train outside is what is moving and not you; you briefly had been the victim of a contraduction . He mentions other contraductions. Noses were created for glasses. The daily crowing of a rooster causes the sun to rise. Obviously, one of the most famous contraductions is that the sun revolves around the earth because it does appear that way until that conclusion is effectively tested. Contraduction   thus is defined by Barker as an informal fallacy that occurs before reasoning begins. It is a hidden fallacy, flipping and inverting the truth.   The truth is opposite to what the person is thinking or asserting. "The verb 'contraduce' means simply to flip around" he notes. The debates between scientists and apologists regarding the vertebrate eye are extensive on the Internet and are wonderful examples of creationist contraductions. The creationists will list the RPE, cabling systems, oil droplets in some photoreceptor cells, etc. as wonderful designs without realizing that a closer look at vertebrate eyes indicates it's just the opposite. They have inverted the truth; as in cosmology it is we who orbit the sun and not the other way around. In nature the vertebrate eye has had to undergo several "tweaks", "patches", workarounds, or compensatory changes to make it work well. When you come across a car with it's back tail light broken, the red duct tape someone put on it is not an original "great design" of the car. Four compensatory adaptations through evolution have been discussed in the previous sections showing that the vertebrate eye is not well "designed"; rather, it has needed fixes and changes to make it work well. Creationists who list these adaptations and claim them as wonderful designs have tripped and fallen into a hole of contraductions. These co-adaptations really represent profound evidence of evolution attempting to lessen the evolutionary constraints  of the vertebrate eye with its inverted retina. * Barker, Dan. 2024. Contraduction. Hypatia Press, UK. 111pgs. Analogies for the eye and Intelligent Design advocates. DISH TV . Arguing that all the needed compensatory adaptations necessary to make the vertebrate eye work well are original and good is like hiring a DISH TV installation. The technician arrives at your house. Instead of putting the antenna on the roof pointed at the satellite, they go to the basement and install it there (retina), point the antenna away from the signal (photoreceptors direction), place it so it will try and grab signals through several walls and floors (the support vessels and cells blocking the retina), run a long electrical cord down to the basement because there's not a wall socket for electricity (the RPE for support), adding a second antenna to make up for poor signal strength (the oil droplets), then punching holes in the walls and floors to try and get more signal in (the cabling system). You assert this is a great design? You'd recommend this tech person to your family and friends? Meanwhile your neighbor with their DISH antenna on their roof pointed at the satellite is wondering if you've lost your mind (cephalopod eye). Broken tail light.  The car you just purchased has a broken tail light. Someone has not replaced it but compensated only and patched it with red duct tape. You think this is a great original design to the car rather than use a better solution - replace the light (the cephalopod eye works without all those vertebrate eye "fixes") Eyeglasses.  Focusing on eyeglasses for vision instead of why they are needed for an eye with vision problems is like creationists declaring all the workarounds and compensatory structures for the vertebrate eye to have good vision wonderful designs instead of noting the fundamental eye problems requiring the eyeglasses to begin with. Contraduction - inverting the real reason for the observations. Other Problems with an Inverted Retina Novella has noted the inverted retina also causes problems for the vertebrate eye not mentioned discussed above. The retina is prone to detachment . Novella notes, " the cephalopod eye does not suffer from retinal detachment because the axons from the photoreceptors anchor them to the layers beneath." A second issue is that the vertebrate eye is prone to macular degeneration.   " The macula is that part of the retina that has the densest concentration of rods and cones for detailed vision. Within the macula is a smaller area called the fovea which contains only cones and has the highest density of these receptors. The very existence of the macula, however, is a partial fix for the “backward” arrangement of retinal layers with the nerve and blood vessels between the receptors and the direction of light. This limits the density of rods and cones, and so the partial fix is to have one small area cleared of nerves and blood vessels where rods and cones can be denser. However, if the human retina were designed like that of the squid and other cephalopods, this would not be necessary. "The dependence of the human eye on the macular for sharp vision creates a vulnerability, for any problem with that small area will have a dramatic effect on visual acuity. The rest of the retina will not be able to adequately compensate for the loss or compromise of the macula because the density of rods and cones is just too diffuse. " Third, the human eye is prone to glaucoma.  This occurs because there is a narrow space between the iris and cornea called the anterior chamber which can become blocked and disrupt the flow of fluid through this chamber, producing narrow angle glaucoma. The eye configuration makes the eye more prone to this problem. " The most susceptible populations are Asians and Inuit. There is speculation that the narrow angle may have been a thermoregulatory adaptation to colder climates—a compromise exacerbating an already existing design weakness." https://evolution-outreach.biomedcentral.com/articles/10.1007/s12052-008-0092-1 ? Other Problems with an Inverted Retina Novella has noted the inverted retina also causes problems for the vertebrate eye not mentioned discussed above. The retina is prone to detachment . Novella notes, " the cephalopod eye does not suffer from retinal detachment because the axons from the photoreceptors anchor them to the layers beneath." A second issue is that the vertebrate eye is prone to macular degeneration.   " The macula is that part of the retina that has the densest concentration of rods and cones for detailed vision. Within the macula is a smaller area called the fovea which contains only cones and has the highest density of these receptors. The very existence of the macula, however, is a partial fix for the “backward” arrangement of retinal layers with the nerve and blood vessels between the receptors and the direction of light. This limits the density of rods and cones, and so the partial fix is to have one small area cleared of nerves and blood vessels where rods and cones can be denser. However, if the human retina were designed like that of the squid and other cephalopods, this would not be necessary. "The dependence of the human eye on the macular for sharp vision creates a vulnerability, for any problem with that small area will have a dramatic effect on visual acuity. The rest of the retina will not be able to adequately compensate for the loss or compromise of the macula because the density of rods and cones is just too diffuse. " Third, the human eye is prone to glaucoma.  This occurs because there is a narrow space between the iris and cornea called the anterior chamber which can become blocked and disrupt the flow of fluid through this chamber, producing narrow angle glaucoma. The eye configuration makes the eye more prone to this problem. " The most susceptible populations are Asians and Inuit. There is speculation that the narrow angle may have been a thermoregulatory adaptation to colder climates—a compromise exacerbating an already existing design weakness." https://evolution-outreach.biomedcentral.com/articles/10.1007/s12052-008-0092-1 ? The evolution of the vertebrate eye - a few comments 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 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 45% 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] Conclusion Debates surrounding the vertebrate eye as an example of poor design over the years have produced many competing articles from both sides. The case of the vertebrate eye being poorly structured for vision is a strong one because when comparing various vertebrate eyes we find compensatory adaptations to lessen the vertebrate eye deficits. These include the RPE  which an eye with an everted retina does not need, the pecten oculi  in birds, the conus papillaris  in many reptiles, the tapetum  in many vertebrates for night vision, a cabling system  to shuttle photons more cleanly to the photoreceptors, and oil droplets  in some vertebrate eye photoreceptors. Instead of realizing these vertebrate eye structures are a result of evolution diminishing and attenuating problems with the eye, creationists and apologists have inverted their true meaning, falling victim to contraductions . The problems with the vertebrate eye are a result of the evolutionary inverted retina constraint imposed upon it. The irony is that what they think will defend their views, actually represents powerful evidence for evolution. In addition, an example of creationist quote-mining is discussed that is often encountered in debates with creationists regarding the inadequacy of the vertebrate eye. Without tweaks and patches to make it work efficiently the vertebrate eye is hardly intelligently and wonderfully "designed".

“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   Soft tissues in fossil bones.  Extensive answer to creationists misconceptions. https://palaeo-electronica.org/content/2022/3739-soft-tissues-in-fossil-bone 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.

"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/ Why not singularity and how inflation is supported: 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/ 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

"The 'hairy quadruped furnished with a tail, and pointed ears, probably arboreal in his habits', this good fellow carried hidden in his nature, apparently, something destined to develop into a necessity for humane letters." ~ Matthew Arnold, 1885. Introduction Our ears are divided into three major sections. The visible part includes our outer ear, also called the pinna, and the ear canal that leads to the eardrum.  Going deeper, the next section is the middle ear that contains the three small bones called the incus, malleus, and stapes. The last section is the inner ear located in the temporal bone of the skull and contains the organs for balance, the semicircular canals and the organ for hearing, the cochlea.  Science has revealed how each of these three main auditory sections evolved. A look especially at our outer ear alone provides important clues to our evolutionary past. 1. Our visible ears - clues to our evolutionary ancestry.   A. Darwin’s Tubercle   - Some people have a small thickened area on their outer ear that scientists and medical researchers have named Darwin’s Tubercle. It matches an ear prominence found in many monkeys.  Left: For educational purposes only. Fair use attribution. https://jcdr.net/articles/PDF/20343/74434_CE%5BRa1%5D_F(SHU)_QC(SD_IS)_PF1(VD_SHU)_PFA(KM)_PN(IS).pdf Right: For educational purposes only. Fair use attribution. https://commons.wikimedia.org/wiki/File:Darwin-s-tubercle.jpg B. Vestigial Pinna Muscles   - It takes at least 6 vestigial muscles to hold the human outer ears to our skull. Although some of us can move our ears slightly, our ability to do so pales in comparison to that of other some other animals. Those vestigial muscles, where simple connective tissue would have sufficed, attest to distant human ancestors who could move their ears in many directions. The best and most harmonious explanation is evolution because we evolved from ancestors that could move their ears in many directions. For educational purposes only. Fair use attribution https://commons.wikimedia.org/wiki/File:Musculushelicismajor.png A deer demonstrates how it can move its ears 180 degrees with muscles From: https://x.com/faintsun/status/1275538865512755206 C. Preauricular Sinus Tracts   -  Below is a typical sinus tract that can occur in human ears. They are not uncommon and represent congenital abnormalities. How do they point us to human evolution? In human and vertebrate embryogenesis, tissue arches form next to the developing throat or pharynx. They are called pharyngeal or branchial arches. In fish they are called gill arches because they develop into gills. In tetrapods (four legged animals) the first and second arches develop several tissue thickenings that give rise to the external ear (pinna) after fusion. If they fail to fuse they can form small tunnels or sinus tracts and these are called preauricular (before the auricle, or outer ear) sinus tracts showing us our common ancestry with fish. Further evidence of our connection with fish ancestors can be demonstrated in at least two ways. First, with the rare condition of Otocephaly  which occurs due to disruption of the 1st branchial arch. The external ears then form and fuse below the chin. The mandible is missing because it arises also from the 1st branchial cleft. The fetus is stillborn or a miscarriage occurs; the disorder arises from a mutation of the PRRX1 gene on chromosome 1. For educational purposes only. Fair use attribution. https://en.wikipedia.org/wiki/Otocephaly Second, in 2025 researchers published a study showing a genetic connection between gill development in fish and the tetrapod external ear. The abstract: "... Here we show that the outer ear shares gene regulatory programs with the gills of fishes and amphibians for both its initial outgrowth and later development of elastic cartilage. Comparative single-nuclei multiomics of the human outer ear and zebrafish gills reveals conserved gene expression and putative enhancers enriched for common transcription factor binding motifs. This is reflected by transgenic activity of human outer ear enhancers in gills, and fish gill enhancers in the outer ear. Further, single-cell multiomics of the cartilaginous book gills of horseshoe crabs reveal a shared DLX-mediated gill program with vertebrates, with a book gill distalless enhancer driving expression in zebrafish gills. We propose that elements of an invertebrate gill program were reutilized in vertebrates to generate first gills and then the outer ear." For educational purposes only. Fair use attribution https://www.nature.com/articles/s41586-024-08577-5 Furthermore, a summary of the above cited regulatory gene confirms the repurposing of a fish gene for vertebrate outer ear formation. " Fish gills and human ears share the same genetic blueprint. Gills and mammalian ears bear little resemblance, yet examination of gene regulation reveals that key supportive cartilage tissue arises from similar embryonic cells guided by an evolutionarily conserved genetic program." https://www.nature.com/articles/d41586-025-00342-6?fbclid=IwY2xjawITEytleHRuA2FlbQIxMQABHbg9vZRZEbCgBWtYQB3KD9968urAaLxRbw1OHOS9QoNE87tAjI9gUXmF3Q_aem_GP_lEoE3E0zis45OJYvLwA *** See footnote end of this blog article about a similar issue that happened when a nerve (the Recurrent Laryngeal Nerve in all tetrapods) that travels to our larynx or voice box was trapped under a branchial arch in fishes as the neck evolved and how it now must travel a crazy course because of it. 2. Evolution of the middle ear  The middle ear of mammals contains three bones - the incus, malleus, and stapes (“hammer, anvil, and stirrup”) that connect to the tympanic membrane (ear drum). Scientists have discovered in detail how all these bones evolved.  When paleontologists classify mammalian fossils, they can’t use common defining characteristics of mammals such as fur and milk production since these don’t normally fossilize. They instead look for the auditory bulla, a bony structure that encases these three bones.  In reptiles, amphibians, and birds the eardrum is connected to the middle ear by a single bone called the columella. This corresponds to the mammalian stapes. During evolution a bone from the upper jaw (quadrate) migrated to form the incus and a bone from the lower jaw (the articular) migrated to from the malleus. The details of how this happened and when is a triumph of science contributed by many diverse and independent fields of research. The columella became the stapes.  How do we know this happened? The fossils tell a wonderful story of   gradual evolution . But there are several other lines of evidence that also tell the story of this amazing gradual evolution. These are best discussed by Anthwal, et al. in their 2012 article. “ Having three ossicles in the middle ear is one of the defining features of mammals. All reptiles and birds have only one middle ear ossicle, the stapes or columella. How these two additional ossicles came to reside and function in the middle ear of mammals has been studied for the last 200 years and represents one of the classic example of how structures can change during evolution to function in new and novel ways. From fossil data, comparative anatomy and developmental biology it is now clear that the two new bones in the mammalian middle ear, the malleus and incus, are homologous to the quadrate and articular, which form the articulation for the upper and lower jaws in non-mammalian jawed vertebrates. The incorporation of the primary jaw joint into the mammalian middle ear was only possible due to the evolution of a new way to articulate the upper and lower jaws, with the formation of the dentary-squamosal joint, or TMJ in humans. The evolution of the three-ossicle ear in mammals is thus intricately connected with the evolution of a novel jaw joint, the two structures evolving together to create the distinctive mammalian skull… Although the fossil record provides clues to the transition it is often incomplete and relies on a few isolated specimens. The ideal solution would be to be able to follow the transition from primary to novel articulation in a living animal. This is indeed possible in marsupials ( Maier, 1987 ). In marsupials the neonate must be able to suckle at an early developmental stage, prior to the formation of the bones that will make up the normal mammalian jaw joint. Marsupials, therefore utilise the joint between the incus and malleus as their primary jaw joint for the first few weeks after birth ( Muller, 1968 ) ( Fig. 5 ). A clear synovial joint between the malleus and incus has been reported at postnatal day (P) 3 in the opossum Monodelphis ( Filan, 1991 )."In conclusion, the evolution of the mammalian middle ear and jaw joint were pivotal steps in the evolution of mammals. It is also a great example of how classical comparative anatomy, paleontology and developmental biology have come together to piece together how this remarkable transformation of jaw joint to ear ossicles was able to come about. The homologies of the malleus, incus and stapes to the articular, quadrate and columella, and tympanic ring and gonial to the angular and prearticular suggested by comparative anatomy 175 years ago have been recently confirmed by molecular and developmental biology. The recent discovery of new mammaliform fossils has allowed careful documentation of the shift from primary to secondary jaw articulation, creating an opportunity to follow the transformation of the post-dentary skeletal elements. This fossil data has been complemented by the study of marsupial development, providing insight into the changing role of the malleus and incus, and the relationship of the primary and secondary jaw joints.” From: Evolution of the mammalian ear and jaw: adaptations and novel structures https://pmc.ncbi.nlm.nih.gov/articles/PMC3552421/ For educational purposes only. Fair attribution. From: https://www.talkorigins.org/faqs/comdesc/section1.html#morphological_intermediates_ex2 Other references: https://en.wikipedia.org/wiki/Evolution_of_mammalian_auditory_ossicles https://carnegiemnh.org/press/researchers-announce-surprising-clue-in-the-evolution-of-mammalian-middle-ear/ 3. Evolution of the cochlea The cochlea (Latin for "snail or screw") is the coiled structure in the inner ear of mammals that converts vibrations into nerve impulses. These vibrations come from the middle ear bones that are eventually in contact with the eardrum, thus vibrating as air pressure waves. The middle ear bones transfer their vibrations to fluid waves that move hair cells of the Organ of Corti inside the cochlea. By studying the fossil record especially with micro-CT and present comparative anatomy, scientists have been able to show basically how this organ evolved although the exact evolutionary steps are still under investigation. Lizards and snakes, birds and crocodilians have a basilar papilla for hearing. The Organ of Corti evolved from this probably about 120 million years ago. Manley notes: " Evolution of the cochlea and high-frequency hearing (>20 kHz; ultrasonic to humans) in mammals has been a subject of research for many years. Recent advances in paleontological techniques, especially the use of micro-CT scans, now provide important new insights that are here reviewed. True mammals arose more than 200 million years (Ma) ago. Of these, three lineages survived into recent geological times. These animals uniquely developed three middle ear ossicles, but these ossicles were not initially freely suspended as in modern mammals. The earliest mammalian cochleae were only about 2 mm long and contained a lagena macula. In the multituberculate and monotreme mammalian lineages, the cochlea remained relatively short and did not coil, even in modern representatives. In the lineage leading to modern therians (placental and marsupial mammals), cochlear coiling did develop, but only after a period of at least 60 Ma. Even Late Jurassic mammals show only a 270 ° cochlear coil and a cochlear canal length of merely 3 mm. Comparisons of modern organisms, mammalian ancestors, and the state of the middle ear strongly suggest that high-frequency hearing (>20 kHz) was not realized until the early Cretaceous (~125 Ma). At that time, therian mammals arose and possessed a fully coiled cochlea. The evolution of modern features of the middle ear and cochlea in the many later lineages of therians was, however, a mosaic and different features arose at different times... " Obviously, no old fossil provides remnants of soft tissues except as far as they influence or are shaped by bone. It is, however, possible to use the cladistical outgroup analysis method to investigate comparative structural questions regarding the soft tissues of the hearing organ. If we compare the structure of the cochleae of modern therian mammals with that of modern monotreme mammals and these again to the structures in nonmammals, we come to the conclusion that all modern mammals have similar and unique structural features (synapomorphies) and all their hearing organs deserve to be called “organs of Corti.” No nonmammals have anything similar." https://pmc.ncbi.nlm.nih.gov/articles/PMC3505590/ A more complete examination of the evolution of the inner ear including components of the vestibular system for balance can be referenced in the article by Koppl and Manley: " This review summarizes paleontological data as well as studies on the morphology, function, and molecular evolution of the cochlea of living mammals (monotremes, marsupials, and placentals). The most parsimonious scenario is an early evolution of the characteristic organ of Corti, with inner and outer hair cells and nascent electromotility. Most remaining unique features, such as loss of the lagenar macula, coiling of the cochlea, and bony laminae supporting the basilar membrane, arose later, after the separation of the monotreme lineage, but before marsupial and placental mammals diverged. The question of when hearing sensitivity first extended into the ultrasonic range (defined here as >20 kHz) remains speculative, not least because of the late appearance of the definitive mammalian middle ear. The last significant change was optimizing the operating voltage range of prestin, and thus the efficiency of the outer hair cells’ amplifying action, in the placental lineage only." https://pmc.ncbi.nlm.nih.gov/articles/PMC6546037/#s3 Conclusion The evolution of the mammalian ear is evident in all three basic ear sections. These are the outer ear or pinna, the middle ear consisting of three bones, and the inner ear containing the auditory structures and vestibular apparatus. The evolution of the mammalian outer ear and its connections to fish anatomy was discussed along with how a genetic abnormality can help support these connections. The middle ear bones are perhaps one of the best documented evolutionary examples of gradual evolution. The history of ear evolution with scientists detailing their gradual formation from jaw bones through the fossil record is introduced. Lastly, the evolution of the inner ear structures involved in auditory nerve processing have been discussed in the literature and several references were provided for readers wanting to know further details. What would seem to be a near impossible task for science to reveal how a complex organ such as the mammalian ear could have evolved through natural processes and gradually has indeed yielded to careful study, driving curiosity, and new technologies. [ Note: just as our outer ear can be traced to the gill arches in fish, so also the long course of the recurrent laryngeal nerve can be explained by evolution and our ancestry with fish. In some dinosaurs it would have been ridiculously long. Instead of branching off the vagus nerve at the level of the larynx as the superior nerves do, the RLN is forced to travel all the way to the heart before coming back up to where it was originally at the level of the voicebox to finally innervate the lower side of the larynx. It became trapped by the 6th gill arch in fish as the neck evolved. For a discussion of this bizarre adaptation route and why evolution explains it, see the first section of Why Not Intelligent Design . ] "Nothing in Biology Makes Sense Except in the Light of Evolution" ~ Theodosius Dobzhansky, 1973. Evolutionary Biologist, Christian

“Natural selection has no analogy with any aspect of human behavior. However, if one wanted to play with a comparison, one would have to say that natural selection does not work as an engineer works. It works like a tinker - a tinkerer who does not know exactly what he is going to produce but uses whatever he finds around him whether it be pieces of string, fragments of wood, or old cardboard; in short it works like a tinkerer who uses everything at his disposal to produce some kind of workable object.” ~ Francois Jacob Part 1 Review and Discussion In the previous part 1 several important points were made about the history of the term junk DNA. Scientists knew especially from the 1960s that there were only about 30,000 genes active in humans. In the last few decades this has been remarkably confirmed with about 20,000 protein producing genes and another 5,000 noncoding genes that produce functional RNA products. Thus, science has pretty much settled on about only 25,000 genes in our genome. This is unlikely to change much or at all in the coming years. To many, this seems difficult to accept that we have the same number of genes as other mammals and yet we appear to be so much more complicated in our brain and social characteristics. There were several reasons why scientists even a half century ago felt that only a small amount of the human genome could be functional. First, the mutation rate of our genome was calculated and confirmed. Based on the number of deleterious mutations that our genome could tolerate, it was predicted that we would only have about 30,000 genes. This was called the argument from genetic or mutation load (1, 4) Secondly, the C-Value Paradox was observed. Some species had very large genomes and others small genomes. Even among closely related species, as with some frogs mentioned in Part 1, there were huge difference in genome sizes. Why would one similar species need a genome so much larger than another? If much of that difference was duplicated and repetitive DNA that built up over millions of years and was mostly nonfunctional, this would be the most parsimonious explanation. The Onion Test by Gregory challenged those who claim that there is little to no junk DNA to explain why an onion needs 5x the amount of DNA compared to a human (2). Third, especially in plants there are many examples of genomes being duplicated, sometimes to 6x the original size. This is called polyploidy and indicates that many species can tolerate this and over millions of years the amount of DNA decreases through mutations - thus the excess DNA was dispensable junk. In modern salmon 96 million years ago a duplication event occurred. (1). Fourth, significant portions of noncoding DNA can be removed from animals without deleterious effects. This indicates it’s most likely junk. If it was mostly or all functional this would not be the result (3). Moran noted that if one totals up all the functional DNA in humans it only adds up to about 8 - 10%. See Table 1 in Part 1 of this blog topic. The other 90% is made up of introns (spliced out during RNA processing), transposons, ERVs and other repetitive DNA. Some even have functions but they are rare. What is defined as functional is any DNA that if deleted reduces fitness. A gene is defined as a DNA sequence that is transcribed to produce a functional product. It’s not the job of the geneticist to prove non function for everything in the genome - 3.2 billion base pairs. One can’t prove a negative. Rather if one is claiming function it is up to that person to show function and not for a scientist to show it does not have function. This is the way evidence works; it’s not up to someone to show unicorns don’t exist, it’s up to unicorn believers to produce the evidence of existence. Those claiming little to no junk DNA need to produce copious evidence of function and not just rare examples. And function means it must have a known product that is functional. Not that it just got transcribed which will be discussed below. ENCODE And then along came ENCODE in September of 2012. The acronym stands for The Encyclopedia of DNA Elements, a consortium of over 400 researchers. There is now an ENCODE 4 in the works. To say that ENCODE made a splash in the news would be a gross understatement. It was all the news in science and the media that year and for years after. ENCODE lists its objectives: “The goal of ENCODE is to build a comprehensive parts list of functional elements in the human genome, including elements that act at the protein and RNA levels, and regulatory elements that control cells and circumstances in which a gene is active.” (5). Importantly, ENCODE defined functional elements as those that produced RNA molecules through transcription, that bind regulatory proteins called transcription factors or that possessed binding sites for methyl groups which can modify the structure of chromosomes (6). Notice that this definition is really a surrogate for function. They did not identify products that were proven to be functional; they primarily assumed that a transcript always indicated a function. There were so many papers that the ENCODE findings were published in a special issue of Nature that year, one of the most prestigious scientific publications in the world (7). Using their definition of function, and relying almost completely on transcription (the DNA was producing RNA products but if they were not immediately destroyed or never produced functioning product was unknown) they found an incredible 80% transcription which they proclaimed meant 80% of the human genome was functional. Anti-evolutionists who were mostly creationists and basically denied any junk DNA were giddy with happiness. Many scientists who could not accept junk DNA or mostly Junk DNA felt vindicated. ENCODE stumbles The definition that ENCODE used for function, transcription = function, soon came under attack by many scientists. It turns out that scientists had previously discovered that about 45% of the human genome was involved in gene activity but also 30% of that were introns that were spliced out and discarded. Only the exons went on to form functional mRNA and other RNAs. Known genes often have large introns and even the ENCODE researchers admitted that only 3 to 8% of the human genome is conserved (1). And genomic conservation between species is one of the best ways to define function because it’s an indication of positive selection in nature; those genes are critical to many species. It turns out that ENCODE was often looking at transcriptions that did not mean anything where their products were quickly destroyed. In other words most of the transcriptions were just genetic noise, spurious transcripts. They were not proven to be functional and have yet to be. “The editors of Nature soon realized they had a serious problem on their hands… Brendon Maher, the feature writer for Nature, took the lead in an article published the very next spring, saying, ‘First up was a scientific critique that the authors had engaged in hyperbole. In the main ENCODE summary paper, published in Nature, the authors had thus far assigned ‘biochemical function for 80% of the genome’. I had long and thorough discussions with Ewan Birney about this figure and what it actually meant, and it was clear that he was conflicted about reporting it in the paper’s abstract.” (1). Maher went on to write that 1% of the genome encodes proteins and 8% of the genome binds transcription factors for a total of 9%. Another 11% he suspected that ENCODE missed due to sampling error giving a real total for function of 20%, the opposite of what ENCODE researchers were claiming (1). This is of course close to the 10% function of our genome that was discussed in Part 1 of this blog. Immediately scientists working in evolutionary biology and genetics wrote papers attacking ENCODE. Eddy (2012), Doolittle (2013), Graur et al. (2013), Hurst (2013), Morange (2013) and Palazzo and Gregory (2014). Moran notes: 1. ENCODE ignored all the earlier scientific evidence and data showing that most DNA is junk. 2. ENCODE ignored all the scientific evidence indicating that much of their “biochemical activity” is spurious and not an indication of biological function. 3. ENCODE and Nature collaborated to deliberately hype their results, thus misrepresenting to the general public the actual conclusions of the experiments. Introns are nearly all junk Evidence that the genome was significantly transcribed was first published in the 1960s. This was called pervasive transcription since most of the genome is transcribed. This was not new to researchers. But researchers also noted that most of the RNA was in the nucleus and very little was mRNA in the cytoplasm. It was later realized that this was explained because it was mostly introns that were being spliced out (1). Introns are mostly junk. “First, intron sequences are not conserved and the lengths of introns are not conserved. Secondly, homologous genes in different species have different numbers of introns, and homologous bacterial genes get along quite nicely without introns. Third, researchers routinely construct intronless versions of eukaryotic genes, and they function normally when reinserted into genomes. Fourth, intron sequences are often littered with transposon and viral sequences that have inserted into the intro and that’s not consistent with the idea of intron sequences being important.” (1) Recall that 30% of the active part of the genome for gene expression (which is 45% of the total genome) are introns in eukaryotic cells. So in terms of function we’re already down to 30% of 45% just with introns alone (13.5% possible function). One of the better reviews of why junk DNA is true and ENCODE wrong was the article by Palazzo and Gregory, “The case for junk DNA” found in PloS Genetics: https://journals.plos.org/plosgenetics/article?id=10.1371/journal.pgen.1004351 Functional DNA apologetics The “junk DNA is dead” drumbeat is very much alive. Of course the anti-evolutionist will never give up their belief that there can be no junk DNA because their religious Intelligent Designer would never make a human genome with 80-90% junk, let alone much of it derived from parasitic viral infections (ERVs, LINE-1s, etc.). But it’s also a huge number of secular scientists who can’t or won’t admit that our genome is mostly junk. Below are some of the most common reasons given for expressing hope that a large percentage of the genome will eventually demonstrate actual function as listed by Moran (1). 1. Alternate splicing. It is known that this occurs - that a single gene can produce more than one product mainly but using different combinations of the exons. There are very few proven examples. This won’t save the mostly function assertion. Splice variants are probably due to errors in splicing anyway. 2. DNA-binding proteins. Even if they regulate certain genes, they will always bind random DNA sequences in the nucleus. Models based on “known promoters and termination sites predict that 66 percent of random DNA sequences will be transcribed due to nonspecific binding… In other words, spurious transcription that has nothing to do with biological function will have two characteristics: 1. The transcripts will be rare, and 2. They will be tissue specific. That’s exactly what we see in the transcription data.” 3. Noncoding RNAs and functions . In Part 1 several types of RNA were listed. There are at least 300 rRNA genes and many small RNAs that have functions. But comparatively they have small numbers of genes. snRNAs - 20 different genes, miRNAs perhaps 1000 genes, several thousand piRNAs genes, etc. A type of RNA called lncRNAs have especially attracted “no junk” advocates as they perform many functions. No one knows for sure how many of these genes are present in the human genome. 4. Humans are more complex due to a sophisticated network of regulatory sequences that fine tune gene expression. The ENCODE scientists hope to solve the problem of humans having the same number of genes as other animals despite our complexity because our genes are more highly regulated. However, “most transcription factor binding doesn’t result in measurable changes in gene expression, an idea that’s consistent with nonfunctional binding,… The crucial element that’s missing in most genomic experiments is the negative control… Mike White is a vocal critic of projects that assume function in the absence of a negative control. He actually did an experiment to see whether DNA fragments could promote transcription, and the answer is yes they can… demonstrating that junk DNA can be mistaken for a functional promoter.” 5. Scaffold attachment regions . The idea is that chromatin (makes up chromosomes - DNA and proteins) is organized by DNA that we call junk and is necessary even if it doesn’t code for proteins or RNA. “There’s very little support for the idea that transposon sequences play a direct role in organizing chromatin. Degenerate transposon sequences are much more likely to be exactly as they seem; once-active transposons that have been degraded by mutation.” 6. The extra DNA and passive transcription is a feature of the genome and not an accident. “But this is just a teleological argument and it fails the Onion Test. ”. This is probably the conclusion the Christian cancer researcher Finlay reaches in his otherwise excellent book on how DNA proves human evolution (8). 7. Epigenetics. Like the term ‘quantum”, this term is the darling of science the past few decades. Eukaryotes can modify the expression of DNA not by changing the bases or duplication but by silencing some genes by methylation. We know that this can fine tune the DNA from environmental pressures. An example would be starvation and mothers passing along physical influences to their offspring’s DNA. But those are stripped off the DNA and usually don’t persist past a few generations. In addition there’s no obvious mechanism for transferring chromatin markers from somatic cells to the egg cells, especially since those egg cells had already formed before the mother was born (1). Any inheritable epigenetic effects are unlikely to be major effects. 8. Natural selection would remove junk DNA . It’s too energy expensive to maintain it. What is called Neo-Darwinism or the Modern Synthesis has been the major way of looking at evolution. Beneficial alleles would be selected for by natural selection and sweep through a population. This is known as adaptationism. It appears to be wrong at the molecular level or at least over emphasized. What has replaced it or is in the process of that, is neutral theory. “The main tenet of the neutral theory is that the great majority of evolutionary changes at the molecular level are caused not by Darwinian selection but by random fixation of selectively neutral (or very nearly neutral) alleles through random sampling drift…” ~ Motoo Kimora, 1989. This approach is derived from population genetics studies and appears to be correct. People may be surprised that natural selection is thought now not to be the main mechanism for evolution. Species with large populations will have streamlined genomes (bacteria, eg) and species with relatively smaller populations will accumulate junk DNA because it is not harmful enough to be purged by natural selection due to the probability of fixation by random genetic drift becomes significant, and slightly deleterious alleles can be fixed by chance (1). Neutral alleles or near neutral ones in small populations will be invisible to natural selection and junk DNA will accumulate. Since mutations in small populations are mostly neutral and invisible to natural selection, the balance between rates of insertion and deletion determines the size of the genome and the increase in the genome initially is unrelated to the fitness of the individual. This is what population genetics is telling us. Dr. Zach Hancock evaluates junk DNA with expert commentary on an interview with a creationist. The point is that no-junk scientists and anti-evolutionists will often write about all the functions that are being identified for noncoding RNAs (really only about 5,000 genes) but the hopes that all or nearly all of the junk DNA in the genome will be found to be functional, usually by noncoding RNAs, in the future is probably a lost cause. Per the Borg , “resistance is futile” (to deny Junk DNA) and it’s a tragedy that so many good scientists have dug a functional hole they cannot or will not acknowledge is wrong. In part because perhaps of all the grant money involved and subconscious motivated reasoning. Follow the money may be applicable. 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 Conclusion Scientists working with DNA and genomes have known that the vast majority of our genome is made up of junk since the 1940s. Introns, transposons mostly from ancient viral infections, ALUs derived from the fusion of two genes plus an ERV insertion, and duplications all have bloated our genome. Attempts like ENCODE to dismiss this have failed if honestly evaluated. The entire ENCODE endeavor for functional claims was a debacle as outlined above. Unfortunately this view appears to still be a minority even in the scientific community. Hopefully Moran’s book will be read widely and discussed and will help to turn the tide to the truth about junk DNA in our genomes. Whether it is 90% as he says or ends up closer to 80-75% remains to be seen but its extremely doubtful it will ever be much less than 75% junk. Creationists and anti-evolutionists will continue to cite ENCODE as evidence for their mostly religious faith commitments and mistaken origin narratives. For the unwary, their claims will probably continue to sound supported and rational when the case is hardly so. Lying by omission is still lying unless they are unaware of why ENCODE should be on their “Don’t Use” list. Transcription involves initiation, elongation and termination. As Moran points out, this entire process is sloppy. Initiation tends to be random; eukaryotes transcribe most of their genomes but as Stuhl writes “little is known about the fidelity… I suggest that ~90% of [RNA] Pol II initiation events in yeast represent transcriptional noise, and that the specificity of initiation is comparable to DNA-binding proteins in other biological process”. (1) Termination also tends to be random. In contrast to bacteria, transcription termination in eukaryotes is a very sloppy business. Because genes are far apart, RNA polymerase [the enzyme that ‘reads’ the DNA to make RNAs] can easily run over the termination site and not stop until it runs into another gene. DNA downstream of a gene is transcribed by accident from time to time which is why much junk RNA transcription comes from regions downstream from active genes (1). Lastly, RNA polymerase sometimes goes in the wrong direction during transcription. “The combination of spurious, accidental low-level transcription at each end of a gene accounts for the observation that a large percentage of junk RNA transcripts occur in the regions around known genes.” (1) The human genome is constantly changing. The average person has about 1000 duplications (see segmental duplications as amazing evidence for human evolution) and 138 unique mutations on average not found in their parents. ALUs are still jumping in our genomes. Evidence shows that ALUs, which make up 11-13% of our genome, are still jumping around - they are polymorphic because everyone has different numbers of them and they have not yet fixed into human genomes. When they land into a gene they often break it and are the cause of some genetic diseases. Transposons by the millions have jumped around in our genomes producing a lot of junk . See Part 1. Introns are cut out and discarded and only the exons go on to produce functional RNAs. The fact that a few introns have functions in no way diminishes the incredible percentage they contribute to junk RNA. Pervasive transcription of most of the genome is part of the genome’s normal activity. According to ENCODE 75% of the genome was being transcribed but 70% of that coverage was from transcripts present at less than one copy per cell. Even ENCODE admitted that this indicated noise and that the transcripts would be less constrained (in effect, junk) (1). Science has known since the 1940s that the human genome and that of other mammals especially have large amounts of junk DNA. And so another topic of misinformation joins the politicization and ideological topics basket we are fighting today. This topic unfortunately has swept up many well meaning scientists to join creationists in spreading the falsehood that junk DNA does not constitute the vast majority of our genome. Citations and References 1. Moran, Laurence A. 2023. What’s In Your Genome?; 90% of your genome is junk. Aevo UTP. University of Toronto Press. 372pp. 2. The Onion Test. April 25, 2007. Genomicron. Exploring genomic diversity and evolution. https://www.genomicron.evolverzone.com/2007/04/onion-test.html 3. https://www.nature.com/articles/news041018-7 4. Surprisingly good article on Junk DNA from Wikipedia https://en.wikipedia.org/wiki/Junk_DNA 5. ENCODE Project Overview. https://www.encodeproject.org/help/project-overview/ 6. https://www.britannica.com/topic/ENCODE 7. Nature: An Integrated encyclopedia of DNA elements in the human genome. https://www.nature.com/articles/nature11247 8. Finlay, Graeme. 2021. Human Evolution: Genes, Genealogies and Phylogenies. Cambridge University Press. 359 pp. 283 pp. not including References and Index. Paperback edition. 2021 - ISBN 978-1-009-00525-8. Original 2013. 9. Paradigm Shift or Paradigm Shaft? https://sandwalk.blogspot.com/2023/09/john-matticks-new-paradigm-shaft.html 10. Junk DNA, TED talks, and the function of lncRNAs https://sandwalk.blogspot.com/2022/12/junk-dna-ted-talks-and-function-of.html Appendix. ENCODE - post by Kenneth Gilmore on FB, 2/2/2025, E-C Open Debate. I have noticed a few creationists appealing to ENCODE in order to bolster their claim that the genome is intelligently designed. ENCODE, which stands for Encyclopaedia of DNA Elements in 2012 made the frankly outrageous claim that up to 80% of the DNA was functional. While this claim has been somewhat walked back, there are still many scientists who do not have expertise in evolutionary biology or population genetics who advance this claim. Creationists needless to say have made much of these unfortunate claims. Therefore, an article rebutting the ENCODE hype is necessary. Puncturing the ENCODE hype In 2012, some scientists made hyperbolic claims that the Encyclopedia of DNA Elements Project (ENCODE) had shown that 80% of our genome was functional. Unsurprisingly, special creationists latched onto this now-refuted claim as if it somehow invalidated common descent. It did not. Apart from the fact that those with the ENCODE project did not declare that their research rebutted evolution, special creationists ignored two points: Functional does not mean essential. Actively transposing retrotransposons writing over essential DNA are functional, but are definitely harmful Once again, the evidence from consonant phylogenetic trees and shared genomic 'errors' is independent of any claim about 'functionality' ENCODE - The truth is that at least 66% of our DNA is worthless junk Anyone who appeals to the ENCODE data in an attempt to rebut the evidence for common descent is merely broadcasting their ignorance of the fact that the ENCODE team and results have been heavily criticised by many evolutionary biologists. For those unaware of what ENCODE is, some context will be provided. In 2001, the human genome was sequenced[1]. Over the past nine years, the Encyclopedia of DNA elements (ENCODE) project has been examining the genome in order to examine what the genome does. Now, the ENCODE project has released several papers announcing the results of its research. One of results of its research is that "more than 80% of the human genome's components have now been assigned at least one biochemical function."[2] How does this square with the fact that much of our genome is made up of non-coding DNA such as retrotransposons (nearly half the DNA), intronic DNA or endogenous retroviral elements? The key word here is 'functional'. I have to stress that functional does not mean essential or beneficial. Retrotransposons for example have been linked with human disease.[3] We would be arguably better off if those SINEs were silent. Special creation already has to accept that if every nucleotide was created by God, then the creator has deliberately inserted genomic material which causes immense misery in the human race. The intelligent designer becomes a malevolent designer if the logic of the special creationist position is carried through to its inevitable conclusion. Another point to remember is that being transcribed counts as biological function, irrespective of whether that transcribed section actually does something beneficial for the organism. Without this context, claims that the 80% figure invalidate what we already know about the genome (that most of it is non-coding junk) can be dismissed. There is of course no substitute for informed commentary (as opposed to special creationist disinformation), which is why the opinions of senior scientists involved in the ENCODE project are worth reading. Ewan Birney, the lead analysis coordinator for ENCODE over the past five years is arguably a man whose opinion would count for something. So what does he say about the 80% figure: It’s clear that 80% of the genome has a specific biochemical activity – whatever that might be. T his question hinges on the word “functional” so let’s try to tackle this first.  Like many English language words, “functional” is a very useful but context-dependent word. Does a “functional element” in the genome mean something that changes a biochemical property of the cell (i.e., if the sequence was not here, the biochemistry would be different) or is it something that changes a phenotypically observable trait that affects the whole organism? At their limits (considering all the biochemical activities being a phenotype), these two definitions merge.  Having spent a long time thinking about and discussing this, not a single definition of “functional” works for all conversations. We have to be precise about the context. Pragmatically, in ENCODE we define our criteria as “specific biochemical activity” – for example, an assay that identifies a series of bases.  This is not the entire genome (so, for example, things like “having a phosphodiester bond” would not qualify). We then subset this into different classes of assay; in decreasing order of coverage these are: RNA, “broad” histone modifications, “narrow” histone modifications, DNaseI hypersensitive sites, Transcription Factor ChIP-seq peaks, DNaseI Footprints, Transcription Factor bound motifs, and finally Exons. [4]  (Emphasis mine) Specific biochemical activity does not mean essential to life. This point needs to be hammered home to every special creationist who latches onto the ENCODE paper and claims that 80% of the genome is functional (though one wonders why they are still happy to accept the implication that God created the human genome with 20% junk). Birney continued by commenting on with what definition of 'functional he is happy: Back to that word “functional”: There is no easy answer to this. In ENCODE we present this hierarchy of assays with cumulative coverage percentages, ending up with 80%. As I’ve pointed out in presentations, you shouldn’t be surprised by the 80% figure. After all, 60% of the genome with the new detailed manually reviewed (GenCode) annotation is either exonic or intronic, and a number of our assays (such as PolyA- RNA, and H3K36me3/H3K79me2) are expected to mark all active transcription. So seeing an additional 20% over this expected 60% is not so surprising.However, on the other end of the scale – using very strict, classical definitions of “functional” like bound motifs and DNaseI footprints;  places where we are very confident that there is a specific DNA:protein contact, such as a transcription factor binding site to the actual bases – we see a cumulative occupation of 8% of the genome. With the exons (which most people would always classify as “functional” by intuition) that number goes up to 9%. Given what most people thought earlier this decade, that the regulatory elements might account for perhaps a similar amount of bases as exons, this is surprisingly high for many people – certainly it was to me!In addition, in this phase of ENCODE we did sample broadly but nowhere near completely in terms of cell types or transcription factors. We estimated how well we have sampled, and our most generous view of our sampling is that we’ve seen around 50% of the elements. There are lots of reasons to think we have sampled less than this (e.g., the inability to sample developmental cell types; classes of transcription factors which we have not seen). A conservative estimate of our expected coverage of exons + specific DNA:protein contacts gives us 18%, easily further justified (given our sampling) to 20% (Emphasis mine) In other words, once we start changing our definition of 'functional' to one more consistent with what the layperson would take it to be (ie: biologically useful or essential) the 80% figure drops to around 20%. As for why ENCODE emphasised the 80% figure, rather than the 20% one more consistent with that the layperson would perceive 'functional' to mean, Birney states: Originally I pushed for using an “80% overall” figure and a “20% conservative floor” figure, since the 20% was extrapolated from the sampling. But putting two percentage-based numbers in the same breath/paragraph is asking a lot of your listener/reader – they need to understand why there is such a big difference between the two numbers, and that takes perhaps more explaining than most people have the patience for.  We had to decide on a percentage, because that is easier to visualize, and we choose 80% because (a) it is inclusive of all the ENCODE experiments (and we did not want to leave any of the sub-projects out) and (b) 80% best coveys the difference between a genome made mostly of dead wood and one that is alive with activity . (Emphasis mine) Alive with activity again does not mean essential to life. A retrotransposon that copies and pastes itself indiscriminately in the genome is functional, but when it causes genetic disorders it is clearly not beneficial. Unsurprisingly, special creationists tend to ignore the 45% of the genome that is retrotransposed DNA, essentially parasitic genetic material. The ENCODE hype has been criticised severely for its misleading 80% figure. Dan Graur   et al have published a takedown of the extravagant ENCODE claims: A  recent slew of ENCODE Consortium publications, specifically the article signed by all Consortium members, put forward the idea that more than 80% of the human genome is functional. This claim flies in the face of current estimates according to which the fraction of the genome that is evolutionarily conserved through purifying selection is under 10%. Thus, according to the ENCODE Consortium, a biological function can be maintained indefinitely without selection, which implies that at least 80 – 10 = 70% of the genome is perfectly invulnerable to deleterious mutations, either because no mutation can ever occur in these “functional” regions, or because no mutation in these regions can ever be deleterious. This absurd conclusion was reached through various means, chiefly (1) by employing the seldom used “causal role” definition of biological function and then applying it inconsistently to different biochemical properties, (2) by committing a logical fallacy known as “affirming the consequent,” (3) by failing to appreciate the crucial difference between “junk DNA” and “garbage DNA,” (4) by using analytical methods that yield biased errors and inflate estimates of functionality, (5) by favoring statistical sensitivity over specificity, and (6) by emphasizing statistical significance rather than the magnitude of the effect. Here , we detail the many logical and methodological transgressions involved in assigning functionality to almost every nucleotide in the human genome. The ENCODE results were predicted by one of its authors to necessitate the rewriting of textbooks. We agree, many textbooks dealing with marketing, mass-media hype, and public relations may well have to be rewritten.[5]   (Emphasis mine) It is worth noting that when Ewan Birney, the lead scientist for ENCODE was pressed on the claim that 80% of the genome is essential to life, he conceded that this was not true. In a BBC Radio interview, Birney admitted: Chris Ponting : So I think we can probably agree between us that between 10% and say 20% is vital for life. Ewan Birney : I mean, I think we would agree with that.  I think, you know, refining that percentage down is quite interesting. I think also the other components that we — biochemical events that we see in the genome, sort of, each one of them are equally likely to be part of that 10% to 20% that we’re looking for. It’s important to realize that it’s not the case that we can spot the 10% to 20% just by looking harder. Each of these different places in the genome that have some biochemical activity associated with it, when there’s some phenotype screen that’s directed there or some evolutionary screen that’s directed to that point, ENCODE can now say “Ah ha! Here is a biochemical thing that this piece of DNA looks like it could be doing”. [6] (Emphasis mine) Evolutionary biologist TR Gregory who is also an expert in genome size evolution - putting him in a perfect position to provide informed commentary on the subject has taken a considerable interest in the subject. In the comments section of one of Gregory's blog posts discussing the ENCODE hype, respected evolutionary geneticist Joe Felsenstein makes a penetrating comment which cuts to the heart of the hype: Ewan Birney is trying to give the impression that the problem is that people have misinterpreted him.  But he was the one who put forward the 80% figure.  It was not added by the popular science press, he wanted it out there and wanted it noticed. And when there was a huge blaze of publicity centered on the (purported) death of junk DNA, publicity that Ryan has done us the great service of listing, I didn’t notice Birney jumping up saying that he had been misinterpreted.Large numbers of laypeople and other scientists are now persuaded that there never was any junk DNA. It will probably take 10 years to unpersuade them. We have Birney to thank for this situation. I’m saddened to see him dance around and try to give the impression that someone else came up with the Death of Junk DNA. [7]  (Emphasis in the original) Birney later admitted on bis bog that the 80% figure represented biological activity, which was not the same thing as essential to life. The problem with 'science by press release', is that in order to gain the attention of your audience, there is a very real temptation to succumb to hyperbole, and when you are dealing with the general public, terms such as 'functional' need to be defined properly, otherwise there is the chance that they will get the wrong idea. Certainly, when most people hear 'functional', they are likely to think that 80% of the genome is essential to life, which is simply false. As project leader Ewan Birney acknowledged later, the 80% figure represents biological activity, which is definitely not the same thing as functional: Q. Ok, fair enough. But are you most comfortable with the 10% to 20% figure for the hard-core functional bases? Why emphasize the 80% figure in the abstract and press release?A. (Sigh.) Indeed. Originally I pushed for using an “80% overall” figure and a “20% conservative floor” figure, since the 20% was extrapolated from the sampling. But putting two percentage-based numbers in the same breath/paragraph is asking a lot of your listener/reader – they need to understand why there is such a big difference between the two numbers, and that takes perhaps more explaining than most people have the patience for. We had to decide on a percentage, because that is easier to visualize, and we choose 80% because (a) it is inclusive of all the ENCODE experiments (and we did not want to leave any of the sub-projects out) and (b) 80% best coveys the difference between a genome made mostly of dead wood and one that is alive with activity. We refer also to “4 million switches”, and that represents the bound motifs and footprints.We use the bigger number because it brings home the impact of this work to a much wider audience. But we are in fact using an accurate, well-defined figure when we say that 80% of the genome has specific biological activity. [8] In other words, between 10-20% of the genome consists of 'hard core functional bases' with the rest simply being biologically active, which is   not  the same thing as essential to life. Retrotransposable elements that copy and paste themselves randomly into the genome are biologically active, but hardly essential - or beneficial, as evidenced by the genetic diseases connected to retrotransposable DNA. Even if one grants that the entire 80% figure refers to essential genomic material, that still leaves 20% of the genome non-coding, non-functional junk, which is inconsistent with the idea that the genome is the product of an intelligent designer. Since then, the much-touted 80% figure is changing. Science journalist Faye Flam contacted John Stamatoyannopoulos, one of the ENCODE researchers to clarify the 80% figure. It turns out that it is more like 40%: He said he thought the skeptics hadn’t fully understood the papers, and that some of the activity measured in their tests does involve human genes and contributes something to our human physiology. He did admit that the press conference mislead people by claiming that 80% of our genome was essential and useful. He puts that number at 40%. Otherwise he stands by all the ENCODE claims. [9]   (Emphasis mine) So, we can safely bin the "80% of the genome is functional" claim as even researchers from ENCODE are backing away from it. Max Libbrecht, another ENCODE researcher also commented on the ENCODE debacle, showing that even members of the project realised just how damaging the "80% is functional" hype was: After I took part in an AMA ("Ask Me Anything") on reddit, there has been some discussion elsewhere (such as by Ryan Gregory and in the comments of Ewan Birney's blog) of what I and the other ENCODE scientists meant. In response, I'd like to echo what many others have said regarding the significance of ENCODE on the fraction of the genome that is "junk" (or nonfunctional, or unimportant to phenotype, or evolutionarily unconserved).In its press releases, ENCODE reported finding 80% of the genome with "specific biochemical activity", which turned into  (through some combination of poor presentation on the part of ENCODE and poor interpretation on the part of the media) reports that 80% of the genome is functional.   This claim is unlikely given what we know about the genome (here is a good explanation of why), so this created some amount of controversy.I think very few members of ENCODE believe that the consortium proved that 80% of the genome is functional; no one claimed as much on the reddit AMA, and Ewan Birney has made it clear on his blog that he would not make this claim either. In fact, I think importance of ENCODE's results on the question of what fraction of DNA is functional is very small, and that question is much better answered with other analysis, like that of evolutionary conservation. Lacking proof either way from ENCODE, there was some disagreement on the AMA regarding what the most likely true fraction is, but I think this stemmed from disagreements about definitions and willingness to hypothesize about undiscovered function, not misinterpretation of the significance of ENCODE's results. I think many members of the consortium (including Ewan Birney) regret the choice of terminology that led to the misinterpretations of the 80% number. Unfortunately, such misinterpretations are always a danger in scientific communication (both among the scientific community and to the public). Whether the consortium could have done a better job explaining the results, and whether we should expect the media to more accurately represent scientific results, is hard to say. I think the contribution of ENCODE lies not in determining what DNA is functional but rather in determining what the functional DNA actually does. This was the focus of the integration paper and the companion papers, and I would have preferred for this to be the focus of the media coverage.[10] (Emphasis mine) In short: The claim that 80% of the genome is essential to life is false. The figure is more like 10-20% The value of ENCODE, to quote one of its researchers is in determining what the functional DNA actually does, rather than how much is functional. The question of functionality does not take away the considerable evidence for common descent. Burges has completely failed to address in any substantive way this evidence, and the ENCODE diversion merely demonstrated his ignorance of the controversy surrounding ENCODE and the acknowledgement that the 80% figure was hype. How much of the genome is actually essential to life? Not much. Around 45% of the genome is made up of mobile genetic elements - retrotransposons - that copy and paste themselves into the genome randomly, often causing disease in the process. This is very much an unguided, random process. A significant fraction of the human genome owes its origin to ancient retroviral infection. In fact, there is more retroviral genetic material – the evidence of past retroviral infection – in our genome than there is direct protein coding material. Only a a small percentage of the human genome directly codes for protein or has specific regulatory function. Breaking down the human genome into the various classes of genetic material we find there, the scale of how much parasitic DNA, decayed viral remnants and genetic equivalent of gibberish[11] is astonishing: Transposable Elements : 44% junk DNA transposons: functional < 0.1%, defective 3% Retrotransposons: active < 0.1%, co-opted < 0.1%, junk 41% Viruses : 9% junk DNA Viruses: active < 0.1%, defective ~1% RNA Viruses: active < 0.1%, co-opted < 0.1%, defective 8% Pseudogenes : 1.2% junk Derived from protein-coding genes: 1.2% junk Co-opted pseudogenes: < 0.1% useful, secondarily acquired new function Ribosomal RNA genes : 0.19% junk Essential: 0.22% Junk: 0.19% Other RNA encoding genes tRNA genes: < 0.1% essential known small RNA genes: < 0.1% essential putative regulatory genes: ~2% essential Protein-encoding genes : 9.6% junk (intron sequences), 1.8% essential transcribed Regulatory Sequences : 0.6% essential Origins of DNA replication : < 0.1% essential Scaffold attachment regions : < 0.1% essential Highly repetitive regions : 1% junk, 2% essential Intergenic DNA : 26.3% unknown function, most likely junk, 2% essential Essential / Functional DNA : 8.7% Junk DNA : 65% Unknown : 26.3% Even if most of the intergenic DNA turns out to have a function, nearly 66% of our genome is rubbish consisting of remnants of ancient retroviral infection, damaged genes that can no longer work, mobile genetic elements that copy and insert themselves randomly around the genome irrespective of what benefit or harm that action does, and introns, the non-coding sections of DNA that interrupt genes. For those wanting an informed view of the subject, Lawrence Moran's recent book is excellent. [12] Population geneticist Zach Hancock has produced a video detailing why junk DNA is very much real. [13] References [1] International Human Genome Sequencing Consortium Initial sequencing and analysis of the human genome   Nature  (2001) 409:860-921 [2] Skipper M, Dhand R, Campbell P "Presenting ENCODE"   Nature  (2012) 489 :45 doi:10.1038/489045a [3] Prescott L. Deiningera PL and Batzerc MA "Alu Repeats and Human Disease"   Molecular Genetics and Metabolism  (1999) 67:183-193 [4] Birney E "ENCODE: My own thoughts" Ewan's Blog; bioinformatician at large September 5th 2012 http://genomeinformatician.blogspot.com.au/2012/09/encode-my-own-thoughts.html [5] Graur D et al "On the Immortality of Television Sets: “Function” in the Human Genome According to the Evolution-Free gospel of ENCODE"   Genome Biol Evol  (2013) 5 :578:590 [6] Gregory TR "BBC Interview with Ewan Birney"   Genomicron  April 1 2013. https://www.genomicron.evolverzone.com/2013/04/bbc-interview-with-ewan-birney/ [7] Gregory TR "BBC Interview with Ewan Birney"   Genomicron  April 1 2013. Comment [8] Birney E "ENCODE: My Own Thoughts"   Ewan's Blog: Bioinformatician At Large  5 Sep 2012 https://ewanbirney.com/2012/09/encode-my-own-thoughts.html [9] Flam F "Skeptical Takes on Elevation of Junk DNA and Other Claims from ENCODE Project"   Tracker: Peer Review Within Science Journalism 12 Sep 2012 https://ksj.mit.edu/tracker-archive/skeptical-takes-elevation-junk-dna-and-o/ [10] Libbrecht M "On ENCODE's results regarding junk DNA"   mlibbrecht  Oct 8 2012 http://mlibbrecht.blogspot.com/2012/10/on-encodes-results-regarding-junk-dna.html [11] Moran L “What’s in Your Genome?”   Sandwalk  May 8th 2011 https://sandwalk.blogspot.com/2011/05/whats-in-your-genome.html [12] Moran, Laurence A.. What's in Your Genome? 90% of Your Genome Is Junk. Canada: University of Toronto Press, 2023. [13] https://youtu.be/0SEKs4bAlHM?si=ifgpeooW089lkwcB

“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. From: Dinosaur Expo, 2009. The Miracle of the Deserts. 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. Scientists announced brain neurological pathway discovered that activates when people are intensely trying to hear that would normally move the outer ears towards the sound. Of course the muscles are vestigial so this is ineffective. " The study revealed distinct responses from two different ear muscles. The posterior auricular muscles reacted to sound direction, while the superior auricular muscles activated more intensely during difficult listening conditions. This activity increased notably when participants reported struggling to follow the target audio." https://scienceblog.com/553483/ear-muscle-we-thought-humans-didnt-use-except-for-wiggling-our-ears-actually-activates-when-people-listen-hard/?utm_source=substack&utm_medium=email Originalsource: https://www.frontiersin.org/journals/neuroscience/articles/10.3389/fnins.2024.1462507/full 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.

“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

"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

“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

"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/