"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

"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/

"My family tree spreads wide as well. I am a great ape, and you are a great ape, and so are chimpanzees and orangutans and bonobos, all of us distant and distrustful cousins." ~ Katherine Applegate Human Chromosome 2 Fusion: The case of the missing DNA Some History As early as the mid 1800’s when the nuclei of eukaryotes (non-bacteria; we are eukaryotes) were stained, small condensed bodies were noted and called chromosomes, from the Greek meaning “color” and “body”. Because microscopes did not have high enough resolution, some scientists felt humans had 48 chromosomes rather than 46. It wasn’t until 1958 that the true number of human chromosomes was confirmed to be 46. Previously in 1953, many years of controversy regarding the molecule of inheritance was finally agreed upon when Watson and Crick published their famous paper proving that the instructions for inheritance was DNA. Before that many scientists including Linus Pauling thought that the DNA letters of ATCG were too limited to code for the complexity in life and they favored proteins instead as the repository of inheritance. Now we knew DNA in the chromosomes was the molecule of inheritance and humans had 46. Genetic studies of the other great apes in the early 1960s (chimps, bonobos, gorillas, orangutans) showed that they all had 48 chromosomes. Since science knew evolution was true and that we shared common ancestors with the great apes, how then did we end up with 46 chromosomes and evolve from all our common ancestors with 48 chromosomes? Chromosome Basics A chromosome is made up of DNA but also contains different compounds in addition to the DNA. The DNA is combined with proteins called histones that look like small balls in diagrams. DNA normally exists in an unraveled state that appears messy to our eyes. Think of a bowl of cooked spaghetti. When a cell divides and makes new cells the DNA is condensed down into small packets for easier moving. After duplication to make new DNA, the packages - called chromosomes - are lined up at a stage called metaphase and pulled apart with one set going into the new cell and the other set remaining in the parent cell. Note the chromosome below at metaphase and that there is a constriction in the pairs like a belt has been tightened called the centromere that will be discussed shortly. See Figure 1. Figure 1. From nuclear chromosomes to DNA with bases exposed When you look at chromosomes today microscopes and staining techniques have improved to the point where the banding patterns from various dyes result in stunning photos. When we compare human chromosomes to chimp chromosomes for example, the banding is almost identical. To the evolutionary scientist that’s because they share an ancestor. To the anti-evolutionist it’s only due to common design; since humans and chimps are both primates and very similar, a Designer in creating these two separate species would have of course used some of the same DNA. To the anti-evolutionist, humans and chimps never shared a common ancestor. This is based almost entirely on a priori beliefs. If you look at Figure 2 the only way to make all the human (H) and chimp (C) chromosomes match is to take chimp's 12 and 13 and stick them together end on end and now the banding of those two fused chromosomes match human chromosome 2. This is what was announced in 1991, that the fusion point of chimp chromosomes 12 and 13 had been found in human chromosome 2. Figure 2. Fair Use applicable. For education purposes. https://www.kqed.org/quest/586/chromosome-fusion-chance-or-design The Fusion of Our Chromosome 2 This discrepancy in chromosomes between humans and the other great apes theoretically initially presented a problem for evolution since it was settled science that humans evolved from a shared ape ancestor that must have had 48 chromosomes. It was not until 1991 that it officially was solved. A paper from Yale University School of Medicine (yes, evolution is necessary for modern medicine. See Evolutionary Medicine) showed what happened to the missing chromosome material; it was there all along, or more specifically the DNA. Human evolution from a shared ancestor with the great apes was vindicated by genetics and confirmed the fossil record. To keep the numbering alignment working for the two species, chimp chromosomes 12 and 13 were renamed 2A and 2B in 2004. See Figure 3. Figure 3. JW Schmidt. https://en.wikipedia.org/wiki/Chimpanzee_genome_project#/media/File:Humanchimpchromosomes.png Now it gets interesting and the fusion shows that Evolution is a scientific theory because it can be tested and makes predictions, which means it can be falsified. And as a reminder, the Theory of Evolution has withstood 150 years of testing. Chromosomes have ends on them called telomeres that protect them when copying and moving around. These collections of DNA are called tandem repeats and are the sequence of TTAGGG and then the opposite on the other side of the DNA “ladder” would be CCTAAA. As we age telomeres become smaller and worn down and much research is ongoing into slowing that process down to help us with aging. So, telomeres should not be found in the middle unless the chromosome had become fused in the past. In addition there is a constricted area in the chromosomes best seen in metaphase before the chromosomes are pulled apart. This is where the cell attaches molecular “ropes” to pull them apart into the now two cells. And you can’t have two because that would cause the pulling points to attach at two points instead of one. So besides old telomeres in the middle of a chromosome there should be an old vestigial inactivated centromere that is no longer in use if there was a fusion. If humans evolved from a great ape ancestor shared with chimps that had 48 chromosomes, we should find a fused chromosome with telomeres in about the middle and a second dead vestigial centromere. Furthermore, by looking at chimps 2A and 2B when the ends are put together we can even see where the two centromeres should be. One is active in HC2 now, so we even know where to look to find a second inactive one! See Figure 4 diagram below of what happened and where we can look on HC2 for the evidence. Also look at figure 2 again and see where we can look for the evidence more specifically on HC2. Do you see that the inactivated vestigial centromere should be just below the active one that is presently in HC2? Figure 4. SaudiPseudonym, CC BY-SA 3.0 , via Wikimedia Commons As previously mentioned, in 1991 the area shown to be a fusion site was found to have the sub-teleomere sequences predicted and is located at 2q13 - 2q14.1 (the chromosome is divided into a top “p” and bottom “q” from the centromere). In 1992 the second vestigial centromere was located on HC2 where predicted at 2q21.3 - 2q22.1 . In 2005 the exact fusion point was sequenced. See Figure 5 and find the arrow which points to the exact fusion point. This sends shivers up my spine because we are looking at an event that happened millions of years ago in a single individual of our distant ancestors. And he or she spread that chromosome event through inbreeding first in a small population and then to all modern humans (and also Neanderthals and Denisovans). Figure 5. https://i.imgur.com/CJRRUGo.png From: Chromosome 2 fusion - a response to a question on biology stack exchange To further confirm the findings, in 2006 Stefan Muller tagged HC2 with a dye and then applied the same dye tags to an orangutan. See Figure 6. The HC2 photo is on the right and the orangutan chromosomes are on the left. Note that the tagged DNA is found in two human chromosomes 2 (we get one each from a parent) but 4 in the orangutan because the DNA is not in a fused state (chromosomes 12 and 13 in chimps) essentially proving the fusion observation in humans because there are four places with the same matching HC2 DNA in the orangutan as in the 2 locations in humans, exactly as predicted. Figure 6. Human tagged karyotype on the right, Orangutan on the left. From: Verena Schubel, Stefan Müller, Department Biologie der Ludwig-Maximilians-Universität München., CC BY-SA 2.5 , via Wikimedia Commons Here is the explanation of his experiment: "DNA of the human chromosome 2 was labeled, applied to Orang-Utan (left) and human metaphase chromosomes (right) by fluorescence in situ hybridization and detected in green. While in the human metaphase spread only the two copies of chromosome 2 were detected, in the Orang-Utan metaphase spread the two original chromosome pairs were painted: Human chromosome 2 is the evolutionary derived fusion product from two separate ancestral chromosomes. In non-human primates - like for example in the Orang-Utan (chromosomes on the left side) - as well as in several other mammals, two chromosomes are observed which carry human chromosome 2 orthologous genes and syntenic segments of orthologous DNA sequences. The fusion in human 2q13-14 at approximately 114 Mbp of the human reference sequence (see Ensembl) occurred after the split of the human and chimpanzee lineages from that of their last common ancestor.” Here is a short summary of the fusion and how it relates to human evolution. Also discussed is how an individual with this chromosomal number could reproduce and how that 46 number could become fixed in a small population and then spread. Lastly, some of you may be wondering how going from 48 to 46 chromosomes could have happened. The 46 number can actually occur in just two generations with inbreeding. A Punnett square at the end of this article shows how it probably happened. Potential Objections Various people have raised some observations that they perceive as negating the claim that HC2 is a fusion product. All of them have answers, however. HC2 is definitely a product of a fusion of an ancestor to humans, specifically what now resembles chimp's 12 and 13 chromosomes. 1. There is too much degradation in the fused telomeres. This is discussed in an online debate between the Discovery Institute and Carl Zimmer: https://carlzimmer.com/the-mystery-of-the-missing-chromosome-with-a-special-guest-appearance-from-facebook-creationists/ 2. The DDXL112 gene in the fusion area. This and several other objections are addressed in a 28 min video. https://www.youtube.com/watch?v=qVeriF1OL54&t=762s 3. The claim that there are numerous telomere sections throughout chromosomes so a fusion by noting telomeres in the middle of chromosomes is unjustified. Why there are short telomere sections found in chromosomes is explained by Graeme Finlay in his book, "Human Evolution: Genes, Genealogies, and Phylogenies". This book is actually the finest presentation of DNA evidence for human evolution that I have ever found. Highly recommended. This from his section on "Old scars on DNA", and how these scars are randomly generated but shared across humans and the other great apes, indicating shared ancestry. "Some 50 short, well-conserved interstitial telomeric repeats, (TTAGGG)n, are present in the human genome. Sequencing studies indicated that they arose as distinct insertion events, probably generated by the action of the enzyme telomerase, which has the function of adding TTAGGG units at the authentic telomeres. These inserts have the characteristics of emergency DNA repair patches that were recruited to hold double stranded breaks together." (p. 146-147). Numerous DNA patches and repairs that are randomly produced and randomly repaired are exactly shared between humans and the other great apes. Some of these patches contain telomeres so the anti-evolutionist objections are disproven. To understand how DNA repair patches point to near proof of human evolution as explained by Finlay, see the short blog on evolution and DNA patches. Instead of being a problem for evolution, interstitial telomeres actually support evolution because they nest in evolutionary phylogenetic trees confirming evolution. As usual, a close examination of anti-evolutionist objections reveals motivated reasoning and lazy "research"; pushing out "possibilities" without testing them and not knowing the literature. 4. Chromosomal fusions and splits occurred in our distant past. As early as the 1980s scientists were able to piece that history together. During meiosis crossing over occurs and also chromosome sections can break out and be inserted in the opposition direction (inversion = Inv). In comparing our chromosomes to other great apes, insertions, deletions and inversions were noted and these events can be seen as part of our genetic history. Roman numerals refer to chromosome numbers. 5. A comment regarding a person making claims that HC2 can't be a fusion. Comments from a geneticist on Reddit and the creationist Tomkins. 6. Actually there was some shuffling of both ends of the chromosomes before the fusion took place. A study published in August of 2022 appears to have narrowed the fusion time between 800,000 and 1 mya before modern humans, Neanderthals and Denisovans split off. In addition, another study showed there probably was a bottleneck in our ancestors about that time and so it would have been easier for the fusion to become fixed in a smaller population. From: Hawks, John. August 31, 2023. When did Human Chromosome 2 Fuse? Full explanation and discussion in: https://johnhawks.net/weblog/when-did-human-chromosome-2-fuse/?fbclid=IwAR0ScYtuG_g7a8ZcGkDWKQOdkrT4enoI4VnWBlPuf7l3SnL2ziSPgFaqEhM Robertsonian fusions, which are a different type involving centromeres near chromosomal ends, are not rare; they occur in 1:1000 people so if you are in a city of 2 million there are about 2,000 people walking around with 45 chromosomes and are perfectly healthy and probably some may be ignorant that their chromosome number is unusual. They have the same basic DNA we have but one less chromosomal luggage piece. After the HC2 fusion event, other mutations occurred to our chromosome 2 including in the fusion site, and duplications of chromosome 9 moved into 2. When compared to the orangutan genome, HC2 carries two inversions. The first shows after a break after orangutans and the second differentiates chimps from gorillas. This all is explained elegantly by evolution but not by common design. There is no reason these inversions happened as they did unless common descent is true; they do not fit into common design as an explanation. See below: What fossil evidence is known that points to the earliest hominid candidate branching from chimps and bonobos 6 - 7 mya? Looking for Mr. Goodlink? - https://pandasthumb.org/archives/2024/07/looking-for-mr-goodlink.html?fbclid=IwZXh0bgNhZW0CMTEAAR1tqB8ZjQYkNc9xiw7Y-JeQu8kHQp-Xv_F4lkb0RGcrO_cTtbgMgHbKVAQ_aem_gSjMcNZ_alEk8DVfk13n3w#more Summary - all the potential objections put forward to discount that our chromosome 2 is a fusion that I know of have been answered. There are no rational reasons why HC2 is not a fusion that I am aware of. Lastly, some of you may be wondering how going from 48 to 46 chromosomes could have happened. It actually can occur in just two generations with inbreeding. A Punnett square at the end of this article shows how it probably happened. Conclusion Why then did I choose shared ERVs and not HC2 fusion as one of my two best examples for evolution? Because I suppose someone could still claim that chimps and the other great apes were created first with 48 chromosomes, and then two chromosomes were fused together when creating humans. That’s possible I guess, but HC2 fusion is still best explained by evolution and not common design. How it was determined shows that evolution is science. With shared ERVs, there is no getting around that these old parasitic viral tags rise to the level of proof of evolution and common ancestry in humans (see shared ERVs, this site). Indeed, in my opinion all attempts to date have failed to discount shared ERVs and human evolution. Human chromosome fusions are not rare. For example it's not rare for Robertsonian Translocations to occur where two chromosomes accidentally fuse during meiosis. Often they have the centromeres near the tips (acrocentric chromosomes), so little DNA is damaged. The person is usually phenotypically normal but since they have 45 instead of 46 chromosomes they may not know this until they try and have children. This occurs in 1:1,000 people so in a city of 2 million for example, there are 2,000 people walking around looking normal but with 45 chromosomes instead of 46! There is even a case of three children that are normal physically with 44 chromosomes because two people who had 45 chromosomes from Robertsonian translocations mated. Human Chromosome 2 is a fusion of an ancestor that appears similar to current chimps' chromosomes 12 + 13, now called 2A and 2B (our closest living relative). We did not evolve from modern chimps but we shared a common ancestor about 6- 7 million years ago with them. The fusion happened after we split from our chimp/bonobo ancestor. It is consistent with human evolution and our shared ancestry with our great ape cousins. It represents human evolution and an example of "macroevolution". References There's Proof of Evolution Hiding in Your DNA https://www.youtube.com/watch?v=2GfKZlTRNjA Human Evolution: Genes, Genealogies and Phylogenies. 2013. Finlay, Graeme. 2021 Paperback ed. University Printing House, Cambridge, CB2 8BS, UK. 359pp. Addendum: going from 48 to 46 chromosomes in a pre-human population with just two generations. It would then need to be fixed. Eggs are represented on the vertical axis and sperm on the horizontal axis. Diagram by the author.

Is the Theory of Evolution vital for good medical practice? "Not one example can be put forth of the need for evolution (or belief in its tenets) in order to practice modern medicine." ~ Robert Mitchell, MD. 11/22/2005 "If evolution were thrown out of consideration, it would have no negative impact (in medicine)—it plays no necessary role in either the teaching or practice of medicine." ~ David Menton, PhD. 7/21/2008 "No biological problem is solved until both the proximate and the evolutionary causation has been elucidated. Furthermore, the study of evolutionary causes is as legitimate a part of biology as is the study of the usually physicochemical proximate causes." ~ Ernst Mayer, 1982. Introduction Are those statements by Drs. Mitchell and Menton true? That there are no examples where an evolutionary context adds to understanding of the human body, behavior or disease? Where evolution plays no role in treating patients or developing new treatments? I often hear the religious tell me that evolution has no role in the practice of medicine, and indeed can be harmful. I would like to assert that the answer is yes and no. A medical provider can practice clinical medicine without considering evolution; it just won’t be the best medicine. One can’t really understand the anatomy, physiology and psychology of humans without evolution. And for researchers at medical schools and other research institutions, it’s vital for them to ground their medical work in evolution. For example, a surgeon can be taught to diagnose a gallbladder problem and to remove it laparoscopically. Someone can learn to change a tire on a car without knowing how the car works or even how to drive it. But that person would be unable to diagnose a problem in the auto’s electrical or transmission, let alone work on improved designs for future models. Likewise, surgeons for example don’t necessarily need to know the origins of this organ or why we are built the way we are with all kinds of clues to our evolutionary past (see the section on unintelligent design). In that case ultimate “whys” do not matter much and the providers are acting like highly paid technicians only (not that technicians don’t need to know why something is in their work). But as I will discuss, in basic medical research such as oncology (the study of cancer) and many other areas, evolutionary principles are vital. Mitchell, Menton and other antievolutionists who claim that evolution is not important in modern medicine would do a severe disservice to the medical field by their deleterious approach to health and disease. After all, medicine is an applied discipline that is grounded in biology and biology’s foundation is evolution. American medical providers (and probably those in other countries) are now pressured more and more to use algorithms in medicine - without necessarily knowing why the steps are there. Theoretically this should help medicine to be more standardized by various providers that are trained differently (MD, DO, DNPs, PAs e.g.), reduce unnecessary testing, and reduce missed diagnoses. However, it also potentially disconnects the provider from novel thinking and curiosity. For example, if you had a complicated problem with your car transmission, would you want someone who has actually taken one apart, who knows how they work, what factory it was made in (its origin) and if that year the factory had manufacturing issues? Or would you use a mechanic who just knew it was broken and supposedly had been taught what to do only to fix it? Today that can mean just replacing part after part until it is fixed. Expensive diagnostic tools to read error codes can help narrow the origin of the problem, but auto systems are interconnected so one still needs to understand the basic interplay and integration of the car systems. Knowing ultimate “whys” is a much superior approach. What if a problem arises that does not fit the medical algorithms? I can tell you from experience that the human body has not read the medical books. And that transmission problem? I’m sure that someone who actually knows how that complicated machine works will be much better at diagnosing and fixing it properly. The “why” can be so important. Have a patient with an anemia? What about just giving them iron without knowing what type of anemia it is? If it is an iron deficiency anemia isn’t it mandatory that you find out why -where the red blood cells are being lost or why they not being produced? Anti-evolutionists insist that medical providers don’t need to understand the evolutionary history of life and disease to practice medicine. Some claim that there is not even one example of why knowing evolution is important in medicine. But is that true? Evolutionary Medicine This new field of medicine became established in the 1990s, especially with the publication of the 1996 book by Nesse and Williams, “Why We Get Sick: The New Science of Darwinian Medicine”(1). Nesse, now at the Center for Evolution and Medicine at Arizona State University, notes that Evolutionary Medicine (EM) “… is the field at the intersection of evolution and medicine… Instead of only asking how bodies work and why some people get sick, EM also asks why natural selection has left all of us with traits that make us vulnerable to disease. Why do we have wisdom teeth, narrow coronary arteries, a narrow birth canal, and a food passage that crosses the windpipe? Evolution explains why we have traits that leave us vulnerable to disease, as well as why so many other aspects of the body work so well.”(2). Low notes that EM “… infuses traditional medical thinking, which primarily centers on proximate explanations and reductionist approaches, with evolutionary concepts to offer ultimate explanations for why diseases may occur, thus providing a more complete framework for understanding the origins of disease risk”. (3) As has been noted, “An evolutionary view of medicine can be extremely useful to help patients understand the “whys” of medicine… why are many cancers more common now than they used to be? Why do so many people struggle with obesity? [they’ve inherited survivor genes]. Why does depression exist?”. (4) Centers for Evolutionary Medicine This new field is so promising that multiple departments and centers for EM have been established at medical schools and universities in America and around the world (in the UK for example). UC Berkeley includes a section on evolution and medicine in its Understanding Evolution course. Johns Hopkins University offers a PhD through their Center for Functional Anatomy and Evolution. UCLA has established an Evolutionary Medicine Program and interdisciplinary center that combines faculty from Biology, Medicine, Geography, Psychiatry and Psychology, Anthropology, Veterinarian Medicine, and other allied disciplines (5). As previously noted, a significant research center for EM is located at Arizona State University and its Center for Evolution and Medicine. Several top American medical schools use or have used paleontologists to teach anatomy to their medical students. Why would top medical schools like The University of Chicago’s Pritzker School of Medicine have a fish paleontologist teaching human anatomy to medical students (Neil Shubin, author of “Your Inner Fish”)? Why would the Northeastern Ohio Medical University have probably the most famous cetacean paleontologist alive today teaching human anatomy to medical students (Hans Thewissen)? Because a doctor won’t understand the crazy course of the Recurrent Laryngeal Nerve in the human neck without evolution (see the section on unintelligent design), nor why our ears are attached to our heads with vestigial muscles, why human males develop inguinal hernias (embryologically the testes develop at the level of the heart as they are in adult sharks for example, and in humans they must move all the way down into the scrotal sac at birth, leaving a tract that can later delaminate and open), why our coccyx (tail bone) is derived from smaller fused bones that hark back to when our ancestors had tails, why humans are rarely born with tails that can even be moved, why the plantaris muscle in the human calf is vestigial in humans and even missing in about 10% of the population (it flexes all the digits at once in the monkey - good for swinging in trees), why we form goose bumps to cold and surprise, and other anatomical features that can only rationally be explained by our evolutionary roots. We can’t really understand human behaviors unless Psychology and Psychiatry are ultimately rooted in evolutionary theory. For example, why do people not understand correct odds and continue to invest badly? Where does nationalism and tribalism come from if not from millions of years of selection that kept us alive and those we love safe when we were hunter-gatherers? Why do men and women often approach partnership so differently due to biological factors of investment cost in offspring - which can, like tribalism, be overcome. We don’t need to be slaves to what was successful in our past evolution but may be harmful to us now. Journals have been established for publishing research in EM. These include ISEMPH, the International Society For Evolution, Medicine & Public Health which publishes through Oxford University Press a journal of the same name, and The Evolution & Medicine Review. There is a database of 1600 online teaching resources for EM in EvMedEd. Cancer Perhaps in no other field of medicine has an area of research benefitted more from an evolutionary perspective than oncology. Oncology is the study and treatment of cancer. Cancer is basically cells that are no longer under control by the body. In order to grow, spread (metastasize), and evade the immune system they must acquire a whole host of mutations beneficial to them. As they grow they crowd out normal cells, use up precious energy, and cause destruction. Joshua Swamidass, MS, MD, PhD and on the faculty of the Washington University School of Medicine in St. Louis where he is an Associate Professor of Laboratory and Genomic Medicine, writes about the importance of EM to understanding cancer: “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.” He further writes: “A common misconception about evolution is that it is dominated by natural selection acting on beneficial mutations (this is often what is meant by “Darwinian” mechanism). However, brilliant mathematical work and genetic experiments in the 1960s and 1970s by scientists like Haldane and Kimura demonstrated that evolution, at the genetic level, is usually dominated, instead, by the drift of neutral or near-neutral mutations. So most of the genetic differences between different lineages were either non-functional or not beneficial enough for natural selection…This is one reason biologists say that Darwinian evolution is quantitatively less important than non-Darwinian evolution (e.g. neutral drift, neutral draft, and other mechanisms) in explaining the complexity in genetic differences between species. Cancer evolution independently confirms that neutral theory is correct. We see the same patterns here, but the terminology is different.” “Phylogenetics is foundational to modern evolutionary theory, with deep roots in information theory, population genetics, and neutral theory. It bears repeating, the exact same math, software, and theory that so accurately reconstructs a cancer’s history, is also used to reconstruct the evolutionary history of species…cancer demonstrates that evolutionary theory itself is useful. Going a small step farther, understanding evolution is centrally important in medical research. Fundamentally, cancer is an evolutionary disease. It only arises because life evolves.”(6) [all emphasis mine]. Many other authors agree. “Neoplasms are microcosms of evolution. Within a neoplasm, a mosaic of mutant cells compete for space and resources, evade predation by the immune system and can even cooperate to disperse and colonize new organs. The evolution of neoplastic cells explains both why we get cancer and why it has been so difficult to cure. The tools of evolutionary biology and ecology are providing new insights into neoplastic progression and the clinical control of cancer.” (7) “The dynamics of evolution are fully in play within the environment of a tumor, just as they are in forests and meadows, oceans and streams. This is the view of researchers in an emerging cross-disciplinary field that brings the thinking of ecologists and evolutionary biologists to bear on cancer biology.”(8) Aktipis notes in her article “How Evolution Helps Us Understand Cancer and Control it” how cancer cells break down normal cooperation and increase cellular cheating in the body, similar to species that must evolve to move onto other resource areas. She writes, “This ecological and evolutionary perspective highlights new ways of identifying cancerous cells, beyond the typical hallmarks such as excessive replication.”(9). Her book is a wonderful journey through why evolution is so important to modern medicine (24). Somarelli et. al. also note the importance of ecology and evolutionary concepts in understanding cancer: “Cancer progression is an evolutionary process. During this process, evolving cancer cell populations encounter restrictive ecological niches within the body, such as the primary tumor, circulatory system, and diverse metastatic sites. Efforts to prevent or delay cancer evolution - and progression - require a deep understanding molecular evolutionary processes. Herein we discuss a suite of concepts and tools from evolutionary and ecological theory that can inform cancer biology in new and meaningful ways.” (10). Tollis, Boddy, and Maley in 2017 wrote about how evolution solved Peto's Paradox - why some large long lived animals did not develop cancer, since cancer tends to develop in longer lived organisms as the cells age and total more cell divisions. (11). Hanahan (2022) noted that there are core new functions that cancer cells must acquire to be successful. He goes on to detail some of these changes at the molecular DNA level: "The eight hallmarks currently comprise the acquired capabilities for sustaining proliferative signaling, evading growth suppressors, resisting cell death, enabling replicative immortality, inducing/accessing vasculature, activating invasion and metastasis, reprogramming cellular metabolism, and avoiding immune destruction. In the most recent elaboration of this concept, deregulating cellular metabolism and avoiding immune destruction were segregated as “emerging hallmarks,” but now, eleven years later, it is evident that they, much like the original six, can be considered core hallmarks of cancer, and are included as such in the current depiction." https://aacrjournals.org/cancerdiscovery/article/12/1/31/675608/Hallmarks-of-Cancer-New-DimensionsHallmarks-of?fbclid=IwAR3woOcRLSyMeNxCiHEToJJbNukst1osH4wcBf2CjLtpHcKOQJKuJOh3BhM How Cancer Shapes Evolution and How Evolution Shapes Cancer https://www.ncbi.nlm.nih.gov/pmc/articles/PMC3660034/ DNA Findings Other than oncology perhaps no other area of medicine has benefited from evolutionary principles the past few decades than the study of human genetic diseases and population genetics. Mitochondria - these are small organelles in cells that produce energy for the cell to survive and grow. They are basically only inherited matrimonially (through the mother’s egg). Biologists noted something strange about them early in the study of cytology (cells) compared to the many other cellular organelles. They have their own DNA and it’s in a circular configuration, unlike the chromosomes in the nucleus of the cell, but like bacteria. They have their own ribosomes and tRNAs and these look bacterial. Unlike other cell organelles, they have two membranes, an outer and inner. They reproduce by fission, just like bacteria. They lack the protective mechanisms found in the cell’s nucleus. For these reasons and others it became apparent that mitochondria were bacteria at one time and then were captured in the past. This theory is called the endosymbiotic theory of their origin in our cells and when approaching mitochondria diseases, this evolutionary past is important (15,16). For example, as you might expect they can be affected by antibiotics we give for bacterial infections. Mitochondria are discussed in a separate blog here.Knowing ultimate origins informs the “why" of medical aspects of disease and treatment. Many mitochondrial diseases are genetic due to various mutations (17) and current medical research to cure mitochondrial genetic diseases using CRISPR-Cas9 gene editing techniques look promising (18). This would potentially offer a cure and not just treatment. Knowing the evolutionary bacterial origin of mitochondria is important in treating mitochondrial diseases. Retroviruses - These are viruses that parasitize us differently than other viruses. In the ultimate evil to us, they insert their genetic material into our chromosomes and use the cell’s normal copying systems to instead make more copies of themselves, eventually killing the infected cells and spilling millions more viruses to invade other cells. An example is HIV, the virus that can produce AIDS if untreated. If a retrovirus inserts into a cell destined to become an egg or sperm the insertion will even be passed onto offspring. It can then spread throughout the population to the point it becomes fixed or endogenized. To the surprise of many, it turns out after the human genome was sequenced, 8% of our genome is made up of dead, fossilized retroviruses that we call endogenous retroviruses or ERVs because they no longer can make retroviral offspring. A few years later when the chimp genome was sequenced and compared to our genome, it was observed that 200,000 of these were in the exact same location and many had the exact same mutations. Since retroviruses insert randomly to DNA address (locus) in the chromosomes the only rational conclusion is that these inserted before humans and chimps split from a common ancestry (see the discussion of how this essentially proves human evolution). Common design as an explanation for similarity of DNA across the great apes is thus dead. Besides knowing the origin of ERVs and how it’s only explained rationally by evolution, ERVs are responsible for disease. We already know that some non retroviral genes can cause cancer, such as in breast and cervical cancer. Human ERV (HERV) genetic material has been found in tissue associated with Lou Gehrig’s disease, MS, and schizophrenia (19) and Kurt et. al. note that “The resulting production of envelope (env) proteins from HERV-W and HERV-K appears to engage pathophysiological pathways leading to the pathognomonic features of MS and ALS, respectively. Pathogenic HERV elements may thus provide a missing link in understanding these complex diseases. Moreover, their neutralization may represent a promising strategy to establish novel and more powerful therapeutic approaches.” (20). Many ERVs are silenced by the host using methylation and other mechanisms as a defense against them. This however, is far from a complete evaluation of ERVs and human co-evolution over millions of years. We have used parts of ERVs to our advantage and co-opted many of them for beneficial uses. For example, one env gene is necessary for producing the placenta and others have been used to help fine tune our immune system in a process called exaptation. It is estimated that 50 - 70% of our genome is derived from viral components and outside elements. Alus - our genome is full of one type of transposable element (TE) called an Alu. They constitute 10% of our genome alone. These are pieces of DNA that can jump in and out of our DNA. We have over a million copies of this TE alone. If we add up all the TE insertions, about 45% of our genome is made up of these elements that jump in and out of our genome, often causing damage. Over a 100 million years ago a gene called 7SL fused to another 7SL at the same time a retroviral infection was occurring. The retrovirus picked up this double 7SL RNA and began to make copies of it and inserting it back into the host DNA. Most of the insertions did not cause problems, but a million insertions did occasionally land into expensive DNA territory. We can identify today damaged gene alleles from Alu and other TE insertions that are responsible for such diseases as hemophilia A & B, familial hypercholesterolemia, severe combined immunodeficiency, porphyria, and Duchenne muscular dystrophy. Many other diseases such as type 2 diabetes, Alzheimer’s disease and cancers of the colon, breast, and lung are victims of genetic susceptibilities due to TE damage. In this case the genes are damaged but not completely destroyed (21). Knowing human evolution is necessary for understanding certain genetic diseases, when and how they entered our germ line and possibly how to correct or control them. Pseudogenes - It has been noted that we have about 20,000 genes that are directly involved in making “us”. These are the genes that produce proteins, commonly enzymes, that control almost everything in our cells. This only represents about 1.5% of all our DNA. Much of the rest is derived from TEs as discussed above and probably mostly “junk” DNA. Indeed, about 98% of our DNA is exactly the same as a chimp’s. But outside that 1.5% are many regulatory and other sequences in our genome that instruct when for example to make products and how long so those elements are probably what really differentiate us from other apes. Scientists have also identified thousands of genes that are damaged and not functional but look like similar normal, active genes. It is thought that there are about 20,000 of these broken, duplicated genes (pseudogenes) but functions have been found for many now that can be partially read so some state the total may be closer to about 12,000. Finlay points out that pseudogenes have always been defined by their original function and if this changed it is still a pseudogene; function does not matter. Christina Sisu notes: “Integrative analyses of cancer data have shown that pseudogenes can be transcribed and even translated, and that pseudogenic DNA, RNA, and proteins can interfere with the activity and function of key protein coding genes, acting as regulators of oncogenes and tumor suppressors. Capitalizing on the available clinical research, we are able to get an insight into the spread and variety of pseudogene biomarker and therapeutic potential. In this chapter, we describe pseudogenes that fulfill their role as diagnostic or prognostic biomarkers, both as unique elements and in collaboration with other genes or pseudogenes. We also report that the majority of prognostic pseudogenes are overexpressed and exert an oncogenic [cancer] role in colorectal, liver, lung, and gastric cancers.” Sen wrote in his paper titled “Relevance of Pseudogenes to Human Genetic Disease”: “Pseudogenes are observed to harbour sequence variations that become degenerative disease-causing mutations when transmitted to their colocalised progenitors through gene conversion event. The issue of pseudogene deregulation in several genetic diseases including cancer is now of the essence in the context of disease progression in humans. Different aspects of the involvement of pseudogenes and their relevance to human genetic disease are recaptured here… Pseudogenes can partially retain or totally resurrect their original functions. Being the paradigm of neutral evolution pseudogenes provide snapshots of the evolutionary history of the human genome. The neutral characteristic of all pseudogenic regions renders them relevant to determine the nature of neutral sequence evolution among different regions in the genome.”(23) Scientists have been using comparative pseudogene analysis for decades to look back at our evolutionary past since we share some of the same pseudogenes (same locations, same mutations) with our ape cousins and thus they confirm our evolutionary history with them. Knowing the ultimate reasons for why we have shared pseudogenes with other apes can explain the origins of some human deficiencies such as our need for vitamin C due to a shared defective gene. We even still make an egg yolk sac and have egg yolk pseudogenes, in the same homologous location as in chickens. And as Sisu writes above, it appears now many of the pseudogenes can have a role in cancer. However, both Moran and Finlay note that pseudogenes can have functions and a proper definition has been confused by more recent researchers. See pseudogenes, this site. Here again a deep dive into where this DNA damage occurred and how will help target therapies. Other examples Obesity - I wrote earlier that many people in developed countries are obese and obesity has been called a pandemic. Many are obese because food is abundant and activity can be diminished. Basically we’ve inherited survivor genes that served our ancestors well thousands of years ago when starvation was always looming but these genes for promoting eating and the efficient extraction of calories are now killing us. Researchers Salazar-Tortosa and Fernandez-Rhodes wrote about this in their 2019 article “Obesity and climate adaptation" where they note using evolutionary perspectives that include genetic changes in metabolic rates, the leptin receptor and brown adipose tissue uncoupling proteins after our ancestors left Africa to increase survivability in colder climates helps us to understand this pandemic via ultimate causes" (12). This will allow medical researchers to attack the problem from its root causes and not just apply drugs or surgery to the issue. Women’s Healthcare - Power, Michael L. et.al. write in their 2020 abstract: “Evolution is a fundamental principle in biology; however, it has been neglected in medical education. We argue that an evolutionary perspective is especially important for women’s health care providers, as selection will act strongly on reproductive parameters, and the biological costs of female reproduction are generally more resource expensive than for men (e.g. due to gestation and lactation) with greater effects on health and wellbeing. An evolutionary perspective is needed to understand antibiotic resistance, disease and health risks associated with mismatches between our evolved adaptations and current conditions, and the importance of breastmilk as a biochemical signal from mothers to their babies. We present data that obstetrician-gynecologists’ views regarding inclusion of evolution within their training is generally positive, but many barriers are perceived. Requiring coursework in evolutionary medicine prior to enrollment in medical school may be a solution.” (13) Sickle Cell Disease and Malaria - 1 million people were dying every year from malaria as of 2010, especially children. Individuals with sickle cell trait, a genetic defect, have red blood cells that are less accommodating to the Plasmodium parasite’s life stage that infects red blood cells. A homozygote normal hemoglobin (HbA/HbA) individual will suffer from malaria more than an heterozygote individual (one HbA and one HbS gene). Those who are homozygous for sickle cell trait having two HbS genes (HbS/HbS) suffer and die more frequently from sickle cell anemia and disease. Thus it is impossible to understand why sickle cell disease persists and is not removed by natural selection without understanding the evolutionary roots of the disease. In this case the carrier state, the heterozygous condition, is being selected for at the expense of the homozygous normal and homozygous sickle cell diseased individuals (14). Ancient DNA As a Tool for Medical Research - "Paleogenomics can help elucidate the genetic basis of modern diseases, including inborn errors of immunity that impair the response to infections, providing a tool for drug development... These discoveries have shed new light on the origins of human populations, their migratory history, and the extent of admixture between humans and ancient, now-extinct hominins, such as Neanderthals, and between modern human populations. However, ancient genomics is also of value for medical research, making it possible to reconstruct the history of human health over time, including past epidemics. This research allows increased understanding of the present-day links between genomic diversity and disease... It is increasingly clear that paleogenomics is a discipline of interest well beyond purely anthropological questions, as it can provide answers to questions of fundamental importance in medical research. It may be time to adopt a slightly rephrased version of Theodosius Dobzhansky’s famous phrase: “Nothing in medicine makes sense except in the light of evolution.” https://www.nature.com/articles/s41591-023-02244-4 Conclusion Anti-evolutionist medical providers have claimed that evolutionary theory has no use in modern medicine. A review of the many Centers for Evolutionary Medicine would indicate otherwise. It is true that one can practice medicine on a more superficial level without considering evolutionary principles if all that is required is a “fix it” mentality. However, in research and often in clinical settings, needing to know ultimate causes is necessary to apply or develop potential effective treatments for various human conditions and this requires an evolutionary context and lens. Ernst Mayer was correct. Numerous examples were discussed revealing the willful ignorance of those physicians who think the best medicine can be practiced without an evolutionary perspective. The study of cancer especially is incredibly illuminated and mirrors evolution, along with the newer genetic medical disciplines as Swamidass especially discusses. Citations 1. Darwin in medical school. 2009. Baker, Mitzi. Stanford Medicine Magazine. Stanford School of Medicine. https://sm.stanford.edu/archive/stanmed/2006summer/evolutionary-medicine.html 2. What is Evolutionary Medicine: Ten Questions Answered. 2016. Randolph Nesse. https://evmed.asu.edu/blog/evolutionary-medicine-top-ten-questions 3. https://www.sciencedirect.com/topics/medicine-and-dentistry/evolutionary-medicine 4. https://askabiologist.asu.edu/evolutionary-medicine-doctors 5. https://www.evmed.ucla.edu/people/ 6. https://peacefulscience.org/articles/cancer-evolution/ 7. https://www.nature.com/articles/nrc2013 8. https://www.sciencedaily.com/releases/2006/11/061117114616.htm 9. https://www.scientificamerican.com/article/how-evolution-helps-us-understand-cancer-and-control-it/ 10. https://academic.oup.com/mbe/article/37/2/320/5603308?login=false 11. https://bmcbiol.biomedcentral.com/articles/10.1186/s12915-017-0401-7 12. https://academic.oup.com/emph/article/2019/1/104/5509505?login=false 13. https://academic.oup.com/emph/article/2020/1/60/5816598?login=false 14. https://www.pnas.org/doi/pdf/10.1073/pnas.0906198106 15. https://www.nature.com/articles/d44151-022-00006-8 16. https://www.labroots.com/trending/microbiology/2279/how-bacteria-became-mitochondria 17. https://www.medicalnewstoday.com/articles/320875#disease 18. https://pubmed.ncbi.nlm.nih.gov/36275864/ 19. https://theconversation.com/humans-are-8-virus-how-the-ancient-viral-dna-in-your-genome-plays-a-role-in-human-disease-and-development-192322 20. https://pubmed.ncbi.nlm.nih.gov/20477095/ 21. Human Errors: A Panorama of Our Glitches, from Pointless Bones to Broken Genes. 2019. Lents, Nathan H. Houghton Mifflin Harcourt. 223pp. 22. https://pubmed.ncbi.nlm.nih.gov/34165724/ 23. https://onlinelibrary.wiley.com/doi/abs/10.1002/9780470015902.a0025002 24. The Cheating Cell: How Evolution Helps Us Understand Cancer and Treat It 2020. Princeton University Press. 256pp. Amazon books Summary: "When we think of the forces driving cancer, we don’t necessarily think of evolution. But evolution and cancer are closely linked because the historical processes that created life also created cancer. The Cheating Cell delves into this extraordinary relationship, and shows that by understanding cancer’s evolutionary origins, researchers can come up with more effective, revolutionary treatments. Athena Aktipis goes back billions of years to explore when unicellular forms became multicellular organisms. Within these bodies of cooperating cells, cheating ones arose, overusing resources and replicating out of control, giving rise to cancer. Aktipis illustrates how evolution has paved the way for cancer’s ubiquity, and why it will exist as long as multicellular life does. Even so, she argues, this doesn’t mean we should give up on treating cancer―in fact, evolutionary approaches offer new and promising options for the disease’s prevention and treatments that aim at long-term management rather than simple eradication. Looking across species―from sponges and cacti to dogs and elephants―we are discovering new mechanisms of tumor suppression and the many ways that multicellular life-forms have evolved to keep cancer under control. By accepting that cancer is a part of our biological past, present, and future―and that we cannot win a war against evolution―treatments can become smarter, more strategic, and more humane. Unifying the latest research from biology, ecology, medicine, and social science, The Cheating Cell challenges us to rethink cancer’s fundamental nature and our relationship to it."

“Expanses of duplicated DNA are situated around our genomes…Genome science has revealed that 5% of our genome is composed of large duplicated segments of DNA or segmented duplications (SDs). Each such duplication that is a common genomic character of our species must have occurred in an ancestor that was common to us all… Any duplicon [a duplicated unit] shared with another species establishes common ancestry” ~ Graeme Finlay Introduction New genes arise naturally. It happens all the time. Where can we find that? In the labs of cell biologists and medical centers with cancer researchers for one thing. Also, other studies have shown that new genes arise with new functions and some de novo. Many of these scientists are Christians and evangelicals; Graeme Finlay, Joshua Swamidass and Francis Collins are examples. It turns out we can prove new genes arise, take on new functions and even develop novel gain of function because cancer tumors begin as a single rogue mutated cell that must evade the immune system and develop novel, new genes in a complex sequential manner in order to survive and grow into tumors of millions of cells. The ability to spread (metastasize) involves many new functions and genes not present in the original normal cell. And this has been demonstrated to happen through random mutations and natural selection, exactly how biologists have demonstrated evolution. See the blog on Evolutionary Medicine, the Cancer section where the Christian and evangelical Swamidass details this. Gene Duplications Biologists have documented for decades that the genomes of animals and plants contain large chunks of duplicated DNA. The human genome contains about 3 billion base pairs and only about 20,000 protein coding genes. That represents only about 1.5% of our genome. Many other genes including regulatory, promoters, inhibitory and enhancer genes are found outside this 1.5%. But the vast majority of that other DNA is derived from viral infections, duplications and jumping genes. They usually represent junk that travels with us. That most of our genome is junk DNA has powerful evidence. See blogs here about pseudogenes as an example of junk DNA that has accumulated in our genome over millions of years often due to duplications and how when shared between species they rise to the level of proof for human evolution. Many have been co-opted for functions and some even have developed new functions, something that most anti-evolutionists claim can’t happen. The Type IA form of Charcot-Marie-Tooth disease is an inherited genetic disease caused by a gene duplication in chromosome 17 resulting in too much production of a protein called PMP22 (1). Ice Fish have a gene that functions as antifreeze that is a duplication of a digestive gene and then evolved a new function. If complexity in organisms were correlated with genome size - which is a prediction of anti-evolutionists since they insist usually that there is no such thing as junk DNA - it is impossible or difficult for them to explain why a species of amoeba has 200x the amount of DNA as humans, or some species of salamanders 100x, or even an onion species with 10x the amount of DNA as humans (Prothero/Shermer debate vs Meyer/Sternberg, 2015). Why would you need that many genes compared to humans to make an onion? This actually has a name as a challenge for anti-evolutionists; The Onion Test (4). Indeed it’s common to find plant species where their chromosomes have undergone complete whole genome wide duplication and not just once. This is called polyploidy in plants and is common. It’s importance is that these duplicated sections are no longer under stabilizing selection pressures since they are just copies. Mutations are often not corrected and the genes are allowed to evolve into new genes or to degrade and become pseudogenes. “The prevalence and recurrence of polyploidization in plant species make it one of the most important evolutionary events in plants, and as a result, polyploidization is an extensively investigated research field. Due to the rapid development of sequencing technologies, there is increased evidence to support that polyploidization plays an important role in the diversification of plant species, evolution of genes, and the domestication of crops…The occurrence of many independent polyploidization events in plants was found to be tightly associated with the timing of extreme climate events or natural disasters on earth, leading to mass extinctions while possibly facilitating increased polyploidization… Moreover, polyploidization was found to significantly impact species diversification, with subsequent effects on crop domestication and the development of traits with agronomic importance”(2). Copy Number Variants Humans contain many genes that have been copied. Genomic analysis has revealed 11,700 locations in our genomes. Any two people differ at about 1,100 of these and nearly 1,000 variable locations involving more than 50,000 bases have been found. Out of 385 olfactory receptor genes, any two humans can vary in the number of copies we have. Same for taste receptor genes and the number of opsin genes (for vision) we have (3). In other words, individuals can vary slightly in how we smell, taste and see because we all vary in the number of receptor genes we have making sensory receptors. A clear example is in the salivary amylase gene, which begins breaking down carbohydrates (starch) in our mouth. Amylase is also produced by our pancreas. I have a confession; while in training on a few occasions I would send a single amylase test for a patient with an inflammation of their parotid gland to see if it could help show an infection vs a blocked salivary duct vs a tumor perhaps not producing a lot of inflammation. I knew that a high level would result in an emergency notice to a sleeping resident on call because the lab would assume it was due to potentially life threatening pancreatitis. This would result in an unhappy resident as they are pulled out of bed only to find it had nothing to do with pancreatitis. There are ways to differentiate the two sources, including combining it with another blood test like a lipase level or even an isoamylase test, but the latter was not available to me and I purposely skipped combining it with a lipase level (another pancreatic enzyme). Anyway, it turns out that our copy number of this gene can matter. People with more copies digest starch better and individuals of European and Japanese descent have higher number of copies of AMY1 genes than those of African descent. Having more AMY1 gene copies lowers insulin levels via accelerated digestion of starches and reduces the chances of developing insulin resistance and diabetes (3). Segmental Duplications (SDs) In the previous section, it was shown that genes are often copied and duplicated. This can be advantageous as new genes and functions can arise through mutation and selection. Scientists studying animals that live long but yet don’t develop cancer often for example have found one reason is because they have more copies of tumor suppressor genes (elephants and the TP53 gene). It turns out that our genome contains also a huge number of copied large chunks of DNA segments containing genes that are shared by all of us, in contrast to various copy number in different human groups and individuals. About 5% of our 3 billion base pairs represent large duplicated DNA segments called segmental duplications (SDs). Recall that 8% of our genome is made up of ERVs that originally were placed randomly millions of years ago by retroviral infections. See ERVs. SDs have been defined as copies of large sections of DNA (> than 1,000 bases) that show a greater than 90% similarity with copies (3). These copies can even be found on different chromosomes or crammed into areas near centromere or telomere repeats. When these large blocks of duplications occur, they can destabilize genomes, cause genetic diseases, can duplicate genes within them and because they are unique and can be found to be shared across species, comparing them can support evolution to the level of proof (3). Finlay notes the following examples: Scientists have found that a large fragment of chromosome 1 (100,000 bases long) has been copied and pasted onto the Y chromosome in humans, chimps and bonobos. It is not present in gorillas, orangutans, gibbons or old world monkeys however. Duplicate segments on human chromosome 17 are 24,000 bases long and flank a 1.5 million base region that contains the PMP22 gene. The duplicated segments cause genetic instability and results in a neurological disease. In part of the CD8B1 gene, the first seven of the nine exons [these are the parts left over that are spliced together after the introns are cut out during transcription processing] has been duplicated as a truncated pseudogene that is present in humans, chimps and gorillas but not orangutans. One end of the duplicated segment has a breakpoint precisely in the same spot in each species having the pseudogene. A segment of DNA 76,000 bases long has been copied from chromosome 9 to chromosome 22, promoting mis-pairing of the chromosomes during cell reproduction and promoting a translocation between the two chromosomes that generates two genes fusing to form a chimeric BCR-ABL fusion gene that is a cause of a type of leukemia (CML). “The paired blocks of DNA are found in the genomes of humans, chimps and gorillas but not of orangutans or monkeys, indicating that the duplication event occurred in an ancestor of the African great apes.” (3) We have a cancer suppressor gene called CHEK2. It is located on chromosome 22 but part of it has been duplicated and inserted into chromosome 16. This event occurred in an ancestor of the great apes because humans, chimps, gorillas and orangutans all have this large duplicated segment. It underwent further duplication; in humans, five of the duplications are interrupted by a particular LINE-1 element, and in two of these cases a corresponding chimp duplicon (SD section) exists (3). These are but a few of thousands of SDs discovered. As Finlay notes, “Duplications of huge tracts of DNA arise as an inevitable outcome of the biochemical nature of DNA and of the enzymatic systems that maintain it. The presence of a particular, randomly arising duplication in multiple cells or in multiple species indicates that those cells or species are monoclonal, descendants of the cell in which the unique structure arose.” The fact that these duplications are unique events and are shared by some of the great apes but not others means we can use them to see if there is a repeatable pattern to their distribution across primate species. "Of all the bases present in SDs in the human genome, approximately 2/3rds are shared with chimps, and were already present in the genome belonging to the ancestors of humans and chimps. Some of these SDs are concentrated near telomeres, and these tend to be younger than SDs found elsewhere. Accordingly, a lower proportion of the telomeric SD’s (50% instead of 66%) is shared by humans and chimps." (3). What all this means If you have hopefully been following along you’ve seen the gene duplications are common. Sometimes they are in large segments of DNA that are copied called SDs (segmental duplications) and these chunks can be in many places in the genomes from next to their original source, to near telomeres and centromeres which involve lots of repeat DNA, to even different chromosomes. "High quality sequence data have allowed the comparison of SDs at single base resolution. The rigorous analysis has confirmed that some SDs are shared by humans and chimps, others by humans, chimps and gorillas and still others by humans, the other great apes and also with old world monkeys such as baboons" (3). If we just simply note which SDs are shared by which groups of primates we can test evolution. Hundreds of SDs have been noted and they generate a primate family tree that is identical to other DNA markers’ trees such as ERVs, DNA repair patches and pseudogenes discussed in the other blogs and sections on this site. If we just compare many SDs and note which are shared between primate groups a family tree based on shared SDs is produced. If evolution was not true a phylogenetic tree could not be produced like this, let alone scores of them using independently derived observations. See Figure 1. Figure 1. Shared Segmental Duplications (SDs) between primate groups. Numerals indicate the numbers of duplication events and when they occurred. See text. From: Finlay, Graeme. 2013. Human Evolution: Genes, Genealogies and Phylogenies. p 204. Figure 4.2. Cambridge University Press. 2021 ed. Social sharing and Fair dealing applied per publisher's web instructions. For example, in Figure 1 above 133 segmental duplications unique to humans have been found. In humans and chimps/bonobos 121 SDs have been found to be shared. Gorillas, chimps and humans have 220 SDs in common. If evolution were not true we could not put together an evolutionary tree from SDs that matched the fossil record, and also the trees produced by shared ERVs, DNA repairs, and pseudogenes. The concept where independent lines of evidence come together and jump towards a firm conclusion is called consilience. We can also approach the same test of evolution with SDs by looking at a single duplication that has kept duplicating, called an expansion. One gene that duplicated more than once can be evaluated in different species. If evolution is true we should find the most recent duplications in species in the newer species and the more recent species should have more copies. And that's exactly what we do find. See Figure 2. Figure 2. Expansion of the SPANX gene family through primate evolution. Gene content is depicted to the right of the phylogenetic tree: X chromosome (thick line), centromere (oval), SPANX genes (open boxes). SPANX-N genes (N), SPANX-N5 (N5), And SPANX-B,C, A1, A2, and D (B, C, A, and D). OWM = Old World Monkeys. See text below. From: Finlay, Graeme. 2013. Human Evolution: Genes, Genealogies and Phylogenies. p 212. Figure 4.6. Cambridge University Press. 2021 ed. Social sharing and Fair dealing applied per publisher's web instructions. The SPANX genes are located on the X chromosome and are largely active in the testes producing a protein in sperm cells. They also can cause premature ovarian failure in women lacking or having damaged genes. This is how Finlay describes the finding of these genes across species. Refer to Figure 2: "In non-primate mammals such as dogs and rodents, a single SPANX-N gene is found located on the long arm of the X chromosome. Primates, in contrast, possess multiple SPANX genes. The gene family has expanded in a stepwise manner through primate history, and the rate has accelerated especially in the great apes. The original SPANX-N gene underwent two duplications in an ancestor of the apes and OWMs (which share three SPANX-N genes), and another duplication in an ancestor of the great apes (which share four SPANX-N genes). Further duplications occurred in the linage giving rise to the African great apes. These species share an additional five genes. These are SPANX-A1, A2, B, and D on the long arm of the X chromosome. Finally, humans have acquired a further gene (SPANX-C) and up to 14 copies of SPANX-B. The flanking and intronic sequences of the SPANX-A to D genes are very similar to each other, indicating that they are located on segmental duplications approximately 20,000 bases long." (3) For those with more knowledge of DNA genomics and perhaps a glutton for evolution DNA punishment, LOL there is a little more regarding the SPANX family of duplicated genes. This is not needed to understand the basic concept of how shared duplications demonstrate evolution to near proof but is featured as an example of how much these scientists know about the genome and the findings that prove human evolution. Reading my blogs on ERVs and DNA repairs would be very helpful if interested. He goes on to note: " The mechanism by which the SPANX-C gene arose has been elucidated. A DNA break occurred in an L1PA7 element [a retrotransposon] that was located some considerable distance upstream of SPANX-B. A segment of DNA (containing SPANX-B) was imported to join the broken ends, and this was selected on the basis of close similarity between the broken L1PA7 element and an L1PA4 element upstream of SPANX-B. The reorganized locus has features of a repair job performed by a non-homologous end-joining (NHEJ). The product contains a chimaeric LINE-1 element, the brand new SPANX-C gene and a chimaeric LTR1B/LIPA7 element." DNA breaks and repairs that are shared between species are powerful evidence of evolution. See my blog on shared DNA repairs here to begin to understand what he is saying and the power of these observations to prove evolution. LINE-1s are a type of jumping gene that randomly inserts into DNA. LTRs are promoters inserted into DNA by retroviruses and are discussed in my ERV section. Conclusion When studying human and the other great ape genomes it was discovered that there are many duplicated genes and many large segments that have been duplicated. We can study the genomes of many species including humans and compare these duplications. When we find the same duplications, defined as greater than 90% of the exact same DNA sequences (ATCG nucleotides) we can be certain that they are indeed the same and represent copies. The only way to have the same duplications at the same chromosomal homologous locations between species is they had to have inherited them from a common ancestor. There is no other rational explanation. Numerous shared duplications can be summed into groups and a phylogenetic tree is produced showing shared common ancestry. The evolutionary phylogenetic trees of segmental duplications match the trees produced by paleontology and the other DNA markers including ERVs, DNA breaks/repairs, pseudogenes, and retroelements. That the same confirming results are produced by independent areas of research means the possibility of evolution being wrong by DNA findings must be essentially zero and represents strong consilience. In addition, some duplicons continued to make copies and within a single family of duplications the number of duplicated copies increases in newer species, as predicted by evolution, and can be nested to form another evolutionary tree from the DNA raw data. As new duplications arise the more recent copies are also found closer to newer species. The comparative segmental DNA duplication findings between primates represents some of the best and most solid evidence we have for human evolution, "macroevolution", and rises to the level of proof in my opinion. References and Citations 1. https://www.genome.gov/genetics-glossary/Duplication 2. https://www.sciencedirect.com/science/article/pii/S2468014119301980 3. Finlay, Graeme. 2021. Human Evolution: Genes, Genealogies, and Phylogenies. Cambridge University Press. 359 pp. Paperback edition. 4. The Onion Test. https://www.genomicron.evolverzone.com/2007/04/onion-test.html

"Supposedly, summer vacation happens because that's when the kids are home from school, although having the kids home from school is no vacation. And supposedly the kids are home from school because of some vestigial throwback to our agricultural past" ~ P.J. O'Rourke Introduction That the term vestigial has been and is currently being misused is supremely unfortunate. The definition of “ without function” is only half correct. The correct definition is without function, diminished function, or the loss of the original function.  Compounding this many scientists are also unaware of the exact definition.  As will be demonstrated, this has been the correct concept for many decades and applies at the anatomical and genetic levels. It is especially unfortunate that even biology textbooks have not used a proper definition. This issue is similar to the misuse and confusion over the terms atheism and theory in many cultures.  Dictionaries are often of no help in clarifying because their primary function is usage and not delineating best or correct utilization. “The writer of a dictionary is a historian, not a lawgiver. . . To regard the dictionary as an 'authority,' therefore, is to credit the dictionary writer with gifts of prophecy which neither he nor anyone else possesses.” https://www.thoughtco.com/what-is-a-dictionary-1690450 First, if one looks at better definitions of the term we can see that without function or without the original function not only is the more accurate definition but it goes back at least to the 1960’s. This is not a dodge by evolutionary biologists, who have always looked at the concept of vestigial this way. For example: 1. Vestigial structures are those that appear in a rudimentary form in some organisms but in a fully developed, functional form in other, closely related animals; or they are poorly developed structures thought to have been fully functional in ancestors of the modern form (pg. 777) ~ Biology by Leland Johnson 1983 2. [Vestigial] - refers to an organ or part which is greatly reduced from the original ancestral form and is no longer functional or is of reduced or altered function. ~ www.biologyonline.com 3. Vestigial - a degenerate or imperfectly developed organ or structure that has little or no utility, but in an earlier stage of the individual or in preceding evolutionary forms of the organism performed a useful function ~ www.dictionary.com 4. Vestigial - (of certain organs or parts of organs) having attained a simple structure and reduced size and function during the evolution of the species: the vestigial pelvic girdle of a snake ~ Collins English Dictionary, 2014. 5. Vestige - a small, imperfectly developed, or degenerate structure which represents an organ or structure which was fully developed and functional in an ancestor or in an earlier state of development. ~ Dictionary of Biology, Edwin Steen. 1971 Secondly, it clarifies much regarding evolution and what we see in nature. A few examples will be discussed that show the loss of original function applies to many of the structures and facts we observe in nature. 1. The pelvis of modern cetaceans (whales and dolphins) are vestigial. We know this because the entire fossil record shows it changing from associated with a small 4 legged terrestrial animal to the vestigial bone today. Anatomists can identify within the modern whale vestigial pelvis what represents the ischium, ilium, and other pelvic structures. All the atrophied muscles and other structures are still attached in modern cetaceans but at least in males in terms of copulation the vestigial pelvis still has some functions. But they sure can’t walk with them.The current tiny vestigial pelvis sits outside the vertebra and is not attached to any bones. See Figure 1. Figure 1a: Modern whale tiny vestigial pelvises showing anatomical structures that were previously only useful for walking. Several have vestigal femurs and all are not attached to the spinal cord. For educational purposes only. Fair use attribution From: www.http://um.uib.no/fagsider/osteologi/hvaler/b_bekken.htm Figure 1b shows the evolutionary shrunken hind limbs of the fossil Basilosaurid that lived 37 - 40 million years ago (left) compared to a modern Right Whale's vestigial hind limbs (right). Figure 1b. Left = Basilosaurid fossil whale species showing actual size of vestigial pelvis. NOTE ARROW. Magnified view shows bones used for walking. Right = photograph of actual living Right whale vestigial leg bones. From: https://faculty.msj.edu.kritskg/evolab/Site/Vestigial_structures.html Fair use, for educational use only. B. The appendix has been shown to have functions in terms of repopulating the intestinal flora after severe diarrhea and it also contains lymphatic tissue. But the shape and location of the structure indicates it probably served other primary purposes in the past. It is officially called the “vermiform appendix” because in some people it’s very long like a worm and can loop back towards the liver behind the cecum. Not an efficient design for repopulating the gut after a wash out of severe diarrhea. Having a function today does not invalidate it being vestigial. See Figure 2. Figure 2. Diagram of human vermiform appendix. From: Henry Vandyke Carter, Public domain, via Wikimedia Commons C. Pseudogenes are genes we share with other species that have been disabled and knocked out by various mutations. By noting which pseudogenes are shared between species and which are not we can even construct evolutionary phylogenetic trees that rise to the level of proof of macroevolution (see pseudogenes, this site). We have about 20,000 pseudogenes and some have functions. Some are only partially transcribed whereas others have even taken on new functions. They still are vestigial even if they are partially transcribed or have acquired new functions because they have lost their original functions. Finlay notes, 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" ... and "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." (1)  A few pseudogenes have been noted to exhibit gain of function as noncoding RNAs. (2) Moran notes: “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... 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.” (3) If so disabled that they have lost all functions they are basically molecular fossils. If they are shared with the same random knock-out mutations between species we are justified in claiming common ancestry as the only rational explanation. For examples and discussion see pseudogenes this site. D. The coccyx is vestigial. It obviously looks like a shrunken tail because it has 5 small bones. It still supports some attachments but it’s small enough that if a Designer didn’t want to make it look like a shrunken tail from our past ape descendants why not just use one or at the most two bones? Since it still has muscles and other tissues attached it still plays a small role in human anatomy, but not it's original function. Figure 3. Diagram of the human coccyx showing how this small bone is really a shrunken remnant of a tail. Functionality is not critical to the vestigial designation. The bone is small enough that one or two bones could easily suffice to be functional instead of having the appearance of 5 fusions. E. Yolk sac . As an embryo we make an empty yolk sac that is vestigial. It still has important functions today such as providing lymphatic and blood cell precursors for the developing embryo but no yolk is produced. Yet it is indeed called a yolk sac because that's what it resembles in other animals that lay eggs. More conclusively, scientists have found 3 human yolk pseudogenes that match the same genes and locations in chickens. We do indeed hark back in deep evolutionary time to a point where our ancestors laid eggs and we have the structure and genes to demonstrate it. Our temporary yolk sac no longer has the function it had in the past and is vestigial. See Figure 4. Figure 4. Human yolk sac which begins development in the embryonic stage and then disappears about the 3rd month. It has important functions but has lost its original evolutionary function. For attribution and additional information, see Why Not Intelligent Design?. Figure 5. Diagram showing three human egg yolk pseudogenes (VIT 1, 2, 3) found also in homologous locations in chickens. Conclusive evidence that the human yolk sac is vestigial, having lost it's original function. For attribution and additional information, see Why Not Intelligent Design?. Third, sometimes a modern species will form an atavistic structure. The DNA is still present to form most of an ancient structure and becomes accidentally turned on. This exposes the ancient connection to it’s past ancestors. These are technically not a vestigial structure because they are uncommon or rare; obviously every individual of the species does not have them, unlike vestigial structures. Notice the decapitated snake in Figure 5. It accidentally grew a leg. It was beaten to death by a homeowner in China, who thought it was trying to crawl up a wall. Notice the leg grew at about the anatomical location we would expect. It did not grow a feather and it did not grow elsewhere like a HOX gene mistake. It grew where an evolutionary ancestor would have had a leg. Figure 5. Atavistic snake leg. From: http://pleiotropy.fieldofscience.com Also: Evolutionary throwback. Snake with foot. Gizmodo.com. 2009, Sept. 15 About 1:5,000 sperm whales grow hind limbs. The DNA instructions for doing that are still present but damaged and normally not expressed. At least six cases are known of whales being caught with hind legs growing. A dolphin was caught in 2006 off the coast of Japan with hind flippers. See Figure 6. Figure 6. Left - a dissected sperm whale atavistic hind limb exposing a femur, tibia and metatarsal caught in 1919 off the coast of British Columbia. Right - a photo of hind flippers growing from a dolphin caught near Japan in 2006. For more discussion of cetacean leg atavisms and attribution see Overwhelming Evidence for Whale Evolution, this site Part 1 Conclusion The proper definition of vestigial is loss of function, diminished function or loss of original function. Repeatedly anti-evolutionists will claim "checkmate" when a function is found for a structure or gene. The finding of a function does not discount that a form can be vestigial. That this complete definition for vestigial is nothing new was demonstrated. It is unfortunate that even within the sciences researchers and teachers may be communicating a wrong concept of vestigial. The actual definition as defined here of vestigial applies not only to structures but also down to the molecular and genetic level and has resulted in unnecessary controversy more recently over pseudogenes in the field of genetics, where some claim there is no junk DNA and few or no pseudogenes (see Junk DNA, this site for example). Vestigial structures, which are present in each individual in a population, were contrasted with atavisms which are rare occurrence of structures that hark back to appropriate evolutionary ancestry. Whales can grow hind limbs but never feathers. Boas and pythons have a vestigial pelvis with rudimentary femurs that are used in courtship which in no way negates them as being vestigial since the original function of the structures was for walking. Citations 1. Finlay, Graeme. 2021. 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. Hardback edition 2013. 2. https://onlinelibrary.wiley.com/doi/abs/10.1002/9780470015902.a0020836.pub2 3. https://sandwalk.blogspot.com/2020/01/are-pseudogenes-really-pseudogenes.html#more

“It is generally stated that half of our genome is derived from ERVs and TEs. The application of more-sophisticated software allows the identification of more degenerated (fragmented) TEs has raised this estimate to two-thirds of our genome. TEs have expanded, modified, and elaborated our ancestors’ genomes at least as far back as genetic analysis can detect.” ~ Graeme Finlay, Human Evolution: Genes, Genealogies, and Phylogenies. 2013. Introduction The year 1953 was an incredible year for biology. A paper by Watson and Crick was published that finally ended the search for the source of heredity and cell functioning for all living things. Proteins, the early candidate, had been toppled by DNA. No one could imagine initially that a molecule with only four nucleotide bases - A,T,C,G - could be the holder of the instructions for life. Shown without her knowledge, Rosalind Franklin’s photograph of DNA helped Francis and Crick put one of the final pieces of the puzzle in place. Watson, Crick and Wilkins later received the Nobel Prize in Physiology or Medicine in 1962 for the discovery that DNA encoded the genetic information for life. DNA was thought by many to be like a blueprint, locked away safely in the nucleus. Messenger RNA (mRNA) would make a copy of one side of the unzipped double helix master code and then the mRNA would travel outside of the nucleus to the ribosome factories to help assemble proteins. Perhaps you also have thought of DNA as a master blueprint. Decades later as scientists studied DNA more closely one of those scientists, Barbara McClintock, shocked the world when she demonstrated that large amounts of DNA jumped around randomly copying and pasting back into the DNA, often causing disabled genes. Genomes were not this rigid instruction blueprint as imagined. Indeed, the corn she was studying was made up a whopping 90% of these mobile DNA segments. Humans were found to have nearly 50% of our 3 billion DNA nucleotides made up these mobile elements alone, called transposable elements or TEs. (1) Transposable Elements (TEs) There are over 1,000 different types of TEs, or jumping genes, and about 50% of our genome is made of them but there are only two basic categories of TEs. DNA transposons and ones that use RNA as an intermediate, and are called retrotransposons. No, the retro does not refer to 1960’s bright plastic furniture or 1970’s colors of gold and green. This latter variety must convert their RNA to DNA so it can be randomly spliced into the DNA genome rather than the normal route of DNA to RNA to proteins. The DNA transposons only represent about 2% of our genome and won’t be discussed since they are not necessary to establish evolution (2). The more common retrotransposon TEs are represented by several types important to our discussion. One type makes up 8% of our genome and includes the endogenous retroviruses (ERVs) that were discussed in a section on this site. They are fantastic evidence for evolution and common ancestry by themselves. ERVs have 3 major viral genes (gag, pol, env) for producing their nasty retroviral cellular parasites; an example is the retrovirus HIV that can produce AIDS. Some have lost the env gene and are called LTR-retrotransposons. As was discussed in the section on ERVs, ERVs are fossilized by mutations and the retroviruses are no longer able to produce infectious particles. Most are so degraded only their LTRs are left behind. But initially they were inserted randomly by retroviruses, and if we find thousands of the same ERVs in the same locations between species the only rational conclusion is shared ancestry - evolution. They must have inserted before the species split. The LTRs are made by the viruses before insertion since they will need promoters to get transcription started to make new viral progeny during an infection. Most retrotransposon varieties however do not have an LTR attached and are non-LTR retroelements. Two are especially important for our purposes here. LINEs are long elements of about 6,000 base pairs and SINEs are short and only about 300 bases long. The most common SINE are called Alu elements, named after the bacteria Arthrobacter luteus where their enzyme product was studied. LINE-1 elements alone make up a staggering 17% of the human genome (626,000) and Alus another 11% (1.1 million). There are also L-1 and L-2 retroposons in our genome for another 340,000 (2). Thus LINE-1s, Alus, and LTR retrotransposons alone make up 36% of the human genome! Considering humans have only 25,000 genes and 20,000 protein coding genes make up only 1.5% of our genome, the 50% of our genome that are retrotransposons is amazing. Much of the TE’s are selfish jumping DNA that cause disease when they land and disable genes or adversely affect them. But nature through shared interspecies TEs has supplied us with rock solid evidence for evolution because when they move they insert randomly and since we find thousands of them in identical homologous locations (called loci) in the genomes of different species, we have evidence for evolution that rises to the level of proof. Indeed, “macroevolution” level proof. These shared TEs must have inserted before then species split. And yes technically science rarely if ever proves - but evidence can be amassed to such a level that to deny a conclusion is perverse. Fortunately, most have lost the ability to move but for millions of years many did, leaving a record that can only be rationally explained by evolution. 1. LINE-1 Elements As with other retrotransposons when LINE elements land in genes they often disrupt them. A LINE-1 that is found in an exon (active part) of a gene called the APC gene, a tumor suppressor gene, together with other mutations inactivated the gene; it is not working in 80% of all human colon cancers. A canine tumor (CTVT) has a LINE-1 element inserted near an important proto-oncogene. LINE-1s insert like ERVs insert (2). Recall that retroelements copy and then randomly paste themselves back into the DNA. Of the approximately 600,000 LINE-1 elements in the human genome all but 2,000 are shared exactly with chimps and bonobos. As with ERVs, this means that over 99% of the LINE-1s in our genome have exact matches by location and ATCG sequences with chimps. Our genomes share all LINE-1 elements with gorillas except for 1,860. Some LINE-1 elements on rare occasions will grab a random RNA segment and then make a two-component element with the usual LINE-1 portion and an ‘innocent bystander RNA” (2). This results in a very unique LINE-1, a chimeric retrotransposon that have been found in human genomes and are especially solid evidence for evolution since they produce very unique shared markers also present between species; a common ancestor is the only rational conclusion. Not only can we find thousands of the same retrotransposons in the same genomic positions between species establishing evolution because they insert randomly and must have done so before the species split, but some are shared by some species and some not. If we collect hundreds and note which are shared between and which are not a pattern is produced that shows evolution in remarkable detail. Using molecular clock calculations we can also determine when the species split and compare those results to the paleontology (fossil) data. The data cries out evolution because there is so much of it across so many independent areas of science. In the case of DNA findings it rises to the level of proof of even macroevolution. Notice that this evidence for evolution is independent from function or not. More will be said about function. See Figure 1 below: Figure 1. Various LINE-1 insertions entered into the Primate Germ line, from their presence or absence in the genomes of primate species. LINE-1 elements: Open boxes. Chimeric inserts = grey boxes. Numbers indicate the number of individual inserts mapped. See text for discussion. From: Finlay, Graeme. 2021. Human Evolution: Genes, Genealogies and Phylogenies. p 85. Figure 2.5. Cambridge University Press. Social sharing and Fair dealing applied per publisher's web instructions. Paperback edition. 2. Alu Elements The origin of most retroelements have been lost in deep time. We do know however how Alus arose. Millions of years ago a gene called 7SL gene, important in signal recognition, fused to form a double DNA piece (called A and B sides) with a short section of an A-rich region between. It has an internal RNA promoter. Each Alu is unique in terms of accumulated mutations, the length, and the 3’ end. (3). Alus are only found in primates so we can determine evolutionarily about when primate evolution occurred. Of the 1.1 million Alus in the human genome, all but 7,000 are shared by chimps and bonobos. That again is greater than 99% shared Alus. Only a few thousand Alus in the human genome are not found in gorillas, establishing that Alus demonstrate the African great ape ancestor also had 99% of the Alu elements that humans, chimps and gorillas have. The only rational explanation is that these Alus must have copied and pasted back into the DNA in a common ancestor to the great apes. As in LINE-1s, some are shared by all primates and some by only some. By just collecting these raw observations one can produce an evolutionary phylogenetic tree demonstrating primate evolution, which most people would describe as “macroevolution” since it involves so many primate species, from macaques to humans. Out of the 1.1 million Alus found in humans, all are shared by orangutans except for 250, establishing a common ancestor between humans and orangutans. (2). Figure 2 shows an Alu insert into the HPRT gene found in multiple species including humans, chimps and gorillas but not other primates establishing evolutionary relationships. Notice the target site of [GAATGTTGTGA] where the insert happened and how the target site was duplicated and placed on either side of the changed DNA, confirming the insertion. Inactivation of this gene produces Lesch-Nyhan syndrome, a condition in children that produces gout, mental retardation, and self mutilation (2). Figure 2. The insertion of an Alu element in the HPRT gene. From: Finlay, Graeme. 2021. Human Evolution: Genes, Genealogies and Phylogenies. p 90. Figure 2.7. Cambridge University Press. Social sharing and Fair dealing applied per publisher's web instructions. Paperback edition. See text for discussion. Below in Figure 3 is the distribution of many Alu elements in various primate genomes. By simply noting which are shared by what groups an evolutionary phylogenetic tree is produced. This transposon evidence for evolution not only agrees with thousands of other DNA trees produced by shared ERVs, shared duplications, shared DNA breaks/repairs, and shared pseudogenes but also agrees with evolutionary trees produced by fossil observations (paleontology). Figure 3. Distribution of various Alu elements in primate genomes. Check marks and circles indicate presence and absence of particular inserts. Shading corresponds to the shading of the boxes and arrows, indicating when the Alu elements were added to the primate germ line. From: Finlay, Graeme. 2021. Human Evolution: Genes, Genealogies and Phylogenies. p 91. Figure 2.9. Cambridge University Press. Social sharing and Fair dealing applied per publisher's web instructions. Paperback edition. Are the insertions really random? Yes, they are. Turns out that LINE-1s and Alus do have some site preferences, but still not exact site insertion locations, or loci (4). Looking at any figures such as Figure 2, we can see that when they insert into a target site in the DNA, that area is duplicated on either side of the target, called Target Site Duplications (TSDs). Thus, we can find LINE-1s and Alus not only by their signatures but also by these TSDs. They are not original to the DNA. The idea that millions of TEs would randomly insert in the same exact genomic locations between species is mathematically impossible. What about hot spots? TEs do have preferences for insertions. They tend to insert around genes and also some prefer to insert into existing TEs. But these are preferences and not exclusive to the exact loci. As an analogy, there are car accident hot spots in cities where car accidents are more prone, but they are still accidents and each one is unique. Some cities have large numbers of people moving to them but they don’t all move onto the same street and certainly not into the same house. In neurofibromatosis type 1 the NF1 gene is mutated. “…of all the NF1 mutations, 0.4% are caused by retrotransposon insertions. In one study, 18 TE insertion mutations were identified in unrelated people, and six of these were clustered in a region of 1,500 bases. Three insertion sites were used twice…of the three sites that were targeted twice, all could be shown to be independent events… the TSDs were of different lengths, the initial cleavage events were on opposite strands of the DNA, or Alu elements of different sub-families were involved.”(2). In one study, 500 LINE-1 elements associated with the human genome were studied. In any other species did any LINE-1 element insert into any of those 500 sites? Not a single one. (2). Studies with Alu elements have also shown the same result. Human specific Alus were studied and “in no case was an Alu element characteristic of sub-families belonging to other species found in the same site as the human insert… It has been concluded that ‘no instances of insertion homoplasy in hominids have been recovered from the analysis of >2,500 recently inserted human Alu insertions’ (2). Exceptions: Incomplete Linkage Sorting It turns out that when comparing genomes there are many exceptions to the clustering of inserts into evolutionary phylogenetic trees. As an example, TEs have been found to be inserted into gorillas and humans but not chimps. Doesn’t this invalidate using TEs or other DNA changes as 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 a particular gene 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 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 (6). 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. Macroevolution deeper in time You may have noticed that the few examples I’ve extracted from Finlay’s book are primate centered. Perhaps you are wondering if these jumping TEs can be traced further back in time to show evolution earlier with even more distant shared common ancestors, like those evolutionary trees that scientists have produced through anatomy and fossils - a tree of life or more accurately a bush of life? And the answer is yes. Of course after millions of years TEs have become so degraded that there are limits. After the mouse genome was sequenced it was compared to our genome and studies showed there were large numbers of shared TEs. In particular LTR, LINE-1, LINE-2 and MIR (mammalian repeat) elements. “In a DNA segment encompassing 1 million DNA bases from the two species, 13 LINE-2 and 30 MIR elements were shown to be shared…inherited from the ancestor in which each element entered the DNA” (2). Finlay notes: “Computational searches have identified five TEs that are shared by primates and tree shrews, and in one case, by the flying lemur. These are all absent from rodents. On the one hand nine TEs were found to be shared by rodents and rabbits but are absent from primates. Primates, tree shrews, and flying lemurs form one monophyletic group; rodents, rabbits comprise another. But ultimately, we and the mice in the garden share many TEs each which arose in the genome of a Euarchontoglires [a clade and superorder of mammals that groups rodents, rabbits, primates and a few others based on TEs] ancestor” (2, pg. 105). Multi-species genomic comparisons have found several well-preserved TEs that corroborate shared ancestry in many species. One is an insertion site of a L1MB3 element. Humans share this TE with cows, horses, cats, dogs, bats and shrews. The degenerated undisturbed target site TACCTGGGAAACTTT is duplicated from the insertion on either side of the L1MB3 transposon (2). “As an illustrative example, an ancient MIR element in an intron of the beta-fibrinogen gene as been identified in the genomes of 22 species (Figure 4 below). The target site where the DNA was cut has the five base TTACT sequence. That sequence is retained in one of the target-site duplications of 8 species… and can be obtained by a one-base change in 18 other cases. We share this ancient TE with elephants” (2). Figure 4. Insertion of a MIR element in intron 7 of the beta-fibrinogen gene of various species demonstrating shared ancestry well beyond primate common ancestry. E - Euarchontoglires. L - Laurasiatheria. A - Afrotheria. From: Finlay, Graeme. 2021. Human Evolution: Genes, Genealogies and Phylogenies. p 107. Figure 2.15. Cambridge University Press. Social sharing and Fair dealing applied per publisher's web instructions. Paperback edition. A set of TEs was found to be shared by whales and hippos demonstrating that whales and hippos shared a common ancestor. Scientists moved whales into the order containing hippos, pigs, deer, sheep, cattle and giraffes based on this finding. Fossil whales were also found to have a special bone in their ankle confirming their artiodactyla ancestry. See my video on whale fossil evidence for evolution. A retrotransposon insertion in baleen whales led to the loss of enamel-capped teeth. See also a short video on DNA evidence for whale evolution. TEs show all living birds are monophyletic (2). Using shared TEs between genomes one can demonstrate evolution and clustering of species. We share common ancestors by shared TEs with elephants, sloths, armadillos and even birds and reptiles. We do live during a second Galileo moment for theology. Evolution, macroevolution, is true just as Darwin worked out 150+ years ago. The DNA evidence is sound, robust, and will withstand the best anti-evolutionists can bring to bear. TEs can be beneficial and functional Until this point the impression has been that TEs jumping around randomly damage a lot of genes and cause disease. They do, but they also have had many positive effects on genomes. Over long ages primate genomes have been invaded by millions of segments of LTRs, LINE-1s, Alus, and SVA elements. Mammals share genomic records of ancient invasions by LINE-2, LINE-3 and MIR retroelements (2). As Finlay points out TEs have provided DNA sequences for new genes. It is incorrect that evolution has not produced new genes and novel genetic information. By jumping in genomes they have also added to the variety of genes when they land into exons (the parts of genes that are left after splicing out the introns during processing the final gene mRNA). Lastly they have donated segments of DNA that have been co-opted by the host into regulatory networks (2). New gene examples include the BCYRN1 gene that is functional in nerve tissue. It was formed when an Alu was spliced into the genome of an ancestor to apes and monkeys. Another Alu element produced a family of genes eventually through a series of mutations to form an ASR element then into a CAS element and finally after two duplications into snaR genes. These are transcribed into small RNA regulatory molecules that probably regulate protein synthesis (2). The PMCHL1 and PMCHL2 genes were assembled from genetic parts, one of which was an Alu element. Besides the Alu element, the genes include several downstream exons and a gene duplication. These genes are active in the testes, fetal brain and encode non-coding RNA transcripts (2). Several Alu elements were used to form the FLJ33706 gene that was spliced into the primate germ-line line and later provided a protein-coding sequence (2). TEs also have provided DNA material for new exons. As mentioned, when the DNA is read to make a final mRNA product that will go to the ribosomes to make proteins, it must first be processed. Most of the transcription is DNA that is nearly always thrown away as introns, leaving only the exons to be spliced together. In the human genome TEs have contributed repeatedly as novel exons. TEs occur in 4.4% of all transcripts and in 0.5% of all DNA sequences that code for proteins. A survey of 330 Alu-derived exons has shown that most are minor components of gene output (2). TEs have also assumed many regulatory roles. An analysis of eutherian genomes showed at least 16% of all the studied conserved non-coding elements were shown to be formed either wholly or in part by TEs representing multiple families including ERVs, LINE elements, MIR elements and DNA transposons. Non-coding genes produce RNA products for regulation instead of protein products. It appears that "6% of all TEs have acquired stable functions as shown by the fact that they contain sequence motifs that resist change.” (2). Many transcripts in human tissues are initiated from specific sites within TEs and include some fibroblasts, liver, brain and 16% of embryos. As discussed extensively in another blog about ERVs at this web site regarding retroviruses and the fossilized ERVs they produced, the LTRs present in ERVs have been repeatedly co-oped to be used by the host as promoters for DNA transcription. About 90% of the ERVs in our genome consist only of LTRs, which are functional and 8% of our genome are made of ERVs. About 10% of ERVs have all three genes that hark back to their parasitic infectious origin. Importantly, most jumping genes either land in areas that cause no damage or have caused few problems. Sometimes two TEs of the same class can join, deleting the DNA between them producing a single chimeric TE (2). "On short timescales, recombination events, leading to the loss of intervening sequences, cause genetic damage. But on evolutionary timescales, the same processes reorganize genome content, contributing to the transformation of the genome of progenitor species into those of descendent species.” After humans split off from our shared chimp ancestor, more than 70 recombination events occurred between LINE-1 elements resulting in the loss of 450,000 bases… and more than 490 recombination events occurred between Alu elements also and these excised another 400,000 bases from the human genome.”(2). One gene, SIGLEC13, is present in chimps and Old World Monkeys, accompanied by several Alu elements, but the gene is absent in humans. During our evolution “the entire gene was neatly excised by a recombination event between the left-handmost Alu element and the Alu element just to the right of the last exon.” (2). Our genome contains many repeated units. If the basic repeat unit is very short, such as only three bases as in -AAG-, the repeat is called a microsatellite. Repeated sequences are often found within LINE-1s and Alu elements. “Microsatellites tend to have high mutation rates… They underlie some 40 genetic diseases…The ability of TEs to introduce such sequences into genomes destabilizes them”. Myotonic dystrophy type 2 developed from an Alu element that appeared in our ancestor and stimulated many repeats perturbing gene function and leading to a genetic disease (2). Host genetic systems do have ways to suppress jumping through epigenetic tags like methyl or acetyl groups. “Organisms possess regulatory mechanisms to suppress the insertional mutagenesis associated with TE activity. However, such genomic stability may be incompatible with adaptive change over the long term. A high mutational burden is disadvantageous to individuals, but promotes variation upon which natural selection can work, and hence promotes the development of adaptations… Patterns of long-term stability interspersed by bursts of active speciation [by waves of Alu insertions into primate genomes] are well recognized and have been called punctuated equilibrium “ (2, pg. 129). Conclusion This discussion of transposable elements (TEs) has been more technical and longer than wished for. Sometimes when it comes to science, brevity is sacrificed for accuracy. Three major types of retrotransposon TEs were discussed: ERVs, LINE-1s, and Alu elements. These three types are examples of non-DNA jumping genes and together constitute 36% of our genome alone. They are called TEs because they can or have in the past jumped around randomly in genomes. Although they have insertional preferences, they insert randomly by specific location (locus). TEs that are shared exactly between species constitute spectacular evidence for evolution, specifically macroevolution. Shared ERVs were discussed in a separate composition about how they are derived from random viral insertions and essentially rise to the level of proof of common ancestry. Why anti-evolution objections fail is also addressed. The two LTRs at the ends of the provirus have in most cases swung around in the distant past during recombination events producing solo LTRs. Most ERVs are only LTRs now and make up an astounding 8% of our genome. Shared LINE-1s and Alu elements between species were discussed in this entry as amazing evidence for evolution also because they also insert randomly and produce nested trees of linked ancestry. Three important takeaways need to be emphasized. First, TEs insert randomly and we find over 50% of our genome is TE derived. So many unique TEs are shared by other species in the exact same locations often with the same mutations, that the only rational conclusion is species that share the same TEs must have shared a common ancestor in the past. Shared TEs indicate insertions before the compared species split. Like the same scratches on two different rifle bullets must have come from the same rifle (origin) and are admissible in a court of law, so also shared TE’s constitute proof of a shared biological origin since they insert randomly. So much for genomes being like blue-prints and unchanging! Secondly, the millions of TEs can be nested in evolutionary phylogenetic trees. Some are shared by species being compared and some are not. If we combine them into groups, nested phylogenetic trees are produced and multiple independent trees all rationally point to only one conclusion: macroevolution even going deep in time is a fact. This disproves attempts to explain TEs as a result of a “Fall” since any disease or breaks in the DNA introduced at a proposed "Fall" would not produce nested evolutionary trees. Third, this jumping is independent of function. Many TEs are functional but the vast majority are not. Most of the time the jumps and new inserts are neutral or cause damage and disease through disabling genes. Over millions of years the host has evolved means to suppress them (methylation and acetylation, e.g.). "Sometimes they jump into very important spots, either genes themselves or in areas of the genome that is important for regulating genes... Joshua-Tor and Ipsaro examined a mouse protein called Asterix/Gtsf1 that immobilizes LTRs" (8). The host as also co-opted many for the host’s own use (especially LTRs which act as promoters and enhancers). To repeat, if TEs were mostly functional or none were, functionality would not matter. It’s the random inserts and the fact that they share the same TEs at the same locations between species that establishes evolution and common ancestry. The topic of functionality is not applicable to the observation of them being randomly inserted and shared between species. This sharing of TEs, producing hundreds of independent phylogenic trees that reach into the deep past, is what also proves macroevolution. A theological and historical appeal to a “Fall” becomes what it always was - a mythological solution to natural observations that only appears on the surface to be explanatory. It was destined to be displaced by science and exposed as fantasy; a literal belief unfortunately that persists and is accepted by billions of people on our planet still. This is the fifth and final article on this site based on a simple principle - the observation that shared random DNA changes between species can only be rationally explained by evolution and common ancestry. It is suggested if possible that readers just read Finlay’s book that these articles are based on. Only a few examples from his book can be showcased in these articles. The previous four associated articles are ERVs, DNA repairs/patches, segmental duplications and pseudogenes. A proper examination of how we actually observe DNA in compared genomes cries out evolution, and even “macroevolution”. People need only look inward to their bodies for definitive evidence for evolution in themselves. It was there all the time. To help emphasize the simple principle of shared random DNA markers between species and how they can only be explained by evolution, an organizing post with links to all DNA five articles was produced. In order to counter anti-evolution false objections many of the articles contain answers to common proposed objections. That made the articles longer to be more complete. Even those who accept evolution may not know how strong the evidence from DNA is for “macroevolution” and are encouraged to consider reading those contra-apologetic sections. Some may have realized that all this jumping within genomes would also produce junk DNA. That is a controversial topic unfortunately in biology with even non-religious scientists thinking we have little to no junk DNA. On the contrary, here is an entry arguing junk DNA ?  for the opposite situation and based on sound genomic principles. References and Citations 1. Transposons: The Jumping Genes https://www.nature.com/scitable/topicpage/transposons-the-jumping-genes-518/ 2. Finlay, Graeme. 2021. Human Evolution: Genes, Genealogies and Phylogenies. Cambridge University Press. 359 pp. Paperback edition.  ISBN 978-1-009-00525-8. 3. Alu elements: know the SINEs https://rdcu.be/drIPT 4. Levin, H.L. and Moran, J.V. 2011. Dynamic interactions between transposable elements and their hosts. Nature Reviews Genetics 12: 615-27. 5. Gorilla Genome Is Bad News for Evolution https://www.icr.org/article/gorilla-genome-bad-news-for-evolution 6. Understanding Incomplete Linkage Sorting. https://www.reddit.com/r/evolution/comments/2w42at/understanding_incomplete_lineage_sorting/# 7. A Tiny Bit of Knowledge is a Dangerous Thing https://freethoughtblogs.com/pharyngula/2012/03/11/a-tiny-bit-of-knowledge-is-a-dangerous-thing/ 8. How to Tame a Restless Genome (protein shuts down LTR-transposons) https://www.sciencedaily.com/releases/2021/04/210408131411.htm I think he's wearing blue genes while he jumps........