Biblical Genetics

https://youtu.be/-jpoxCZgZKQ Is the human genome highly functional or mostly junk? This is a question that is not only being asked in the creation-evolution debate; it is a question raging in the ivory tower as well. The 'old guard' is much more likely to resist any claim that large swaths of the genome are useful. The 'young punks' in science is more willing to accept the obvious fact that the genome is highly functional. Who is going to win? In this episode, Dr Rob puts a few more nails in the coffin of junk DNA.. Notes and links:' Carter 2023 What proportion of the human genome is actually functional? And how much variation is tolerable? Chen et al. 2023 A genomic mutational constraint map using variation in 76,156 human genomes Moran 2023 What's in your genomes? 90% of your genome is junk

No, the size of the genome has not changed, but the number of genes we thought it contains certainly has. After lots of double checking, there are fewer known protein coding genes today (~19,000) than there were when the human genome was first published, and even that count (~23,000) was shockingly small, according to the predictions of the world's top geneticists. The nature of the genome has consistently surprised people, but mostly because they applied Darwinian concepts to it. Instead, the genome is a wonderful testimony to the engineering prowess of God, who built something unexpected. LInks: GeneSweep One-gene-one-enzyme Central dogma of molecular biology Amaral et al. 2014 The status of the human gene catalogue, Nature 622(7981):41-47. What on earth is a ‘gene’? Slicing and dicing the genome The Barrier has been breached: new discoveries are challenging neo-Darwinism

Chromosomal recombination is an essential part of the life cycle of all sexually reproducing organisms. Yet, the system is complex, involving hundreds to thousands of proteins and RNAs. It also involves DNA repair pathways, which are themselves incredibly complex. The newest available information on recombination tells us it is mutagenic, meaning that recombination erodes the very places where recombination happens. How did such a system arise by chance? Can we assume the recombination rate has always been the same? What happens when a new allele arises in the protein that controls recombination? What is the mutation burden caused by this important system? Finally, how does this affect the creation-evolution debate? Links and notes: 15 Questions for evolutionists, #8 How did sex originate? Geeking out about DNA damage repair, June 2023. Grey et al. 2018 PRDM9, a driver of the genetic map, PLoS Genet 14(8):e1007479. Altemose et al. 2017 A map of human PRDM9 binding provides evidence for novel behaviors of PRDM9 and other zinc-finger proteins in meiosis, eLife 6:e28383. Robert Carter gets everything wrong?, creation.com, 10 Jul 2021. Hussin et al. 2011 Age-dependent recombination rates in human pedigrees, PloS Genetics 7(9):e1002251. Wang et al. 2012 Genome-wide single-cell analysis of recombination activity and de novo mutation rates in human sperm, Cell 150(2):402–12. African origins and the rise of carnivory, creation.com,19 Dec 2020. Hinch, A.G. et al., The landscape of recombination in African Americans, Nature 476:170–177, 2011. Hinch et al. 2023 Meiotic DNA breaks drive multifaceted mutagenesis in the human germ line, Science 382:eadh2531.

My new video made quite a splash! Apparently, lots of Christians are asking questions about the DNA we can now pull from very old skeletons. How do they do it? What are the data telling us? How is it even there, if the bones are as old as claimed? Without revealing too many details about what is in the main presentation, here I am just talking about ancient DNA and its implications for the creation-evolution debate. I also throw in a few things I was not able to address in the main presentation, including the genetics of ancient Canaanites and Philistines found in and around Israel. Notes and links: You can order Ancient DNA: Illuminating the Tapestry of Biblical Human History at creation.com (physical DVD or streaming format): creation.com/en/landing/ancient-dna How reliable are genomes from ancient DNA? (Creation.com) Patriarchal Drive in the early post-Flood population (Creation.com) Patriarchal Drive (BiblicalGenetics.com) Ancient History vs the Table of Nations (BiblicalGenetics.com) Extensive mixing of Israelites and non-Israelites in biblical history (Creation.com) The genetic history of the Israelite nation (Creation.com) The Israelites: forging of a nation (Creation.com) Genetics of modern Jews (BiblicalGenetics.com) Early Israel was a hotbed of interracial mixing (BiblicalGenetics.com) The Jews, Israel, and false notions of 'race' (BiblicalGenetics.com) Who were the Philistines? (Creation.com) Ötzi Mitochondrial Eve and the Three 'Daughters' of Noah (Creation.com) The High-Tech Cell (Creation.com) Feldman et al. 2019 Ancient DNA sheds light on the genetic origins of early Iron Age Philistines, Sci Adv 3;5(7):eaax0061, 2019. Haber et al. 2017 Continuity and admixture in the last five millennia of Levantine history from ancient Canaanite and present-day Lebanese genome sequences, Am J Hum Genet 3;101(2):274-282, 2017, Rylands Fragment of the Gospel of John Georgia Institute of Technology

African cichlids are a diverse group of fishes that have frequently been used as evidence for evolution. Yet, now that the genomes of several hundred species have been published, the true history of this group has been revealed. All parties must now acknowledge that the many species arose quickly, from a common stock. In many ways, African cichlids fit beautifully into the biblical model of 'created kinds'. Links: Meier et al. 2023 Cycles of fusion and fission enabled rapid parallel adaptive radiation in African cichlids, Science 381:1428. Carter R 2021 Species were designed to change, creation.com. Carter R 2021 Species were designed to change, biblicalgenetics.com. Common aquatic macroinvertebrates Map of the biodiversity of amphibians, etc., in North America

Darwin's finches have long been considered an icon of evolution. A recent analysis included 40 years of morphological measurements and genealogy tracing among four finch species on a small island in the Galapagos chain. This was coupled to 30 years of DNA sampling, including the recent sequencing of nearly 4,000 finch genomes from the same small island. The results tell us a LOT about biblical views of speciation, natural selection, and 'change over time'. Notes and links: Carter R, Galápagos finches, rapid speciation, and recent creation, Creation.com, 9 Nov 2023. Wieland C, Speciation conference brings good news for creationists, J Creation 11(2):135–136, 1997. Kaloyirou N, The remarkable Captain Robert FitzRoy, Creation 40(1):14–17, 2017. Lightner JK, Identification of a large sparrow-finch monobaramin in perching birds (Aves: Passeriformes), J Creation 24(3):117–121, 2010. Enbody ED et al., Community-wide genome sequencing reveals 30 years of Darwin's finch evolution, Science 381(6665):eadf6218, 2023.

A new paper claims that the pre-human population went through an extremely small and extremely long population bottleneck. Starting about one million years ago, the population was reduced to at most 1,280 "breeding individuals" and this lasted for over 100,000 years. To get there, they examined thousands of human genomes and assumed that all mutations are neutral. What would happen if we applied real-world mutation affects to the data? You know it. We would have gone extinct. The mutation burden would have driven us to extinction. Instead, what they really discovered was the we came from a very small founding population with only a little diversity. This fits perfectly within the Adam and Eve model of human ancestry. Links and notes: Hu et al. 2023 Genomic inference of a severe human bottleneck during the Early to Middle Pleistocene transition, Science 381:979–984. Buggs R, Science moves closer to Adam and Eve?, richardbuggs.com, 1 Sep 2023. Evolutionary bottlenecks are disastrous, Biblical Genetics, 2 Jun 2020. Biblical bottlenecks are not bad, Biblical Genetics, 27 May 2020. Sanford J, Critic ignores reality of Genetic Entropy, Creation.com, 7 Mar 2013. Carter R, A successful decade for Mendel's Accountant, J Creation 33(2):51–56, 2019. Carter R, The Neutral Model of evolution and recent African origins, J Creation 23(1):70–77, 2009.

The opponents of biblical creation have made some glaring errors in their criticisms of prior work on human-chimpanzee genetic differences. Specifically, several of their claims are in conflict with both theory and experiment. I document these here in detail. They have also shown a rudimentary understanding of how scientific data needs to be 'weighted' and they completely misunderstand how BLAST is supposed to work. Despite the high level of vitriol I have received so far, I submit this detailed analysis of their work for your review. Links: As promised, example programs etc. can be found at: https://github.com/BiblicalGenetics/Human-Chimp Creationist research is utter, utter poo, Roohif, 14 Sep 2018; https://www.youtube.com/watch?v=D117oXq8yT4 “80% Chimpanzee” | The Bogus Creationism of Jeffery Tomkins, Gutsick Gibbon, 26 May 2023; https://www.youtube.com/watch?v=QtTHlqhRQi0 Tomkins Responded to Me (Kinda?), Gutsick Gibon, 7 Jul 2023; https://www.youtube.com/watch?v=pYw9jl5jArE&t=18s Jeffrey Tomkins, The Creationist Who Can't Math: The Movie, Dapper Dinosaur, 24 Aug 2023; https://www.youtube.com/watch?v=BasDcbzx3AM Human vs Chimp: an honest appraisal of our differences, Biblical Genetics, 15 Aug 2023; https://youtu.be/FHg3LqJI34g The three attempted rebuttal videos: Professional Creationist RESPONDS to my Tomkins Debunk (kinda), 23 Aug 2023; https://www.youtube.com/watch?v=Qq1AcyHfLrA; Robert Carter, Liar | Creationists Have a Bad Relationship with Honesty: Part 2, Dapper Dinosaur, 23 Aug 2023; https://www.youtube.com/watch?v=Sx91ljv32Yc; Creationists Behaving Badly: Dr. Rob Carter, Creation Myths, 23 Aug 2023; https://www.youtube.com/watch?v=9LrhBnVXks0. Human vs Chimp, part 2: Digging deeper into our roots, Biblical Genetics, 5 Oct 2023; https://youtu.be/_vsGVN21TQU.

This is the second installment in a now multi-part series on human and chimpanzee genetic differences. I had a lot of pushback from my last episode, including negative reviews posted by Gutsick Gibbon, Creation Myths, and Dapper Dinosaur. Unperturbed, I push on. Here, I lay out some of the arguments in more detail and discuss many of the problems people are having when using one particular program, BLAST, to assess similarity between the two species. I will address the results of Gutsick Gibbon specifically in Part 3, but this was filmed before I got most of my experimental results back. Links (many of these are for Part 3 also): Background: Creationist research is utter, utter poo, Roohif, 14 Sep 2018. “80% Chimpanzee” | The Bogus Creationism of Jeffery Tomkins, Gutsick Gibbon, 26 May 2023. Tomkins Responded to Me (Kinda?), Gutsick Gibon, 7 Jul 2023. Jeffrey Tomkins, The Creationist Who Can't Math: The Movie, Dapper Dinosaur, 24 Aug 2023. My first installment: Human vs Chimp: an honest appraisal of our differences, Biblical Genetics, 15 Aug 2023. The three attempted rebuttal videos: Professional Creationist RESPONDS to my Tomkins Debunk (kinda), 23 Aug 2023. Robert Carter, Liar | Creationists Have a Bad Relationship with Honesty: Part 2, Dapper Dinosaur, 23 Aug 2023. Creationists Behaving Badly: Dr. Rob Carter, Creation Myths, 23 Aug 2023.

Several anti-creationists have made a hobby out of attacking creationists. Their best efforts, however, have generally failed. For example, see: Sanford 2013 Critic ignores reality of Genetic Entropy: the author of a landmark book on genomic decay responds to unsustainable criticisms creation.com 7 Mar 2013. Price, Carter, and Sanford 2020, Responding to supposed refutations of genetic entropy from the ‘experts’, creation.com, 1 Dec 2020. Unperturbed, "Gutsick Gibbon" has recently tried to discredit Dr Jeffrey Tomkins and his work on human-chimp genetic similarities: "80% Chimpanzee" | The Bogus Creationism of Jeffery Tomkins" 26 May 2023 youtube.com/watch?v=QtTHlqhRQi0. In my analysis of her analysis, I note several flaws in her logic. Note, however, that I deliberately ignored several of her main objections. This was not because I do not have answers, mind you, but because I wanted to focus on the most salient questions. Ignored were questions about why God would have included all the chimp-like non-coding DNA when he made humans and questions about properly weighting samples. The most recent comparison I am aware of claimed 96.6% similarity between humans and chimps: Seaman and Buggs 2020 FluentDNA: nucleotide visualization of whole genomes, annotations, and alignments, Frontiers in Genetics 30;11:292. This comes from the laboratory of Richard Buggs. This is much higher than Tomkins' estimates, that, with one exception, are generally in the 80s. However, I know the first author on that paper, so I called him up to discuss his methods. Sure enough, he used entirely different methodology than earlier work from that same laboratory (which arrived at an estimate of ~85%). To reach the higher percentage similarity, they cut out everything humans and chimps do not share, including the centromeres, telomeres, copy number variations of many annotated genes, and hundreds of thousands of small insertions and deletions that must be included to align the two genomes. This "apples to apples" comparison is fine, as long as everybody acknowledges that the true similarity is necessarily less than 96.6%. Yet, if the percent similarity is much less than 99%, there is no way, mathematically, to explain how so many millions of difference arose in the (imagined) 6.5 million years since our last common ancestor. Additional links: The Waiting Time Problem, BiblicalGenetics.com, 8 Jun 2021. Hierachical clustering complicates baraminiological analysis Carter 2021 Robert Carter gets everything wrong? Responding to even more ridiculous aspersions, creation.com, 10 July 2021. “Dr. Rob Carter Gets Everything Wrong (with Gutsick Gibbon)” 20 May 2021. Sibley and Alquist. 1991. The Phylogeny and Classification of Birds. King and Wilson. 1975. Evolution at two levels in humans and chimpanzees, Science 188(4184):107–116. Moorjani et al. 2016. Variation in the molecular clock of primates, PNAS 113(38):10607–10612. Sibley and Ahlquist. 1984. The phylogeny of the hominoid primates, as indicated by DNA-DNA hybridization, J Mol Evol 20(1):2–15. Sibley, Comstock, and Ahlquist. 1990. DNA hybridization evidence of hominoid phylogeny: a reanalysis of the data, J Mol Evol 30(3):202–36. Wikipedia page on DNA reassociation kinetics. Bergman and Tomkins 2012 Is the human genome nearly identical to chimpanzee?—a reassessment of the literature, Journal of Creation 26(1):54–60, Tomkins and Bergman 2012 Genomic monkey business—estimates of nearly identical human–chimp DNA similarity re-evaluated using omitted data, Journal of Creation 26(1):94–100, Tomkins 2013 Comprehensive analysis of chimpanzee and human chromosomes reveals average DNA similarity of 70%. Answers Research Journal 8:379–390. The version of BLAST he used for this paper had a flaw in the algorithm that only manifested when using extremely large data sets. Tomkins corresponded with the bioinformatics group at the NIH to get the BLAST...

Dr Rob outlines three aspects of genetics that tell us that, scientifically, the human species is doomed to eventual extinction. These include the rate of mutation accumulation in our population over time, the inability of natural selection to remove most of those mutations, and the sheer number of children that would be required to remove the mutations, given perfect selection. These all argue that there is no hope, collectively, in any evolutionary process. Thus, biblically, the only hope for us individually is through belief in Jesus. Links: Genetic entropy Basener et al. 2023 Dynamical systems and fitness maximization in evolutionary biology Fisher’s failure and the dramatic end of neo-Darwinism Genealogy vs Phylogeny: The War Continues

Dr Rob discusses a fundamental aspect of neo-Darwinism (Fisher's Theorem of Natural Selection) and how it fails mathematically. First postulated in 1930, Fisher's idea was promoted as something as firm and settled as the 2nd Law. Problem is, he made several incorrect assumptions that invalidate the whole thing. When you add realistic mutations to the scenario (e.g., Basener and Sanford's 'Fisher's Theorem of Natural Selection with Mutations'), you see that the net trajectory of evolution is downward. Why did it take 90 years to figure this out? Links: Basener and Sanford 2017 The fundamental theorem of natural selection with mutations Basener et al. 2021 Dynamical Systems and Fitness Maximization in Evolutionary Biology Keightley and Lynch 2003 Toward a realistic model of mutations affecting fitness Price 1972 Fisher's 'fundamental theorem' made clear Fisher 1930 The Genetical Theory of Natural Selection (Wikipedia page) Carter 2020 A successful decade for Mendel's Accountant

Dr Rob waxes eloquent about some amazing new revelations involving DNA damage repair systems. Researchers recently turned AI onto the human genome, probing the genes and gene systems that are involved in maintaining and repairing DNA. The results shocked everyone. Many more genes that anyone thought are required, and entire new repair systems were discovered. So what came first, DNA or the amazing repair systems required to maintain DNA that are, in turn, coded into DNA? The point is that these systems are absolutely necessary for living things, yet they are also incredibly complicated. They would never be expected to arise without help, but without them the entire DNA system (not just the code, but the DNA itself) could never exist. Evolution, in this case, simply fails to explain much of anything. Links: Kratz et al. 2023. A multi-scale map of protein assemblies in the DNA damage response. Cell Syst 14(6):447-463.e8; https://pubmed.ncbi.nlm.nih.gov/37220749/

Everybody loves genealogy, but we are severely limited in what we can know about our family histories. There are two main reasons for this. First, family records only go back so far. Even the longest family trees can't go back thousands of years. Second, personal genetics testing can only tell you who your closest relatives are. Yes, genetics can tell you what population you came from, but that is a matter of statistics, not documentation. This is not a problem for belief in the Bible. Adam and Eve are still the (sole) ancestors of everyone who has ever lived, it's just that you cannot prove it with what we have available to us today.

Notes and links: Genetic Entropy, by John Sanford Keffer oak RNA: the epicenter of genetic information, by John Mattick and Paulo Amaral (reviewed by Witold Filipowicz)

Science advances in fits and starts, and it sometimes takes a detour onto a dead-end road. Bacteria represent one of those roads. Studying bacteria gave us a sense that we could easily figure out biology, that there was a direct connection between genes and behavior, and that life was simple. Granted, there was no other way to get started, but the study of bacteria slowed down our understanding of higher organisms in many ways. From the 'one gene, one enzyme' hypothesis to the thought that living systems can be reduced to a binary decision tree, many things about bacteria misled us and prevented science from seeing that the majority of the information in the genomes of higher organisms is in the non-coding DNA. C-value paradox G-value paradox Transcription factors Bathybius (on Creation.com) One gene, one enzyme hypothesis Lac operon Boolean data

Genetic engineering is a controversial topic. From vaccines to fetal cells to transhumanism, the debate rages. Yet, there are certain aspects to genetic engineering that are demonstrably good. How are we supposed to make heads or tails of this new technology, especially since it is impacting every aspect of our lives? I thought that a simple explanation (at least, as simple as I could make it!) of the things I did while earning my PhD could help increase our understanding. I, as a conservative Christian, made the 'frankenfish'. I stole the genes for the bright green and red fluorescent proteins in corals, engineered them into bacteria, then into fish. There is nothing inherently difficult in what I did, but there were a LOT of steps. Perhaps, after this explanation, we can have a more civil discussion on the pros and cons. Links and notes: Gibbs PDL, Carter RW, and Schmale MC (2008) Nucleic acid encoding fluorescent proteins from aquatic species. US Patent #7,413,874. Gibbs PDL, Carter RW, and Schmale MC (2007) Fluorescent Proteins from Aquatic Species. US Patent #7,291,711. Carter RW, Schmale MS, and Gibbs PDL (2004) Cloning of anthozoan fluorescent protein genes. Comparative Biochemistry and Physiology, Part C 138:259–270. Carter RW (2003) Cnidarian Fluorescent Proteins. PhD Dissertation. University of Miami. Manica A, Carter RW (2000) Morphological and fluorescence analysis of the Montastraea annularis species complex in Florida. Marine Biology 137:899–906. Monkeying around with human embryos? Harnessing God’s design to help prevent sickness, but will the new vaccine technology alter our DNA? Unnatural selection: CRISPR on Netflix Gene editing babies? A dangerous, pointless experiment Human/animal hybrids? Human Cloning? Mammoth clones coming to a zoo near you

We are approaching the 100th anniversary of the Scopes "Monkey Trial". Dr Rob was in the neighborhood, so he stopped by the Rhea County Courthouse in Dayton, TN to tell the part of the story most people have never heard. This was the first time evolution was put on 'trial' in a US courtroom and it pitted two of the greatest orators of the 20th century against each other: William Jennings Bryan for the prosecution and Clarence Darrow for the defense. Bryan, the Christian anti-evolutionist, gave a weak performance. Darrow, the anti-theistic evolutionist, made Bryan, and thus by proxy, cultural Christianity, look foolish. Put yourself in the shoes of person living in 1925. Which side would you have chosen? Notes and links: Carter R, Scopes at 100: The “monkey trial” shaped an entire century, Creation.com, 25 Aug 2020. Carter RW, A long-overdue review of Hunter’s A Civic Biology, Creation.com, 1 Sep 2020. Rhea County Courthouse William Jennings Bryan Clarence Darrow Oliver Wendell Holmes Many of the references I made (e.g., to Bryans socialism and Darrow's anti-Christian atheism) were based on facts I have learned over many years. I.e., they were from memory.

Given the biblical accounts of Creation and the Flood, can we draw any conclusions about what we would expect in genetics? That depends on status of the species in question (e.g., 'clean' vs 'unclean and 'on the Ark' vs 'not on the Ark'), its population history, the amount of created diversity initially engineered into that species/kind, difference in mutation rates and DNA repair systems, and things like that. In the end, no, we cannot make many direct predictions, yet much of the genetic data and observations still point straight to the Bible. The biblical model is expansive enough to take in a range of observations. Notes and links: Tallulah Gorge Orphan Brigade Park Jeanson N. 2015. Mitochondrial DNA clocks imply linear speciation rates within "kinds”. Answers Research Journal 8:273–304. Jeanson N. 2013. Recent, functionally diverse origin for mitochondrial genes from ~2700 metazoan species. Answers Research Journal 6:467–501. Carter R.  How to think (not what to think), Creation.com, 1 Nov 2016. Carter R. 2019. A successful decade for Mendel’s Accountant, J Creation 33(2):51–56. Carter R. Species were designed to change, part 3: the tangled web of (intrabaraminic) life, Creation.com, 12 Aug 2021. The Amazing Braided Baramin Concept is Intrinsic to Creation (Species were designed to change, part 4) on BiblicalGenetics.com.

Notes, links, and things to think about: Hinch et al. 2011. The landscape of recombination in African Americans. Nature 476:170–177, 2011. Eberle et al. 2017. A reference dataset of 5.4 million human variants validated by genetic inheritance from sequencing a three-generation 17-member pedigree. Genome Res 27(1):157–164. Altemose et al. 2017. A map of human PRDM9 binding provides evidence for novel behaviors of PRDM9 and other zinc-finger proteins in meiosis. Elife 6:e28383. Grey et al. 2018. PRDM9, a driver of the genetic map. PLoS Genet 14(8):e1007479. Stapley et al. 2017. Recombination: the good, the bad and the variable. Philos Trans R Soc Lond B Biol Sci 372(1736):20170279. Protacio et al. 2022 Adaptive control of the meiotic recombination landscape by DNA site-dependent hotspots with implications for evolution. Front Genet 13:947572. International HapMap Project 1000 Genomes Program CEPH panel (note: In the video/audio I said that the DNA is cultured in bacterial artificial chromosomes. This is probably incorrect as there is mention of lymphoblastoid cell lines in this link. It has been a long time since I read any of the documentation on this project! Biblical Genetics episodes mentioned: There is no Y chromosome clock Did we evolve from 10,000 people in Africa? Was Africa the cradle of humanity? Did Eve live in Southern Africa? Modern humans from Adam and Eve? You bet! Patriarchal Drive Images: A diagram of crossing over from Thomas Hunt Morgan, circa 1917. Two consecutive crossings leads to gene conversion (if they are close enough) HapMap data, Europeans, Chr 15 spanning the XXX gene. Each individual is represented by a pair of rows. Each column is a single letter in the genome, but the letters are separated by an average of ~1000 nucleotides, so this is not full sequence data. Same as above, but for West Africans. Two accidental three-generation families in the HapMap and 1,000 Genomes datasets. The dotted lines show where the two-parent-child trios connect. The three-generation, 17-member CEPH panel A recombination map of Chr1 for one child (child #5, if I remember correctly). Blue = letters that came from the paternal grandfather. Red = letters that came from the paternal grandmother. Green = a spacer region to represent the position of the centromere. The number of recombined blocks vs the length of each block among the 11 children in the CEPH panel. Note: I totally messed up the explanation (and my hand motions) when I was describing this. I had something else in mind, but after filming, when I went looking for the image I had in my head, I realized my mistake. Either way, it is still an interesting image. It cannot be known how many of the singletons are sequencing errors of 1-SNP gene conversions, but see the Eberle reference above and how they claim to resolve many of the apparent errors.