Biblical Genetics Dr. Robert Carter

Human-chimpanzee similarity is a hotly-debated topic in the evolution-creation wars. Are we 98, 95, 90, or 85% similar? One way to get at the question is to ask what is the longest stretch of DNA that is shared between the two species. This is a very difficult question to answer! But, unperturbed, Dr Rob set out to answer it. Will our fearless hero be able to pull it off? Spoiler alert: not quite, but the path of discovery is still very interesting.



LastZ github.com/lastz/lastz

LastZ chaining github.com/hillerlab/make_lastz_chains

Mummer4 mummer4.github.io/

Blast blast.ncbi.nlm.nih.gov/Blast.cgi

Telomere-to-Telomere Consortium primate projects github.com/marbl/Primates

Python python.org/



Standard Bases:



A: Adenine

C: Cytosine

G: Guanine

T: Thymine (in DNA)

U: Uracil (in RNA)



Ambiguous Bases (IUPAC Codes):

These codes are used when there is ambiguity in the nucleotide present at a particular position:



R: A or G (puRine)

Y: C or T (pYrimidine)

S: G or C

W: A or T (Weak)

K: G or T (Keto)

M: A or C (aMino)

B: C, G, or T (not A) (B comes after A)

D: A, G, or T (not C) (D comes after C)

H: A, C, or T (not G) (H comes after G)

V: A, C, or G (not T) (V comes after U; U is replaced with T in DNA)

N: Any base (A, C, G, T) (N for any nucleotide)





Silver Comet Trail silvercometga.com/

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

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 Carter highlights four new studies that ratchet the argument toward high function.



Notes and links:'



Carter 2023 What proportion of the human genome is actually functional? And how much variation is tolerable?

Zhang et al. 2023 FOXP3 recognizes microsatellites and bridges DNA through multimerization

Walter 2024 Are non-protein coding RNAs junk or treasure?

Stepankiw et al. 2023 The human genome contains over a million autonomous exons

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

A slew of videos has recently come out arguing for and against the work of Dr Jeffrey Tomkins, who claims humans and chimps are only about 85% similar. His detractors have made some massive blunders and I attempt to document them here. This is not to gloat, however. I understand that all humans are bigoted, biased, myopic, jealous, envious, etc., including all scientists. So, we'll apply James 3:1 ("Not many of you should presume to be teachers...for know that we will be judged more strictly)  and Philippians 2:3... (Do nothing from selfish ambition or conceit...) to the situation as we outline multiple lapses of logic and analysis that have been done in an attempt to discredit Tomkins' work. To be fair, though, the main person in my crosshairs has admitted to making these mistakes. I am only documenting things for posterity.



Notes and links:



James 3:1–2

patternsofevidence.com/patterns-plus

The 3rd Commandment

Dr Jeffrey Tomkins

Blast

Gutsick Gibbon, A Professional Creationist Agrees with Me: Tomkins Wrong, 30 Dec 2023.

Roohif, Jeffrey Tomkins is allergic to controls, 29 Dec 2023. Note: I made several mistakes when describing Roohif's results. First, he was looking at older trace read datasets, not the contig database I (and Gutsick Gibbon, and Tomikins in his 2018 paper) have been working with, so his conclusions about vector, etc., contamination do not apply here. Second, I stated that he only tested a few of the problematic areas, but he actually performed several thorough tests. Third, I also conflated his analysis on non-aligning subsequences in Blast matches with his analysis of the sequences for which Blast failed to find any alignment at all. After being challenged on a few of these points, and upon re-watching the video, paying attention this time (!) I stand corrected. Yet, that was but a small portion of my presentation and I included it almost as supplementary information, trying to cover all bases. In retrospect, I could easily have left it out entirely.

Gutsick Gibbon's Blast program on Github: GGBlast

Philippians 2:3–11

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.