Creationism in Crisis - Human Genomic Snapshot Shows Evolution Over Hundreds of Thousands of Years

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The Rockefeller University » The clearest snapshot of human genomic diversity ever taken

Creationists hang themselves on a hook by insisting that all humans, and indeed every living thing, were designed by an omniscient, perfect supernatural deity for whom no superlative is enough, because such a designer would design a perfect human species, and a perfect human species would have no genetic diversity because its genome would be the perfect genome with every DNA base the perfect DNA base and every DNA triplet the perfect DNA triplet for the intended purpose.

Save only for a small number of genes for the difference in their sexes, Adam & Eve would have had identical genomes, as would their offspring and their offspring's offspring... down to today's descendants. Indeed, in the biblical myth, Eve was a clone of Adam, so there would not even have been sex chromosomes or genetic sexual differences - which reflects the ignorance of genetics of the authors.

A perfect creator would have no need for genetic diversity. Genetic diversity is the result of an evolutionary process, not of intelligent design!

But even is a slightly less that omnipotent, omniscient creator had lost control of the chemistry and physics that replicates the genome in each new generation, so a little bit of diversity would creep in over time, there is no way the amount of diversity we see today would arise by chance mutation. Even allowing for natural selection which would weed out the less than perfect, there has not been enough time since creationists believe the total human population was reduced to 8 genocidal flood survivors for the present amount of diversity to arise. And what possible mechanism could there be for keeping a mutated form of a perfect gene? Perfection is an absolute, with no possibility of a gene being better than perfect.

The Human Pangenome Reference Consortium.
The Human Pangenome Reference Consortium (HPRC) is a collaborative scientific effort aimed at constructing a comprehensive and representative reference of the human genome. The traditional human genome reference, known as the GRCh38 reference, represents a single individual's genome and does not capture the full genetic diversity of the human population. The HPRC seeks to address this limitation by constructing a pangenome reference that incorporates genetic variation present in different populations.

The HPRC was officially established in 2016 and is composed of researchers from various institutions and organizations, including academic institutions, genome centers, and biotechnology companies. The consortium aims to generate a more complete and accurate representation of the human genome by integrating data from diverse populations worldwide.

The impact of the HPRC's work is significant and has several implications for genomics research and precision medicine. Here are some key points:

1. Capturing Genetic Diversity: The human genome exhibits substantial variation across different populations, and a single reference cannot adequately represent this diversity. The pangenome reference being developed by the HPRC incorporates genetic variants that are absent from the traditional reference, providing a more comprehensive view of human genetic variation.
2. Improved Variant Calling: The pangenome reference enables more accurate variant calling and genotyping in genomic studies. By including a broader range of genetic variants, researchers can better identify and interpret genomic variants specific to different populations. This is particularly relevant for identifying rare or population-specific variants associated with diseases.
3. Precision Medicine: The pangenome reference has implications for personalized medicine and the interpretation of genomic data in clinical settings. It enhances the accuracy of genetic testing and interpretation, especially for underrepresented populations. By considering a broader range of genetic variation, clinicians can provide more precise diagnoses, prognoses, and treatment options tailored to individual patients.
4. Population Genetics and Evolutionary Studies: The pangenome reference facilitates population genetics and evolutionary research. It allows scientists to explore the genetic diversity within and between populations, investigate evolutionary processes, and gain insights into the origins and migration patterns of different human populations.

It's important to note that while the HPRC is actively working on constructing a pangenome reference, as of my knowledge cutoff in September 2021, the consortium had not yet completed and released a final version of the pangenome reference. However, their work has gained recognition and attention within the scientific community due to its potential to revolutionize genomic research and applications.

For more information and updates on the Human Pangenome Reference Consortium, I recommend referring to their official website (https://humanpangenome.org/) and reviewing relevant scientific publications and news articles published after September 2021.

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This, of course, is why Michael J Behe's notion of all mutations being deleterious and all change in the genome being 'devolutionary' is nonsensical and unworthy of someone who purports to be a serious biologist, because there is no known mechanism for keeping a gene less well suited for the environment than a perfect gene in the assortative process that is natural selection, so genetic diversity can't possibly arise by accumulation of deleterious genes.

So, if they understood it, the work of the Human Pangenome Reference Consortium should be worrying the frauds who run the creationist cult, because the only plausible mechanism for the present level of human genetic diversity is evolution, by natural selection, genetic drift, horizontal gene transfer and the occasional historical founder effect, all taking place over several hundred thousand years.

So, the small flurry of papers published in the last few days by the HPRC should be ringing alarm bells in Creation Central and causing the schemers and planners to come up with strategies for ignoring, misrepresenting of dismissing the work of the Consortium.

As the Rockefeller University news release explains:

For more than 20 years, scientists have relied on the human reference genome, a consensus genetic sequence, as a standard against which to compare other genetic data. Used in countless studies, the reference genome has made it possible to identify genes implicated in specific diseases and trace the evolution of human traits, among other things.

But it has always been a flawed tool. One of its biggest problems is that about 70 percent of its data came from a single man of predominantly African-European background whose DNA was sequenced during the Human Genome Project, the first effort to capture all of a person’s DNA. As a result, it can tell us little about the 0.2 to one percent of genetic sequence that makes each of the seven billion people on this planet different from each other, creating an inherent bias in biomedical data believed to be responsible for some of the health disparities affecting patients today. Many genetic variants found in non-European populations, for instance, aren’t represented in the reference genome at all.

For years, researchers have called for a resource more inclusive of human diversity with which to diagnose diseases and guide medical treatments. Now scientists with the Human Pangenome Reference Consortium have made groundbreaking progress in characterizing the fraction of human DNA that varies between individuals. As they recently published in Nature, they’ve assembled genomic sequences of 47 people from around the world into a so-called pangenome in which more than 99 percent of each sequence is rendered with high accuracy.

Layered upon each other, these sequences revealed nearly 120 million DNA base pairs that were previously unseen.

While it’s still a work in progress, the pangenome is public and can be used by scientists around the world as a new standard human genome reference, says The Rockefeller University’s Erich D. Jarvis, one of the primary investigators.

“This complex genomic collection represents significantly more accurate human genetic diversity than has ever been captured before,” he says. “With a greater breadth and depth of genetic data at their disposal, and greater quality of genome assemblies, researchers can refine their understanding of the link between genes and disease traits, and accelerate clinical research.”

Sourcing diversity

Completed in 2003, the first draft of the human genome was relatively imprecise, but it became sharper over the years thanks to filled-in gaps, corrected errors, and advancing sequencing technology. Another milestone was reached last year, when the final eight percent of the genome—mainly tightly coiled DNA that doesn’t code for protein and repetitive DNA regions—was finally sequenced.

Despite this progress, the reference genome remained imperfect, especially with respect to the critical 0.2 to one percent of DNA representing diversity. The Human Pangenome Reference Consortium (HPRC), a government-funded collaboration between more than a dozen research institutions in the United States and Europe, was launched in 2019 to address this problem.

At the time, Jarvis, one of the consortium’s leaders, was honing advanced sequencing and computational methods through the Vertebrate Genomes Project, which aims to sequence all 70,000 vertebrate species. His and other collaborating labs decided to apply these advances for high-quality diploid genome assemblies to revealing the variation within a single vertebrate: Homo sapiens.

To collect a diversity of samples, the researchers turned to the 1000 Genomes Project, a public database of sequenced human genomes that includes more than 2500 individuals representing 26 geographically and ethnically varied populations. Most of the samples come from Africa, home to the planet’s largest human diversity.

“In many other large human genome diversity projects, the scientists selected mostly European samples,” Jarvis says. “We made a purposeful effort to do the opposite. We were trying to counteract the biases of the past.”

It’s likely that gene variants that could inform our knowledge of both common and rare diseases can be found among these populations.

Mom, dad, and child

But to broaden the gene pool, the researchers had to create crisper, clearer sequences of each individual–and the approaches developed by members of the Vertebrate Genome Project and associated consortiums were used to solve a longstanding technical problem in the field.

Every person inherits one genome from each parent, which is how we end up with two copies of every chromosome, giving us what’s known as a diploid genome. And when a person’s genome is sequenced, teasing apart parental DNA can be challenging. Older techniques and algorithms have routinely made errors when merging parental genetic data for an individual, resulting in a cloudy view. “The differences between mom’s and dad’s chromosomes are bigger than most people realize,” Jarvis says. “Mom may have 20 copies of a gene and dad only two.”

With so many genomes represented in a pangenome, that cloudiness threatened to develop into a thunderstorm of confusion. So the HPRC homed in a method developed by Adam Phillippy and Sergey Koren at the National Institutes of Health on parent-child “trios”—a mother, a father, and a child whose genomes had all been sequenced. Using the data from mom and dad, they were able to clear up the lines of inheritance and arrive at a higher-quality sequence for the child, which they then used for pangenome analysis.

New variations

The researchers’ analysis of 47 people yielded 94 distinct genome sequences, two for each set of chromosomes, plus the sex Y chromosome in males.

They then used advanced computational techniques to align and layer the 94 sequences. Of the 120 million DNA base pairs that were previously unseen or in a different location than they were noted to be in the previous reference, about 90 million derive from structural variations, which are differences in people’s DNA that arise when chunks of chromosomes are rearranged—moved, deleted, inverted, or with extra copies from duplications.

It’s an important discovery, Jarvis notes, because studies in recent years have established that structural variants play a major role in human health, as well as in population-specific diversity. “They can have dramatic effects on trait differences, disease, and gene function,” he says. “With so many new ones identified, there’s going to be a lot of new discoveries that weren’t possible before.”

Filling gaps

The pangenome assembly also fills in gaps that were due to repetitive sequences or duplicated genes. One example is the major histocompatibility complex (MHC), a cluster of genes that code proteins on the surface of cells that help the immune system recognize antigens, such as those from the SARS-CoV-2 virus.

“They’re really important, but it was impossible to study MHC diversity using the older sequencing methods,” Jarvis says. “We’re seeing much greater diversity than we expected. This new information will help us understand how immune responses against specific pathogens vary among people.” It could also lead to better methods to match organ transplant donors with patients, or identify people at risk for developing autoimmune disease.

The team has also uncovered surprising new characteristics of centromeres, which lie at the cruxes of chromosomes and conduct cell division, pulling apart as cells duplicate. Mutations in centromeres can lead to cancers and other diseases.

Despite having highly repetitive DNA sequences, “centromeres are so diverse from one haplotype to another, that they can account for more than 50 percent of the genetic differences between people or maternal and paternal haplotypes even within one individual,” Jarvis says. “The centromeres seem to be one of the most rapidly evolving parts of the chromosome.”

Relationship building

The current 47-people pangenome is just a starting point, however. The HPRC’s ultimate goal is to produce high-quality, nearly error-free genomes from at least 350 individuals from diverse populations by mid-2024, a milestone that would make it possible to capture rare alleles that confer important adaptive traits. Tibetans, for example, have alleles related to oxygen use and UV light exposure that enable them to live at high altitudes. A major challenge in collecting this data will be to gain trust from communities that have seen past abuses of biological data; for example, there are no samples in the current study from Native American nor Aboriginal peoples, who have been long been disregarded or exploited by scientific studies. One doesn’t have to go far back in time to find examples of unethical use of genetic data: Just a few years ago, DNA samples from thousands of Africans in multiple countries were commercialized without the donors’ knowledge, consent, or benefit. These offenses have sown mistrust against scientists among many populations. But by not being included, some of these groups could remain genetically obscure, leading to a perpetuation of the biases in the data—and to continued disparities in health outcomes. “It’s a complex situation that’s going to require a lot of relationship building,” Jarvis says. “There’s greater sensitivity now.” And even today, many groups are willing to participate. “There are individuals, institutions, and governmental bodies from different countries who are saying, ‘We want to be part of this. We want our population to be represented,’” Jarvis says. “We’re already making progress.”

Copyright: © 2023 The authors.
Published by Springer Nature Ltd. Open access. (CC BY 4.0)

The team's findings are published, open access, in Nature:

Abstract

Single-nucleotide variants (SNVs) in segmental duplications (SDs) have not been systematically assessed because of the limitations of mapping short-read sequencing data^1,2. Here we constructed 1:1 unambiguous alignments spanning high-identity SDs across 102 human haplotypes and compared the pattern of SNVs between unique and duplicated regions^3,4. We find that human SNVs are elevated 60% in SDs compared to unique regions and estimate that at least 23% of this increase is due to interlocus gene conversion (IGC) with up to 4.3 megabase pairs of SD sequence converted on average per human haplotype. We develop a genome-wide map of IGC donors and acceptors, including 498 acceptor and 454 donor hotspots affecting the exons of about 800 protein-coding genes. These include 171 genes that have ‘relocated’ on average 1.61 megabase pairs in a subset of human haplotypes. Using a coalescent framework, we show that SD regions are slightly evolutionarily older when compared to unique sequences, probably owing to IGC. SNVs in SDs, however, show a distinct mutational spectrum: a 27.1% increase in transversions that convert cytosine to guanine or the reverse across all triplet contexts and a 7.6% reduction in the frequency of CpG-associated mutations when compared to unique DNA. We reason that these distinct mutational properties help to maintain an overall higher GC content of SD DNA compared to that of unique DNA, probably driven by GC-biased conversion between paralogous sequences^5,6.

Vollger, M.R., Dishuck, P.C., Harvey, W.T. et al.
Increased mutation and gene conversion within human segmental duplications.
Nature 617, 325–334 (2023). https://doi.org/10.1038/s41586-023-05895-y

Copyright: © 2023 The authors.
Published by Springer Nature Ltd. Open access
Reprinted under a Creative Commons Attribution 4.0 International license (CC BY 4.0)

Scientists from the University of Californis Santa Cruz (UC Santa Cruz) who were involved in the project have produced a video explaining their work:

What's clear from all this is that the Homo sapiens species is not only far from perfectly designed by a perfect designer, but it could not possibly have achieved the present level of genetic diversity starting with 8 individuals, three of whom were sons of one of the couples, in the last 4 thousand years, or even tens of thousands of years, but must have been diversifying for several hundred thousand years since the species diverged from its ancestral species.

In other words, the notion of intelligent design and recent special creation is entirely inconsistent with the observable evidence, which is perfectly explained by an evolutionary process over a very long period of time.

And, to lay another creationist lie, there is no suggestion that any of the scientists involved believe otherwise. There is never a hint that god-magic might have been involved in the process.