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.

chatGPT3 "Tell me what you know about the Human Pangenome Reference Consortium and the impact of their work, with references, please." [Response to user question]
Retrieved from https://chat.openai.com/

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.

Creationism in Crisis - Not a Founder Couple, Not Even a Founder Species!

Slideshow code developed in collaboration with ChatGPT3 at https://chat.openai.com/

Reconstruction of Neanderthal woman

Photo: Bacon Cph; makeup: Morton Jacobsen
https://doi.org/10.1371/journal.pbio.0020449.g001

Nose shape gene inherited from Neanderthals - UCL News

One of the associated dogmas of creationism, with its slavish adherence to Bible literalism, is the legend of Adam & Eve as a single founder couple of the human species without ancestors, together with a genocidal flood 4000 years ago in which the human population was reduced to just eight octogenarians who were the incestuous ancestors of all living humans.

In order to sustain that belief, creationists need to ignore all the evidence that shows several lines of uninterrupted mitochondrial DNA (female) history going back hundreds of thousands of years and several uninterrupted lines of Y chromosome (male) history.

This same genetic evidence also shows that the last common female ancestor and the last common male ancestor of all living humans could not even have lived contemporaneously, let alone met and committed the 'original sin' that we are all supposedly guilty of and need the vicarious redemption by the blood sacrifice of an innocent person to be saved from being punished for by an invisible, mind-reading sky man.

Another major problem for creationists is the evidence that non-African Homo sapiens all carry evidence not only that there never was a severe bottleneck in evolutionary history but that we interbred with at least two other hominin species, especially Neanderthals, so that non-African humans carry something like 1-4% Neanderthal DNA.

Some paleoanthropologists have even suggested that Neanderthals never died out but were simply absorbed into the growing Eurasian Homo sapiens population to the extent that there is now more Neanderthal DNA in the human population than there ever was in the total Neanderthal population.

So, not only not a founding couple who could have committed the original sin, but not even a single founding species!

Creationism in Crisis - Modern Humans Migrated to America Tens of Thousands of Years Before the Biblical Flood

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The Long Trail Ahead

Howard Terpning

Mitogenome evidence shows two radiation events and dispersals of matrilineal ancestry from northern coastal China to the Americas and Japan: EurekaAlert!

In what would embarrass creationists if their cult beliefs were based on real-world evidence, a team of geneticists has shown that there were two waves of migration from the northern coastal region of China into North America, tens of thousands of years before creationists believe the entire human population of Earth was reduced to just eight individuals in a genocidal flood. The team, led by Yu-Chun Li, together with colleagues at the Kunming Institute of Zoology, Chinese Academy of Sciences, Kunming, Yunnan, China and the Department of Biology and Biotechnology “L. Spallanzani”, University of Pavia, Pavia, Italy, published their findings yesterday, in an open access paper in Cell Reports.

In normal, intellectually honest people, with the humility to allow their opinions to be led by the evidence, having a basic belief refuted would be a reason to change their mind; for a creationist however, it's a reason to find a strategy for dismissing the evidence and retaining a counter-factual belief, because the mere thought of being wrong is an existential threat to a creationist.

To arrive at their conclusions, the researchers analysed mitochondrial DNA (mtDNA) in thousands of ancient samples:

Creationism in Crisis - Exploding the Myth of the Cambrian and Ordovician 'Explosions'

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Fossils from the Lower Cambrian Yu'anshan Formation at Mafang (Figs. A-K) and Ercaicun (Fig. L) near Haikou, Kunming. All bar scales 10 mm except: C, I, 5 mm; L, 1 mm. Abbreviations: an, antenna; ap, appendage; as, axial spine; ex, exopodite; eye, compound eye; fc, free cheek; hs, head shield; leg, tentacle-like leg; te, trunk end. A) Three lobopodians (arrowed separately in different colors) of Microdictyon sinicum coexisting with their host Eldonia eumorpha (RCCBYU 10414). B) Fuxianhuia protensa (RCCBYU 10192), an adult with three juveniles (arrows). C) Eoredlichia intermedia with one free cheek detached (RCCBYU 10199). D) Four laterally compressed Leanchoilia illecebrosa (RCCBYU 10193). E) Concentration of exoskeletons of Yunnanocephalus yunnanensis (RCCBYU 10366). F) Dense accumulation of Yunnanozoon lividum (RCCBYU 10418). G) Eoredlichia intermedia (RCCBYU 10190). H) Xandarella spectaculum (RCCBYU 10191), with head shield, antennae and appendages preserved in separate laminae. I) Naraoia longicaudata (RCCBYN 10367) with nonsymmetry gut fillings (arrow). J) Dorsoventrally compressed Leanchoilia illecebrosa (RCCBYU 10194). K) Paucipodia inermis (RCCBYU 10186) preserved across two thin layers marked by the dark shadow. L) Kunmingella douvillei (RCCBYU 10196) with outstretched appendages and trunk.

Zhang, Xi-Guang & HOU, X.-G (2007)

No (Cambrian) explosion and no (Ordovician) event: A single long-term radiation in the early Palaeozoic - ScienceDirect

The bad news for creationism continues with the publication of yet another paper refuting one of their central dogmas - the lie that the so-called 'Cambrian Explosion' was a sudden creation of all the basic body plans of the major phyla, without ancestors, in a single act of magical design and creation.

The creationist argument of course depends on a deliberate misrepresentation of the metaphorical use of the word 'explosion' in this context, which is used in biology to describe a relatively rapid radiation of new taxa such as frequently happens when the potential evolutionary landscape changes due either to a major geological/cosmological event, or due to the evolution of new capabilities such as air-breathing and terrestrial existence or flight, or, in plants, new methods of fertilisation such as pollen, resulting in the explosive radiation of flowering plants.

Creationist frauds pretend it is used literally, to mean a sudden single event.

There was a lesser-known but similar 'explosive' increase in biodiversity during the Ordovician (approximately 485 to 443 million years ago) - the Great Ordovician Biodiversification ‘Event’ (GOBE).

The Cambrian explosion is a term used to describe a rapid diversification of animal life that occurred approximately 541 million years ago during the Cambrian Period. It is considered to be one of the most significant events in the history of life on Earth, as it marked the appearance of the first complex animal forms

The Cambrian Period, which lasted from approximately 541 to 485 million years ago, was characterized by a rapid increase in biodiversity, with the emergence of a wide variety of animal phyla. Fossil evidence from this period shows the appearance of many new body plans, including those of arthropods, mollusks, echinoderms, and chordates. The diversification of these groups was likely driven by a combination of environmental and evolutionary factors, including the availability of new ecological niches and the evolution of new genetic and developmental pathways.

Creationism in Crisis - What We Can Learn About Evolution From a Single Individual's Genome

Slideshow code developed in collaboration with ChatGPT3 at https://chat.openai.com/

Comparing Genes of 240 Mammal Species—and One Famous Dog—Offers New Insights in Biology, Evolutionary History | HHMI

Still more evidence against creationism is being revealed by data provided by the Zonomia Consortium.

In a series of 11 papers published recently, is one by Professor Beth Shapiro, HHMI Professor at the University of California, Santa Cruz (UCSC) and director of evolutionary genomics at the UCSC Genomics Institute. In this work Professor Shapiro and her team analysed the genome of the famous sled dog, Balto, the hero of the 1925 'Serum run' to Nome, Alaska:

Creationism in Crisis - How Human and Other Mammalian Immune Systems Evolved

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White blood cell

Source: La Jolla Institute for Immunology

Genomes from 240 mammal species explain human disease risks - Uppsala University, Sweden

My recent article about the evolution of mammals was based on research by the Zonomia Consortium which would be spreading despondency throughout the creationist cult if only they weren't so well rehearsed at avoiding and dismissing any information that threatens their superstition.

Another area of research coming out of the data supplied by the Zonomia Consortium is the evolution of the human and other mammalian immune system, and how it has led to some of the diseases currently associated with it.

Creationists who have fallen for the intelligent design hoax and who believe the putative intelligent designer is one and the same as the Abrahamic god, might like to consider why a supposedly omnibenevolent designer would design an immune system that causes suffering. Is that through malevolence or incompetence? The same applies to those creationists who believe a god magically guided evolution, usually to comply with their arrogant, anthropocentric belief that the purpose of evolution was to create modern humans, and them in particular.

Creationism in Crisis - Scientists Have Worked Out The Time Scale for the Evolution of Placental Mammals

Creationism in Crisis

Scientists Have Worked Out The Time Scale for the Evolution of Placental Mammals

Slideshow code developed in collaboration with CHATGPT3 at https://chat.openai.com/

A genomic timescale for placental mammal evolution | Science

It's another dreadful day for creationism as scientists involved in the Zoonomia Project publish yet another paper that refutes creationist dogma and the disinformation that is used to recruit more scientifically illiterate dupes into the money-making and extremist political cult.

This paper, published in Science concerns the gaps in the palaeontological record of the diversification of mammals from a single stem species. The gaps are filled with genetic evidence, made possible by the systematic comparison of 241 whole genomes from different existing mammals.

To make matters worse for creationism, the major periods of diversification coincides with major environmental changes as evidenced from geology and show changes over several millions of years - on an Earth that creationists believe is only a few thousand years old!

The work was made possible by the work of the Zoonomia Consortium, which should be keeping creationist cult leaders awake at night, if they grasped the significance of the work:

The Zoonomia Consortium was formed in 2015 by a group of scientists from several institutions, including the University of California, Davis, the University of California, Berkeley, the University of California, Santa Cruz, and the Broad Institute of MIT and Harvard. The goal of the consortium was to develop a comprehensive database of animal genomes that could be used to study and compare the genetic basis of traits across different species.

In 2020, the Zoonomia Consortium published a paper in the journal Nature describing the results of their work. The paper, entitled "Zoonomia Consortium, A comparative genomics multitool for scientific discovery and conservation," provides an overview of the consortium's approach and the tools they developed.

The Zoonomia database includes genomic data from over 100 species of animals, including mammals, birds, reptiles, and fish. The database is freely available to researchers and includes a variety of tools for analyzing and comparing genomic data, such as genome browsers, alignment tools, and gene expression analysis tools.

The Zoonomia Consortium's work has significant implications for conservation biology, as it allows researchers to compare the genetic basis of traits across different species and identify genetic factors that may be important for species survival. For example, researchers could use the Zoonomia database to identify genes that are associated with disease resistance or tolerance to environmental stressors, which could inform conservation efforts.

Reference:

Lewin, H.A., Robinson, G.E., Kress, W.J. et al. Zoonomia Consortium, A comparative genomics multitool for scientific discovery and conservation. Nature 587, 240–245 (2020). https://doi.org/10.1038/s41586-020-2876-6

Tell me about the Zonomia Consortium, please

According to the international team of scientists, led by William J Murphy, of Veterinary Integrative Biosciences, Texas A&M University:

Creationism in Crisis - Evolution by Loss of Genetic Information, or What Made us Human

Creationism in Crisis

Evolution by Loss of Genetic Information, or What Made us Human

Illustration by Michael S. Helfenbein

‘Deletions’ from the human genome may be what made us human | YaleNews

A trio of papers out recently should make creationists feel even more despondent, if only they could find the courage to read them, and if they could understand their contents. I'll write about them over the next couple of days, time willing.

The first, published yesterday in Science, concerns a new study led by researchers at Yale and the Broad Institute of MIT and Harvard, which has shown that, in addition to gaining some new genes that allowed us to speak, for example, what also differentiates us from chimpanzees is about 10,000 lost pieces of DNA, some as small as a few base pairs.

This of course, flies in the face of creationist dogma which says loss of genetic information is always deleterious and so can't contribute to evolution. It's something that creationist guru Michael J. Behe ludicrously calls 'devolution', which is a nonsense term, since there is no mechanism by which deleterious mutations can accumulate in the species gene pool, unless, rarely, they are closely linked to a strongly beneficial mutation.

But then Behe is writing primarily for a readership that doesn't understand what evolution is or the processes that cause it and who have no intention of ever finding out. Instead, they tell themselves that 'evolutionists' believe a mutation can turn a one species into another as a single event. As we've come to expect, creationist dogma is counter-factual because it's based on deliberate misinformation.

These are the same people who have boon fooled into believing that mainstream biologists are turning against the Theory of Evolution and turning to their childish superstition with its magic and an unevidenced supernatural magician. Another creationists delusion refuted by this research paper.

That this is not a case of chimpanzees gaining something that their common ancestor with humans did not have is evidenced by the fact that the genetic information chimpanzees still have is also in the genome of many other mammals. The probability of multiple species all gaining the same small fragments of DNA are incalculably small.

So, what benefits did these deletions convey? That they did so is concluded from the fact that they are present in all humans so must have given a common ancestor and advantage early in. As the Yale News article by Bill Hathaway explains:

Creationism in Crisis - A Large Trove of 'Transitional' Fossil Fish Shows How Jawed, Tetrapod Vertebrates Evolved

Creationism in Crisis

A Large Trove of 'Transitional' Fossil Fish Shows How Jawed, Tetrapod Vertebrates Evolved

Fish Fossils Rewrite Evolutionary History----Chinese Academy of Sciences

According to a series of news items from the Chinese Academy of Sciences last September, which somehow passed beneath my radar, two huge collections of fossils in southwestern Chongqing municipality and Guizhou province, in China, in strata which have been dated to the Silurian Period that began around 440 million years ago, are providing new information about the evolution of fishes and the jawed vertebrates that eventually evolved into terrestrial tetrapods. These were direct ancestors of today’s amphibians, reptiles, mammals and birds.

These finds resulted in four articles in Nature which sadly lie behind paywalls, but according to one of the news releases:

…Chinese researchers reported finding fish fossils that provided the "missing link" about the origin of the jaw, a key trait that gave rise to 99.8 percent of all vertebrate species living on Earth today, from giant whales to humans.

It is the first time for China to publish this many studies by one research team in a single issue of the prestigious journal, which stands as a testament to the importance of the findings and for China's global recognition as a powerhouse in paleontology, experts said.

Deng Tao, the director of the Institute of Vertebrate Paleontology and Paleoanthropology of the Chinese Academy of Sciences, said the recent breakthroughs represented China's original contribution to the basic sciences regarding evolution.

Creationism in Crisis - So What 'Kind' is This Strange Thing?

Creationism in Crisis

So What 'Kind' is This Strange Thing?

George, Emma E., et al.(2023)

Evolutionary oddball has seven genomes inside a single cell | New Scientist

The Bible that creationists turn to for a source of scientific information, is of course, as hopelessly muddled and simplistic about biology as it is about cosmology, morality and medicine. For example, this is how it tries to classify the birds that it is forbidden to eat under the irrational food taboos it mandates for believers:

And these are they which ye shall have in abomination among the fowls; they shall not be eaten, they are an abomination: the eagle, and the ossifrage, and the ospray, and the vulture, and the kite after his kind; every raven after his kind; and the owl, and the night hawk, and the cuckow, and the hawk after his kind; the little owl, and the great owl, and the swan, and the pelican, and the gier eagle, and the cormorant; and the stork, the heron after her kind, and the lapwing, and the bat.

Leviticus 11:13-19

Not surprisingly, and not just because of the hilarious gaff of including 'the bat' in a list of birds, and the muddle over the different 'kinds' of owl, biologists soon realised how hopelessly inadequate the Biblical notion of 'kinds' is as a means of classifying biological taxons, so had the devise the modern classification system.

And, presumably because the authors didn't realise that plants are alive because they don't breath like vertebrates do, there is no attempt to classify plants. In fact, the author's show their muddle over plants by this strange piece from Genesis:

Then God said, 'Let the earth put forth vegetation: plants yielding seed, and fruit trees of every kind on earth that bear fruit with the seed in it. ' And it was so. The earth brought forth vegetation: plants yielding seed of every kind, and trees of every kind bearing fruit with the seed in it.

Genesis 1:11-12

Clearly the Bible's authors thought there were only angiosperms (the most advances plants) since they are the only ones mentioned. Incidentally, more of their muddle is illustrated by the fact that this creation of green plants occurs before the sun is created, showing the authors knew nothing of photosynthesis.

And of course, there is no hint that the authors were even aware of single-celled micro-organisms, otherwise they might have mentioned germ theory, of which there is not a single word. Imaging how many lives could have been saved and how much suffering would have been avoided if God had thought to mention bacteria and viruses and how to avoid being infected by them, assuming it didn't know what it had created them for in the first place...

But that's an aside. The real muddle comes with the authors attempt to come up with a classification system, as Bible-literalist creationists assume that's what they were trying to do.

So, here is a curveball inadvertently thrown to creationists by researchers led by Emma E. George, now of the Scripps Institution of Oceanography, Integrative Oceanography Division, University of California, San Diego, La Jolla, CA, USA, when working at the University of British Columbia in Canada.

Her team have discovered single-celled algae that are not single organisms at all, but a complex community of seven different organisms, each with its own genome, and each playing a part in a complex relationship within the algal cell body.

Figure 3
Microscopy of Cryptomonas gyropyrenoidosa SAG 25.80 with bacterial endosymbionts.

(A) DIC; (B) DAPI; (C) FISH-M. polyxenophila probe; (D) FISH-G. numerosa probe; (E) overlay of (C) and (D); (F) endosymbionts clustered in the host cytoplasm, including endosymbionts with virus-like particles (Sv); (G) endosymbiont with virus-like particles within the bacterial cytoplasm and attached to the bacterial cell’s surface (arrowhead); and (H) bacterial endosymbionts and a membrane-like structure (i.e., putative autolysosome vacuole) that potentially contains virus-like particles (arrowhead). See also Figures S4A and S4C and Table S2.

George, Emma E., et al.(2023)

Creationism in Crisis - How a Complex Process Evolved From Simplicity. It's Those Blinking Mudskippers Again

Creationism in Crisis

How a Complex Process Evolved From Simplicity.
It's Those Blinking Mudskippers Again

Mudskippers Could Be Key to Understanding Evolution of Blinking | Research

Indian mudskipper, Periophthalmodon septemradiatus

Mudskippers are the thing of nightmares for creationists because, although not directly ancestral to terrestrial tetrapods, they show how fish left the water and moved onto land, to become the terrestrial vertebrates - amphibians, reptiles, mammals and birds - we have today.

Another thing creationists dread is evidence of complexity evolving naturally from simplicity, because that conflicts with another of their counter-factual dogmas.

So, news today that simple beginnings of the evolution of blinking can be seen in the way mudskippers keep their eyes clean when out of water, will need to be rigorously ignored or misrepresented by creationists who are too afraid to consider that they could be wrong.

The news comes in the form of an open access research paper published a couple of days ago in the online journal PNAS by researchers from Georgia Institute of Technology, Seton Hill University, and Pennsylvania State University, and an accompanying news release from the Georgia Institute of Technology (Georgia Tech):

Creationism in Crisis - Stuff The Bible's Scientifically illiterate Authors Never Imagined

Creationism in Crisis

Stuff The Bible's Scientifically illiterate Authors Never Imagined

Figure 1: Illustration of gravitational lensing by a galaxy. Light from a more distant and reddish galaxy is bent by a more nearby and bluish galaxy, which acts like a natural cosmic telescope to magnify the more distant galaxy. In this instance, multiple images of the reddish galaxy are created, forming a reddish ring-like feature referred to as an Einstein ring around the bluish galaxy.

Image credit: ALMA, L Calcada, Y. Hezaveh et al.

Howe the authors of Genesis saw the Universe

HKU Astrophysicists Reveal the Nature of Dark Matter through the Study of Crinkles in Spacetime - All News - Media - HKU

Back in the bronze Age, in the days that Christopher Hitchens described as 'the fearful infancy of our species', before we had even invented the wheel and isolated tribes still thought Earth was flat, the best explanation they could think of for where everything came from was the result of some magic spells cast by an invisible magician who lived above the sky. Agency in all things and magic, were assumed to be behind everything, just as they are today by creationists.

So, imagine these ignorant hill farmers, who thought stars were hanging from a dome over a flat Earth, struggling to come to terms with concepts such as deep space where celestial bodies are millions of light years apart and most of it is composed of invisible matter?

Magic and agency in all things
(Bible moralisée, French, 13th century)

How on Earth were these simple, ignorant people going to guess at an accurate description of the cosmos and its origins?

They weren’t of course. The best they could do was to describe a world which ran on magic and give magical explanations for everything they didn't understand, confident that those who were going to read their guesses were equally ignorant.

Contrast that situation about 3000 years ago with today's astrophysicist trying to make sense of what can be observed.

Having abandoned magic and supernatural agency as an explanation for anything, about 200 years ago, modern scientists have to rely on what can be observed, either directly or indirectly, and one of their observations is that the Universe has far more mass in it than can be accounted for by observation of that which can be seen. In other words, the observable universe has a lot of stuff that can't be seen but which is giving it mass.

How then do we know about it? Because we now understand the relationship between mass and gravity, so we can observe dark matter indirectly by observing the effect its gravity has on things we can see, such as galaxies.

You wouldn't expect the simple-minded hill farmers who wrote Genesis to have any inkling that such substance even existed, let alone come up with an explanation of what this 'dark matter' is, other than the product of magic words, of course.

This is why there is no mention, not even the tiniest hint, of dark matter in the Bible, or even that the universe is as massive as it is. In the ignorant minds of the authors, 'stars' (whether galaxies or suns) were points of light stuck on the underside of the dome that kept the water above the sky out. Of course, you wouldn't expect scientifically illiterate and ignorant people to describe and explain the origins of dark matter, but you WOULD expect any creator god who filled the Universe with dark matter to be able to describe and explain it.

Creationism in Crisis - What Internet Creationists Tell us About Creationists

Creationism in Crisis

What Internet Creationists Tell Us About Creationists

Listening to creationists can strengthen our understanding of evolution

Back in the 1980,s in the early days of the Internet, I was what was known as a 'SysOp' for a few CompuServe fora. I first got involved in the old UK Medical forum because of my interest in medical science as an Ambulance paramedic, then I joined a couple more fora - UK Forum and UK Current Affairs. Each forum had several sections for which particular SysOps were responsible. UK Forum, for example, had sections on Religion and Science as well as Politics. UK Current Affairs had sections on NHS, Northern Ireland, Economics, UK Constitution, etc. I also joined SciMath, a US-based forum.

It was in one of those fora that I first encountered American Creationists and Bible literalists, in addition to run-of-the-mill fundamentalists.

At first, I assumed they were joking, as it was hard to believe the childishness and scientific ignorance being displayed. As a child, we used, 'He/she still believes in Noah's Ark', to call someone childish and believing in fairy stories. In due course, we also stopped believing in the Tooth Fairy and Santa.

No-one I knew took the Bible literally anymore and no-one believed Earth was just a few thousand years old, any more so than they believed the sun orbits Earth, or the Earth is flat, or that we really are all descended from Adam and Eve. Sure, they were in the Bible, which some people still took seriously as a historical document, but it was generally assumed that the creation stories in Genesis were some sort of metaphor or allegory, although no-one seemed entirely sure for what. The tales, like those of Noah and Lot's wife, were so patently counter-factual that they must have had some deeper meaning...

So, it was amazing to discover that in America, the most advanced of countries and 'leader of the Free World', there really were a large number of people who still believed what our grandparents once believed, and who knew so little of science, geology and history that they couldn't see any flaws in the arguments they were putting forward.

But what that did for me at the time was to spur me on to learn, to understand their arguments and more importantly, to refute them with scientific facts. In short, it was debating with creationists that convinced me more and more that not only were they wrong, but that they were deluded victims of fraud who came from a culture that made them believe they could only be important enough if they had a close personal relationship with the creator of the universe who made it all with them in mind.

And the more I learned about science the more obvious it became why their cults expend so much energy trying to rubbish it, and why you can never get a creationist to read primary science sources, preferring to stick to their safe echo-chambers. To them, science is toxic.

So, what else can we learn from creationists?

Creationism in Crisis - How to Expose a Creationist's Scientific Illiteracy in Online Debate

Creationism in Crisis

How to Expose a Creationist's Scientific Illiteracy in Online Debate

How to slam dunk creationists when it comes to the theory of evolution

I find that the easiest way to expose creationists in online debate as gullible, scientifically illiterate dupes who have been fooled by other creationist frauds, is to let them expose themselves. Just give them a platform for them to perform on, shine a spotlight on them and away they go.

Don't try to win over the creationists; this would men them having to consider being wrong, and most creationists will never do that because to them the prospect of being wrong is too terrifying to even contemplate. Treat them as an asset to win over the audience for you.

The only problem with that tactic is that it only works on an audience who already understand even basic science so will understand the meaning of 'Theory' used as a scientific term and will know that the distinction between 'micro-' and 'macro-' evolution is illusory and meaningless since they both have the same underlying mechanism.

Anyone with a grasp of analytical reasoning will understand why there are gaps in the scientific record, and will understand that evolution is usually, with very few exceptions, a slow process that takes hundreds or thousands of generations, not an event that can be easily witnessed.

Most people with the intellect of a normal adult will understand why a hypothesis that includes magic and unproven supernatural entities, is not a scientific hypothesis, or what an assertion made without evidence is a claim that can be dismissed without evidence.

And most people will readily understand that an unsupported claim does not default to true unless disproved and creationism does not win by default if you prove a scientific hypothesis wrong. Fallacies like the false dichotomy fallacy, God of the gaps fallacy, ad hominem fallacy and special pleading fallacy are not hard to understand as fallacious arguments, and most honest people will recognise confirmation bias when they see it used to support a claim.

The weakness of my approach is that creationists in the audience, who have probably already been fooled by those fallacies and misinformation, will regard it as a win for the creationist because they lack the scientific understanding and critical thinking skill of most normal adults and most of them with have the thinking ability of an arrogant toddler.

Having said all that, the following article is by Professor Paul Braterman Hon. Research Fellow and Professor Emeritus, University of Glasgow, on how to defeat creationists in debate. It is reprinted from The Conversation under a Creative Commons license, reformatted for stylistic consistency:

Psychology News - New Study Confirms a Negative Correlation Between Intelligence and Religiosity

Psychology News

New Study Confirms a Negative Correlation Between Intelligence and Religiosity

Meta-analysis of 83 studies produces 'very strong' evidence for a negative relationship between intelligence and religiosity

Q. Why are so few scientists religious and why do so many fundamentalists have no understanding of science and poor critical thinking skills?

A. Because learning science and thinking are hard, but religion is easy and requires no analytical skill.

In 2013 a team led by Professor of psychology at Rochester University, Miron Zuckerman, reported finding a negative correlation between intelligence and religiosity from a meta-analysis of 63 studies.

In 2019, with more studies being conducted and because his findings have been challenges, Zuckerman and colleagues repeated the meta-analysis with a larger data set of studies. This larger study has confirmed the earlier finding. showing the correlation between intelligence and religiosity is between -0.20 and -0.23. The correlation tends to be stronger in

For non-statisticians, what is a meta-analysis?

Creationism in Crisis - How Mutations, not Magic, Have Helped Killer Hornets Spread

Creationism in Crisis

How Mutations, not Magic, Have Helped Killer Hornets Spread

Asian Yellow-legged hornet, Vespa velutina

Newly sequenced hornet genomes could help explain invasion success | UCL News - UCL – University College London

Today's bad news for Creationists is that scientists have analysed the genomes of both the European common hornet and the Asian yellow-legged hornet and found a number of genetic mutations that contribute to the ability of the latter to quickly adapt to new locations, and so become an invasive species in several parts of the world.

The study was led by Dr. Emeline Favreau and Professor Seirian Sumner of the Centre for Biodiversity and Environmental Research, Department of Genetics, Evolution and Environment, University College London (UCL), London, UK and included scientists from UCL, Spain, Italy, Austria, and New Zealand. Their findings are published, open access, in the journal Scientific Reports. The scientists did not report finding a magical reason for their success or need one to explain how the new genetic information entered the genome; it was those things creationists dread - gene duplication and mutation. Creationist dogma states that no new information can arise without magic and all mutations are deleterious and so can't convey an advantage. Those idiotic and demonstrably false dogmas are both comprehensively refuted by the study, so will almost certainly be ignored, dismissed or misrepresented by creationists.

First a little about the European common hornet, Vespa crabro and the Asian yellow-legged hornet, Vespa velutina:

Creationism in Crisis - Evolving Cancers - Another Devilish Problem for Creationists

Creationism in Crisis

Evolving Cancers
Another devilish Problem for Creationists

Tasmanian devil, Sarcophilus harrisii

Photo: Max Stammnitz

Tasmanian devil, Sarcophilus harrisii

Evolution of two contagious cancers affecting Tasmanian devils underlines unpredictability of disease threat | University of Cambridge

Scientists have unwittingly thrown creationists another curve-ball, in the form of a genetic analysis of the transmissible facial cancers that are devastating the population of the Tasmanian devil, Sarcophilus harrisii. Some estimates put the decline in population at 80% in some areas.

Tasmanian devils are one of the few mammals known to be affected by transmissible cancers, specifically devil Facial Tumor Disease (DFTD). DFTD is an aggressive and usually fatal cancer that is spread from animal to animal through biting and other forms of physical contact.

The cancer is believed to have originated in a single Tasmanian devil over 20 years ago and has since spread rapidly throughout the Tasmanian devil population. DFTD is a clonal cancer, meaning that it is composed of cells that are genetically identical to each other and to the original cancer cell.

The spread of DFTD has had a devastating effect on the Tasmanian devil population, with some estimates suggesting that the population has declined by up to 80% in some areas. The disease is considered a significant threat to the survival of the species.

Researchers have been studying DFTD since its discovery in 1996, and there have been many advances in our understanding of the disease. One of the key discoveries has been that the cancer cells evade the immune system of the host animal by downregulating MHC molecules. This allows the cancer cells to avoid detection by the host's immune system, allowing the cancer to spread unchecked.

There have also been efforts to develop treatments and vaccines for DFTD. Some promising results have been obtained in laboratory studies, but there is still much work to be done before these treatments can be applied in the field.

References:

1. Pye RJ, Pemberton D, Tovar C, et al. A second transmissible cancer in Tasmanian devils. Proceedings of the National Academy of Sciences. 2016;113(2):374-379. doi:10.1073/pnas.1519691113.
2. Stammnitz MR, Coorens THH, Gori KC, et al. The origins and vulnerabilities of two transmissible cancers in Tasmanian devils. Cancer Cell. 2018;33(4):607-619.e15. doi:10.1016/j.ccell.2018.03.013.
3. Tovar C, Pye RJ, Kreiss A, et al. Regression of devil facial tumour disease following immunotherapy in immunised Tasmanian devils. Scientific Reports. 2017;7(1):43827. doi:10.1038/srep43827.

Tell me about the transmissible cancers in Tasmanian devils, please, with references

The study, by an international team from the UK, Australia and USA, led by scientists from Cambridge University, UK, has analyzed the DNA of the devils and their two cancers (DFT1 & 2) and worked out how the cancers evolved by the classic evolutionary process of mutation and selection. They have identified that DFT1 arose in a single individual in the 1980 and this individual infected six other adult devils in Northeast Tasmania, which resulted in six different strains and an explosive spread of the disease across the island. The second, DFT2, arose spontaneously shortly before it was first observed in 2014, since when it has spread slowly but is mutating about three times faster than DFT1, probably because it has a faster growth rate.

So, the problem for creationists is that they either accept that evolution works, or, if they insist there was an intelligent agent causing the observed changes, that that agent, who is invariably the same as the Christian and Moslem god, malevolently designed these cancers and is ensuring their perpetuation in the face of any resistance the devils might evolve. And, not content with creating it once about 40 years ago, it repeated the exercise about 30 years later, presumably because killing 80% of the population was not enough.

Quite why it would have chosen such a nasty way to devastate the Tasmanian devil population rather than simply casting a magic spell to wipe out 80%+ of the population, is a matter for creationists to explain.

As the Cambridge University News release explains:

Creationism in Crisis - Feathered Dinosaurs Had Beetles Living on their Feathers Whose Descendants Now Live on Bird Feathers

Creationism in Crisis

Feathered Dinosaurs Had Beetles Living on their Feathers Whose Descendants Now Live on Bird Feathers

Remnants of dermestid beetle larvae and feathers in 130-million-year-old amber

Dermestid (larder) beetles

Fossils reveal a 100-million-year-old relationship between feathered dinosaurs and feather-feeding beetles | University of Oxford

Is there ever a day goes by when yet another science paper refutes creationism without even trying?

Well, maybe the odd public holiday when scientists take a day off from revealing the facts about the world, but refuting creationism is, and has always been, the incidental result of research into biology, archaeology and geology, and today is no exception.

For instance, we learn today that feathered dinosaurs not only existed 30 million years before birds evolved, but that those feathers were host to dermestid beetles, just as are modern bird feathers.

Dermestid beetles, also known as skin or hide beetles, are a type of beetle belonging to the family Dermestidae. They are found worldwide and are commonly associated with carcass decomposition, but they can also feed on a wide variety of organic material, including dried plant material, feathers, and even leather.

Dermestid beetles are known for their ability to efficiently clean carcasses of flesh, skin, and hair, making them popular among museums, taxidermists, and forensic scientists. The beetles are used to strip flesh and tissue from bones, leaving behind a clean and intact skeleton. This process is known as "dermestid beetle cleaning" or "dermestid beetle taxidermy."

According to a study published in the journal "Forensic Science International" in 2012, dermestid beetles are an effective tool for forensic entomologists in determining the post-mortem interval of human remains. The study found that the presence and activity of dermestid beetles on decomposing human remains can help estimate the time since death, particularly in cases where other insects are not present or are unable to colonize the body due to environmental conditions.

Dermestid beetles are also used in the field of zoology, where they are used to study the diet of animals. By analyzing the contents of dermestid beetle stomachs, researchers can learn about the types of animals a particular species preys upon.

In addition to their practical uses, dermestid beetles are also important ecologically. They play a role in the decomposition of dead animal matter and can help to recycle nutrients back into the ecosystem.

References:

1. "Dermestid Beetles." University of Florida Department of Entomology and Nematology,
   http://entnemdept.ufl.edu/creatures/misc/beetles/dermestid_beetles.htm
2. "Forensic Entomology: Dermestid Beetles and Their Significance in Time of Death Estimation." Forensic Science International, vol. 219, no. 1-3, 2012, pp. 237-240., doi: 10.1016/j.forsciint.2011.12.026.
3. Gordon, Robert D., and Karen M. Hackbarth. "Dermestid Beetles as a Tool in Wildlife and Zooarchaeological Research." Journal of Archaeological Science, vol. 26, no. 6, 1999, pp. 685-690., doi: 10.1006/jasc.1998.0307.

ChatGPT (21 Apr 2023) Tell me about dermestid beetles, please, with references. [Response to user question]
Retrieved from https://chat.openai.com/

Leaving aside the little problem for creationists that these beetles were getting trapped in amber some 300 million years before Earth was created according to the childish creationist fairy tales, this is also lovely evidence that the modern species of dermestid beetles co-evolved with their feathered hosts as the 'avian' dinosaurs evolved into birds.

The analogy is with human lice which co-evolved as the hominids diverged from the chimpanzees and gorillas, so there is now a clear evolutionary relationship between the lice that infect humans and the lice that infect the other African great apes.

Creationism in Crisis - How Trees Evolved Over the Last 21,000 years

Creationism in Crisis

How Trees Evolved Over the Last 21,000 years

The composition of tree species, as here in southern Germany, is linked to climate changes over the past 21,000 years.

The diversity of present tree species is shaped by climate change in the last 21,000 years

Mixed Woodland, Wales

Woodland Trust/Credit: Jordan Mansfield / WTML

In yet another rebuttal of the Creationist claim that the Theory of Evolution is being discarded by mainstream biologists as an explanation for observable evidence, an international team of researchers led by scientists from Aarhus University, Denmark have investigated the beta diversity of woodlands worldwide to assess the effects of climate change since the last ice age, 21,000 years ago.

Incidentally, 21,000 years is more than twice as long ago as creationists believe Earth was magicked into existence by a magic man using magic words. Also, there was no sign of a global flood a few thousand years ago.

Beta diversity is a measure of how diversity differs between locations.

Beta diversity is a term used in ecology to describe the variation in species composition among different habitats or ecosystems. It refers to the differences in species richness (the number of species) and species composition (the identity of the species present) among different communities or sites.

Beta diversity can be measured in different ways, including using indices such as the Jaccard index, the Simpson index, or the Bray-Curtis index. These indices provide a measure of the degree of dissimilarity between communities based on their species composition.

Beta diversity is important in ecology because it provides insights into the distribution of species and the factors that influence their distribution. For example, if beta diversity is high between two habitats, it suggests that the environmental conditions in those habitats are different and may support different sets of species. Conversely, if beta diversity is low, it suggests that the environmental conditions are similar and may support similar sets of species.

Beta diversity can also be used to assess the effects of human activities on biodiversity. For example, if beta diversity is lower in an area that has been impacted by human activities, it suggests that those activities have homogenized the habitat and reduced the diversity of species that can survive there.

In summary, beta diversity is a key concept in ecology that helps us understand the variation in species composition among different habitats or ecosystems, and can provide insights into the factors that influence species distribution and the impacts of human activities on biodiversity.

References:

1. Baselga, A. (2010). Partitioning the turnover and nestedness components of beta diversity. Global Ecology and Biogeography, 19(1), 134-143.
2. Ferrier, S., & Guisan, A. (2006). Spatial modelling of biodiversity at the community level. Journal of Applied Ecology, 43(3), 393-404.
3. Jost, L. (2007). Partitioning diversity into independent alpha and beta components. Ecology, 88(10), 2427-2439.
4. Legendre, P., & De Cáceres, M. (2013). Beta diversity as the variance of community data: dissimilarity coefficients and partitioning. Ecology Letters, 16(8), 951-963.
5. Vellend, M. (2016). The conceptual foundations of ecological diversity revisited. Ecology Letters, 19(8), 912-923.

ChatGPT. (20 Apr 2023). Tell me about beta diversity in the science of ecology. [Response to a user question].
Retrieved from https://chat.openai.com/

The team found a close link between the global pattern of tree biodiversity and global temperature changes since the peak of the last ice age.

The Aarhus University News release explains the study: