Permafrost melts into the Kolyma River outside of Zyryanka, Russia, in 2019. The worms in the new study seem to have survived buried deep in the permafrost for tens of thousands of years.
Michael Robinson Chavez / The Washington Post via Getty Images
Duvannyi Yar thaw site on the banks of the Kolyma River, Siberia, Russia.
The problem with clinging to counter-factual beliefs like Bible-literalist creationism, for fear of having to contemplate being wrong, is that you have to keep deciding whether to believe the Bible or the evidence.
Here, for example, is a (to a creationist) key passage from the Bible:
Fifteen cubits upward did the waters prevail; and the mountains were covered.
And all flesh died that moved upon the earth, both of fowl, and of cattle, and of beast, and of every creeping thing that creepeth upon the earth, and every man:
All in whose nostrils was the breath of life, of all that was in the dry land, died.
And every living substance was destroyed which was upon the face of the ground, both man, and cattle, and the creeping things, and the fowl of the heaven; and they were destroyed from the earth: and Noah only remained alive, and they that were with him in the ark.
Genesis 7:21-23
Leaving aside the absurdity of believing there was a time just 4000 years ago when the highest mountain would have been covered by a fifteen-cubit (i.e., about 22.5 feet) flood, it is necessary to believe that everything outside the Ark was destroyed. The Bible is quite specific on that point - every living substance was destroyed, including the 'creeping things'!
And that claim has to be set against the evidence provided a couple of days ago by an international team of scientists led by Anastasia Shatilovich, of the Institute of Physicochemical and Biological Problems in Soil Science Russian Academy of Science, Pushchino, Russia, and Vamshidhar R. Gade of the Max Planck Institute for Molecular Cell Biology and Genetics, Dresden, Germany, that they have revived, analysed the genome of and C14-dated a nematode worm recovered from Siberian permafrost, shown to be 46,000 years old.
So, not only was this not destroyed as the Bible claims, it was around some 36,000 years before the Earth was created, according to creationist fundamental dogma.
And of course, a corollary to that is that the permafrost containing the nematode in suspended animation, also survived a catastrophic flood a few thousand years ago.
But then, to be fair on the Bronze-Age Canaanite hill farmers who plagiarized that Mesopotamian local flood myth, what did they know of real mountains, as opposed to low hills, permafrost, or nematodes? They thought Earth was small, flat and ran on magic, and the sky was a dome to keep the water above it out.
The account of the discovery, and its significance, is explained in a news release by the Max Planck Institute of Molecular Cell Biology and Genetics:
So often, if only they hadn't learned to ignore it like an elephant in the room, or stay carefully ignorant of it, creationists should be confronting evidence that, if they believe it was designed, could only have been designed by a malevolent or incompetent designer.
Take for example this discovery that sections of mitochondrial DNA (mtDNA) frequently (in about 1 in 4,000 births) cross into the nuclear DNA, where it can cause cancer.
Creationists insist that this must have been intelligently designed by an omniscient designer who would therefore have known the outcome of its designed processes. The presence of mitochondria in cells is of course, good evidence of how simple, prokaryote cells, evolved into more complex, eukaryote cells by endosymbiosis - something creationists insist didn’t happen, so they are already an acute embarrassment for creationists. Now we have this finding that a supposed intelligent design process would look like a design to cause cancer.
This was discovered recently by a team of researchers at the University of Cambridge and Queen Mary University of London. The team were investigating a 2018 claim by researchers at the Cincinnati Children’s Hospital Medical Center in the USA, that there were occasional instances of inheritance of paternal mtDNA, in contradiction to the normally accepted view that mtDNA in inherited exclusively from the maternal line because the sperm head, which fertilizes the egg does not contain any mitochondria.
The Cambridge/London team found that these were in fact examples of the migration of sections of mtDNA into the cell nucleus where they had become incorporated into the nuclear DNA. The process is in theory a two-way process except for two things:
There is only one nucleus with two copies of the DNA, but a cell can contain thousands of mitochondria, each with a copy of its DNA so the odds are greatly in favour of sections of mtDNA becoming free-roaming.
The nuclear membrane has pores which allow RNA to pass out into the cell, whereas the mitochondrial membrane is an intact barrier through which DNA or RNA can't normally pass.
The scientists’ findings are explained in a Cambridge University press release:
A research team from Sweden, Spain and Morocco have found genomic evidence that two waves of migrants took agriculture to North Africa in about 5400 BCE where it was adopted by the local population. One wave came along the north Mediterranean coast and through Iberia, and the second a short time later, from the Levant along the south Mediterranean coat.
For the previous 8,000 years and maybe even longer, the people of the western end of the Maghreb had been more or less isolated and lived as hunter-gatherers. Genetic evidence from 15,000 year old fossils shows that the population were intermediate between the people of the Levant and sub-Saharan Africans, and then, about 7,400 years ago, there was an ingression of Eurasia genes and culture from Spain as agriculturalists migrated to the Maghreb to live alongside the indigenous population, followed about a hundred years later, by a second wave of pastoralists from the Eastern end of the Mediterranean migrating along the North African coast, bringing a third population into the mix.
Later, in the Neolithic, these groups had merged into a single population.
It almost goes without saying that the team found no evidence of the population being exterminated in a flood, to be replaced after about 2000 BCE by a population from the Middle East, all descended from a small, incestuous band of eight related individuals, as they would have been if creationist fairy-tales were real history.
The News release from Uppsala University explains the study:
If their dupes understood them, a number of papers published recently in a special 'Primate Genomes' edition of science would be giving creationist cult leaders panic attacks, because they all show how deeply embedded the Theory of Evolution is in modern biology as the explanation for the observable evidence, and it also shows how human evolution fits completely into the science of primate evolution.
The papers are the result of studies by a large international team of researchers including scientists from the German Primate Center - Leibniz Institute for Primate Research, (Deutsches Primatenzentrum - DPZ). These studies analysed the genomes of 809 individuals from 233 primate species, generating the most complete catalog of genomic information about our closest relatives to date.
It shows, amongst other things that, like the modern humans species, Homo sapiens, which is the result of several periods of diversification then ingression of genes from related species by interbreeding, such as that between H. sapiens, Neanderthals, Denisovans and others inside and outside Africa, some modern baboons also had an ingression of genes from related species.
Recent new findings illustrate the way a species will evolve by diverging into related species that may still be able to interbreed even though other indicators show that they should be regarded as a distinct species. It also shows how a single species can diverge into populations as the precursor to evolving into subspecies and then species.
How are dingoes unique?
Dingoes possess several unique characteristics that distinguish them from domestic dogs and wolves. These characteristics include:
Size and Body Proportions: Dingoes are typically smaller than wolves and many domestic dog breeds. They exhibit a lean and agile body structure with a head that is broader and flatter than that of domestic dogs.
Coat Color and Texture: Dingoes commonly have a sandy or reddish-brown coat color, although variations can occur. Their coat is usually short, dense, and well-adapted to the Australian climate. Some dingoes have a white chest and facial markings.
Cranial Features: Dingoes often have a skull shape that is different from both domestic dogs and wolves. Their skull is generally longer and less domed than that of most dogs, with a narrower zygomatic arch (cheekbone) region.
Dentition: Dingoes possess a unique set of teeth, including relatively large canine teeth and sharp carnassial teeth adapted for cutting flesh. Compared to domestic dogs, their teeth are generally larger and exhibit less size variation.
Behavior and Social Structure: Dingoes are highly adaptable and display behavior suited to their semi-arid and arid habitats. They are generally more independent and less social than domestic dogs. Dingoes often live in small packs or as solitary individuals, whereas wolves form larger, more structured packs.
Reproduction and Breeding: Dingoes typically have a different breeding cycle than domestic dogs, with a once-a-year breeding season. They also exhibit different mating behaviors and have fewer puppies per litter compared to many domestic dog breeds.
It's important to note that while these characteristics are typical of dingoes, there can be variations among individuals and populations. Additionally, some of these traits may be influenced by interbreeding between dingoes and domestic dogs, which can introduce genetic diversity into the dingo population.
ChatGPT3 "What are the unique characteristics that distinguish dingoes from domestic dogs and wolves?" [Response to user question]
Retrieved from https://chat.openai.com/
It also shows how, as science refines and improves its techniques, new information brings about a change of consensus in a classic example of scientific opinion changing when the information changes, unlike religion which needs to find reasons not to change its collective mind despite new information, or risk another fragmentation into mutually hostile sects.
The study is a re-examination and re-evaluation of the status of the Australian dingo, Canis dingo, in view of improved DNA testing. Using earlier techniques which involved comparing just 23 DNA markers, geneticists had concluded that there were very few pure-bred dingoes left as most had DNA derived from hybridization with feral domestic dogs, Canis familiaris. On that basis, the dingo was reclassified as a wild dog and an invasive pest, and several eradication programs were implemented.
But a new study, using newer techniques which enable the scientists to compare not just 23 but 195,000 DNA markers has revealed a very different picture. This shows not only that ingression of familiaris DNA has been very limited in some areas, but that the dingo species can be regarded as four distinct populations. In other words, not only is the dingo still a species distinct from feral dogs but the dingo species is showing early signs of speciating.
It is now accepted that dingoes have not evolved directly from wolves so are not a subspecies of Canis lupus but are descended from the Southeast Asian domestic dog, meaning they were taken to Australia by humans and have evolved to adapt to the Australian environment. They have also been there so long that they have become an important part of the Australian ecosystem as apex predators, so can't now be regarded as an alien species, unlike rabbits, rats, European foxes, mice, cane toads and domestic cats.
The new study, by geneticists from the University of New South Wales and Sydney University, NSW, Australia, with colleagues in the National Human Genome Research Institute, National Institutes of Health, Bethesda, Maryland, USA, is published, open access, in the journal Molecular Ecology.
Three of the scientists, Kylie M Cairns, Research fellow, UNSW Sydney, Mathew Crowther, Associate professor, University of Sydney and Professor Mike Letnic, Evolution and Ecology Research Centre, UNSW Sydney have explained their research and its significance for dingo conservation in an article in The Conversation. Their article is reprinted here under a Creative Commons license, reformatted for stylistic consistency.
Genetic information is stored as long, complex sequences of the four different bases in DNA: adenine (A), thymine (T), guanine (G) and cytosine (C). Triplets of these bases are interpreted by the genetic machinery as instructions to add a certain amino acid to a protein.
Alfred Pasieka/Science Photo Library/Getty Images Plus
By way of an introduction to this article on abiogenesis, I'm going to try to dispel the common, but evidence-free claim from creationists that the genetic code is so complex that it must have been designed by an intelligent designer.
This is, of course, nothing but the usual argument from ignorant incredulity and a false dichotomy fallacy - I don't know enough, I can't be bothered to learn, and I can't imagine how something could have arisen naturally, so God did it - and of course it must be the locally popular god because there are only two possibilities; the current science or the local god. It's an argument that demonstrates better than most the scientific illiteracy, intellectual bankruptcy and cultural chauvinism of creationism.
First, I look at the genetic codes and how it could have evolved naturally, without a supernatural magician making chemistry and physics do things they couldn't do without it, or making the highly improbable happen - as though the notion of an undetectable entity existing outside space and time but able to influence things inside space and time makes any sense.
The first anatomically modern Homo sapiens to migrate out of Africa were almost certainly hunter-gatherers. This much can be deduced from the fact that agriculturalists tend to be relatively sedentary and tied to the land. Our early ancestors, however, were migrants who spread relatively rapidly and one of the best habitats for hunter-gatherers is the coast where food in the form of shell-fish is abundant.
It is often assumed that these migrants travelled up the Nile or the Red Sea coast to the Middle East, and dispersed from there, but there is an alternative coastal route once they arrived at the Horn of Africa.
It is a short sea journey from there to what is now Yemen in Arabia and from there either up the Hijaz to the Middle East or along the south-east coat to what is now Oman. From Oman it is again a short sea-crossing at the Gulf of Hormuz, or even up the Arabian Gulf coast, into what is now Iran. From there, the whole of south and south-east Asia is accessible by coastal spread, as is Mesopotamia and then Central Asia either by going round the Black Sea coast, or the more difficult rout through the Caucasus mountains between the Black Se and the Caspian Sea.
Even Australia could be reached via land at a time when sea-levels were much lower than today at glacial maxima.
And now, a team of Australian researchers led by Raymond Tobler and Yassine Souilmi, of the Australian Centre for Ancient DNA, The University of Adelaide, Adelaide, South Australia, Australia, have found genetic evidence of a 30,000 year period of evolutionary adaptation to a colder environment, probably in Arabia of the immediate area, prior to a rapid dispersal across Eurasia as far as Australia. Functional targets in the genome include multiple interacting loci involved in fat storage, neural development, skin physiology, and cilia function, with associations with multiple modern Western diseases.
The team’s findings were published recently in PNAS, sadly behind a paywall, although the Abstract is published open access.
Three of the team have also written about their research and findings in an article in The Conversation. There article is reprinted here under a Creative Commons license, reformatted for stylistic consistency:
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
chatGPT3 "Tell me about the Zoonomia Consortium, with references." [Response to user question]
Retrieved from: https://chat.openai.com/
Yet more evidence of mammalian common origins and the lack of intelligence in design, or, if we assume design, then evidence of malevolence, has emerged from the Zonomia Consortium this week.
Researchers at the University of Southern California (USC) Keck School of Medicine have used their database of the genomes of 240 different mammal species, to work out why humans suffer from diseases despite being the end-point of millions of years of evolution that might have been expected to weed out predisposition to diseases.
It turns out that most of the genes that lead to diseases are in a group of highly conserved genes that are common to all mammals. These genes appear to be highly constrained in evolutionary terms, meaning that any mutations would have been seriously deleterious so making their carriers less successful in competition with carriers of the normal allele.
As the USC Keck School of Medicine news release explains:
“Why do humans have disease if they went through millions of years of evolution?” It’s a question Steven Gazal, PhD, assistant professor of population and public health sciences at the Keck School of Medicine of USC, hopes to answer.
Gazal is part of an international team of researchers who have become the first to precisely identify base pairs of the human genome that remained consistent over millions of years of mammalian evolution, and which play a crucial role in human disease. The findings were published in a special Zoonomia edition of Science.
Gazal and his team analyzed the genomes of 240 mammals, including humans, zooming in with unprecedented resolution to compare DNA. They were able to identify base pairs that were “constrained” – meaning they remained generally consistent – across mammal species over the course of evolution. Individuals born with mutations on these genes may not have been as successful within their species or were otherwise not likely to pass down the genetic variation. “We were able to identify where gene mutations are not tolerated in evolution, and we demonstrated that these mutations are significant when it comes to disease,” explains Gazal.
The team found that 3.3% of bases in the human genome are “significantly constrained,” including 57.6% of the coding bases that determine amino acid position, meaning these bases had unusually few variants across species in the dataset. The most constrained base pairs in mammals were over seven times more likely to be causal for human disease and complex trait, and over 11 times more likely when researchers looked at the most constrained base pairs in primates alone.
The dataset was provided by the Zoonomia consortium, which according to the project website, “is applying advances in DNA sequencing technologies to understand how genomes generate the tremendous wealth of animal diversity.” Gazal gives credit to Zoonomia for making this type of data available to researchers and anticipates it will be widely used by human geneticists. “It’s a cheap resource to generate, as opposed to datasets generated in human genetic studies,” says Gazal.
His team’s findings are a significant step forward, as Gazal notes, “we do not understand 99% of the human genome, so it is fundamental to understand which part has been constrained by evolution and is likely to have an impact on human phenotypes.” Their discoveries and methods could become crucial tools for further research.
The next step for Gazal and his team is to repeat the process with a primate-only dataset. By restricting the subjects, they hope to focus on functions of DNA that appeared more recently in human evolution. “We expect this to be even more useful in determining information on human disease,” says Gazal.
Thousands of genetic variants have been associated with human diseases and traits through genome-wide association studies (GWASs). Translating these discoveries into improved therapeutics requires discerning which variants among hundreds of candidates are causally related to disease risk. To date, only a handful of causal variants have been confirmed. Here, we leverage 100 million years of mammalian evolution to address this major challenge.
RATIONALE
We compared genomes from hundreds of mammals and identified bases with unusually few variants (evolutionarily constrained). Constraint is a measure of functional importance that is agnostic to cell type or developmental stage. It can be applied to investigate any heritable disease or trait and is complementary to resources using cell type– and time point–specific functional assays like Encyclopedia of DNA Elements (ENCODE) and Genotype-Tissue Expression (GTEx).
RESULTS
Using constraint calculated across placental mammals, 3.3% of bases in the human genome are significantly constrained, including 57.6% of coding bases. Most constrained bases (80.7%) are noncoding. Common variants (allele frequency ≥ 5%) and low-frequency variants (0.5% ≤ allele frequency < 5%) are depleted for constrained bases (1.85 versus 3.26% expected by chance, P < 2.2 × 10−308). Pathogenic ClinVar variants are more constrained than benign variants (P < 2.2 × 10−16).
The most constrained common variants are more enriched for disease single-nucleotide polymorphism (SNP)–heritability in 63 independent GWASs. The enrichment of SNP-heritability in constrained regions is greater (7.8-fold) than previously reported in mammals and is even higher in primates (11.1-fold). It exceeds the enrichment of SNP-heritability in nonsynonymous coding variants (7.2-fold) and fine-mapped expression quantitative trait loci (eQTL)–SNPs (4.8-fold). The enrichment peaks near constrained bases, with a log-linear decrease of SNP-heritability enrichment as a function of the distance to a constrained base.
Zoonomia constraint scores improve functionally informed fine-mapping. Variants at sites constrained in mammals and primates have greater posterior inclusion probabilities and higher per-SNP contributions. In addition, using both constraint and functional annotations improves polygenic risk score accuracy across a range of traits. Finally, incorporating constraint information into the analysis of noncoding somatic variants in medulloblastomas identifies new candidate driver genes.
CONCLUSION
Genome-wide measures of evolutionary constraint can help discern which variants are functionally important. This information may accelerate the translation of genomic discoveries into the biological, clinical, and therapeutic knowledge that is required to understand and treat human disease.
Using evolutionary constraint in genomic studies of human diseases.
(A) Constraint was calculated across 240 mammal species, including 43 primates (teal line). (B) Pathogenic ClinVar variants (N = 73,885) are more constrained across mammals than benign variants (N = 231,642; P < 2.2 × 10−16). (C) More-constrained bases are more enriched for trait-associated variants (63 GWASs). (D) Enrichment of heritability is higher in constrained regions than in functional annotations (left), even in a joint model with 106 annotations (right). (E) Fine-mapping (PolyFun) using a model that includes constraint scores identifies an experimentally validated association at rs1421085. Error bars represent 95% confidence intervals. BMI, body mass index; LF, low frequency; PIP, posterior inclusion probability.
Abstract
Thousands of genomic regions have been associated with heritable human diseases, but attempts to elucidate biological mechanisms are impeded by an inability to discern which genomic positions are functionally important. Evolutionary constraint is a powerful predictor of function, agnostic to cell type or disease mechanism. Single-base phyloP scores from 240 mammals identified 3.3% of the human genome as significantly constrained and likely functional. We compared phyloP scores to genome annotation, association studies, copy-number variation, clinical genetics findings, and cancer data. Constrained positions are enriched for variants that explain common disease heritability more than other functional annotations. Our results improve variant annotation but also highlight that the regulatory landscape of the human genome still needs to be further explored and linked to disease.
The significant points, that creationist will avoid like the plague, are:
The evidence of common ancestry of the mammals in the study.
The lack of any evidence that the scientists were rejecting the TOE as an explanation for the observed facts.
The inevitable conclusion that if a magic designer designed genes to cause diseases, then the designer can only be described as malevolent; it this was an accident, then incompetence is the only explanation.
Even if, as 'theistic evolutionists' argue, an invisible supernatural deity was guiding human evolution, it was either incompetent, or malevolent, in allowing genes that caused diseases to be conserved in the evolving human genome.
But those who want to feel important, as the conscious creation of a mighty god who made everything just for them, are hardly likely to allow little considerations like those to make them feel they might be less important than they want to feel.
How a 'Macro-Evolutionary' Change can be Produced by Changes to a Few Genes.
A transient change in expression of one gene (Shh) can produce a cascade of developmental events leading to the formation of feathers instead of scales
Lurk a while in any Evolution vs Creationism group in the social media and you can guarantee a creationist will try to argue that a given example of evolution which they have probably just deamnded be provided, and which conforms to the scientific definition of evolution - any change in allele frequency over time - is not real evolution because it wasn't 'macro-evolution' which they will define as a change in 'kind' or the evolution of a new species, even the evolution of new structures - whichever definition they think stands the best chance of winning.
I've been at this for long enough to remember how, when the early internet 'bulletin boards' on CompuServe had morphed into thriving debate 'forums', creationists would simply argue that there was no such thing as evolution, full stop! It simply never happened; not in the slightest. No Way! Everything was created exactly as it is today during 'Creation Week' a few thousand years ago! Any evidence to the contrary was a forgery by evil scientists or had been planted by Satan.
Then, in the face of so much evidence, particularly the very large number of living and extinct species and the impossibility of them all being collected together in a few days, herded onto a wooden boat and surviving for a year, they began to concede that there had indeed been evolution, but only limited to evolution withing species, and evolution moreover at a phenomenal rate, far exceeding anthing proposed by biologists, so as to produce the millions of species from a few 'kinds' that survived the genocidal flood their putative creator had inflicted on its creation, just a few thousand years ago.
What creationists are doing is moving the goal-posts by redefining a well-understood scientific term to place it beyond what science actually claims, so they can demand evidence of something that no evolutionary biologist ever claimed - that a single mutation produced a new species or that one species gave birth to another in a single event, ignoring the fact that evolutionary biologists understand the evolution is normally a slow process which takes place in the species gene pool, with the instances of new species arising by, for example, hybridization, being rare exceptions, but nevertheless, natural processes, not requiring supernatural entities to explain.
So, ask a creationist now wedded to the notion that real evolution needs to be 'macro-evolution' to define a reptile 'kind' and a bird 'kind' and they will normally define a reptile 'kind' as having scales and a bird 'kind' as having feathers, ignoring the fact that paleontologists have discovered several feathered dinosaurs (reptiles).
Now, present a creationist with an example such as the one in this research paper, where changes to a small number of genes resulted in what they would define as 'macro-evolution', i.e., a change in 'kind' because that change in chickens results in them growing feathers where they normally grow scales, showing the feathers are simply evolved scales.
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:
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.
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.
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.
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.”
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 data1,2. 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 regions3,4. 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 sequences5,6.
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.
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!
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:
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:
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:
A discovery by scientists at the University of California San Diego School of Biological Science has scuppered yet another creationist fallacy, usually backup up by a blatant misrepresentation of what Darwin actually said (as though that matters anyway).
Creationists like to try to fool their dupes with the lie that Darwin admitted that the eye could not be explained by evolution, as though Darwin was a secret intelligent design creationist who let it slip in a book he wrote, and repeated that blunder in several editions. The quote you'll often see attributed to Darwin is:
To suppose that the eye with all its inimitable contrivances for adjusting the focus to different distances, for admitting different amounts of light, and for the correction of spherical and chromatic aberration, could have been formed by natural selection, seems, I freely confess, absurd in the highest possible degree.
But Darwin, in typical style, was merely setting out the problem before giving the solution. What you'll never see posted by a creationist is the full quote, which continues:
Yet reason tells me, that if numerous gradations from a simple and imperfect eye to one complex and perfect can be shown to exist, each grade being useful to its possessor, as is certainly the case; if further, the eye ever varies and the variations be inherited, as is likewise certainly the case; and if such variations should be useful to any animal under changing conditions of life, then the difficulty of believing that a perfect and complex eye could be formed by natural selection, though insuperable by our imagination, can hardly be considered real.
Charles Darwin, “On the Origin of Species by Means of Natural Selection, or the Preservation of Favoured Races in the Struggle for Life," first edition (1859). Chapter 6, "Difficulties on Theory", page 187, 6th edition, page 217.
Since then, numerous experiments have shown how a patch of light-sensitive cells will quickly evolve into a functional eye if there is a benefit to each step. In other words, Darwinian gradualism perfectly explains the evolution of the eye.
Stages in the evolution of the vertebrate eye
All that remains to explain is the evolution of light-sensitive cells.
And this was done by the University of California San Diego team, who show that mammals acquired light-sensitivity, in a way that also refutes another creationist lie.
They acquired it by horizontal gene transfer. Horizontal gene transfer is the way genes can cross from one taxon to another, giving the lie to creationists dogma which states that new information can only arise withing a genome with the assistance of a magic designer.
The team have shown that the protein needed by cells to respond to light comes from simple bacteria, and, because it is not present in other vertebrates, but have entered the genome of the last common ancestor of mammals.
The University of California, San Diego news release explains the research:
