Creationism in Crisis - How De Novo Genes Arise (And Another Creationist Dogma Bites The Dust)

The whole genome of several tens of primates and mammals is known. Comparison of genomes allows for studying the evolution of individual genes.

Image: Mostphotos

New genes can arise from nothing | HiLIFE – Helsinki Institute of Life Science | University of Helsinki

Present a creationist with a puzzle like, where does new genetic information in the form of new functional genes come from and a typical response will be, "Er... I can't imagine how that's possible... so God did it!". This of course is based on the foundational fallacies of creationism, and most religious apologetics - the argument from ignorant incredulity, and the false dichotomy fallacy.

This intellectual dishonesty appeals to people who are satisfied with not knowing and aren't bothered about the truth, so long as they have an excuse for pretending they know the answer

By contrast, present a scientist with the same question, and the response will probably be, "I don't know, so how can we find out?", because admitting ignorance is the foundation of good science. This approach appeals to people who have the humility to admit they don't know and who are interested enough in truth to want to find out.

An example of this was published recently by three researchers from the Institute of Biotechnology, Helsinki Institute of Life Science, University of Helsinki, Helsinki, Finland, who decided to address the question of where de novo genes arise in the genome, seemingly from nowhere.

This question arose from the observation that a comparison between human and other primate genomes shows that a number of microRNA (miRNA) sequences arose within the human genome, and the genome of other apes apparently as single mutation events.

In addition to the 20,000 genes in the human genome, there are thousands of miRNA sequences of about 22 base-pairs which have a regulatory function. Their role is to stop messenger RNA (mRNA) from continuing to make proteins when enough have been made. They do this by blocking the mRNA molecules and to do this they need to be folded in half like a hairpin. This folding means that they need to be 'palindromes', i.e., reading the same forward as backward, so, when folded in half, each base lines up with a copy of itself.

So, the question was, how do these palindrome miRNAs arise?

Creationism in Crisis - A Monster Virus Is A BIG Problem For Creationists

Pithovirus sibericum

Legendre, Matthieu; Bartoli, Julia; Shmakova, Lyubov, et al. (2014)

Pithovirus sibericum

Pithoviruses Are Invaded by Repeats That Contribute to Their Evolution and Divergence from Cedratviruses | Molecular Biology and Evolution | Oxford Academic

Regular readers with very long memories may remember how I wrote about something big and potentially nasty emerging from Siberian permafrost back in 2014.

The 30,000-year-old monster in question was a form of giant virus then unknown to science, now named Pithoviruses sibericus. It came back to life when thawed. Since then, several other related pithoviruses have been discovered in soil and aquatic sources. Fortunately, all those discovered so far are parasitic only on one species of amoeba, Acanthamoeba castellanii and don't pose a threat to humans or multicellular life.

The question was, why are they so large, or more particularly, why do they have such a massive genome, including some genes normally found in complex cells. the Pithovirus species so far discovered have a genome of between 460 to 686 kb. Their genome, moreover, is similar to that of bacteria and archaea, in that it is DNA-based and forms a single circular 'chromosome'.

But it's not the fact that the first one was found in permafrost dating back 20,000 before 'Creation Week', difficult though that little inconvenience is for creationists; it is the account of how they acquired this massive genome that is the thing of nightmares for any creationists who understand the biology.

They acquired it by processes that give the lie to their basic dogma that new genetic information can't arise in a genome without 'God magic'.

A team of researchers have shown that they acquired new genetic information and such a massive genome by:

1. Horizontal gene transfer (5% -7 %)
2. Gene duplication (14% - 28%)
3. Massive inversions of repeated sequences of DNA.

All these are familiar mutations in which the genome size is increased, and by which 'spare' copies of genes and novel sequences are free to mutate and give rise to new genes and new functions.

And this gives the lie to the ludicrous creationist dogma that no new information can arise by mutation because all mutations are deleterious. There is nothing deleterious in having a spare copy of a gene, nor in mutations in that spare copy, least of all if it gives a new function that increases fitness.

The researchers, from the Institut de Microbiologie de la Méditerranée, FR3479), IM2B, IOM, Aix–Marseille University, Centre National de la Recherche Scientifique, Marseille, France were led by Matthieu Legendre. Their findings are published, open access, in Molecular Biology and Evolution:

Creationism in Crisis - Evolution of Rock Doves & Domestic Pigeons

Rock dove, Colmba livia neglecta (Iran)

Picture: Γεωργός via Wikimedia (CC BY-SA 4.0)

Rock dove, Columba livia.
The wild ancestor of the domestic or town pigeon

Redefining the Evolutionary History of the Rock Dove, Columba livia, Using Whole Genome Sequences | Molecular Biology and Evolution | Oxford Academic

A great deal is understood about how the many different varieties of domestic pigeon were produced ever since Charles Darwin used them to illustrate the role of selection in evolution. In this case, selection is human selection rather than natural selection, although the difference is a matter of semantics if you regard human selective breeders as part of the domestic pigeon's environment.

Incidentally, creationists should note that Darwin never claimed evolution always resulted in new species. As he showed with his selective breeding examples, it produced new varieties too. Some of these have become so far removed from their wild ancestors that they rank as subspecies, like the domestic pigeon, Columba livia domestica

Although the radiation of domestic varieties is now well understood, the wild ancestors, the rock doves, have received far less attention until now. Now a paper by a team led by Germán Hernández-Alonso of the Center for Evolutionary Hologenomics, The Globe Institute, University of Copenhagen, Copenhagen, Denmark, redresses that discrepancy by analysing the entire genomes of 65 historical rock doves that represent all currently recognized subspecies and span the species’ original geographic distribution. 3 of these specimens were from Charles Darwin's collection.

This works shows that rock doves have diversified into a number of subspecies across their range, stemming from a subspecies now restricted to a small coastal strip of Northwest Africa, C. livia gymnocyclus. One of these subspecies received a substantial ingression of genes from a related species, C. rupestris after it split from the West African population but before it became domesticated. The result is that C. livia gymnocyclus should now probably rank as a species in its own right, C. gymnocyclus.

First a little about the evolution of domestic pigeons:

Creationism in Crisis - Evolution of a Carnivorous Pitcher Plant by Gene Duplication - New Genetic Information Created Naturally

Genomic study sheds light on how carnivorous Asian pitcher plants acquired signature insect trap - University at Buffalo

East Asian pitcher plants, Nepenthes gracilis.

Photo: Pierre-Louis Stenger

East Asian pitcher plants capture insects using their highly specialized pitcher-shaped leaves, which may have resulted from duplicated genomes.

Photo: Pierre-Louis Stenger.

Genomic study sheds light on how carnivorous Asian pitcher plants acquired signature insect trap - University at Buffalo

Unlike so many biology, geology and palaeontology papers published recently, this paper doesn't refute creationism by showing how much of Earth's history occurred before creationism's mythical 'Creation Week', although the genetic changes almost certainly did occur in the long period of 'pre-Creation' history.

Instead, it refutes two more of creationism's favourite fallacies:

1. Genetic information can't be created without the magical assistance of a creator god. This is a fundamental axiom, taught to creationists by cult leaders such as William Dembski, who fooled them by equating 'information' with energy and citing the Third Law of Thermodynamics. It's a belief clung to despite the repeated evidence of gene duplication and repurposing of resulting redundancy.
2. The fallacy of irreducible complexity which wrongly assumes that a complex system must have arisen as a single event and was so highly unlikely that a magic god must have created it. This is taught to them by another cult leader, Michael J. Behe, despite the evidence that 'irreducibly complex' systems can and do arise by exaptation of pre-existing, redundant structures or steps in a metabolic pathway that arise in parallel in the species gene pool, not all at once in a single event in one individual or cell.

The paper, by a large team of researchers that included Victor Albert, PhD, Empire Innovation Professor in the University at Buffalo Department of Biological Sciences, within the College of Arts and Sciences, concerns the evolution of the carnivorous East Asian pitcher plant, Nepenthes gracilis, in particular the 'pitcher' traps and the condition of dioecy, which is unique in this genus of plants.

And, just in case creationists declare that mere gene duplication wouldn't create enough new genetic information, this species doesn't have just one or a few genes duplicated and repurposed; they don't even stick with a whole genome duplication, They actually have five whole genome duplications making them decaploid, an extreme example of polyploidy!

Creationism in Crisis - The Multiple Origins of Homo Sapiens Over Hundreds of Thousands of Years

View of the village of Kuboes, on the border of South Africa and Namibia. DNA samples were collected from Nama individuals who have historically lived in the region.

Photo: Brenna Henn/UC Davis

Nama women of Namibia
The Nama are an indigenous population known to carry exceptional levels of genetic diversity compared to other modern groups.

New UC Davis Research Using DNA Changes Origin of Human Species, Researchers Suggest | UC Davis

In an article which passed beneath my radar last May, a team of anthropologists led by Professor Brenna Henn of the Genome Center at the University of California, Davis, cast doubt on the theory that modern humans all originated in a single population in East Africa.

Instead, they propose a model in which early Homo sapiens spread across Africa forming partially isolated populations, between which there was limited gene flow by interbreeding.

The earliest split which is still detectable in the DNA of contemporary people occurred between 120,000 to 135,000 years ago after two or more weakly genetically differentiated populations had been mixing for hundreds of thousands of years.

Before creationists start to get over-excited by the news that earlier scientists might have been wrong about the exact details of the evolution of modern humans, they should break the habit of a lifetime and find the courage to read the abstract to the paper in Nature, which makes it clear that the debate is about the details of our evolutionary origins in Africa. There is no serious doubt about the truth of that explanation.

As a UC Davis press release explains:

Creationism in Crisis - Damselflies Evolved Their Colours At Least 5 Million Years Before 'Creation Week'

The common bluetail damselfly Ischnura elegans

Photo: Erik Svensson

Common bluetail damselflies, Ischnura elegans

Credit: Quartl, CC BY-SA 3.0, via Wikimedia Commons

Scientists have solved the damselfly colour mystery | Lund University

So much history, especially the evolutionary history of life on Earth, occurred before the mythical Creation Week, when creationists believe a magic man who existed when nothing existed made the universe out of that nothing, that it’s difficult to keep up with it all.

Here, for example, is a scientific account of how damselflies evolved their colours at least 5 million years before Creation Week, by an evolutionary process guaranteed to have creationists going into abject denialism and lying to one another about it in their echo chambers, if not throwing a tantrum, stamping their feet and shouting abuse at the facts to make them go away, or at the scientists who discovered the facts.

The bluetail damselfly, like many other damsel flies is sexually dimorphic with males being brightly coloured and the females more drab, usually brown. Females of the common bluetail occur in three color forms, one of which mimics the male, and the mystery was how, why and when did this evolve? Note here how a creationist would simply declare they were designed that way by a god whose purpose in doing so is unknowable, whilst science looks for the how and why, and so discovers a much more satisfying answer than the creationist one which makes them satisfied with not knowing.

By comparing the genome of the common bluetail, Ischnura elegans with that of a close tropical relative, Ischnura senegalensis, the scientists were able to show that the colour differences are due to mutations in a specific genetic region on chromosome 13 that arose at least 5 million years ago, so the question resolves down to why was it retained? In other words, what were the environmental selectors that spread the mutations in the population then conserved them for 5 million years?

The research was conducted by scientists at Lund University, Sweden, under biologist Professor Erik Svensson with colleagues at Stockholm University, Sweden, Institut Pasteur, Université Paris Cité, Paris, France, the University of Rennes, France and Tohoku and Chiba Universities, Japan. Their findings are published, open access, in Nature Ecology & Evolution and its significance is explained in a Lund University press release:

Creationism in Crisis - Head Lice Bring More Lousy News For Creationists

Contact between Europeans and Native Americans is recorded in the DNA of head lice.

Credit: Vincent Smith,
Natural History Museum, London, CC-BY 4.0

Head lice hitched a ride on humans to the Americas at least twice

Male human head louse, Pediculus humanus capitis

Source: Wikipedia (CC BY-SA 2.0)

According to the creationist favourite arguments - the argument from ignorant incredulity and the false dichotomy - anything which is complex, such as cells, multicellular organisms, cultural ethics, etc., must have been intelligently designed by their particular god by magic, because that is the only answer allowed. Evolution is ruled out by dogmas, as too hard to understand, by someone too lazy to learn biology and too afraid to consider being wrong.

So, following what passes for creationist logic, creationists should believe that the species-specific, obligate parasite, the head louse, Pediculus humanus capitis, must have been intelligently designed by the creationists' god.

Which begs the questions, why would an omnibenevolent designer:

1. design an irritating parasite?
2. design its DNA to look like head lice had co-evolved with humans over millions of years from a common ancestor with the louse, Pediculus schaeffi, that parasitises chimpanzees?

And, as with all host-specific, obligate parasites, like pubic lice, chlamydia, and other STDs, there is the little matter of who on the Ark, was host to them and how did they acquire them?

Of the three lice that can infest humans, the head louse, Pediculus humanus capitis, the closely-related body louse, P. h. humanus and the more distantly-related pubic louse, Phthiriasis pubis, all have their counterparts in our nearest great ape relatives, in the latter case, the gorilla, and all have genomes that map closely onto the evolutionary history of different human populations.

Humans inherited the ancestor of P. humanus when we diverged from the chimpanzees and, as we lost body hair, it became isolated to our head and facial hair. Later, when we started wearing clothes, our lice diverged into two sub-species, P. h. capitis and P. h. humanus (also called P. h. corporis) respectively. How we managed to acquire the sexually-transmitted pubic or crab louse, Phthiriasis pubis, from an ancestor of gorillas about 3.3 million years ago, is a matter for speculation.

What are the three species of lice that infest humans and what can they tell us about our evolutionary history and the history of different human populations? There are three species of lice that infest humans:

1. Pediculus humanus capitis:This is the head louse, which infests the human scalp and hair.
2. Pediculus humanus corporis:This is the body louse, which lives and lays its eggs on clothing and only feeds on the human body.
3. Pthirus pubis:This is the pubic louse, which infests coarse body hair, especially in the genital area but can also be found in other coarse body hair.

These lice can provide insights into our evolutionary history and the history of different human populations through a field known as "phylogeography." Phylogeography involves studying the genetic variation within a species to understand its historical migration patterns and population dynamics. Lice are highly host-specific, meaning that they have evolved to live on and feed exclusively from humans. The divergence of head and body lice is thought to have occurred when humans began wearing clothing. The body louse adapted to live in clothing and only feeds on the human body when needed, while the head louse remained adapted to living in human hair. Research on the genetic diversity of human lice has contributed to our understanding of human evolution and migration. For example, studies have used genetic data from lice to estimate when humans started wearing clothing, which is linked to the migration out of Africa. The idea is that as humans migrated to different climates, the need for clothing increased, leading to the divergence of body lice from head lice. Additionally, the study of lice genetics has been used to investigate the timing and patterns of human migration and to trace the movement of human populations over time. This research helps scientists map out the historical interactions and separations of human populations, providing valuable information about the peopling of different regions of the world. In summary, the genetic diversity of human lice provides clues about our evolutionary history, including migration patterns, the development of cultural practices like clothing use, and the historical interactions among human populations.

Now, a group of scientists led by Marina Ascunce, of the United States Department of Agriculture’s Agricultural Research Service (USDA-ARS), together with colleagues, have used this knowledge to show that head lice came to America twice; once with the first wave of human migration from Siberia via the land bridge, Beringia, which was located between Siberia and Alaska, what is now the Bering Strait, when sea-levels were lower, and again with European colonists. They report these findings in a new study published on November 8 in the open-access journal PLOS ONE.

The new study analysed the DNA of 274 human lice from 25 geographic sites around the world. This analysis revealed the existence of two genetically isolated clusters of lice that only rarely interbred. Cluster I had a worldwide distribution, while cluster II was found in Europe and the Americas. There is also a population found in the Americas which appears to be the result of a mixture between lice descended from populations that arrived with the First People carrying cluster I lice and those descended from European (cluster II) lice, which were brought over during the colonization of the Americas.

The researchers also identified a population of lice in Central America which shows a close genetic with lice in Asia. This is consistent with the idea that people from East Asia migrated to North America and became the first Native Americans. These people then spread south into Central America, where modern louse populations today still retain a genetic signature from their distant Asian ancestors.

Abstract The human louse, Pediculus humanus, is an obligate blood-sucking ectoparasite that has coevolved with humans for millennia. Given the intimate relationship between this parasite and the human host, the study of human lice has the potential to shed light on aspects of human evolution that are difficult to interpret using other biological evidence. In this study, we analyzed the genetic variation in 274 human lice from 25 geographic sites around the world by using nuclear microsatellite loci and female-inherited mitochondrial DNA sequences. Nuclear genetic diversity analysis revealed the presence of two distinct genetic clusters I and II, which are subdivided into subclusters: Ia-Ib and IIa-IIb, respectively. Among these samples, we observed the presence of the two most common louse mitochondrial haplogroups: A and B that were found in both nuclear Clusters I and II. Evidence of nuclear admixture was uncommon (12%) and was predominate in the New World potentially mirroring the history of colonization in the Americas. These findings were supported by novel DIYABC simulations that were built using both host and parasite data to define parameters and models suggesting that admixture between cI and cII was very recent. This pattern could also be the result of a reproductive barrier between these two nuclear genetic clusters. In addition to providing new evolutionary knowledge about this human parasite, our study could guide the development of new analyses in other host-parasite systems.

Fig 1. Humans and lice.
The map shows the geographic distribution of the modern human head lice included in this study using green dots. Archeological findings of human lice are shown with the figure of a human louse on the map with the corresponding estimated dates from: [3, 5, 6, 21, 22]. In addition, the map reflects the approximate locations of hominin fossil remains and their proposed distribution based on: [23–38]. Each hominin is color coded as follows: Neanderthal (Blue), Denisovan (Black), and Anatomical Modern Humans (Orange).

The outline map was downloaded from Wikimedia: Map author: Maulucioni (https://commons.wikimedia.org/wiki/File:World_map_with_the_Americas_on_the_right.png).
This file is licensed under the Creative Commons Attribution-Share Alike 4.0 International license. https://creativecommons.org/licenses/by-sa/4.0/legalcode.

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Fig 5. Proposed global co-migration of human lice and humans.
Top: Map depicting the collection sites of the human lice included in this study. The color of each circle corresponds to the majority nuclear genetic cluster to which sampled individuals were assigned. Sites with admixed lice are indicated with patterned circles including colors of the two major genetic clusters at that site. The proposed migrations of anatomically modern humans out of Africa into Europe, Asia and the Americas, as well as the more recent European colonization of the New World are indicated with thick grey arrows. Hypothetical human louse co-migrations are indicated with orange and blue arrows. At the bottom, the STRUCTURE plot from Fig 3A corresponding to the assignment of 274 lice from 25 geographical sites at K = 4 (Table 1) is shown.

The outline map was downloaded from Wikimedia: Map author: Maulucioni (https://commons.wikimedia.org/wiki/File:World_map_with_the_Americas_on_the_right.png).
This file is licensed under the Creative Commons Attribution-Share Alike 4.0 International license. https://creativecommons.org/licenses/by-sa/4.0/legalcode.

Ascunce MS, Toloza AC, González-Oliver A, Reed DL (2023)
Nuclear genetic diversity of head lice sheds light on human dispersal around the world.
PLoS ONE 18(11): e0293409. https://doi.org/10.1371/journal.pone.0293409.

Copyright: © 2023 The authors.
Published by [publisher] Open access.
Reprinted under a Creative Commons CC0 1.0 DEED (CC0 1.0 Universal)

As the author point out, analysis of the DNA of host-specific obligate parasites such as lice can help fill in gaps in the fossil record because their evolution is closely linked to their host's evolution, patterns of migration and , in our case, to cultural changes such as wearing cloths. Again, in the case of humans, a clear pattern emerges which maps exactly onto other evidence of migration, isolation and remixing, confirming the value of DNA analysis in this respect. There is a clear line of migration out of Africa into Asia and from Asia into the Americas with the earliest human migrants. The lice Europeans inherited, had been partially isolated in the European Peninsula with their hosts, or possible had evolved with Neanderthals who then passed them on the modern humans, were the able to remix with the Asian/American variety from the 15th century onwards.

So what creationists need to explain, as well as why their putative designer went to the trouble of designing an obligate parasite to live on us, is why it then gave them DNA that looked like they had evolved over millions of years, share a ecommon ancestor with those of chimpanzees and reflected our pattern of migration out of Africa and across the world over a period of several tens of thousands of years.

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Creationism in Crisis - A Population of Greenland's Ringed Seals Has Been Isolated Since 90,000 Years Before 'Creation Week'

North Atlantic Ringed Seal

The Kangia Ringed Seal of Greenland's Ilulissat Icefjord

The ringed seals in Ilulissat Icefjord, Greenland, are special

How an isolated population of a species diverges from the 'parent', both genetically and phenotypically, is illustrated by a population of Arctic ringed seals, Pusa hispida hispida which is normally a wide-ranging circumpolar species but a population of which is more or less sedentary in the Ilulissat Icefjord in Western Greenland, and so is isolated from the main population.

This population, known locally as the Kangia, differs markedly in coat pattern and size from the usual ringed seal and genetic studies have shown that it has been isolated from the main population for about 100,000 years, which, to the embarrassment of creationists, means since about 90,000 years before they believe Earth existed.
The ringed seal of the Ilulissat Icefjord have been identified as a distinct subspecies by a research team led by Greenlandic and Danish researchers. Their results are published open access in the journal Molecular Ecology.

Tell me all about the Arctic ringed seal, especially the Kangia from western Greenland. The Arctic ringed seal (Pusa hispida), often referred to as simply the ringed seal, is a species of seal found primarily in the Arctic and subarctic regions of the Northern Hemisphere. These seals are well adapted to cold environments and are considered the smallest and most abundant of the Arctic seals. Here are some key facts about the Arctic ringed seal:

Creationism in Crisis - Some of Our Mental Heath Problems Could Be the Result of Denisovan Genes

Super-resolution STED microscopy image of HEZ293 cells transfected with the zinc transporter ZnT9 (in green). In magenta the mitochondrial protein TOM 20 and in white the localization in mitochondria.

Credit: Rubén Vicente.

Geographic distribution of the substitution identified in the SLC30A9 gene in current human populations and possible scenarios of Denisovan introgression. Ancestral SLC30A9 corresponds to the version of the gene prior to interbreeding between Denisovans and sapiens. SLC30A9 variant, refers to the version shared with Denisovans.

Credit: Jorge Garcia and Elena Bosch.
Licensed under Creative Commons 4.0. Created with mapchart

Denisovan genetic inheritance may have left a mark on our mental health - Focus UPF (UPF)

A team of researchers led by the Institute of Evolutionary Biology (IBE), a joint center of the Superior Council of Scientific Research (CSIC) and Pompeu Fabra University (UPF) , and by the Department of Medicine and Life Sciences (MELIS) of the UPF, has identified one of the most widespread traces of the genetic inheritance of the extinct Denisovans in modern humans.

These genes probably played an important role in helping early Homo sapiens adapt quickly to a cold climate, but, because they are involved in the regulation of zinc and play a part in cellular metabolism could also be a contributory factor in predisposition to mental health disorders such as depression and schizophrenia.

It's tempting to assume that they may also have contributed to a growth in religion since many 'prophets' seem to have had schizophrenic disorders in which they heard voices. However, that's not the main worry for creationists in this research. What they need to cope with is the fact that all this happened in that vast expanse of time before 'Creation week' when creationists believe the universe was magicked up from nothing, just 10,000 years ago.

There is also the matter of Homo sapiens not having a single founding couple who were created without ancestors, and don't even come from a single species, but are a hybrid between several related species.

So, just who were these Denisovans?

Creationism in Crisis - How Grasses Acquired New Genetic Information - By Horizontal Gene Transfer

Natural GM crops: grasses take evolutionary shortcut by borrowing genes from their neighbours | News | The University of Sheffield

Alloteropsis semialata, acquired genes by lateral transfer from other species.

Despite Creationist dogma that no new genetic information can arise in a genome without the active intervention of a magic man in the sky, who can magically create information at will, there are several known mechanisms by which this can occur - for example, gene or even whole genome duplication, which leaves spare DNA which can mutate without harming the carrier and which, when filtered through the sieve of natural selection, can give rise to novel genes and new genetic information.

And there is horizontal gene transfer, normally thought of in terms of bacteria sharing genes in the form of plasmids with other bacteria, even from a different species. And scientists are constantly discovering new examples of horizontal gene transfer, sometimes with startling results such as the fruit fly, Drosophila ananassae which has the entire genome of the bacterium Wolbachia incorporated into its genome.

Now a team of researchers at the University of Sheffield, UK, have discovered that the evolution of grasses included frequent horizontal (or lateral) gene transfer, the effects of which were to enable them to grow taller and faster. This is a natural version of genetic modification. The research is reported in the journal New Phytologist and explained in the University of Sheffield press release:

Creationism in Crisis - How African Genetic Diversity Refutes Creationist Origin Myths - It's Those Pesky Facts Again!

Kuvale settlement in Virei, Namibe province of Angola.

© Sandra Oliveira

San people, Southern Africa

Probing the deep genetic structure of Africa | Max-Planck-Gesellschaft

Creationist dupes believe that all human life on Earth was reduced to a small band of 8 related individuals who survived a global genocidal flood and then got off a boat in Turkey and repopulated Earth from there.

Their problem is that this ludicrously implausible tale gives us a testable hypothesis - that an analysis of human genetics should show this bottle neck and the distribution of humans from that geographical point. We would also expect the greatest diversity to be found around the area of modern Turkey.

And of course, this hypothesis is easily and repeatedly falsified, which normally spells the death of any scientific hypothesis.

The scientific explanation for human origins is that modern Homo sapiens evolved in Africa and spread to the rest of the world from there, preceded, probably by archaic hominids such as H. erectus. A hypothesis stemming from this theory is that the greatest genetic diversity is to be found in Africa, because humans have been evolving there for longer than anywhere else. A recent refutation of it was found in an analysis of the genome of ancient people in the Angola/Namib region of Africa, which also validates the 'out of Africa' theory of human origins.

The work was done by a research team from the University of Bern in Switzerland, the University of Porto in Portugal and the Max Planck Institute for Evolutionary Anthropology in Germany. The Maz Planck Institute News release explains it:

Malevolent Designer News - How Creationism's Favourite 'Designer' Made Alzheimers More Likely

[left caption]

[Right caption/credit]

IU researchers identify new gene mutation that alters Alzheimer’s disease risk

The terrible week for creationism continues unabated: Following yesterday’s news of more evidence of common descent of the great apes, including humans, we have news that creationism's putative designer has apparently given some people a gene variant that increases their risk of developing Alzheimer’s dementia in later life, while some others get a variant the reduces that risk.

A problem of creationists' own making is the insistence that mutations don't happen by chance but need the deliberate intervention of their favourite putative designer, without whom nothing happens.

This means they need to ignore the existence of parasites, which, if they were designed deliberately, can only be regarded as evidence that whatever designed them had malevolent intent, and intended to increase the suffering in the world, since that is what they do.

It also means they need to ignore the evidence that a lot of diseases are caused by mutations, especially the degenerative diseases in older people, which don't manifest until after they have produced their offspring, and so passed on their genetics, including any mutations.

This is where we come to the news that a large team of researchers, led by scientists from Indiana University School of Medicine, USA, have identified a mutation in a critical gene for the brain's immune system, so greatly increasing the risk of developing Alzheimer's.

Creationism in Crisis - An Acute Bottleneck in Early Hominin Ancestral History - Almost a Million Years Ago

The core formula of the new inference method is shown. The image depicts a cliff painting, illustrating the population of human ancestor pull together to survive the unknown danger in the darkness during the ancient severe bottleneck.

Image by Shanghai Institute of Nutrition and Health, CAS

Early Ancestral Bottleneck Could’ve Spelled the End for Modern Humans----Shanghai Institute of Nutrition and Health, Chinese Academy of Sciences

African savannah in the Middle Pleistocene (Artist's Impression)

Credit: Peter Schouten

Creationists claim, without any understanding of the biological absurdity of the claim, that the human population on Earth went through a genetic bottleneck of 8 related individuals about 4,000 years ago following a genocidal flood inflicted on Earth by an angry god, annoyed that his design wasn't working as intended.

The one thing right about that claim is the bottleneck, although it wasn't so narrow that it would have almost guaranteed extinction within a few generations because of accumulated deleterious genes and a lack of genetic diversity, it was about 1,280 individuals and it happened about 900,000 years before creationists believe the universe was created, before anatomically-modern humans had evolved.

This is the findings of Chinese researchers led by Haipeng Li, of the Chinese Academy of Science (CAS) Key Laboratory of Computational Biology, Shanghai Institute of Nutrition and Health, and Yi-Hsuan Pan of the Key Laboratory of Brain Functional Genomics of Ministry of Education, School of Life Science, East China Normal University, Shanghai, China.

First, a little about evolutionary bottlenecks and the consequences for humanity had the mythical genocidal flood actually occurred as creationists believe:

Unintelligent Design News - How the Human Y Chromosome Evolved

Rost9/Shutterstock

The 'weird' male Y chromosome has finally been fully sequenced. Can we now understand how it works, and how it evolved?

An international team of scientists led by researchers from the National Human Genome Research Institute, National Institutes of Health, Bethesda, MD, USA, together with colleagues from the University of California Santa Cruz, Santa Cruz, CA, USA, the University of Connecticut, Storrs, CT, USA, Johns Hopkins University, Baltimore, MD, USA, have finally completed the task of sequencing the entire human Y chromosome from end to end or T2T (Telomere-to-Telomere). This completes the entire human genome now sequenced T2T.

Unsurprisingly, they found that most of the DNA was non-functional junk, containing the remnants of ancient retroviruses and duplicated genes that had then mutated.

The X and Y chromosomes, or sex chromosomes, are how gender is determined in humans and other mammals. Females have two copies of the X chromosome while males have one of each. Males inherit their Y chromosome from their father.

The significance of the research, and how it informs our understanding of the evolution of the Y chromosome from one of the two X chromosomes that females carry is the subject of an article in The Conversation by Professor Jenny Graves Jenny Graves, La Trobe University, Australia. Her article is reprinted here under a Creative Commons Licence, reformatted for stylistic consistency:

Creationism in Crisis - How a Deleterious Gene Can Survive in a Population

Coyote tobacco Nicotiana attenuata is a plant species native to the Great Basin Desert of the western United States.

© Ian T. Baldwin
Max Planck Institute for Chemical Ecology

Coyote tobacco, Nicotiana attenuata

Stan Shebs via Wikipedia (CC BY-SA 3.0)

It all depends on the genetic diversity | Max Planck Institute for Chemical Ecology

Mutations in genes that are essential for defence against predator attack are usually deleterious and would be expected to be quickly eliminated from a population, however, occasionally, the same mutation can convey an advantage which it is able to assert in conditions where predator populations are low, and this is especially true if wide genetic diversity within the population makes it more likely that the mutation can operate synergistically with other genes.

This can lead to a dynamic situation in which, in periods of low predation, the mutation can increase, or at least remain at a stable level in the population, and, in periods of high predation, it can be reduced. This dynamic can result in deleterious genes being retained in a population for much longer than would be expected if they were wholly deleterious.

An example of this was found recently by researchers from the Max Planck Institute for Chemical Ecology, Jena, Germany, in a wild member of the tobacco family, Nicotiana attenuata. Their finding is published in Proceedings of the National Academy of Science (PNAS)

The research and its significance are explained in a press release:

Creationism in Crisis - In Just 2000 Years Humans In Central Asia Had Diverged into Multiple Cultures Each with Distinctive DNA, If Creationists Are to be Believed

The Xiongnu built a multiethnic empire on the Mongolian steppe that was connected by trade to Rome, Egypt, and Imperial China.

© Artwork by Galmandakh Amarsanaa, courtesy of Christina Warinner and the DairyCultures Project

Multiethnic structure of Mongolia’s first nomadic empire | Max-Planck-Gesellschaft

The Xiongnu Empire, from 300BC, had a significant impact on the political economies of Central, Inner and East Asia and created extensive trade networks.

Photo: Weibo

Following the news that Ötzi the Iceman, who died just 700 years after creationists believe the human population of the world was reduced to 8 related individuals, was a brown-skinned 'outsider' in Europe, descended from people who had migrated from Anatolia a couple of thousand years earlier, comes news that an early empire in Central Asia, the Xiongnu Empire, had a multi-ethnic origin.

Each of these pieces of news give the lie to creationist claims of a genocidal flood just 4000 years ago because there would simply not be enough time for the human populations of Europe or Asia to diversify to the extent that different genetic populations would be identifiable.

Taken together, they mean even the traditional claim that the scientists knowingly used inaccurate radiometric dating is redundant. Ötzi was dated partly by dendrochronology, which is not a radiometric dating technique, and the dates of the Xiongnu Empire are from contemporaneous records kept by their neighbours in China.

First a little background, courtesy of the AI source, ChatGPT3.5:

The Xiongnu were a significant nomadic confederation that originated in Central Asia, particularly in the regions of modern-day Mongolia, Kazakhstan, and northern China. They played a crucial role in shaping the history and dynamics of the ancient Eurasian steppe region. Here are some key points about the Xiongnu:

1. Origin and Expansion: The Xiongnu are believed to have emerged around the 3rd century BCE and quickly established themselves as a dominant power in the steppe region. They were known for their skilled horsemanship and nomadic lifestyle, which allowed them to traverse vast distances and exert control over large areas.
2. Society and Culture: Xiongnu society was organized along tribal lines, with a hierarchical structure. They had a chieftain or "shanyu" at the top, followed by subordinate tribal leaders. Their culture was heavily influenced by steppe traditions, including horse riding, pastoralism, and archery. They were also known for their use of mounted warriors and chariots in warfare.
3. Conflict with China: One of the most significant aspects of Xiongnu history is their interaction with the Chinese dynasties, particularly the Han Dynasty. The Xiongnu frequently raided northern Chinese territories and established a tense relationship with the Han rulers. The Chinese even built the Great Wall as a defense against Xiongnu incursions.
4. Diplomacy and Alliances: Throughout their history, the Xiongnu engaged in both military conflicts and diplomatic negotiations with China. At times, they formed alliances or signed treaties with the Chinese in exchange for tribute or gifts. These interactions were often marked by a delicate balance of power and a mutual understanding of the benefits of maintaining stable relations.
5. Decline and Disintegration: By the 2nd century CE, the Xiongnu confederation began to weaken due to internal conflicts, external pressures, and changes in the geopolitical landscape. The rise of other nomadic groups, such as the Xianbei and the Huns, also contributed to their decline. Eventually, the Xiongnu fragmented into smaller groups, some of which merged with neighboring societies, while others faded into history.
6. Legacy: The Xiongnu left a lasting impact on the cultural and historical development of Central Asia and the surrounding regions. Their interactions with China influenced Chinese policies, military strategies, and diplomatic approaches. Additionally, the Xiongnu's nomadic lifestyle and military techniques contributed to the broader cultural and societal dynamics of the Eurasian steppe.
7. Historical Sources: Much of what is known about the Xiongnu comes from Chinese historical records and archaeological findings. Ancient Chinese texts, such as the "Records of the Grand Historian" by Sima Qian, provide valuable insights into the interactions between the Xiongnu and China.

Overall, the Xiongnu were a significant force in the ancient world, shaping the geopolitical landscape of Central Asia and leaving a lasting mark on the history of the region.

An interesting finding from the study is that genetic diversity was widest amongst the lower status individuals and much lower amongst the social elite, suggesting that a culture had developed where a narrow ethnic group had gained control of diverse populations.

And all this diversity in the two thousand years following the genocidal flood, is the Bible and its creationist advocates are to be believed. Clearly a preposterous proposition.

As with the genetic analysis of Ötzi the Iceman, the research into the origins of the per-Mongolian Xiongnu included scientists from the Max Planck Institute for Evolutionary Anthropology, Leipzig, Germany. As the Max Planck Institute’s newsletter explains:

Creationism in Crisis - Ötzi The Iceman Had Anatolian Ancestors

'Ötzi the Iceman'

© South Tyrol Museum of Archaeology/Eurac/Marco Samadelli-Gregor Staschitz

A facial reconstruction of Ötzi the Iceman. New evidence suggests he had male-pattern balding and was brown-skinned.

Image credit: Reconstruction by Kennis © South Tyrol Museum of Archaeology, Foto Ochsenreiter

Dark skin, bald head, Anatolian ancestry | Max-Planck-Gesellschaft

In about 3,300 BCE, some 700 years after Bible literalist creationists believe the human population was reduced to just 8 survivors of a genocidal flood inflicted on the world by their 'loving' God, a brown-skinned man, possibly being pursued over the Alps north of Italy, fell into a glacier. He may have died before he fell or he may have died of his injuries from the fall, but a fresh arrow wound in his shoulder may have contributed to his death.

The significance of his genome is that is shows how far the human population of Europe had diversified into distinct groups each with a characteristic DNA signature - something that would not have been possible if the entire human population of the world had evolved from such a narrow genetic bottleneck. Not only had they diversified but had developed distinct cultures and life-styles.

Another significance of this research is that it shows how science is never certain, but constantly reassesses the evidence and revises its collective opinion when the evidence demands it.

Ötzi the Iceman

Ötzi, also known as the Iceman, is a well-preserved mummy of a man who lived during the Copper Age, around 3300 BCE. He was discovered in the Ötztal Alps, hence the name "Ötzi," by German tourists on September 19, 1991, near the border between Austria and Italy. The mummy was found at an altitude of around 3,210 meters (10,530 feet) in the Schnalstal Glacier. Here are some key facts and details about Ötzi the Iceman:

1. Discovery and Preservation: Ötzi's mummy was preserved due to the unique conditions of the glacier, which acted as a natural freezer. His body was naturally mummified over the centuries, allowing researchers to gain insights into his life and the environment he lived in.
2. Age and Appearance: Ötzi was estimated to be around 45 years old at the time of his death. He stood about 1.6 meters (5 feet 3 inches) tall and had a stocky build. He had brown eyes, wore a beard, and had tattoos on various parts of his body, likely created by making small incisions and rubbing charcoal or other pigments into them.
3. Clothing and Equipment: Ötzi's clothing included a coat made of woven grass and leather, a loincloth, leggings, a belt, and a hat. He also wore shoes made of grass and leather. He carried a variety of tools and equipment, including a copper-bladed axe, a flint knife, a quiver with arrows, a backpack, a birch bark container, and a wooden bow.
4. Diet and Lifestyle: Examination of Ötzi's stomach contents and isotopic analysis of his teeth and bones provided insights into his diet. He primarily consumed a diet of meat (from ibex and red deer) and various grains and plants, including einkorn wheat. This indicates a diet typical of the time, as well as evidence of mobility in the alpine region.
5. Health and Injuries: Ötzi's body revealed evidence of several injuries and health conditions. He had a number of broken ribs, possibly indicating a fall or accident. He also had wear-and-tear on his joints, suggesting a physically demanding lifestyle. Additionally, Ötzi had an arrow wound on his left shoulder that likely contributed to his death, as well as signs of head trauma.
6. Copper Axe: One of Ötzi's most significant possessions was a copper-bladed axe, which is one of the earliest examples of metal use in human history. This suggests a level of sophistication in his society's technology and craftsmanship.
7. Genetic Analysis: Ötzi's DNA has been extensively studied, providing insights into his ancestry and genetic traits. This analysis revealed that he had a genetic predisposition for cardiovascular disease, lactose intolerance, and a higher risk of certain autoimmune disorders.
8. Cultural and Historical Significance: Ötzi's discovery has offered a unique window into the life of an individual from the distant past. Researchers have gained valuable information about ancient diets, clothing, tools, and health conditions. Ötzi has also helped to reconstruct aspects of Copper Age society, including trade routes and cultural practices.
9. Exhibition and Research: Ötzi's mummy is preserved and displayed at the South Tyrol Museum of Archaeology in Bolzano, Italy. Researchers continue to study his remains using various advanced techniques to uncover more information about his life, death, and the world he lived in.

Overall, Ötzi the Iceman is a remarkable archaeological discovery that has provided invaluable insights into the lives of our ancient ancestors and their interactions with the environment and technology of their time.

"Tell me all you know about the 'Iceman' known as Ötzi’s." [Response to user request]
Retrieved from https://chat.openai.com/

Creationism in Crisis - How Watermelons Evolved, With Gene Loss AND Gene Duplication

Cultivated watermelon, Citrullus lanatus

Photo: James E. Scarborough
via Wikipedia Public Domain

Behind the Rind: New Genomic Insights into Watermelon Evolution, Quality, and Resilience - Boyce Thompson Institute

Fig. 6 Fruits types in C. lanatus, C. mucosospermus, C. amarus, and C. colocynthis: a, b C. colocynthis, c C. lanatus subsp. lanatus, d-f C. lanatus subsp. vulgaris, g, h C. mucosospermus, i: Citrullus sp.

Fig. 8 Fruit flesh colour in C. lanatus, C. mucosospermus, C. amarus, and C. colocynthis: a, b C. lanatus subsp. vulgaris, c, d C. mucosospermus, e C. amarus, f C. lanatus

Achigan-Dako, E.G., et al., (2015)

The embarrassment for creationism continues unabated with news that scientists from the Boyce Tompson Institute, Itheca, New York, USA, have worked out how the cultivated watermelon evolved.

This might seem trivial to normal people, but to creationists, it shatters several cherished pieces of dogma and exposes them as bogus.

1. Firstly, the scientists have shown that the process of domestication from wild ancestors included an incident of gene doubling, so creating new genetic information (and increasing the sweetness of the watermelon). Creationists claim there is no mechanism for increasing the information in the genome without the intervention of a magic man doing magic.
2. Secondly, the scientists have also discovered that the process of domestication involved the loss of several genes from the cultivated watermelon genome, yet creationist dogma says all genetic loss is fatal and all mutations are deleterious, and yet here we have an improved cultivar, resulting in millions more watermelons than had the mutations not happened.
3. Thirdly, the Bible claims all life on earth was created by God for its special creation, mankind, and yet here we have evidence that the cultivated watermelon is the result of selective breeding, meaning that, even if we allow for the sake of argument that watermelons were created for mankind, whoever created them didn't do a very good job, or failed to anticipate what humans would require from a watermelon, so we needed to improve on what was provided. Imagine buying an intelligently designed motor car, then finding it needs considerable modification and improvement to make it fit for purpose! Would you buy from that designer again?

That latter point can be made for all domesticated animals, by the way, since very few of them have remained unchanged compared to their wild ancestors.

So, what is the evolutionary history of watermelons?

According to the press release by Aaron Callahan, from the Boyce Thompson Institute :

Creationism in Crisis - The Evolution of Batesian Mimicry in a New Zealand Stonefly

Similar ‘warning’ colouration of the non-toxic mimic Zelandoperla fenestrata stonefly (left), and cyanide-producing Austroperla cyrene (right).

A cyanide-producing Austroperla cyrene sits at the top of this picture, with a mimicking Zelandoperla fenestrata in the center and non-mimicking Zelandoperla fenestrata at the bottom.

Credit: University of Otago

When cheating pays – survival strategy of insect uncovered, News, University of Otago, New Zealand

I've written before about Batesian mimicry as an example of environment-driven evolution and how it depends on an evolutionary arms race - which makes no sense as the work of a single creator god, as creationists believe is responsible for the 'design' of all living organisms.

Batesian mimicry

Batesian mimicry is a fascinating concept in evolutionary biology named after the English naturalist Henry Walter Bates. It refers to a form of mimicry in which a harmless species closely resembles the appearance of a toxic or dangerous species to deceive predators. This phenomenon is commonly observed in the animal kingdom, particularly among insects, although it can also occur in other groups of organisms.

The key components of Batesian mimicry are:

1. Model Species: The toxic or harmful species that possesses some form of defense mechanism, such as toxicity, stinging, or bad taste. Predators learn to associate the distinct appearance of this model species with the negative consequences of attacking or consuming it.

Creationism in Crisis - A Newly-Discovered Non-Genetic Mode for Inheritance, But It's No Comfort For Creationists

Because babies acquire their first gut microbes passing through their mother’s birth canal, mothers’ microbiomes form the basis of their offspring’s.

Photo: Sarah Chai/Pexels

Hardship affects the gut microbiome across generations | UCLA

Human gut microbiome

Source

The old scientific debate from the early 19th century between Darwinian evolution and Lamarckian evolution all hinged on whether characteristics acquired after birth could be inherited by offspring, as Lamarck thought, or whether what we inherit from our parents is a variation (within limits) of what they inherited from their parents:

Darwinian and Lamarckian evolution are two contrasting theories of evolution that were proposed in the past. Though both sought to explain the process of biological change over time, they differ in their fundamental mechanisms and assumptions.

1. Darwinian Evolution (Theory of Natural Selection):
   • Proposed by Charles Darwin and Alfred Russel Wallace in the mid-19th century.
   • Central concept: Natural selection is the main driving force behind evolution.
   • Mechanism: Variation exists within populations, and individuals with traits better suited to the environment are more likely to survive and reproduce. Over time, these advantageous traits become more common in the population, while less favorable traits are selected against.
   • Inheritance of acquired characteristics: Darwinian evolution does not rely on the inheritance of traits acquired during an organism's lifetime. Instead, it is based on the passing down of genetic information from parents to offspring.
   • Example: Consider a population of giraffes with varying neck lengths. If the environment favors individuals with longer necks (e.g., taller trees for feeding), those with longer necks have a survival advantage and are more likely to pass on their long-necked genes to the next generation.
2. Lamarckian Evolution (Theory of Inheritance of Acquired Characteristics):
   • Proposed by Jean-Baptiste Lamarck in the early 19th century.
   • Central concept: Evolution is driven by an organism's effort to adapt to its environment and the inheritance of acquired traits.
   • Mechanism: Lamarck proposed that if an organism acquires new characteristics or traits during its lifetime due to its environment's demands, these acquired traits can be passed on to its offspring.
   • Example: Lamarck suggested that if a giraffe stretches its neck throughout its lifetime to reach higher leaves, the elongated neck acquired during its life will be passed on to its offspring, leading to the gradual evolution of longer-necked giraffes over generations.

The key difference between the two theories lies in their view on the inheritance of acquired characteristics. Darwinian evolution relies on natural selection acting on existing genetic variation, while Lamarckian evolution suggests that acquired traits during an individual's lifetime can be inherited by their offspring, driving evolutionary change. Lamarckian evolution, however, has been largely discredited by modern genetics and molecular biology, as it does not align with the principles of inheritance through genes and DNA. Instead, the modern understanding of evolution is based on the principles proposed by Darwin, which include the processes of mutation, genetic variation, and natural selection acting on heritable traits.

ChatGPT3 "What is the difference between Darwinian and Lamarckian evolution?" [Response to user request]
Retrieved from https://chat.openai.com/

That debate has now been opened up again in an unexpected way with the news that an international team of scientists led by UCLA psychologists has shown that information produced during hardship suffered by a woman during pregnancy can be passed on to her baby via its microbiome.