Unintelligent Design - Neurodegenerative Diseases Such As MS & Alzheimer's Traced Back To Early North European Farmers - 24,000 Years Before 'Creation Week'

Bronze Age Genes.

Credit: SayoStudio

Life in Bronze Age Britain (artist's impression)

Ancient DNA reveals reason for high MS and Alzheimer's rates in Europe

Researchers have just completed a massive gene bank for ancient humans who lived in Eurasia up to 34,000 years ago (i.e., up to 24,000 years before creationist dogma says the universe and everything in it was magicked out of nothing by a god made of nothing who self-assembled out of nothing before there was time and space to self-assemble in.

The gene bank has enabled researchers to trace the historical and geographical spread of genes and diseases, producing four papers published in Nature. This article deals with just one of them; others will follow.

The results should disturb any creationists who has the courage to read about them because, not only did it all occur long before the mythical 'Creation Week' that is central to their superstition, but is shows that any designer either could not have been omniscient, or must have been malevolent, because it shows how the genes for Multiple Sclerosis (MS) arose in North Europe, probably as a side-effect of evolving genes to increase resistance to the diseases carried by domestic animals. An omniscient designer who deigned them should have been aware of what they would also cause, so either isn't omniscience and didn't know what its design would do, or created MS deliberately.

As the University of Cambridge News release explains:

Creationism in Crisis - The Evolution of African Primates

Cercopithecus diana

Complex Evolutionary History With Extensive Ancestral Gene Flow in an African Primate Radiation | Molecular Biology and Evolution | Oxford Academic

Cercopithecus diana

Mustached guenon,
Cercopithecus cephus

De Brazza's guenon,
Cercopithecus neglectus

Stuhlmann's Blue monkey,
Cercopithecus mitis stuhlmanni,

Crowned Guenon
Cercopithecus pogonias

12 years ago, I wrote a blog post to explain why, because speciation is a process, not an event, we often don't even know it's happened until well after the event when we can see we have a new population with distinct characteristics. I illustrated this with a hypothetical example of monkeys in a forest being split into isolated populations by climate change.

In it I said:

But, gradually, due to climate change or continental drift, or maybe a change in ocean currents, the forest begins to get drier and turn into grasslands, with trees surviving only close to rivers. In other words, the monkey population is broken up into isolated groups which can no longer interbreed because they simply don't come into contact any more. Each group will be free to evolve according to the local conditions in its woodland. Eventually, maybe after a few hundred thousand years, maybe a million or two, these groups may evolve to the point where they not only look different to each other but may not be able to interbreed even if they do meet up.

So where and what was the 'speciation event'? At what point in the process could an observer say, "Hey! I've just seen speciation occur! It happened when...". In fact, we only know that speciation has occurred retrospectively because, according to our rules of taxonomy, failure to interbreed means they are now different species. Maybe if we had been able to examine them a hundred thousand years ago we might have found that they could still interbreed. Maybe we would have found an incompletely speciated 'ring species'.

There was no sudden emergence of a new species; no sudden branching of the 'tree of life'; no mutation which brought a new species into being and no 'macro-evolution' event. There was no event which creation pseudo-scientists proclaim to be impossible and which they claim has never been seen. All there was was a slow accumulation of difference, directed by natural selection with each group doing nothing but struggling to survive and reproduce with the ones which left the most descendant contributing the most genes to the gene-pool.

Now, take the same scenario, only this time the climate changed again after a few tens of thousands of years and the isolated scattered groups could once again mix freely. But this time maybe they had not diverged sufficiently to prevent interbreeding, or maybe one group now had a significant advantage over the others. In these cases, the group with the genes which gave them greater success would come to dominate and possibly replace the others.

Is this speciation? Is this the point at which we can say a new species arose and the 'archaic' form went extinct? Or is this merely evolution of the entire species? Were those groups isolated for a few thousand years new twigs on the monkey branch of the tree of life, or were they merely groups of individuals with the potential to become new species, but which never quite made it? Certainly, the day they came back into contact, nothing happened to their genes. It was not a change on their part which caused them to re-establish contact. It was the environment which changed.

Rosa Rubicondior: Evolution - Making a Monkey (4 July 2012)

And now, as though to confirm my hypothetical example was close to the real thing, a team of archaeologists and geneticists, led by Axel Jens and Katerina Guschanski of the Department of Ecology and Genetics, Animal Ecology, Uppsala University, Uppsala, Sweden, have carried out a whole genome analysis of 22 species of West African guenons (monkey of the Cercopithecini tribe - one of the world's largest primate radiations) and shown how the different species diverged with frequent gene flow across species boundaries and hybridization events playing a part in the process of radiation and diversification.

The team have published their findings, open access, in the journal Molecular Biology and Evolution. In it they say:

Creationism in Crisis - How New Genetic Information Arises Naturally

Top left: Bread Wheat, Triticum aestivum (hexaploid)
Bottom left: Arabica Coffee, Coffea arabica (tetraploid)

Top right: Strawberry, Fragaria x ananassa (Octoploid)
Bottom right: Coxes Orange Pippin, Malus domestica var (tetraploid)

The 'Christmas tree (Norwegian spruce) Picea abies
Seven times more DNA than a human.

It is a basic axiom of creationism that no new genetic information can arise in a species genome without the assistance of a magic designer. This is based on some half-baked interpretation of 'Shannon Information Theory' and misrepresentation of the second law of thermodynamics in which 'information' is confused with energy and a species genome with a closed system.

Try to get a creationist to explain the science behind that claim and you're likely to get nothing but rehearsed parrot squawks made in response to trigger words, if they don't run away hurling abuse and passive aggressive threats over their shoulder, or quickly change the subject. There will be no understanding of either information theory or thermodynamics.

The natural world is full of examples of how gene or even whole genome duplication creates redundant DNA and copies of genes than can mutate and be selected by natural selection to create new meaning in the genetic information. The Christmas tree, or Norwegian spruce, Picea abies, has about 29,000 functional genes (marginally more than a human) yet it has a genome seven times larger than the human genome, all packed into 12 chromosomes. The reason for this, according to a research team from Umeå universitet, Sweden, is because the mechanism for correcting duplication errors broke millions of years ago, so these duplications have been accumulating in the Picea abies genome ever since.

Creationists seem incapable of understanding the difference between information and the meaning in that information or how meaning is given by the environment. For example, a mutation which gave Streptococcus aureus resistance to the antibiotic, methicillin, would have had no meaning before medical science invented methicillin; now the same information makes MRSA an intractable condition and a highly successful pathogen. The point being that new meaning can arise without any change in the genome simply by a change in the environment, so evolution is not always dependent on change in genetic information.

Creationism in Crisis - The Woolly Dogs Of The American Coast Salish People Predate 'Creation Week'

Researchers, Coast Salish People Analyze 160-Year-Old Indigenous Dog Pelt in the Smithsonian’s Collection | Smithsonian Institution

The reconstructed woolly dog shown at scale with Arctic dogs and spitz breeds in the background to compare scale and appearance; the portrayal does not imply a genetic relationship.

Credit: Karen Carr.

During that long period of Earth's 'pre-Creation Week' history, before anyone told the people of Siberia that they should wait to be created then wiped out in a genocidal flood before forgetting all about it and only then going to live elsewhere, they migrated to North America, taking their domestic dogs with them.

This is the sort of nonsense that creationism requires you to believe in order to reconcile the scientific evidence with the creation myths of a bunch of Bronze Age Canaanite farmers who thought Earth was small, flat and had a dome over it to keep the water above the sky out. Obviously, these people had almost certainly never heard of Siberia or North America or realised that there were other people living there and were as ignorant of most of Earth's long history as they were of cosmology, biology and geology.

One of the things the Bronze Age Canaanites would never have guessed was that some of the domestic dogs the Siberians took with them had genes for a dense wooly fur that could be woven into blankets and other fabrics, but now a team of researchers from the Smithsonian’s National Museum of Natural History have carried out a detailed DNA analysis of the pelt of the last known example of this breed of dog (a dog known as Mutton). Mutton died in 1859 and his pelt was sent to the Smithsonian Institute where it remained until it was rediscovered in the early 2000's.

The analysis has shown that the line diverged from the other dogs about 5,000 years ago (i.e., before creationist superstition says all life on Earth was exterminated in a genocidal flood when their 'all-loving' god flew into a rage because its creation wasn't working as intended).

They have shown that its closes genetic relationship is with the pre-colonial dogs from Newfoundland and British Columbia. The Indigenous Coast Salish communities in the Pacific Northwest (in Washington state and British Columbia) for millennia held these wooly dogs in high esteem, regarding them almost as family members and often keeping them in pens or on islands to prevent them interbreeding with other dogs, to maintain the quality of their wool. This isolation prevented the ingress of genes from other dogs and even from the dogs later colonists brought with them. The genes recovered from Mutton's pelt show that 85% of his genes were from pre-colonial dogs.

The Smithsonian researchers have, with the assistance of Coast Salish Elders, Knowledge Keepers and Master Weavers, now traced the place of the woolly dogs in Coastal Salish culture and the reasons for its decline. Their findings are published in Science and tell a sorry tale of colonial destruction of a people and their culture. Instead of, as has been suggested, the arrival of machinery and woven blankets made the wooly dogs expendable, the truth is that, due to disease and colonial policies of cultural genocide, displacement and forced assimilation, it likely became increasingly difficult or forbidden for Coast Salish communities to maintain their woolly dogs and a 1000 years or more of careful selective breeding was wiped out within a couple of generations.

Creationism in Crisis - How Early Humans Caused A Decline In Megafauna Numbers Thousands Of Years Before 'Creation Week'

Illustration: First printed in Bryant & Gay, 1883. Wood carving by E. Bayard.

Peré Davids deer, Elaphurus davidianus. Now extinct in the wild.

People, not the climate, caused the decline of the giant mammals

About 90,000 years before creationist superstition says the Universe was created, humans, who had been evolving in Africa, began to expand their range into Eurasia and eventually into Austronesia and the Americas.

About 500,000 years later most large species show a sudden decline in their numbers, and now researchers led by Professor Jens-Christian Svenning, head of the Danish National Research Foundation's Center for Ecological Dynamics in a Novel Biosphere (ECONOVO) at Aarhus University, believe they have shown that this was due to human predation and habitat destruction.

They reached this conclusion from an analysis of the genomes of 139 species. This involved crunching the data from 3 billion or so data points to build evolutionary trees of the mutations in the genomes. The bigger the population, the more mutations there will be in the species genome, so this data shows the population changes over time.

Their work is published, open access, in Nature and is explained in a news release from Aarhus University:

For years, scientists have debated whether humans or the climate have caused the population of large mammals to decline dramatically over the past several thousand years. A new study from Aarhus University confirms that climate cannot be the explanation.

About 100,000 years ago, the first modern humans migrated out of Africa in large numbers. They were eminent at adapting to new habitats, and they settled in virtually every kind of landscape - from deserts to jungles to the icy taiga in the far north.

Part of the success was human's ability to hunt large animals. With clever hunting techniques and specially built weapons, they perfected the art of killing even the most dangerous mammals.

But unfortunately, the great success of our ancestors came at the expense of the other large mammals.

It is well-known that numerous large species went extinct during the time of the world-wide colonization by modern humans. Now, new research from Aarhus University reveals that those large mammals that survived, also experienced a dramatic decline.

The eastern gorilla is one of the mammals that have declined the most. Today it's only living in small areas in DR Congo.

Foto: Michalsloviak / Creative Commons

By studying the DNA of 139 living species of large mammals, the scientists have been able to show that abundances of almost all species fell dramatically about 50,000 years ago.

This is according to Jens-Christian Svenning, a professor and head of the Danish National Research Foundation's Center for Ecological Dynamics in a Novel Biosphere (ECONOVO) at Aarhus University, and the initiator of the study.

We’ve studied the evolution of large mammalian populations over the past 750,000 years. For the first 700,000 years, the populations were fairly stable, but 50,000 years ago the curve broke and populations fell dramatically and never recovered. For the past 800,000 years, the globe has fluctuated between ice ages and interglacial periods about every 100,000 years. If climate was the cause, we should see greater fluctuations when the climate changed prior to 50.000 years ago. But we don't. Humans are therefore the most likely explanation.

Professor Jens-Christian Svenning, Lead author
Center for Ecological Dynamics in a Novel Biosphere (ECONOVO)
Department of Biology
Aarhus University, Aarhus, Denmark.

Who killed the large mammals?

For decades, scientists have debated what is behind the extinction or rapid decline of large mammals over the past 50,000 years.

On one side are scientists who believe that rapid and severe fluctuations in the climate are the main explanation. For example, they believe that the woolly mammoth went extinct because the cold mammoth steppe largely disappeared.

On the opposite side are a group who believe that the prevalence of modern humans (Homo sapiens) is the explanation. They believe that our ancestors hunted the animals to such an extent that they either became completely extinct or were severely decimated.

So far, some of the most important evidence in the debate has been fossils from the past 50,000 years. They show that the strong, selective extinction of large animals in time and space roughly matches the spread of modern humans around the globe. Therefore, the extinction of animals can hardly be linked to climate. Nevertheless, the debate continues.

The new study presents brand new data that sheds new light on the debate. By looking at the DNA of 139 large living mammals – species that have survived for the past 50,000 years without becoming extinct – the researchers can show that the populations of these animals have also declined over the period. This development seems to be linked to the spread of humans and not climate change.

DNA contains the long-term history of the species

In the past 20 years, there has been a revolution within DNA sequencing. Mapping entire genomes has become both easy and inexpensive, and as a result the DNA of many species has now been mapped.

The mapped genomes of species all over the globe are freely accessible on the internet – and this is the data that the research group from Aarhus University has utilized, explains assistant professor Juraj Bergman, the lead researcher behind the new study.

We’ve collected data from 139 large living mammals and analysed the enormous amount of data. There are approximately 3 billion data points from each species, so it took a long time and a lot of computing power. DNA contains a lot of information about the past. Most people know the tree of life, which shows where the different species developed and what common ancestors they have. We’ve done the same with mutations in the DNA. By grouping the mutations and building a family tree, we can estimate the size of the population of a specific species over time.

The larger the population of an animal, the more mutations will occur. It’s really a question of simple mathematics. Take elephants, for example. Every time an elephant is conceived, there’s a chance that a number of mutations will occur, and it will pass these on to subsequent generations. More births means more mutations.

Assistant professor Juraj Bergman, First author
Center for Ecological Dynamics in a Novel Biosphere (ECONOVO)
Department of Biology
Aarhus University, Aarhus, Denmark.

The large mammals

The 139 large mammals examined in the study are all species that exist today. They include elephants, bears, kangaroos and antelopes, among others.

It is estimated that there are 6,399 species of mammals on the Earth, but the 139 extant megafauna were selected in this study to test how their populations changed over the past 40,000 to 50,000 years, when similar large animals went extinct.

The large mammals are also called megafauna – and are defined as animals weighing more than 44 kg when fully grown. Humans are therefore also considered megafauna. In the study, however, the researchers examined species weighing as little as 22 kg, so that all continents have been represented - except Antarctica.

Source: Journal of Mammalogy

Looking at the neutral parts of the DNA

However, the size of the elephant population is not the only thing that affects the number of mutations.

If the area in which elephants live suddenly dries up, the animals come under pressure – and this affects the composition of mutations. The same applies if two isolated groups of elephants suddenly meet and mix genes.

If not only the size of the population affects how many mutations occur, you would think that the results are rather uncertain. But this is not the case, explains Juraj Bergman.

Only 10 per cent of mammalian genomes consist of active genes. Great selection pressure from the environment or migration will primarily lead to mutations in the genes. The remaining 90 percent, on the other hand, are more neutral. We have therefore examined mutations in those parts of the genome that are least susceptible to the environment. These parts primarily indicate something about the size of the population over time.

Assistant professor Juraj Bergman

Peré Davids deer, shown in this picture, does not live in the wild anymore. The only animals left today is living in Zoos and animal parks.

Foto: Tim Felce / Creative Commons.

The woolly mammoth is an atypical case

Much of the debate about what caused the large animals to either become extinct or decline has centered around the woolly mammoth. But this is a bad example because the majority of the megafauna species that went were associated with temperate or tropical climates, as Jens-Christian Svenning explains.

The classic arguments for the climate as an explanatory model are based on the fact that the woolly mammoth and a number of other species associated with the so-called "mammoth steppe" disappeared when the ice melted and the habitat type disappeared. This is basically an unsatisfactory explanatory model, as the vast majority of the extinct megafauna species of the period did not live at all on the mammoth steppe. They lived in warm regions, such as temperate and tropical forests or savannahs. In our study, we also show a sharp decline during this period in populations of the many megafauna species that survived and come from all sorts of different regions and habitats.

It seems inconceivable that it is possible to come up with a climate model that explains how, across all continents and groups of large animals, there have been extinctions and continuous decline since about 50,000 years ago. And how this selective loss of megafauna is unique for the past 66 million years, despite huge climate change. Given the rich data we now have, it’s also hard to deny that instead it is because humans spread across the globe from Africa and subsequently grew in population.

Professor Jens-Christian Svenning

The final full stop in the debate has probably yet to be set, but Jens-Christian Svenning finds it difficult to see how the arguments for the climate as an explanation can continue.

The team’s findings are explained in detail in their open access paper in Nature:

Abstract

The worldwide extinction of megafauna during the Late Pleistocene and Early Holocene is evident from the fossil record, with dominant theories suggesting a climate, human or combined impact cause. Consequently, two disparate scenarios are possible for the surviving megafauna during this time period - they could have declined due to similar pressures, or increased in population size due to reductions in competition or other biotic pressures. We therefore infer population histories of 139 extant megafauna species using genomic data which reveal population declines in 91% of species throughout the Quaternary period, with larger species experiencing the strongest decreases. Declines become ubiquitous 32–76 kya across all landmasses, a pattern better explained by worldwide Homo sapiens expansion than by changes in climate. We estimate that, in consequence, total megafauna abundance, biomass, and energy turnover decreased by 92–95% over the past 50,000 years, implying major human-driven ecosystem restructuring at a global scale.

Introduction

The late-Quaternary extinction event^1,2 is characterised by the selective extinction of large-bodied animals (megafauna) at a global scale. At the present date, only a small fraction of this prehistorically speciose group^2,3,4,5 persists in rapidly diminishing communities, many of which face an immediate threat of extinction^6,7. The causes of megafauna decline have been subject to long-standing debate, with fluctuations in paleoclimate and the spread of Homo sapiens emerging as the predominant explanatory factors^{3,5,8,9,10,11,12,13,14,15,16,17,18}.

According to the climate-driven hypothesis of megafauna dynamics, a temporal dependency of population sizes on the glacial–interglacial cycle is expected. On the other hand, modern humans are expected to start influencing megafauna densities in recent times, mainly following the Last Interglacial period, corresponding to their worldwide expansion out of Africa¹⁹. To distinguish between these two scenarios, previous studies have focused on inferring past species distributions and extinction chronologies based on fossil data^{3,5,8,9,10,11,12,13,14,15,16,17,18}. However, while the fossil record provides valuable insight into species’ histories, its fragmentary nature allows for only a limited temporal resolution of past population dynamics.

An alternative approach to fossil-based analyses is using genomic sequence data to reconstruct time-resolved trajectories of species population sizes^20,21. Genomics-based methods commonly provide population size estimates for most of the Quaternary period (consisting of the Pleistocene period between 2.58 million and 11,700 years ago and the Holocene period between 11,700 years ago and present), thereby covering multiple glaciation cycles, as well as recent periods of human expansion^{22,23,24,25,26,27,28,29,30,31,32}. Thus, genomics-based trajectories of population sizes should provide a more comprehensive framework for modelling the impact of climatic shifts and humans on megafauna dynamics compared to fossil-based approaches. However, a global analysis of genomics-based megafauna histories and their driving factors is currently lacking.

We focus our study on the Late Pleistocene and Early Holocene population trajectories of extant megafauna to address the following hypotheses. On the one hand, the surviving species may have experienced similar dynamics as the species undergoing extinction, showing widespread population declines linked to Homo sapiens or climate. Alternatively, surviving megafauna communities may have exhibited compensatory dynamics³³, resulting in an increase in population size due to mechanisms such as competitive release. These scenarios have widely different ecological implications, whereby co-occurrence of population declines and extinctions would result in the exacerbation of ecosystem degradation, while compensatory dynamics would stabilise ecosystem functioning34. Thus, studying population dynamics of the surviving megafauna species during the Late Pleistocene and Early Holocene extinction period has major implications for our understanding of past and contemporary biosphere functioning^4,35.

We curated a genomic dataset comprising 139 high-quality reference genome assemblies and short-read sequence data of extant terrestrial megafauna and implemented a bioinformatic pipeline to infer their Quaternary population histories. We studied the population dynamics of megafauna as a function of species’ ecology, geographical distribution, climate, and anthropogenic influence. We detect a global, severe decline in megafauna population sizes over the past 50,000 years and show that this observation is best explained by the influence of the worldwide expansion of H. sapiens rather than past climate dynamics. This lack of compensatory dynamics has had major impacts on ecosystem structure and functioning as reflected in a dramatic reduction of wild megafauna abundance, biomass and energy turnover.

Fig. 1: Effective population size (N_e) dynamics of 139 extant megafauna species.

a Each step line represents changes in Ne with respect to time for a single megafauna species, coloured by a gradient based on average adult mass. The dashed line represents the fit of the piecewise linear model, as determined by breakpoint analysis. The grey-shaded area represents the 95% confidence interval of the linear model prediction. The blue rectangle represents the timespan of realm-specific breakpoints (Supplementary Fig. 2). Both axes are log10-transformed. Credit information for photographs of Antilocapra americana, Elephas maximus, Ursus arctos, Macropus giganteus and Giraffa tippelskirschi are available in Supplementary Table 2. All photographs are under CC-BY copyright (https://creativecommons.org/licenses/by/4.0/) and adapted for the purpose of the figure. b Relationship between species’ adult mass and the rate of population size change (slope). The x-axis is log10-transformed. Points are median slope values with 95% HPDI ranges indicated by bars (each distribution is derived using n = 1000 posterior samples). c Distribution of species’ decline severity. Source Data for this figure are in Source Data 1–4.

Bergman, J., Pedersen, R.Ø., Lundgren, E.J. et al.
Worldwide Late Pleistocene and Early Holocene population declines in extant megafauna are associated with Homo sapiens expansion rather than climate change.
Nat Commun 14, 7679 (2023). https://doi.org/10.1038/s41467-023-43426-5

During that long period that creationists believe was before 'Creation Week', when they think Earth was magicked up out of nothing by a magic man made of nothing, mammalian megafauna such as elephants and mammoths, giraffes, kangaroos and antelopes had evolved, and the humans (who hadn't been created yet, but had been evolving in Africa for several millions of years) had spread out of Africa and across most of the Earth and were busy hunting and killing these large animals, leaving their descendants to tell the tale in the number of mutations in the neutral parts of the genome.

Creationists will need to ignore this evidence and the fact that the Theory of Evolution is the underpinning theory of biology that explains these observations.

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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