Biodiversity News - Australia's Exotic Invertebrates

Mating Repsimus scarab beetles

Credit: Nick Porch

Photos from the field: zooming in on Australia’s hidden world of exquisite mites, snails and beetles | The Conversation

Most people will be familiar with Australia's unique set of mega- (and not so mega) fauna such as kangaroos, wallabies, koalas, dingoes, wombats, marsupial mice, and of course the egg-laying monotremes, the platypus and the echidna or spiny ant-eater, but how many people are aware of the equally unique and often bizarre array of invertebrates, apart from the dangerous spiders, that is?

In this article in The Conversation, 'Photos from the Field' series, from January 2021 Nick Porch, Senior Lecturer in Environmental Earth Science, Deakin University, Australia, shares some photographs of a small sample of the several hundred thousand uniquely Australian organisms, most of which will be almost completely unknown, even to Australians.

Creationists might like to ignore the bits about 150 million years, Gondwana and allusions to plate tectonics, in the explanation for why Australian bugs tend to be more closely related to South American bugs than those from New Zealand. Evidence of evolution on an old Earth will probably upset them.

The article is reprinted here under a Creative commons licence, reformatted for stylistic consistence. The original can be read here:

Malevolent Designer News - Has Creatonism's Divine Malevolence Lost the Plot?

Yellow-legged frogs killed by chytrid fungus in Sixty Lakes Basin area of the Sierra Nevada, California, USA

Photo credit: Joel Sartore/Natural History Museum.

A deadly disease has driven 7 Australian frogs to extinction – but this endangered frog is fighting back

I've written several times both in this blog and in my popular, illustrated book, The Malevolent Designer: Why Nature's God is not Good, about the deadly fungus, Batrachochytrium dendrobatidis, that is decimating the world population of amphibians, especially frogs.

As a piece of intelligent [sic] design, taking a previously harmless soil fungus and modifying to kill frogs, is about as good an example of the sheer nasty malevolence of any designer that could do such a thing as you could wish for.

Yet Creationists continue to insist only their favourite designer god could do such a thing, because evolution isn't capable of doing it. For some unexplained reason, chemistry and physics need magic to make them work.

God Hates Frogs

But now the news from Australia, is that frogs may be staging something of a fight back by developing resistance to it - again something that Creationists will insist must have been done by the same malevolent designer that designed the fungus to kill frogs in the first place.

Or that's to sort of bizarre belief system Creationists dupes have been fooled into.

As always though, the facts of biological science offer a more rational explanation. Here for example is a report by Matthijs Hollanders and David Newell of Southern Cross University, Australia, which gives evidence of this fightback. It is reprinted from The Conversation, reformatted for stylistic consistence, under a Creative Commons licence. The original article can be read here:

Creationism in Crisis - Transitional Forms in Recent Human Evolution

Comparing the Boxgrove and Atapuerca (Sima de los Huesos) human fossils: Do they represent distinct paleodemes? - Journal of Human Evolution

Figure 1. A) Location map and B) chronology of key European Middle Pleistocene hominin samples relative to the benthic foraminiferal oxygen isotopic stratigraphy (Lisiecki and Raymo, 2005).

One of the difficulties with palaeontology is fitting individual fossils into a taxonomic system that was designed for classifying contemporaneous organisms. This difficulty is inevitable given that species change over time as they evolve so it is not a flaw in the theory but a confirmation of it, rather like the problem of deciding exactly where one colour changes into another in a rainbow is not a flaw in the theory of why sunlight can be split into different colours but a confirmation of the theory.

Where do the colours change?

Just such a problem was illustrated by a paper published recently by a team of paleoanthropologists from England and Spain, led by Lucile Crété of the Centre for Human Evolution Research (CHER), The Natural History Museum, London, UK.

The team set out to decide whether hominin fossils from Boxgrove in West Sussex, England were of the same paleodeme as those found at the Sima de los Huesos (Pit of Bones) at Atapuerca, Castile and León, Spain.

Creationism in Crisis - The Evolutionary Origins of Nitrogen Fixation by Prokaryotes

Origin and Evolution of Nitrogen Fixation in Prokaryotes | Molecular Biology and Evolution | Oxford Academic

Despite ludicrous claims by Creationist frauds and their dupes that the Theory of Evolution (TOE) is about to be abandoned by mainstream biomedical science and replaced by an evidence-free Bronze Age superstition involving magic, the TOE continues to be the fundamental principle of biology and the framework which explains what can be observed, without the need for magic and unknowable mysteries.

Take for example the question of the origin of nitrogen fixation.

Nitrogen is essential for all biological organisms, being an integral part of all proteins, yet, despite the abundance of molecular nitrogen (N₂) in the atmosphere at about 78%, no eukaryote organisms can extract it directly. The problem is that N₂ is a very stable molecule with a triple bond between the two atoms, so, to be biologically active, it needs to be converted to ammonia (NH₃) which takes an enormous amount of energy and sixteen molecules of ATP. A significant proportion of ammonia comes from lightning strikes which convert a molecule of N₂ and three molecules of water (H₂O) into two molecules of NH₃ and a molecule of ozone (O₃)

N₂ + 3H₂O → 2NH₃ + O₃

But by far the most significant source of biological nitrogen is 'nitrogen fixation' by bacteria living often in symbiosis with plants. One example is nitrogen fixation by prokaryote bacteria is the relationship between rhizobia bacteria (Rhizobiaceae, α-Proteobacteria) which live in nodules in the roots of plants of the legume family. Other free-living nitrogen-fixing bacteria contribute to soil and marine nitrogen when the nitrogen in their bodies is released when they die.

Nitrogen Fixation by Legumes (Guide A-129) - New Mexico State University

The question for evolutionary biology was where and when did this ability to fix nitrogen originate? The prevailing consensus was that it originated in archaea and was acquired by bacteria by horizontal gene transfer. That consensus has now been challenged by a team of researchers from National Chung Hsing University and Academia Sinica, Taiwan, in an open access paper which argues that the process arose in bacteria first and was acquired by archaea later.

The evidence is in the form of an in-depth analysis of the >30,000 prokaryotic genomes that have so far been sequenced, to test the two competing hypotheses. This analysis produced nested hierarchies, in which the nitrogen-fixing archaea were nested inside the bacterial clades, and the fact that the majority of archaea use the bacterial Mo (molybdenum) transporter (ModABC) and not the archaeal Mo transporter (WtpABC). In other words, the majority of archaea use the bacterial process, not the archaeal process.

These observations, of course, only make any sense as the result of an evolutionary process. Certainly, there is no evidence of intelligent design here. After all, why design two different methods to achieve the same result. Also, why not designs eukaryotes to fix nitrogen directly by giving them the same processes used in bacteria and archaea, or one less demanding of energy, instead of opting for the much more complex system of symbiosis and dependence on dead bacteria releasing their fixed nitrogen?

In evolutionary terms of course, there was no evolutionary pressure on eukaryotes to evolve independent nitrogen fixation because bacteria and archaea were already abundant when the first eukaryotes and the first multicellular organisms arose, so biological nitrogen was not in short supply. That situation did not apply in the early evolution of the prokaryotes, for whom nitrogen would have been in very short supply, so the expenditure of energy in the process of fixing atmospheric nitrogen was cost-effective.

The resulting eukaryote plant life evolved to fit the environment in which they were evolving. The additional energy needed by an independent nitrogen fixing metabolic process would have made any evolution in that direction, deleterious, so it never evolved. For the legumes, it proved advantageous with little additional resource, to have nitrogen fixing bacteria living symbiotically in their roots.

An example there of how the process of evolution by natural selection results in a compromise solution which tends to provide the greatest benefit for the least cost.

Copyright: © 2022 The authors.
Published by Oxford University Press on behalf of Society for Molecular Biology and Evolution. Open access. (CC BY-NC 4.0)

The Taiwan team's paper is published open access in the Oxford Academic journal, Molecular Biology and Evolution:

Abstract

The origin of nitrogen fixation is an important issue in evolutionary biology. While nitrogen is required by all living organisms, only a small fraction of bacteria and archaea can fix nitrogen. The prevailing view is that nitrogen fixation first evolved in archaea and was later transferred to bacteria. However, nitrogen-fixing (Nif) bacteria are far larger in number and far more diverse in ecological niches than Nif archaea. We, therefore, propose the bacteria-first hypothesis, which postulates that nitrogen fixation first evolved in bacteria and was later transferred to archaea. As >30,000 prokaryotic genomes have been sequenced, we conduct an in-depth comparison of the two hypotheses. We first identify the six genes involved in nitrogen fixation in all sequenced prokaryotic genomes and then reconstruct phylogenetic trees using the six Nif proteins individually or in combination. In each of these trees, the earliest lineages are bacterial Nif protein sequences and in the oldest clade (group) the archaeal sequences are all nested inside bacterial sequences, suggesting that the Nif proteins first evolved in bacteria. The bacteria-first hypothesis is further supported by the observation that the majority of Nif archaea carry the major bacterial Mo (molybdenum) transporter (ModABC) rather than the archaeal Mo transporter (WtpABC). Moreover, in our phylogeny of all available ModA and WtpA protein sequences, the earliest lineages are bacterial sequences while archaeal sequences are nested inside bacterial sequences. Furthermore, the bacteria-first hypothesis is supported by available isotopic data. In conclusion, our study strongly supports the bacteria-first hypothesis.

Hong-Wei Pi, Jinn-Jy Lin, Chi-An Chen, Po-Hsiang Wang, Yin-Ru Chiang, Chieh-Chen Huang, Chiu-Chung Young, Wen-Hsiung Li,
Origin and Evolution of Nitrogen Fixation in Prokaryotes, Molecular Biology and Evolution, 39(9), September 2022, msac181, DOI: 10.1093/molbev/msac181

Copyright: © 2022 The authors.
Published by Oxford University Press on behalf of Society for Molecular Biology and Evolution. Open access
Reprinted under a Attribution-NonCommercial 4.0 International (CC BY-NC 4.0)

Creationism in Crisis - How Our Extended Genome of Micro-Organisms Killed Rivals For Land During the European Imperial Expansion

A Tongan Village

Photo: State Library of New South Wales

New data reveals severe impact of European contact with Pacific islands - CHL - ANU

In his Pulitzer Prize-winning book, Guns, Germs and Steel, Professor Jared Diamond, makes the point that it was not just superior technology (guns and steel) that enabled European imperialists to colonise much of the undeveloped world, but also our armoury of lethal germs that we unwittingly took with us.

Our germs, many of which are derived from related varieties in our domestic cattle, had being living with us for thousands of years in Europe where the population had developed a degree of natural resistance. However, when we came into contact with people who had lived, for example, on remote Pacific Islands, these people had little or no natural immunity, so diseases like measles and mumps were lethal and spread quickly, going ahead of us like a fifth column, working in secret to kill or severely weaken the indigenous population, making it easy to take control through force of arms.

This is an example of a sudden environmental change giving a big advantage to one group and being severely detrimental to a rival group. In evolutionary terms, this could be one reason why we have failed to develop complete resistance to our commensal and sometime pathogenic microbes and viruses; as we evolved, it was advantageous to us to have this invisible 'fifth column' to help us take over new territory. It's a classic example of how genes can form alliances and don't even need to belong to the same species, just so long as both benefit from the alliance.

Now two researchers from the Australian National University (ANU) School of Culture, History & Language, PhD candidate Phillip Parton and Professor Geoffrey Clark, have shown that this devastation of the population on Pacific islands was even worse than previously thought, with the population of the island of Tongatapu in the kingdom of Tonga being reduced to just 10,000 in 50 years, from 50-60,000 when Europeans first landed.

Their work, published in the Journal of Archaeological Science, indicates population declines were a lot larger than previously thought.

As the ANU news release explains:

Creationism In Crisis - Another 'God-Filled' Gap Just Got a Lot Smaller

Molecular dynamic simulation of ADP and acetyl phosphate

Aaron Halpern, UCL (CC-BY 4.0)

What is perhaps the favourite of all Creationism's 'God-filled' gaps - abiogenesis - just go a lot smaller with the news today that Nick Lane and colleagues of University College, London, UK, have shown how ATP became the universal energy currency used by all living organisms, so adding another layer to our understanding of how the earliest self-sufficient, self-replicating organisms arose from pre-existing molecules.

As always, the process evicts Creationism's shrinking little god because it is explained using just the natural laws of chemistry and physics acting on pre-existing molecules, with no place for magic or supernatural powers.

The mystery was, how the system for producing ATP could have evolved when the process used by cells today is a multi-step process which itself utilises ATP at six different points. Clearly, there must have been a simpler process for creating ATP early on in the evolution of living organisms and, because of it's universality, this was almost certainly in a common ancestor to all forms of life.

In prokaryote cells such as bacteria, the process occurs in the cell itself but in eukaryote cells the process takes place in the mitochondria - the descendants of bacteria originally incorporated into other prokaryote cells to give rise to the eukaryotes.

What is ATP and how is it synthesised? Wikipedia - Adenosine triphosphate

As explained in information provided ahead of publication by PLoS Biology:

Creationism in Crisis - Evolutionary Palaeontologist, Svante Pääbo, Wins Nobel Prize for Medicine

Svante Pääbo

Sweden's Pääbo wins Nobel Medicine Prize for sequencing Neanderthal DNA

This is the sort of news that the leading frauds in the Creationist cults must be dreading, if they still have an hope of convincing their dupes that the Theory of Evolution is a theory in crisis, about to be overthrown and replaced by religious superstition. It is the news that leading evolutionary palaeontologist and geneticist, Professor Svante Pääbo, director of the Max Planck Institute for Evolutionary Anthropology, Leipzig, Germany has been awarded a Nobel Prize for his work in the field of human evolution.

Far from being a theory in crisis, the Theory of Evolution is very much mainstream biomedical science, to the extent that the work Pääbo and his team are doing is central to our understanding of our recent history and how we relate to the archaic hominins that were our direct ancestors and the direct ancestors of other species of the Homo genus.

One of Pääbo's first major contributions to evolutionary biology was in sequencing Neanderthal genomes, then discovering that modern non-African Homo sapiens have at various times in recent history, had a significant ingression of Neanderthal DNA due to interbreeding between the two species. This horizontal gene transfer meant anatomically modern hominins acquired genes that had evolved in Neanderthals over a period of some 250,000 years, giving us significant adaptations to the cold, cloudy northern climates in Eurasia. Today, modern non-African humans have 2-4% Neanderthal DNA, most of it acquired about 40,000-60,000 years ago when the two species co-existed in Eurasia.

Human Evolution - Sex With Neanderthals
So What Did The Neanderthals Ever Do For Us?
More Evidence For a Human Ring Species
Evolution News - Women with Neanderthal Genes are More Fertile
Ancient Teeth Show Human Roots

Pääbo and his team then succeeded in sequencing the genome of a previously unknown hominin from a finger bone found in the Denisova Cave in Siberia and showed that this was a third distinct species of hominin, the Denisovans, who coexisted with Neanderthals, with whom they interbred extensively, and with H. sapiens with whom they also interbred. This led to the discovery that south East Asian and Melanesian people today have a significant proportion of Denisovan DNA, indicating frequent interbreeding as Homo sapiens spread out of Africa across central, southern and south-eastern Asia and into Indonesia, New Guinea and Australia.

There is also a mysterious fourth hominin whose DNA has been found in Neanderthals and some Homo sapiens. Neanderthals and Denisovans were the descendants of an earlier migration out of Africa of an archaic hominin, probably H. erectus. H. sapiens are almost certainly the descendants of those H. erectus who stayed in Africa.
What this tells us is that for much of recent human history, we have co-existed with several other hominin species whose evolutionary divergence from us and each other was not sufficiently advanced to prevent interbreeding, probably because for most of the 250,000 years that Neanderthals had lived in Eurasia, during which the ancestors of H. sapiens lived in Africa, interbreeding was a rare event so there was no evolutionary pressure to either reintegrate into a single species or to establish barriers to hybridization.

Having said that, though, there is a recent explanation for the disappearance of Neanderthals which suggests that they were never exterminated but simply merged into the growing population of H. sapiens which quickly outnumbered them, to the extent that there is now more Neanderthal DNA in the world than there ever was prior to 40,000 years ago.

Human Evolution News - We have More Neanderthal DNA Now Than They Ever Had

When Homo sapiens came out of Africa, the period of co-existence was too short for barriers to hybridization to evolve, so for much of our recent history, the Homo complex of species behaved very much like a ring species of incompletely speciated regionals species and subspecies.

Ring species

Creationist frauds now have the task of explaining to their credulous dupes why, if the TOE is a theory in crisis, one of its main exponents, whose work only makes any sense in the context of evolving hominin species, has been awarded the most prestigious prize in science - a Nobel Prize. We can now expect a proliferation of childish conspiracy theories as they seek to cope with the cognitive dissonance.

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Malevolent Designer News - How Creationism's Divine Malevolence Gives us Dementia

Viral infections including COVID are among the important causes of dementia – one more reason to consider vaccination

What is not generally recognised is the role of viruses, such as SARS-CoV-2 which caused COVID-19, have in causing dementia. Now recent research has shown that 'Long Covid' is emerging as one ot the most important causes of dementia.

Now, with many countries discontinuing the policy of isolating people with COVID-19 and allowing them to continue to work and mix socially, the virus is becoming endemic in the population, so the long-term effects, such as dementia are going to increase.

The following article by Professor John Donne Potter of the Research Centre for Hauora and Health, Massey University, New Zealand, reproduced from The Conversation under a Creative Commons open access licence, reformatted for stylistic consistency, highlights the role of viruses in dementia. The original article can be read here.

Viral infections including COVID are among the important causes of dementia – one more reason to consider vaccination

Credit: Sven Hoppe/picture alliance via Getty Images

John Donne Potter, Massey University

With more of us living into old age than at any other time, dementia is increasing steadily worldwide, with major individual, family, societal and economic consequences.

Treatment remains largely ineffective and aspects of the underlying pathophysiology are still unclear. But there is good evidence that neurodegenerative diseases – and their manifestation as dementia – are not an inevitable consequence of ageing.

Many causes of dementia, including viral infections, are preventable.

COVID and other viral infections are centrally involved in insults to the brain and subsequent neurodegeneration. COVID-positive outpatients have a more than three-fold higher risk of Alzheimer’s and more than two-fold higher risk of Parkinson’s disease.

A study of almost three million found risks of psychiatric disorders following COVID infection returned to baseline after one to two months. But other disorders, including “brain fog” and dementia, were still higher than among controls two years later.

🚨I wrote about “brain fog”—one of the most common & disabling symptoms of long COVID (and many other pre-pandemic conditions), and one of the most misunderstood.

Here’s what brain fog actually is, and what it’s like to live with it. 1/ https://t.co/Gq8iylgfBr

— Ed Yong is on sabbatical (@edyong209) September 12, 2022

Among more than six million adults older than 65, individuals with COVID were at a 70% higher risk than the uninfected for a new diagnosis of Alzheimer’s disease within a year of testing positive for COVID.

More than 150,000 people with COVID and 11 million controls have been involved in a study of long-term consequences of acute COVID infection. A year after infection, there was an overall 40% higher risk (an additional 71 cases per 1000 people) of neurologic disorders, including memory problems (80% higher risk) and Alzheimer’s disease (two-fold higher risk). These risks were elevated even among those not hospitalised for acute COVID.

These 12 things can reduce your dementia risk – but many Australians don't know them all

SARS-CoV-2, the virus that causes COVID, can invade brain tissue. Other viruses can also cause direct damage to the brain. A study of almost two million people showed the risk of Alzheimer’s was markedly lower in those who had been vaccinated against influenza.

The cost of dementia

Dementia is characterised by progressively deteriorating cognitive function. This involves memory, thinking, orientation, comprehension, language and judgement, often accompanied by changes in mood and emotional control.

It is one of the major causes of disability among older people. Worldwide prevalence exceeds 55 million and there are almost ten million new cases annually. It is the seventh leading cause of death. In 2019, the estimated global cost of dementia was US$1.3 trillion and rising.

The best known form of dementia – Alzheimer’s – was first described in 1907. Dementia is generally described as developing in three stages:

• impairment of memory, losing track of time and becoming lost in familiar places
• further deterioration of memory with forgetfulness of names and recent events, becoming confused at home, losing communication skills and personal care habits, repeated questioning, wandering
• increased difficulty walking, progressing to inactivity, marked memory loss, involving failure to recognise relatives and friends, disorientation in time and place, changes in behaviour, including lack of personal care and emergence of aggression.

Omicron-specific vaccines may give slightly better COVID protection – but getting boosted promptly is the best bet

Treatments largely unsuccessful

There are no cures and no resounding treatment successes. Management involves support for patients and carers to optimise physical activity, stimulate memory and treat accompanying physical or mental illness.

Dementia has a disproportionate impact on women, who account for 65% of dementia deaths and provide 70% of carer hours.

We may know less about the pathology of dementia than we imagined: some key data are under scrutiny for possible inappropriate manipulation.

Alzheimer's theory undermined by accusations of manipulated data – but does not bring dementia research to its knees

But we do know about many of the causes of dementia and therefore about prevention. In addition to viral infections, there are at least four other contributing causes: cardiovascular disease, type 2 diabetes (especially if untreated), traumatic brain injury and alcohol.

The brain has its own immune system – cells called microglia. These play a role in brain development, account for 5-10% of brain mass and become activated by damage and loss of function. They are also implicated in Alzheimer’s and their inflammation has been shown to be central to its pathology.

Dementia is preventable

In the absence of effective treatment, prevention is an important goal. The association with viral infections means we should pay careful attention to vaccine availability and uptake (for influenza, COVID and any future variants) and place greater emphasis on combatting misinformation regarding vaccines.

The association with atherosclerosis and stroke, as well as diabetes, supports primary prevention that involves healthier diets (plant-based diets low in salt and saturated fats), physical activity and weight control.

Alcohol consumption is a major problem globally. We have allowed high intake to be normalised and talk about no more than two glasses per day as though that is innocuous. Despite the myth of some beneficial aspects of alcohol, the safest intake is zero drinks per week.

My article speaks about a study that showed that people who chronically consume alcohol and become unconscious because of it, their chances of having dementia increase 10 fold. https://t.co/0DOFf9X5Zx @mrcopsych

— Hannah (@Hannah46221416) September 29, 2022

This requires a complete national rethink around the availability and acceptability of alcohol as well as assistance with alcohol addiction and treatment of alcohol-related disorders.

Traumatic brain injury is associated with sport and, more importantly, falls and car crashes. It is recognised as a global priority and there is increasing awareness of the preventability of falls among older people. The management of head injuries is being ramped up in contact sports.

However, data on the impact of best management of the initial injury on subsequent risk of dementia are lacking and risk remains elevated even 30 years after the initial trauma.

The evidence that dementia has preventable causes, including viral infection, should better inform policy and our own behaviour.

John Donne Potter, Professor, Research Centre for Hauora and Health, Massey University

Published by The Conversation.
Open access. (CC BY 4.0)

It seems then, that if you've fallen for the intelligent [sic] design hoax, you must now accept that the malevolent designer who designed the SARS-CoV-2 virus intended it to cause dementia in those who survived the initial attack. Unless, of course, you believe that it is a stupid designer who doesn't know what the organisms it is designing will do and is incapable of correcting its designs when it realises the consequences of what it’s done, if it has any concerns for those consequences. If the latter, you believe the designer has all the characteristics of a mindless natural process without a plan, exactly like evolution by natural selection.

Malevolent Designer News - How Ticks Are Designed to Make Us Sick

European tick, Ixodes ricinus

Study demonstrates for the first time that ticks weaken skin's immune response

Creationism's divine malevolence is nothing if not a fanatical perfectionist for whom no detail is too small in its quest to find ways to make its creation sick - or so you must believe if you've fallen for the intelligent [sic] design hoax.

Here for example is a paper in which the scientists have shown how well-designed ticks are for passing on infections to its victims, including humans and our livestock. The scientists found that tick saliva contains a powerful immuno-suppressant the prevent the body from reacting to the nasty little organisms it injects along with its saliva when it takes a meal. This also solves the mystery of why ticks are such powerful disease vectors. It almost seems they were designed for it.

The team of scientists led by led by Georg Stary (MedUni Vienna's Department of Dermatology, CeMM Research Center for Molecular Medicine of the Austrian Academy of Sciences, Ludwig Boltzmann Institute for Rare and Undiagnosed Diseases) in collaboration with the research group of Hannes Stockinger (Center for Pathophysiology, Infectiology and Immunology at MedUni Vienna) have published their paper, open access, in the Journal of Clinical Investigation.

The Medical University of Vienna news release, explains the research and its significance:

Creationism in Crisis - How the Precursors of Paired Fins and Limbs Evolved

Life reconstructions of the fossil Tujiaaspis vividus.

Qiuyang Zheng

September: Galeaspids | News and features | University of Bristol.

There is little doubt now that the paired terrestrial tetrapod limbs, possessed by all terrestrial vertebrates, and those such as whales and turtles that he reverted to a marine existence, evolved out of the paired pectoral and pelvic fins of fish that first crawled onto land. The remaining question was how did these paired limbs evolve in the early fish? Because of gaps in the fossil record, it had looked as though fins suddenly appeared fully formed.

That question has now been answered by an international team, led by Min Zhu of the Institute of Vertebrate Palaeontology and Palaeoanthropology, Beijing and Professor Philip Donoghue from the University of Bristol’s School of Earth Sciences, whose discovery shows the primitive condition of paired fins before they separated into pectoral and pelvic fins, the forerunner to arms and legs.

The evidence was found in fossils in the rocks of Hunan Province and Chongqing and named Tujiaaspis after the indigenous Tujia people who live in this region. Unlike previous fossils records which are mostly just the heads, these fossils contain the whole body.

Earlier fossils either had fins or they didn't, with no fossil record of transition to paired fins. That gap has now been filled by Tujiaaspis. There had been a hypothesis that fins probably began as folds but is was just that - a hypothesis awaiting confirmation or falsification. That confirmation has now been provided.

As the press release from the University of Bristol explains:

Creationism in Crisis - Scientists Have Reconstructed the Genome of the Earliest Mammalian ancestor

Morganucodon, one of the oldest known mammal-like species

Source: FunkMonk (Michael B. H.), CC BY-SA 3.0
via Wikimedia Commons

Revealing the Genome of the Common Ancestor of All Mammals - Leibniz Institute for Zoo and Wildlife Research

The creationist delusion that the Theory of Evolution is a theory in crisis, about to be replaced in mainstream biology with their childish, evidence free superstition based on the ludicrous idea that nothing evolves and everything is made by magic, took another blow today when an international team of scientists led by scientists from the University of California Davis and the Leibniz Institute for Zoo and Wildlife Research (Leibniz-IZW), Berlin, Germany, published their computed genome of the stem species from which all mammals evolved.

Such a project would not have been mooted had the scientists had the slightest doubt about evolution being the explanation for biodiversity, nor would it have been possible to compute this ancestral genome if the DNA of mammals did not form consistent hierarchy of nested clades resulting in evidence that the genomes of the ancestors of modern mammals form a family tree with a single origin, which lived about 200 million years ago.

The scientists' work is published in the scientific journal Proceedings of the National Academy of Sciences (PNAS).

As the scientists explain in the news release from Leibniz-IZW:

Malevolent Designer News - Yet Another SARS-CoV-2 Variant and Another Wave of COVID-19 is On The Way

Big COVID-19 waves may be coming, new Omicron strains suggest | Science | AAAS

According to this article in Science, another wave of COVID-19 infections is on the way because several different sub-strains of the Omicron variant have converged on a similar way to evade the antibodies our immune systems manufacture in response to vaccination and/or infection.

It's not possible to say which of the various emerging strains will come to predominate, but one variant, known as BA.2.75.2, is a likely candidate. It is proving to be especially successful at evading antibodies because changes at half a dozen key sites in its genome that affect the way antibodies bind to the spike proteins on the viral coat, mean the antibodies don't bind very successfully.

Creationism in Crisis - Scientists Show How Large Molecules Self-Assemble - No Gods Required Again

Attraction between the dipoles of several macromolecules leads to their mesomorphic assemblies, in contrast with typical polyelectrolyte behavior.

Credit: Shibananda Das

Game-changing New Theory Upends What We Know About How Charged Macromolecules Self-assemble : UMass Amherst

The recent rum of bad news for Creationism just got worse, with the news that scientists from the University of Massachusetts Amherst have discovered how large molecules such as proteins and DNA can self-assemble with nothing more than the laws of chemistry and physics. As always when one of Creationism's favourite gaps is snapped shut by science, no gods were found and the 'mystery' required nothing more than the operation of the natural laws of chemistry and physics.

In the words of one of the researchers:

The significance of the discovery that dipoles drive the assembly of polymers is immense because it throws new light on one of the fundamental mysteries of life’s processes, [how biological materials know how to self-assemble into coherent, stable structures]. The theory changes the paradigm of how we think about these systems, and highlights the unacknowledged role that dipoles play in the self-assembly of biological materials.

Professor Murugappan Muthukumar, senior author
Department of Polymer Science and Engineering, University of Massachusetts, Amherst, MA, USA

What is a dipole? Dipole Definition in Chemistry and Physics

As the University of Massachusetts Amherst news release explains:

Malevolent Designer News - The Asian Longhorned Ticks Are Spreading Fast in USA

Asian longhorned tick, Haemaphysalis longicornis

Longhorned tick discovered in northern Missouri for first time, MU researchers find // Show Me Mizzou // University of Missouri

News today of another stunning triumph for Creationism's malevolent designer!

The Asian longhorned tick, Haemaphysalis longicornis is spreading fast in the USA. Worldwide is causes millions of dollars in lost revenue for cattle farmers. It was first reported in New Jersey in 2017 and has now spread to Missouri. The tick is responsible for spreading the organisms that cause bovine theileriosis, which is similar to anaplasmosis in that it causes weight loss, reduced milk yield and death in cattle.

Wikipedia - Theileria

The longhorned tick is closely related to other ticks in the Haemaphysalis genus which are found extensively in Asia and Australasia, all of which can and do transmit bacterial and viral diseases.

I described in The Malevolent Designer: Why Nature's God is not Good how another tick, the black-legged tick, Ixodes scapularis transmits the disease anaplasmosis in humans by injecting the rickettsia bacterium, Anaplasma phagocytophilum when it bites.

The Malevolent Designer: Why Nature's God is not Good

Map showing the spread of the tick from New Jersey since 2017 (as of July 2022.

Source: Drovers

The spread of this nasty little arachnid has probably been facilitated by two things:

1. Climate change, meaning the warmer temperatures in the US mid-west are creating a more conducive environment for it.
2. the fact that females can breed parthenogenically, meaning they don't need to mate to produce thousands of fertile eggs - all of which are female with the same ability. This mean in a few years, a single female can quickly establish a very large population.

Creationists might like to marvel at that stroke of genius in their putative designer's design for the tick, while wondering how, what is so obviously an advantageous adaptation can be presented as 'devolution', to comply with the latest attempt to replace the failed 'Intelligent [sic] Design' hoax.

The University of Missouri news release explains the problem and how it was discovered:

Evolution News - How The Bird-Hipped Dinosaurs Evolved

Shaking the dinosaur family tree: how did ‘bird-hipped’ dinosaurs evolve?

Two Herrerasaurus chasing a Silesaurus down a stream in the Triassic period. Two Plateosaurus are in the background.

Mohamad Haghani/Stocktrek Images

It's been another terrible week for Creationists.

First there was the news that plants have a ludicrously complex process for correcting the mistakes made when DNA is replicated, and how this shows common descent of plants and animals with the news that this process works when inserted into a human cell. Then there was yet more evidence of the malevolence of any creator who could come up with a design for a trypanosome flagellum that makes it easier for tsetse flies to inject it into us and cause sleeping sickness, and the news that a redesigned fungus is killing the frogs that would eat the mosquitoes that spread malaria. And lastly there is the news that the Theory of Evolution shows no signs of being abandoned as the best explanation for biodiversity but can even be applied to cultures with the finding that chimpanzees, like humans, form different cultural groups.

In fact, of course, most weeks are bad news weeks for Creationists because so many new scientific papers, especially in the fields of biology, archaeology and geology, refute Creationism without even trying, simply because, unlike Creationism, science is firmly grounded in observable and verifiable reality.

Now there is news that scientists from Cambridge University, UK, have shown how a group of dinosaurs, the remote ancestors of modern birds - the bird-hipped dinosaurs - evolved from a 'transitional', i.e., stem group, of dinosaurs, the silesaurs, which had been identified ten years earlier. They have published their finding in the Zoological Journal of the Linnean Society.

The Cambridge University News release explains how this discovery was made:

Malevolent Designer News - How Creationism's Divine Malevolence Made Tsetse Flies to Pass on Sleeping Sickness

African Sleeping Sickness Microscopic African trypanosomes (left), the parasites that cause African sleeping sickness, are spread by the bite of the tsetse fly (right).

Photo by Nikolay Kolev (left) and Geoffrey Attardo (right)

African sleeping sickness: How the pathogen colonizes t … - LMU Munich

This news item should please devotees of Creationism's putative intelligent [sic] designer, if for no other reason than that it involves a flagellum. Those who fell for Michael J Behe's opening ploy in his intelligent design hoax were fooled into believing that a flagellum is an irreducibly complex structure so must have been designed by an intelligent designer because it could not have evolved by Darwinian gradual evolution.

Of course, Behe ignored the fact that the component parts of the flagellar proton motor pre-existed the flagellum, in the Type II Secretion System, which was a development of the proton pump, so all that was needed was for them to be exapted for a different function, and to give the organism an advantage. It also ignores the fact that there are lots of different flagella found in nature, some with even fewer components than those of E. coli, which he had claimed was the minimum necessary for a functional flagellum. Clearly, if other flagella can work with less components, that of E. Coli is not irreducibly complex

Wikepedia - Type II secretion system

And, unwittingly, Behe gave us the idea of a malevolent designer, because E. coli is much better at making us sick because it has a flagellum, than it would be without it. Given that Creationists believe their putative designer is omniscient, it must have been aware of that when it designed the flagellum.

Anyway, no matter how comprehensively the hoax is refuted, or how malevolent it makes their favourite god look, Creationists will ignore the science and stick with the refuted notion, so those are the people who should be thrilled by this discovery. It is the discovery that the trypanosomes carried by the tsetse fly, which causes sleeping sickness in humans and debilitating diseases in cattle and horses, has a flagellum specially designed to enable the tsetse fly to pass it on in its saliva when it takes a blood meal.

Origins of the English

From Continental Europe to England | Max-Planck-Gesellschaft

The Alfred Jewel
Believed to have been commissioned by King Alfred the Great and inscribed "AELFRED MEC HEHT GEWYRCAN" (Alfred me had made) in the West Saxon dialect.

Ashmolean Museum, Oxford

Where did the English come from?

The answer might surprise those little Englander nationalists who took us out of the European Union, as well as those on the far right who foster daft notions of English racial purity, because even in the Early Middle Ages, the average English person was actually only about 40% Anglo-Saxon, and even that proportion of the 'English' genome came from continental regions bordering the North Sea, including the Netherlands, Germany and Denmark. 20%-40% came from what is today Belgium and France. The rest is derived mostly from the indigenous population that was present at the time of the Roman occupation - Brythonic Welsh. The evidence is that the Germanic immigrants sometimes integrated and intermarried in some area, while in other places they formed which might have been an elite upper class.

Grave goods from inhumation grave 3532 at Issendorf cemetery in Lower-Saxony, Germany. Individuals buried at Issendorf cemetery during the Middle Ages are genetically closely related with people who migrated into England during the Anglo-Saxon period.

© Landesmuseum Hannover

The language they brought with them is as comprehensible today to a Dane, a Swede or a Flemish/Dutch speaker as it is to an English speaker, as anyone who has read Beowulf in the original West Saxon dialect of Old English can testify. I once worked with a girl who had been brought up in Norway with a Norwegian mother and an English father. She spoke Swedish, some Danish and a little German in addition to her native Norwegian and English. She could understand parts of Beowulf that I was reading during a coffee break because all the languages she spoke were related to the Germanic West Saxon dialect of Old English, the epic poem was written in.

That fact is confirmed by the work done by the Max Planck Institute and University of Central Lancashire, scientists.

Cultural Evolution - In Chimpanzees

Chimpanzee stone tool diversity | Max-Planck-Gesellschaft

Female chimpanzee cracking Panda oleosa nuts using a granodiorite hammerstone on a wooden (panda tree root) anvil.

© Liran Samuni, Taï Chimpanzee Project

Archaeologist and primatologists from the Max Planck Institute for Evolutionary Anthropology, Leipzig, Germany, have discovered cultural differences between different groups of chimpanzees.

Ask any Creationist and they'll assure you that the fact that humans have developed art, music and architecture, to name just a few of our cultural developments, is evidence that there is something very special about humans, showing that we were specially created separate from the rest of 'creation' and given these 'gifts' to enable us to have 'dominion over the planet - which was provided for our benefit.

The problem with that argument from personal incredulity and wishful thinking, is that humans are far from being the only species to have cultures, albeit, our cultural developments of language and writing, combined with our ability to learn and recall facts, and to pass them on to our children, has enabled us to build on out innate ability to form cultural groups, to build advanced cultures. The difference is one of magnitude, not presence/absence. The analogy is with the elephant’s trunk, which is an example of variation on the same basic body plan, and so evidence of common ancestry, not special creation of elephants, although that analogy is probably too subtle for the simple binary thinking of Creationists.

The fact that our cultures have much in common with each other but vary considerably between different geographical groups is evidence of the evolutionary process involved in building those cultures. Sometimes, these cultural variations are very subtle, but most people who have been to other countries will be aware of them, especially with food, drink and language, and with little differences between driving behaviour, as I once showed with a blog post about the difference in driving customs between the UK and Naples, in Italy.

Driving Ethical Evolution

What the scientists at the Max Planck Institute have discovered is that chimpanzees not only use stone tools as hammers to open nuts, but that the stone tool preferred varies between different social groups.

As the Max Planck Institute news release explains:

Malevolent Designer News - Creationism's Divine Malevolence is Killing the Frogs That Help Protect Us from Malaria

Malaria Spike Linked to Amphibian Die-Off | UC Davis

Panamanian golden frog, Atelopus zeteki, a victim of the fungus, Batrachochytrium dendrobatidis.

On the face of it, there is no connection between frogs and malaria, but scientists have discovered a correlation between the decline of frogs due to the fungus, Batrachochytrium dendrobatidis, and a spike in malaria cases in parts of Latin America, particularly in Costa Rica and Panama.

Readers may remember how I described the world-wide devastation of amphibian populations with the fungus, B. dendrobatidis (Bd), and how a team of researchers from the University of California at Davis had reported a link between these deaths and an increase in malaria, probably due to this removal from the ecosystem of major predators on mosquitos.

To be a Creationists is to believe this fungus, the effects it is having on global amphibian populations and the knock-on effects this is having on the ecosystem and human health, is the intended outcome of a supernatural intelligent [sic] designer, with this obviously malevolent intent.

Unintelligent Design - God Hates Frogs
Malevolent Designer News - God Doesn't Hate Frogs; He Just Loves Mosquitos and Malaria More.

I also write about this fungus in my popular, illustrated book, The malevolent Designer: Why Nature's God is not Good, as an example of what can only be described as malevolent intent, if the modification to this otherwise harmless soil fungus to turn it against the world's amphibians, really was the work of Creationists' putative intelligent [sic] designer, as their dogma obliges them to believe.

The Malevolent Designer: Why Nature's God is not Good - Rosa Rubicondior

The mystery, as ever, is why Creationists would prefer us to see their favourite god as a malevolent monster, forever scheming to increase the amount of suffering in the world, rather than ascribe these things to a natural process with no mind or morality involved.

The same UC Davis team has now reported a close correlation between the major die-off of amphibians in Costa Rica and Panama with a spike in malaria cases in the region. At the spike’s peak, up to 1 person per 1,000 annually contracted malaria that normally would not have had the amphibian die-off not occurred, the study found.

According to the UC Davis news release:

Unintelligent Designer News - A Moss RNA Repair Mechanism That also Works in Human Cells

Moss repair team also works in humans — University of Bonn

The editor PPR56, - which only acts in mitochondria in the moss, edits more than 900 different positions in nuclear transcripts in human cells. The size of the respective nucleotide (A, U, C, G) shows how often it occurs at this position of the targets additionally edited by PPR56 in the human transcripts.

© Elena Lesch/University of Bonn

If ever a scientific discovery was designed to embarrass Creationist's, this is it. It is the discovery by scientists at the University of Bonn, Germany, that an RNA editing process which is normally used in plant mitochondria and chloroplasts, works in animal cells, including human cells.

What the scientists discovered is that if they transfer the RNA editing machines PPR56 and PPR65 from moss into human cells, they still work and edit RNA as they would in plants cells.

The process repairs mistakes in the RNA transcribed from the DNA. Although the mistakes are in the RNA, they are correct transcriptions of mistakes in the DNA itself. The mistakes in the DNA are left alone - which means they accumulate over the generations. In animal cells DNA is repaired (albeit imperfectly) when the cell is replicated, but not so in plant mitochondria and chloroplasts.

Now, there may be advantages in allowing mistakes to accumulate over time because this means there are more mutations for natural selection to work on so giving the organelles more evolvability. However, since the transcribed RNA is repaired, this doesn't seem to be an explanation because the resulting proteins will be the same, regardless.

Overview of Transcription - Khan Academy

What plant organelles have ended up with is the equivalent of a master document which it to be photocopied lots of times, but which has spelling mistakes in it. Then, instead of correcting the master copy, each photocopy is scanned for mistakes and corrected, while the mistakes are left in the master copy. When a new master copy is needed, it is made by copying the old master copy, mistakes and all, and any new mistakes intoduced in that process also go unrepaired.

On the face of it, this doesn't seem to be a process that could be described as intelligently designed!

As the University of Bonn news release explains:

Moss repair team also works in humans

Researchers at the University of Bonn transplant RNA editing machine of a moss into human cells

If everything is to run smoothly in living cells, the genetic information must be correct. But unfortunately, errors in the DNA accumulate over time due to mutations. Land plants have developed a peculiar correction mode: they do not directly improve the errors in the genome, but rather elaborately in each individual transcript. Researchers at the University of Bonn have transplanted this correction machinery from the moss Physcomitrium patens into human cells. Surprisingly, the corrector started working there too, but according to its own rules. The results have now been published in the journal "Nucleic Acids Research".

In living cells, there is a lot of traffic like on a large construction site: In land plants, blueprints in the form of DNA are stored not only in the cell nucleus, but also in the cell’s power plants (mitochondria) and the photosynthesis units (chloroplasts). These blueprints contain building instructions for proteins that enable metabolic processes. But how is the blueprint information passed on in mitochondria and chloroplasts? This is done by creating transcripts (RNA) of the desired parts of the blueprint. This information is then used to produce the required proteins.

Errors accumulate over time

However, this process does not run entirely smoothly. Over time, mutations have caused errors to accumulate in the DNA that must be corrected in order to obtain perfectly functioning proteins. Otherwise, the energy supply in plants would collapse. At first glance, the correction strategy seems rather bureaucratic: instead of improving the slip-ups directly in the blueprint - the DNA - they are cleaned up in each of the many transcripts by so-called RNA editing processes.

Why living cells make this effort, we do not know. Presumably, these mutations increased as plants spread from water to land during evolution.

Dr. Mareike Schallenberg-Rüdinger, co-senior author
Institute of Cellular and Molecular Botany (IZMB)
University of Bonn, Bonn, Germany.

Compared to letterpress printing, it would be like correcting each individual book by hand, rather than improving the printing plates.

In 2019, the IZMB team led by Prof. Dr. Volker Knoop succeeded in transplanting RNA editing processes from the moss Physcomitrium patens into the bacterium Escherichia coli. It was shown that the repair proteins of the moss can also modify the RNA of these bacteria.

Our results showed that the land plant correction mechanism also works in human cells. This was previously unknown.

Elena Lesch, first author
Institute of Cellular and Molecular Botany (IZMB)
University of Bonn, Bonn, Germany.

Now, researchers from the Institute of Cellular and Molecular Botany, together with the team led by Prof. Dr. Oliver J. Gruss from the Institute of Genetics at the University of Bonn, have gone one step further: They transferred the RNA editing machinery from the moss into standard human cell lines, including kidney and cancer cells, for example.

But that's not all: the RNA editing machines PPR56 and PPR65, which only act in mitochondria in the moss, also introduce nucleotide changes in RNA transcripts of the cell nucleus in human cells.

More than 900 targets

Surprisingly for the research team, PPR56 makes changes at more than 900 points of attack in human cell targets. In the moss, on the other hand, this RNA corrector is only responsible for two correction sites." There are many more nuclear RNA transcripts in human cells than mitochondrial transcripts in the moss," explains Dr. Mareike Schallenberg-Rüdinger. "As a result, there are also many more targets for the editors to attack." Although the editors follow a particular code, at this stage, it is not yet possible to accurately predict where the editing machines will make changes in human cells.

However, the abundance of RNA editing targets in human cells also offers the opportunity to find out more about the basic mechanisms of the correctors in further studies. This could be the basis for methods of inducing a very specific change in RNA in human cells by means of a corrector. "If we could correct faulty sites in the genetic code with RNA editing methods, this would potentially also offer starting points for the treatment of hereditary diseases," says Schallenberg-Rüdinger, looking to the future. "Whether that will work remains to be seen."

Copyright: © 2022 The authors.
Published by Oxford University Press on behalf of Nucleic Acids Research. Open access. (CC BY 4.0)

The team have published their findings in an open access paper in the journal Nucleic Acids Research:

Abstract

RNA editing processes are strikingly different in animals and plants. Up to thousands of specific cytidines are converted into uridines in plant chloroplasts and mitochondria whereas up to millions of adenosines are converted into inosines in animal nucleo-cytosolic RNAs. It is unknown whether these two different RNA editing machineries are mutually incompatible. RNA-binding pentatricopeptide repeat (PPR) proteins are the key factors of plant organelle cytidine-to-uridine RNA editing. The complete absence of PPR mediated editing of cytosolic RNAs might be due to a yet unknown barrier that prevents its activity in the cytosol. Here, we transferred two plant mitochondrial PPR-type editing factors into human cell lines to explore whether they could operate in the nucleo-cytosolic environment. PPR56 and PPR65 not only faithfully edited their native, co-transcribed targets but also different sets of off-targets in the human background transcriptome. More than 900 of such off-targets with editing efficiencies up to 91%, largely explained by known PPR-RNA binding properties, were identified for PPR56. Engineering two crucial amino acid positions in its PPR array led to predictable shifts in target recognition. We conclude that plant PPR editing factors can operate in the entirely different genetic environment of the human nucleo-cytosol and can be intentionally re-engineered towards new targets.

Graphical Abstract

Plant mitochondrial PPR-DYW deaminase specifically edits cytidines in nuclear-cytosolic transcripts in human cells. The editing enzyme can be re-directed to new targets via modification of single binding motifs.

Elena Lesch, Maximilian T Schilling, Sarah Brenner, Yingying Yang, Oliver J Gruss, Volker Knoop, Mareike Schallenberg-Rüdinger
Plant mitochondrial RNA editing factors can perform targeted C-to-U editing of nuclear transcripts in human cells
Nucleic Acids Research, 2022;, gkac752, https://doi.org/10.1093/nar/gkac752

Copyright: © 2022 The authors.
Published by Oxford University Press on behalf of Nucleic Acids Research. Open access
Reprinted under a Creative Commons Attribution 4.0 International license (CC BY 4.0)

This raises several problems for Creationists, especially those who believe an intelligent [sic] designer is responsible for these processes:

1. Why is this not evidence of a common origin of plants and animals?
2. Why would an intelligently designed process by an omnipotent, omniscient designer result in mistakes that need repairing?
3. Why would an intelligent designer use such an unncessarily complicated process to correct the mistakes in DNA replication when it uses a simpler process in animal cells, which doesn't mean mistakes continue to accumulate in the Genome?
4. If there are no advantages in carrying out the repair at the RNA level instead of at the DNA level, why 'design' two different processes to achieve the same result?
5. If there are advantages, why not use the advantageous process for animals as well as plant organelles?

No doubt all those problems will be waved aside with the ultimate in non-answer, "God works in mysterious ways!", whilst still insisting that intelligent [sic] design is real science, not religion in a lab coat.