Creationism in Crisis - More Lousy News For Creationists - Human Evolution Mapped In The Genome Of Head Lice Symbiotic Bacteria

Human head louse, Pediculus humanus capitis

Gilles San Martin via Wikimedia (CC BY-SA 2.0)

Phylogenetic trees for primate lice and their vertebrate hosts redrawn from Reed et al . [9]. Trees are shown as cladograms with no branch length information, and are based on molecular and morphological data. Dashed lines between trees represent host-parasite associations. Humans are unique in being parasitized by two genera (Pediculus and Pthirus). (Herd, K.E., Barker, S.C. & Shao, R.(2015))

Photo credits: J. W. Demastes, T. Choe, and V. Smith.

Genomic Diversity in the Endosymbiotic Bacteria of Human Head Lice | Molecular Biology and Evolution | Oxford Academic

It's a basic principle of evolutionary biology that an obligate commensal, symbiotic or parasitic organism is evolutionary bound to the organism on which it is dependent, It follows then that the genomes of two or more organism in such a relationships will reflect the same major changes which drive evolution.

I have previously described how the evolutionary tree of the human head and body lice, Pediculus humanus, fits exactly on the evolutionary tree of Homo sapiens as we diverged from the common ancestor with chimpanzees. At the same time, our lice diverged from a common ancestor they share with the lice which are obligate parasites on chimpanzees, Pe. schaeffi.

Interestingly, our lice also reflect when we started wearing clothes having lost our body hair. This loss of body hair meant our lice became head lice which are closely related to the chimpanzee's body lice. When we started wearing clothes our lice diverged into two subspecies - head lice, Pe. h. capitis, and body lice, Pe. h. humanus.

And now, something even more interesting and confirmative of evolution, is the discovery that an obligate, symbiont bacteria on which the lice depends, shows exactly the same pattern of divergence, mapped onto the evolutionary tree of the lice.

The symbiotic bacterium, Candidatus Riesia pediculicola, in a typically Heath-Robinson solution to a problem which is a characteristic of mindless, unplanned evolution, and unlike anything an intelligent designer would design, is essential to the lice because they can't make essential B-vitamins and don't get them from the blood on which they exclusively feed.

And, incidentally, these bacteria have evolved by loss of genetic information - something that creationist frauds tell their dupes is impossible because "every loss of genes is invariably fatal" [sic].

This discovery is the subject of a recent open access paper in the journal Molecular Biology & Evolution:

Creationism in Crisis - Saharan Rock Art From 8,000 Years Ago 'Missed' By the Biblical Genocidal Flood

Acacia forests in the Atbai Desert, near Bir al-Ajjami

Atbai Survey Project, Yale University

Ring tombs of likely Late Antique age (c. 1st Millennium CE) at Di’irabab

Atbai Survey Project, Yale University

New rock art discoveries in Eastern Sudan tell a tale of ancient cattle, the ‘green Sahara’ and climate catastrophe

From my own experience, the Sahara Dessert, at least the Tunisian part of it, is cold and wet!

At least that was what we experience a few years ago when we went there in early June, to avoid the heat of summer. That was a mistake, as Tunisia was experiencing one of the coldest Springs in living memory, when, at times, it felt like it was about to snow. We shivered at the Roman amphitheater at Al Jem where we were back on the coach within 20 minutes, asking for the heating to be turned on, and a trip to the Bardot Mosaic Museum in Tunis was spoilt by the rain.

But it was in the desert near Tozeur, dressed only in summer clothes, that we experienced a cold, wet Sahara, much as it may have been between 15,000 and 5,000 years ago when cattle herders were painting images of their cattle on the rocks at Atbai, east of Wado Halfa in Eastern Sudan. This period of Saharan 'greening' was when the West African subspecies of Rock dove (Columba livia lividor) managed to interbreed with a hybrid between C. rupestris and an Asian subspecies of C. livia, probably somewhere in the Sahara. And from that, probably all domestic and feral (town) pigeons are descended, as I described recently.

It was also where humans herded the cattle they had obtained from North African pastoralists, as described in the following article by Julien Cooper, Honorary Lecturer, Department of History and Archaeology, Macquarie University, Australia, reprinted here from The Conversation under a Creative Commons license. His article has been reformatted for stylistic consistency, but the text is unaltered:

Antivaxxer Idiot News - How An mRNA Vaccine Is Proving Effective Against A Highly Malignant Brain Cancer

Sadeem Qdaisat, Dr. Hector Mendez-Gomez and Dr. Elias Sayour
discuss their new study.

Photo by Nate Guidry

Dr. Elias Sayour, Chong Zhao and Arnav Barpujari discuss the mRNA cancer vaccine developed at the University of Florida

New mRNA cancer vaccine triggers fierce immune response to fight malignant brain tumor - UF Health

Contrary to the bizarre antivaxxer claims that the mRNA vaccines used against the SARS-CoV-2 virus that causes COVID-19 somehow causes cancer, based on nothing more substantial than the fact that some people who developed cancer had previously been vaccinated, there is now an mRNA vaccine that is proving spectacularly effective against a highly malignant form of brain cancer.

Curiously, the fact that some people who developed cancer will previously have sung Christmas carols or eaten potatoes, is never given as a probable cause, but then few people who believe antivaxxer disinformation will understand statistics or statistical correlations.

The mRNA vaccine against the brain cancer known as Glioblastoma has shown very promising results in a small-scale study of four adults by scientists at Florida University, repeating the results of a trial in 10 dogs and preclinical trials in mice.

The vaccine successfully, and very quickly, reprograms the immune system to produce highly specific antibodies against the tumour. Intelligent design proponents (or 'cdesign proponentcists' as they have been known since the Kitzmiller trial) might like to explain why the immune system, supposedly intelligently designed to protect us, needs to be artificially reprogrammed by human medical science.

The trick has been to create clusters of nanoparticles of lipid-enclosed mRNA wrapped around one another like a miniature onion. These means the mRNA will be released slowly and reprogram the immune system more effectively than a single burst would. The specific mRNA is tailor-made for the patient's tumour and creates antibodies against specific tumor proteins, in the same way the mRNA anti-COVID vaccines target the virus's spike proteins, so is specific to that particular cancer.

The results are reported in the journal Cell and are also explained in a University of Florida Health News release:

In a first-ever human clinical trial of four adult patients, an mRNA cancer vaccine developed at the University of Florida quickly reprogrammed the immune system to attack glioblastoma, the most aggressive and lethal brain tumor.

The results mirror those in 10 pet dog patients suffering from naturally occurring brain tumors whose owners approved of their participation, as they had no other treatment options, as well as results from preclinical mouse models. The breakthrough now will be tested in a Phase 1 pediatric clinical trial for brain cancer.

Reported May 1 in the journal Cell, the discovery represents a potential new way to recruit the immune system to fight notoriously treatment-resistant cancers using an iteration of mRNA technology and lipid nanoparticles, similar to COVID-19 vaccines, but with two key differences: use of a patient’s own tumor cells to create a personalized vaccine, and a newly engineered complex delivery mechanism within the vaccine.

“Instead of us injecting single particles, we’re injecting clusters of particles that are wrapping around each other like onions, like a bag full of onions,” said senior author Elias Sayour, M.D., Ph.D., a UF Health pediatric oncologist who pioneered the new vaccine, which like other immunotherapies attempts to “educate” the immune system that a tumor is foreign. “And the reason we’ve done that in the context of cancer is these clusters alert the immune system in a much more profound way than single particles would.”

Among the most impressive findings was how quickly the new method, delivered intravenously, spurred a vigorous immune-system response to reject the tumor, said Sayour, principal investigator of the RNA Engineering Laboratory within UF’s Preston A. Wells Jr. Center for Brain Tumor Therapy and a UF Health Cancer Center and McKnight Brain Institute investigator who led the multi-institution research team.

“In less than 48 hours, we could see these tumors shifting from what we refer to as ‘cold’ — immune cold, very few immune cells, very silenced immune response — to ‘hot,’ very active immune response,” he said. “That was very surprising given how quick this happened, and what that told us is we were able to activate the early part of the immune system very rapidly against these cancers, and that’s critical to unlock the later effects of the immune response.”

Glioblastoma is among the most devastating diagnoses, with median survival around 15 months. Current standard of care involves surgery, radiation and some combination of chemotherapy.

The new publication is the culmination of promising translational results over seven years of studies, starting in preclinical mouse models and then in a clinical trial of 10 pet dogs that had spontaneously developed terminal brain cancer and had no other treatment options. That trial was conducted with owners’ consent in collaboration with the UF College of Veterinary Medicine. Dogs offer a naturally occurring model for malignant glioma because they are the only other species that develops spontaneous brain tumors with some frequency, said Sheila Carrera-Justiz, D.V.M., a veterinary neurologist at the UF College of Veterinary Medicine who is partnering with Sayour on the clinical trials. Gliomas in dogs are universally terminal, she said.

After treating pet dogs that had spontaneously developed brain cancer with personalized mRNA vaccines, Sayour’s team advanced the research to a small Food and Drug Administration-approved clinical trial designed to ensure safety and test feasibility before expanding to a larger trial.

In a cohort of four patients, genetic material called RNA was extracted from each patient’s own surgically removed tumor, and then messenger RNA, or mRNA — the blueprint of what is inside every cell, including tumor cells — was amplified and wrapped in the newly designed high-tech packaging of biocompatible lipid nanoparticles, to make tumor cells “look” like a dangerous virus when reinjected into the bloodstream and prompt an immune-system response. The vaccine was personalized to each patient with a goal of getting the most out of their unique immune system.

“The demonstration that making an mRNA cancer vaccine in this fashion generates similar and strong responses across mice, pet dogs that have developed cancer spontaneously and human patients with brain cancer is a really important finding, because oftentimes we don’t know how well the preclinical studies in animals are going to translate into similar responses in patients,” said Duane Mitchell, M.D., Ph.D., director of the UF Clinical and Translational Science Institute and the UF Brain Tumor Immunotherapy Program and a co-author of the paper. “And while mRNA vaccines and therapeutics are certainly a hot topic since the COVID pandemic, this is a novel and unique way of delivering the mRNA to generate these really significant and rapid immune responses that we’re seeing across animals and humans.”

While too early in the trial to assess the clinical effects of the vaccine, the patients either lived disease-free longer than expected or survived longer than expected.

The 10 pet dogs lived a median of 139 days, compared with a median survival of 30 to 60 days typical for dogs with the condition.

The next step, through support from the Food and Drug Administration and the CureSearch for Children’s Cancer foundation, will be an expanded Phase I clinical trial to include up to 24 adult and pediatric patients to validate the findings. Once an optimal and safe dose is confirmed, an estimated 25 children would participate in Phase 2, said Sayour, an associate professor in the Lillian S. Wells Department of Neurosurgery and the department of pediatrics in the UF College of Medicine, part of UF Health.

For the new clinical trial, Sayour’s lab will partner with a multi-institution consortium, the Pediatric Neuro-Oncology Consortium, to send the immunotherapy treatment to children’s hospitals across the country. They will do this by receiving an individual patient’s tumor, manufacturing the personalized vaccine at UF and sending it back to the patient’s medical team, said Sayour, co-leader of the Immuno-Oncology and Microbiome research program at the UF Health Cancer Center.

Despite the promising results, the authors said one limitation is continued uncertainty about how best to harness the immune system while minimizing the potential for adverse side effects.

“I am hopeful that this could be a new paradigm for how we treat patients, a new platform technology for how we can modulate the immune system,” said Sayour, the Stop Children's Cancer/Bonnie R. Freeman Professor for Pediatric Oncology Research. “I am hopeful for how this could now synergize with other immunotherapies and perhaps unlock those immunotherapies. We showed in this paper that you actually can have synergy with other types of immunotherapies, so maybe now we can have a combination approach of immunotherapy.”

Graphic abstract

Highlights

• RNA-LPAs mimic dangerous emboli for lymphoreticular entrapment and systemic immunity
• Systemic immunity resets both the peripheral and intratumoral milieu via IFNAR1/RIG-I
• RNA-LPAs are safe and effective tumor re-modulators in canines with spontaneous gliomas
• RNA-LPAs reprogram the TME and elicit adaptive immunity in human GBM patients

Summary Cancer immunotherapy remains limited by poor antigenicity and a regulatory tumor microenvironment (TME). Here, we create “onion-like” multi-lamellar RNA lipid particle aggregates (LPAs) to substantially enhance the payload packaging and immunogenicity of tumor mRNA antigens. Unlike current mRNA vaccine designs that rely on payload packaging into nanoparticle cores for Toll-like receptor engagement in immune cells, systemically administered RNA-LPAs activate RIG-I in stromal cells, eliciting massive cytokine/chemokine response and dendritic cell/lymphocyte trafficking that provokes cancer immunogenicity and mediates rejection of both early- and late-stage murine tumor models. In client-owned canines with terminal gliomas, RNA-LPAs improved survivorship and reprogrammed the TME, which became “hot” within days of a single infusion. In a first-in-human trial, RNA-LPAs elicited rapid cytokine/chemokine release, immune activation/trafficking, tissue-confirmed pseudoprogression, and glioma-specific immune responses in glioblastoma patients. These data support RNA-LPAs as a new technology that simultaneously reprograms the TME while eliciting rapid and enduring cancer immunotherapy.

Mendez-Gomez, Hector R.; DeVries, Anna; Castillo, Paul; et al.(2024)
RNA aggregates harness the danger response for potent cancer immunotherapy Cell https://doi.org/10.1016/j.cell.2024.04.003

© 2024 Cell Press.
Reprinted under the terms of s60 of the Copyright, Designs and Patents Act 1988.

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ID is not a problem for science; rather science is a problem for ID. This book shows why. It exposes the fallacy of Intelligent Design by showing that, when examined in detail, biological systems are anything but intelligently designed. They show no signs of a plan and are quite ludicrously complex for whatever can be described as a purpose. The Intelligent Design movement relies on almost total ignorance of biological science and seemingly limitless credulity in its target marks. Its only real appeal appears to be to those who find science too difficult or too much trouble to learn yet want their opinions to be regarded as at least as important as those of scientists and experts in their fields.

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

This book presents the reader with multiple examples of why, even if we accept Creationism's putative intelligent designer, any such entity can only be regarded as malevolent, designing ever-more ingenious ways to make life difficult for living things, including humans, for no other reason than the sheer pleasure of doing so. This putative creator has also given other creatures much better things like immune systems, eyesight and ability to regenerate limbs that it could have given to all its creation, including humans, but chose not to. This book will leave creationists with the dilemma of explaining why evolution by natural selection is the only plausible explanation for so many nasty little parasites that doesn't leave their creator looking like an ingenious, sadistic, misanthropic, malevolence finding ever more ways to increase pain and suffering in the world, and not the omnibenevolent, maximally good god that Creationists of all Abrahamic religions believe created everything. As with a previous book by this author, "The Unintelligent Designer: Refuting the Intelligent Design Hoax", this book comprehensively refutes any notion of intelligent design by anything resembling a loving, intelligent and maximally good god. Such evil could not exist in a universe created by such a god. Evil exists, therefore a maximally good, all-knowing, all-loving god does not.

Illustrated by Catherine Webber-Hounslow.

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Creationism in Crisis - A Microorganism That Manipulates It's Host To Make The Nutrients It Needs

Electron microscopy showing the parasitic Candidatus Nanohaloarchaeum antarcticus: the small circular shape, attached to its host, Halorubrum lacusprofundi.

Image Credit: Joshua N Hamm

Another example of the parasitic Candidatus Nanohaloarchaeum antarcticus attached to its host, Halorubrum lacusprofundi.

Image Credit: Joshua N Hamm

Archaea can be picky parasites - NIOZ

The Bible is silent on the subject of microorganisms because they were unknown to the Bronze Age authors. But now we know better than them, we can see other ways in which they refute several basic creationist dogmas.

Firstly, there is the problem that creationists always struggle with when they don't avoid it altogether - that of parasites and how they fit into a world 'designed' by an omnibenevolent god who wishes to minimise the about of suffering in the world. More on this later…

Then the fact that archaea and bacteria could be different forms of life which arose independently showing that abiogenesis is not only possible but may have happened twice on Earth. And as they both have the same genetic 'code' this suggests that the 'code' was inevitable, not some special creation requiring a magician to produce it.

But that's a minority view; the consensus being that they have a common ancestor from which they diverged about 3.5 billion years ago.

Creationism in Crisis - How Neanderthals Were Burying Their Dead - 65,000 Years Before 'Creation Week'

Scientists have produced a remarkable reconstruction of what a Neanderthal woman would have looked like when she was alive. It is based on the flattened, shattered remains of a skull whose bones were so soft when excavated they had the consistency of "a well-dunked biscuit". Researchers first had to strengthen the fragments before reassembling them. Expert palaeoartists then created the 3D model.

BBC Studios

Shanidar Z: what did Neanderthals do with their dead?

Illustrated reconstruction of a Neanderthal man.

Hermann Schaaffhausen, 1888.

65,000 years before creationists believe the Universe existed, and before anatomically-modern humans had migrated out of Africa, a community of Neanderthals were living in a the Shanidar cave in what is now northern Iraq.

These Neanderthals also appear to have used the same cave in which to bury their dead, the skeletons of which are now being excavated to learn more about how these hominins lived.

And the picture emerges of a sophisticated people, very different from the brutal sub-human animals Victorian archaeologists depicted them as when Neanderthal remains were first discovered. Like many Creationists and US white supremacists today, Victorians were so wedded to the idea that modern (European) humans are the pinnacle of creation, that they could not conceive of the idea that there may once have been earlier humans who had anything approaching their level of sophistication.

One of the skeletons is of a man with a disabled arm who was probably deaf and had a head trauma that would have made him disabled and dependent, yet he had lived a long time, showing evidence of care and compassion.

Readers of Jean M. Auel's excellent series of imaginative, but painstakingly researched books about a Homo sapiens girl, Ayala, raised by Neanderthals will probably recognise Mog-ur, the Neanderthal tribal elder and shaman who befriended Ayala from that description...

The burials also suggest a sense of an after-life and care for the dead in that after-life. One skeleton is placed with its head pillowed on its hand presumably to make it comfortable.

One of the assembly of (female) skull fragments has been carefully removed from the rock matrix in which it was embedded and used to reconstruct her skull and then build a 3D reconstruction of how she would have appeared in life, for a BBC Netflix documentary on the excavation of the 35 individuals in the cave.

The work is the subject of an open access paper in the journal Antiquity and of a Cambridge University news article by Fred Lewsey:

Bible Blunders - What The Authors Of The Bible Never Even Guessed At

Horsehead nebula in near-infrared light from NASA’s Hubble Space Telescope

Webb Captures Top of Iconic Horsehead Nebula in Unprecedented Detail - NASA Science

A portion of the Horsehead Nebula from NASA’s James Webb Space Telescope that is about 0.8 light-years in width. The ethereal clouds that appear blue at the bottom of the image are filled with a variety of materials including hydrogen, methane, and water ice. Red-colored wisps extending above the main nebula represent both atomic and molecular hydrogen. Distant galaxies are sprinkled in the background.

Credits: NASA, ESA, CSA, K. Misspelt (University of Arizona) and A. Abergel (IAS/University Paris-Saclay, CNRS)

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Left: Released in November 2023, features the Horsehead Nebula as seen in visible light by ESA’s Euclid telescope.
Middle: View of the Horsehead Nebula in near-infrared light from NASA’s Hubble Space Telescope, which was featured as the telescope’s 23rd anniversary image in 2013. This image reveals a beautiful, delicate structure that is normally obscured by dust.
Right: A new view of the Horsehead Nebula from NASA’s James Webb Space Telescope’s NIRCam (Near-Infrared Camera) instrument.

Credit: NASA, ESA, CSA, Karl Misselt (University of Arizona), Alain Abergel (IAS, CNRS), Mahdi Zamani The Euclid Consortium, Hubble Heritage Project (STScI, AURA)

The Universe as described in Genesis 1: 3-18

And God said, Let there be light: and there was light. And God saw the light, that it was good: and God divided the light from the darkness. And God called the light Day, and the darkness he called Night. And the evening and the morning were the first day.

And God said, Let there be a firmament in the midst of the waters, and let it divide the waters from the waters. And God made the firmament, and divided the waters which were under the firmament from the waters which were above the firmament: and it was so. And God called the firmament Heaven. And the evening and the morning were the second day. And God said, Let the waters under the heaven be gathered together unto one place, and let the dry land appear: and it was so. And God called the dry land Earth; and the gathering together of the waters called he Seas: and God saw that it was good.

Gen 1:3-10

[…]

And God said, Let there be lights in the firmament of the heaven to divide the day from the night; and let them be for signs, and for seasons, and for days, and years: And let them be for lights in the firmament of the heaven to give light upon the earth: and it was so.

And God made two great lights; the greater light to rule the day, and the lesser light to rule the night: he made the stars also. And God set them in the firmament of the heaven to give light upon the earth, And to rule over the day and over the night, and to divide the light from the darkness: and God saw that it was good.

Gen 1:14-18

NASA’s James Webb Space Telescope has captured the sharpest infrared images to date of a zoomed-in portion of one of the most distinctive objects in our skies, the Horsehead Nebula. These observations show the top of the “horse’s mane” or edge of this iconic nebula in a whole new light, capturing the region’s complexity with unprecedented spatial resolution.

Webb’s new images show part of the sky in the constellation Orion (The Hunter), in the western side of a dense region known as the Orion B molecular cloud. Rising from turbulent waves of dust and gas is the Horsehead Nebula, otherwise known as Barnard 33, which resides roughly 1,300 light-years away.

The nebula formed from a collapsing interstellar cloud of material, and glows because it is illuminated by a nearby hot star. The gas clouds surrounding the Horsehead have already dissipated, but the jutting pillar is made of thick clumps of material and therefore is harder to erode. Astronomers estimate that the Horsehead has about five million years left before it too disintegrates. Webb’s new view focuses on the illuminated edge of the top of the nebula’s distinctive dust and gas structure.

The Horsehead Nebula is a well-known photodissociation region, or PDR. In such a region, ultraviolet (UV) light from young, massive stars creates a mostly neutral, warm area of gas and dust between the fully ionized gas surrounding the massive stars and the clouds in which they are born. This UV radiation strongly influences the chemistry of these regions and acts as a significant source of heat.

Compare this and the following image from the laughably naive picture painted in Genesis of how the authors saw the Universe, based on their parochial and ignorant view of the world.

Creationism in Crisis - Batty Evolution On Solomon Islands

Islands in the Vona Vona Lagoon of the New Georgia Group, Solomon Islands. This island group hosts four species of Hipposideros bats, including the two featured in the study of convergent evolution across the archipelago.

Credit: RG Moyle

Diadem leaf-nosed bat, Hipposideros diadema

Michael Pennay via Wikimedia (CC BY 2.0)

Researchers parse oddity of distantly related bats in Solomon Islands that appear identical | KU News

There is something strange about the Solomon Islands, lying east of Papua New Guinea and northeast of Australia. The bats that inhabit the islands seem to have evolved in ways that are difficult to understand.

Before creationists get over-excited and think we've found an example of species that didn't evolve but were made by magic, the question is not whether they evolved, but how? The scientists are in no doubt that the process was an evolutionary one and show no signs of concluding that a supernatural entity was involved. The puzzle is that genetically distinct species on different islands, occupying the same niche, have evolved such a high degree of phenotypic convergence that they are almost indistinguishable, so were previously classified as the same species, although genetically they are not even close relatives. The question is what is it about the environment on these islands that has driven this high level of convergence.

Each of the islands in the archipelago has a population of bats, usually 3-5 species on each island, consisting of a small, medium and large species and on islands with four species, an extra-large. One island has five species so gets an extra small bat.

That all seemed fairly straightforward on the assumption that the five distinct species had each found a niche on each island, and they certainly looked identical when comparing the different sized bats on each island. However, that was before we had DNA sequencing techniques.

DNA analysis has shown that the large bats on different islands, although identical in appearance, are not closely related - they have converged on that appearance from different ancestral bats.

This was discovered by a research team of scientists from University of Melbourne, Australia, the University of Kansas, USA, Jame Cook University, Australia and others. Their work is published open access in the journal, Evolution (the National Journal of Organic Evolution). It is explained in a University of Kansas news release:

Creationism in Crisis - Wake UP And Smell The Coffee - It Evolved 600,000 Years Before 'Creation Week'

Arabica coffee - the result of a random hybridization event

Coffea arabica

Newly sequenced genome reveals coffee’s prehistoric origin story — and its future under climate change - UBNow: News and views for UB faculty and staff - University at Buffalo

Creationists insist on seeing evolution as an event, not a process happening slowly over time, but there are a few rare examples where they are right - right by accident because few of them will have the courage to study evolutionary biology or even find out what it is and what processes cause it.

In the plant world, though not exclusively, new species arising by a single event such as hybridization between two related species which goes on to form a stable population that doesn't normally interbreed with either of the parent species, are fairly common. And one of them is the Arabica coffee plant, Coffea arabica, which is the result of a chance crossing between two diploid versions of Coffea canephora and Coffea eugenioides between 600,000 and 1,000,000 years ago to produce a state of allopolyploidia.

Because this represents such a narrow genetic bottle-neck with low genetic diversity, Arabic coffee is susceptible to infections and environmental hazards such as climate variability and soil conditions, so it needs carefully controlled conditions. It may well owe its long-term survival to the fact that it was cultivated by humans.

This was discovered by researchers at the University of Buffalo led by Victor Albert, Empire Innovation Professor in the Department of Biological Sciences, College of Arts and Sciences. Their paper is published, open access, in the journal Nature Genetics and their findings are explained in a University of Buffalo news release by Tom Dinki:

Creationism in Crisis - How Sabretoothed Cats Were Avoiding Broken Teeth - Before 'Creation Week'

Saber-toothed cat. Smilodon fatalis

Massimo Molinero

Smilodon fatalis skull

The double-fanged adolescence of saber-toothed cats | Berkeley

As an example of daft, Heath-Robinson design, the teeth of the North American sabre-toothed cat, Smilodon fatalis is a good as it gets. Obviously, having huge canine teeth with which to rip the throat out of large prey and so subdue it quickly, has some advantages, but the trouble is that the longer they are, the more likely they are to break, and broken teeth for a Smilodon could well have meant starvation and death. There needs to be a trade-off between ever-bigger teeth and death due to breakages.

And typical of creationism’s daft designer is the Heath-Robinson solution to a simple problem - you've guessed it, another layer of complexity. Instead of losing their 'milk teeth' like many mammals do as their head and mouth grows, Smilodon kept its milk teeth to act as a sort of splint for the adult Sabre tooth, reducing the lateral strain on the adult teeth until the adult was about 30 months old, by which time it had probably learned how to minimise lateral stress on its teeth.

This was discovered by Paleontologist Jack Tseng, associate professor of integrative biology at the University of California, Berkeley, who has published his findings in an open access paper in the journal The Anatomical Record. It is also explained in a University of California news release by Robert Sanders:

Reasons to Lose Faith - Suffer Little Children - How The Bible Promotes Child Abuse

Arrest for witchcraft (1866) by John Pettie. NGV

CC BY-NC

‘Witches’ are still killed all over the world. Pardoning past victims could end the practice

A promotional poster for Liberty Gospel Church with Helen Ukpabio, a modern 'witchfinder'(Lady Apostle Helen Ukpabio/Facebook)

You might think that enlightened Humanism had sufficiently civilised Christianity to put a stop to the Medieval sport of burning old ladies alive because someone had accused them of witchcraft and 'God sez' they should be killed, but think again. According to a UN report, the practice is still widespread in sub-Saharan Africa and parts of India and Southeast Asia, where an estimated 20,000 people across 60 countries were victims of abuse and summary killing between 2009 and 2019,⁴ although the true figure is likely to be much higher because such instance often go unreported.

The report is the UN Human Rights Council report entitled, Study on the situation of the violations and abuses of human rights rooted in harmful practices related to accusations of witchcraft and ritual attacks, as well as stigmatization(pdf). It paints a shocking picture of what Biblical, mainly, but now wholly, Christian, beliefs and invocations can lead to amongst those who have swallowed the missionary lie that the Bible is the inerrant word of God which should be followed to the letter to achieve 'salvation' from the horrors that the missionaries has told them await those who fail to carry it out.

The problem is that the belief in Biblical inerrancy and a mind-reading, ever watchful god can make people think the barbarity in the Old Testament especially, is the will of God and 'moral' in some arbitrary definition of morality as "what God sez!"

And 'God sez, Thou shalt not suffer a witch to live. (Exodus 22: 18)

And running throughout the Bible is a belief in evil spirits and a world running on magic in which magic words, signs and thoughts can cause bad things to happen. The result is horrendous abuse of vulnerable people and especially of women and children, as the UN report states:

Creationism in Crisis - Yeast Evolution - Not Whether But How

Electron micrograph of budding yeast cells.

Ira Herskowitz and E. Schabtach

Electron micrograph of budding yeast cells

Photo: Ira Herskowitz and E. Schabtach

Bioinformatics professor discovers surprising evolutionary pattern in landmark yeast study | Inside UNC Charlotte | UNC Charlotte

As I've remarked before, trying to debate with creationists is like boxing with a brain-dead opponent who lacks the cognitive ability to know when they're down and out. Their lumbering body keeps flailing around and like a defeated Donald Trump, insists that they’ve won, and are triumphing over all-comers in the ring.

Creationist frauds have been telling their willfully ignorant cult that they are winning the debate against science and science is about to convert to creationist superstition and abandon the materialist explanations. The science that has produced all of modern technology, including the computers and Internet that they use to inform the world that science is all wrong, and magic done by an unproven supernatural being is a better explanation for the observable facts, endearingly oblivious of the irony.

And yet not a single science paper has ever concluded any such thing and the small handful of pseudo-scientists that the creation cult employs to misinform the world never publish in peer-reviewed science journals. It's almost exactly like science just gazes bemusedly at the hopeless flailings of creationism, which has been on the canvas now for 50 years but still hasn't noticed. The trick has been to remain completely oblivious of real science by never reading anything that might make them wonder if being horizontal on the canvas is the best way of winning a boxing match.

Meanwhile real scientists do real science and science moves on.

An example of this was a paper published recently in Science which is the result on an AI assisted detailed analysis of the genomes of 1,154 strains of the ancient, single-cell yeast, Saccaromycotina, to discover how the different yeasts had evolved. Nowhere in the paper is there the slightest hint that the process that produced the different strains might be magic, not natural evolution. Instead, the research provides more understanding of how the evolutionary processes work.

The research by a team co-led by Professor of Bioinformatics Abigail Leavitt LaBella of the University of North Carolina at Charlotte, is explained in a University of North Carolina news release:

Creationism in Crisis - How Order Emerges From Chaos - Naturally

A 'murmuration' of starlings

Press Releases - SCHOOL OF SCIENCE THE UNIVERSITY OF TOKYO

It's a fundamental mantra of creationism that you'll see chanted over and over again as though it’s a proof that their god must exist, "You can't get order from chaos". It’s as fundamental, and as mindless, as the mantra, "You can't get life from non-life".

Both of them ignore the evidence and neither of them can be explained any more so than a parrot can explain its squawks.

And now a Tokyo University team has demonstrated that order can indeed emerge from chaos at different levels from the quantum to the macro level of flocks of birds, when there is a force acting between the particles to make it what they term an 'active matter'. They explain their findings in a highly technical, mathematical paper, the maths of which is quite incomprehensible to me, in the journal, Physical Review Research. The basic requirements for 'active matter' are that the particles (agents) are moving and that there is repulsion between them. In the case of a flock of birds, the repulsion is in the form of maintaining a distance between the individuals.

The researchers have explained their findings in a news release from Tokyo University:

Uninteligent Design - Bacteria Have A Defence Against The Viruses Designed To Infect Them

Bacterium infected by phage viruses

Illustration: Getty Images

Structural model at atomic resolution of bacteriophage T4

Dr. Victor Padilla-Sanchez, PhD via Wikimedia (CC BY-SA 4.0)

Study details a common bacterial defense against viral infection

Creationism's latest hobbyhorse, designed by Michael J Behe to revive the flagging fortunes of his Discovery Institute’s Wedge Strategy and the abysmal failure of his Intelligent [sic] Design ploy to get creationism inserted into the US public school science curricula at US taxpayers' expense, is the silly notion of 'genetic entropy' and 'devolution'.

This unintelligently designed strategy contains the seeds of its own failure at being regarded as a science because it starts off with the assumption that all species were created perfectly by a perfect creator, in compliance with Christian superstition, and so any mutation must be devolutionary away from that perfection. Mutations are called 'genetic entropy', so incorporating the idiotic notion that genetic 'information' is subject to the same law of physics as energy, so the Second Law of Thermodynamic make evolution impossible.

This is supposed to make creationists think Darwin must have been wrong because mutations can't improve fitness, being devolutionary, not evolutionary because of 'genetic entropy'. It ignores the fact that only an improvement in fitness in a given environment can produce more descendants than a deleterious mutation because fitness is defined as the ability to survive and reproduce. How increased fitness can be defined as a reduction in perfection is never explained because Behe 'forgot' to define 'perfection' leaving his marks to assume it means something made by their god.

And this daft notion is now cited by creationists to explain why an intelligent, omniscient and supposedly omnibenevolent god would design parasites. These are now explained as devolved from some initial perfection because of 'genetic entropy' made possible by Adam & Eve's 'sin' - Which is not religious superstition, because it was a historical fact! Got it!

So, we now have an explanation for bacteria, viruses and other parasites, that absolved creationism's god of any responsibility for them while blaming humans for their 'devolution'. However, the problem for this childish nonsense arises when we have parasites on those parasites, such as viruses that infect bacteria - how are bacteria responsible for Adam & Eve's sin and if they aren't why are they being punished for it?

Then it gets even more bizarre when we discover that many bacteria have mechanisms for protecting themselves from these viruses. How can 'devolution' produce an improvement in the organism's ability to survive and reproduce, and in what sense is an improvement a reduction in perfection?

Unintelligent Design - How the Periodic Cicadas Evolved

17-year cicada, Magicicada septendecim

Image: © Ed Reschke-Stone/Getty Images

13-year cicada, Magicada tridecima

Billions of cicadas are about to emerge from underground in a rare double-brood convergence

If it hasn't happened yet, it will do soon. The largest brood of 13-year locusts is about to emerge simultaneously with the mid-western brood of 17-year locusts - and even that only happens every 221 years.

The mathematically-minded will have noticed something about the periodicity of these insects - they are prime numbers (i.e. numbers that are only divisible by themselves and 1) ad there is a very good evolutionary reason for this - it makes it harder for a potential predator to synchronise with these emergencies because, since there are no periods that would coincide exactly with these primes other than the prime itself and a 2, 3, 4 or more period would only coincide with an emergence of these cicadas every 26, 39 and 52 years respectively for the 13-year locust, longer for the 17-year locust.

Because these broods only emerge in the same year, they form an effectively isolated genetic population and yet these two broods appear to be identical in appearance, song and genetics, so it will be interesting to see how they interact, although they occupy different geographical areas, so overlap is relatively rare.

As a strategy to avoid predation, this takes some beating in terms of intelligent stupid design, but there is a nasty little twist to the story, as I will relate later...

In the following article reprinted from The Conversation under a creative commons license, John Cooley, Assistant Professor of Ecology and Evolutionary Biology, University of Connecticut, USA and Chris Simon, Senior Research Scientist of Ecology and Evolutionary Biology, University of Connecticut, USA explains the significance of this event from the point of view of ecologists and evolutionary biologists. Their article has been reformatted for stylistic consistency: