Malevolent Design - How Creationism's Divine Malevolence Co-opted Red Squirrels To Spread Leprosy in Medieval England

Lepers having magic spells cast over them

Mycobacterium leprae

Ancient Mycobacterium leprae genome reveals medieval English red squirrels as animal leprosy host: Current Biology

Few places in Europe or elsewhere were more pious than Medieval England, but still creationism's pestilential malevolence continued to make people suffer with diseases such as bubonic plague, tuberculosis and the related leprosy. Even the extreme measures taken by believers to atone for imaginary transgressions that had brought about the Black Death had failed to assuage the putative designer god who was believed to be visiting this pestilence upon people.

The superstitious Bible-based belief in evil spirits and 'sin' as the cause of disease led to the social stigma that made the disease so feared and led to the isolation of sufferers in lepper colonies, and often reduced to begging to stay alive. Poor nutrition and poor sanitation led to a worsening of the condition and, although these counter-measures were visibly ineffective, such was the belief in the Bible that it was inconceivable that the disease could be caused by anything other than 'sin' and evil demons being permitted to enter the victim.

The modern equivalent of this victim-blaming superstition can be found in the modern creationist tactic of blaming 'Sin' and 'genetic entropy' for parasites, with demons being replaced by 'entropy' to make it sound sciencey. It is of course, Bible-based superstition without supporting evidence.

And now, if you believe that stuff, there is evidence that creationism's putative designer god designed M. leprae to also infect red squirrels so they would act as a repository to spread leprosy. Red squirrels were common in those days and were often captured in the wild for pets or pelts. Their skins, when used for clothing, would have carried M. leprae and infected anyone who wore them - a brilliant strategy, if you hate people and want them to be sick, suffer and die.

Unintelligent Design News - How Creationism's Putative Designer 'Brilliantly' Designs Solutions To Problems It Supidly Designed

Two-spot spider mite, Tetranychus urticae

Two-spot spider mite (yellow form), Tetranychus urticae

Plants utilise drought stress hormone to block snacking spider mites | Sainsbury Laboratory

To start at the beginning because that's always a good place to start, plants need to get water and nutrients up to their leaves, so their 'designer' gave them a vascular system but without a pump, so, to maintain the upward flow, they need to evaporate away (or transpire) the water that just arrived in their leaves. They do this through tiny pores (or stomata; singular=stoma) that are just about visible to the naked eye, and clearly visible under a hand lens or a microscope.

These stomata are guarded by guard cells, one on either side, which can swell to close the stoma or shrink to allow the stoma to open, as the need arises.

However, these stomata are an open invitation to sap-sucking arthropods such as mites and aphids, which are cleverly designed, reputedly by the same designer that designed the stomata, which can push their mouthparts into the stoma to get at the nutrient-rich watery contents of the leaf.

So, having designed these sap-suckers to exploit the transport system it designed for plants, creationism's putative designer clearly saw the sap-suckers it had designed as a problem to be solved.

How it added this Heath-Robinson layer of additional complexity to solve the problem the earlier layer of complexity had caused is the subject of a research paper by a collaboration of researchers from the Centre for Plant Biotechnology and Genomics (CBGP), Spain, and Sainsbury Laboratory, Cambridge University (SLCU), Cambridge, UK and a news release from Cambridge University:

Malevolent Designer News - How Creationism's Favourite Pathogen Is Designed to Cause UTIs

Escherichia coli,
The usual cause of urinary tract infection (UTI)

UTI's will affect 50% of women at some time in their lives

How E. coli get the power to cause urinary tract infections | Michigan Medicine

Despite their protestations that their god doesn't create pathogens - some other creative entity does that, apparently - they have been in love with Escherichia coli, or E. coli ever since their guru and Deception Insitute flunky, Michael J Behe, persuaded them that he had 'proved' their god exists and designs things because he couldn't work out how the E. coli flagellum could have evolved - so God did it!

There problem then, courtesy of Michael J Behe is that they have accepted that, if there was a designer involved in E. coli's design, it is the god that Michael J Behe 'proved' designed it, so their god designs pathogens, and even designs clever way to make them good at making us sick.

With that in mind, which creationist is going to argue against Michael J Behe's clever 'proof' that their god designs things so must exist, and insist that it isn't also behind the newly discovered way it manages to cause urinary tract infections (UTIs)?

The discovery that they can live, reproduce, and do their nasty thing in the otherwise near-sterile urinary tract, was made by researchers at the laboratory of Professor Harry Mobley in the University of Michigan Medical School.

Having been filtered by the kidneys, while urine contains some chemicals such as metabolites, it is about as sterile as it gets, with anything in it entering through the urethral meatus, in women, stupidly placed near the anus and inside the vulva where it can become infected during sexual intercourse by a penis cleverly designed with a foreskin to harbour pathogens under.

It has now been discovered that E. coli is also cleverly 'designed' to grab the nutrients it needs but can't manufacture itself by have a highly efficient transport system for taking them from its victims at a rate of thousands of molecules a second. One of the genes responsible for this, codes for an enzyme known as ATP-binding cassette (ABC).

Typical of creationism's 'intelligent' [sic] designer, if you believe in such a thing, is the Heath-Robinson workaround for the lack of genes for manufacturing these amino acids, where the parasite needs an energy-intensive ATP-based transport system, complete with multi-layered back-up systems to keep them working - the needless waste and needless complexity, so typical of evolved systems and the antithesis of intelligently designed systems. The researchers have published their findings, open access, in the journal PNAS and explained them in a University of Michigan news release:

Creationism in Crisis - Humans Had Domesticated Dogs At Least 10 Thousands Years Before 'Creation Week'

Siberian grey wolf, Canis lupus

Source: Pinterest

Siberian wolf, Canis lupus

Ancient Mitogenomes Reveal the Maternal Genetic History of East Asian Dogs | Molecular Biology and Evolution | Oxford Academic

These days, no serious scientist sets out to prove the Bible is wrong; discovering truth does that anyway - for anyone who can join the dots and do the simple logic. For example, humans could not have domesticated dogs some 23,000 years ago in Siberia by domesticating the local variety of grey wolf, if the Universe is just 10,000 years old.

And yet a paper published recently in the journal Molecular Biology & Evolution shows that they did exactly that.

In the context of mitochondrial DNA, what are haplotypes? In the context of mitochondrial DNA (mtDNA), haplotypes refer to specific combinations of genetic variants or polymorphisms within the mitochondrial genome. Unlike nuclear DNA, which is inherited from both parents, mtDNA is passed down exclusively from the mother to all of her offspring. This maternal inheritance pattern makes mtDNA useful for studying ancestry, population genetics, and evolutionary history.

A haplotype represents a unique combination of nucleotide variations or mutations along the mtDNA sequence. By analyzing these haplotypes, researchers can track maternal lineages, study population migrations, and infer evolutionary relationships among different groups of individuals. Haplotypes are often used in studies of human populations, as well as in forensic genetics and medical research related to mitochondrial disorders.

Refuting the Bible was almost certainly not the intention of the authors, jointly led by Songmei Hu, of Joint International Research Laboratory of Environmental and Social Archaeology, Shandong University, Qingdao, China, and Xijun Ni and Qiaomei Fu, both of the Institute of Vertebrate Paleontology and Paleoanthropology, Center for Excellence in Life and Paleoenvironment, Chinese Academy of Sciences, Beijing, China, but the facts they discovered do just that. They had set out to resolve the question of where exactly dogs had been domesticated, based on an analysis of the mitochondrial DNA.

Mitochondrial DNA (mDNA) is inherited through the maternal line, so an analysis of the geographical and temporal distribution of the various haplotypes of mDNA and how they relate to one another should give an indication of where and when the ancestral haplotype lived.

How the team did this is explained in their paper:

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:

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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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.

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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 - 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:

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:

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:

Creationism in Crisis - How Human Society Was Changing When Creationists Believe There Was A Genocidal Global Flood

A Patrilineal Central Asian population

Social change may explain decline in genetic diversity of the Y chromosome at the end of the Neolithic period | CNRS

The problem with having a childish superstition based on the campfire tales of primitive people who knew nothing of the world outside their own narrow horizons and folk memory is that it can cause you to believe the most ludicrous things that require you to maintain a pristine ignorance in order to retain your superstition.

This is especially true if an integral part of your irrational superstition is that there is a mind-reading bogeyman in the sky who will become angry if you have the slightest doubt or learn things that cause you to question your superstition. Your irrational phobia imposes a sort of information filter on your perception that doesn't allow anything to pass through that might cause you to change your mind.

This is why creationists will believe such absurdities as a global genocidal flood that left no geological evidence and reduced the human population to such a low number that the lack of genetic diversity would have guaranteed extinction within a handful of generations, yet this left no mark on human genetic diversity. Instead, what we see in the genetic record of human history in the Y chromosome is a change in the demographic profile just about the time when the Bronze Age story-tellers were setting their genocidal flood tale.

This shows that not only were there far more humans alive than the tales relate, but that there was a significant change in the form of society, probably as a result of technological change, to a more patrilineal society. This created the conditions for powerful male tribal leaders to inherit the powers to dominate other males and so to father many more children, resulting in a functional reduction in the male population, and fall in genetic diversity in the Y chromosome, while the female population continued to grow.

Some time ago I wrote about how gene-meme co-evolution can result in genetic changes which are not directly related to fitness of those genes, as this phenomenon illustrates. One of the examples I gave was that of Western Ireland where there is a cluster of Y chromosomes inherited from the legendary founder of the Uí Néill, Niall Noígíallach (Niall of the 9 hostages). In that part of Ireland an estimated 21% of males carry his Y chromosome and 8% in the rest of Ireland. I also cited another such cluster in China where an estimated 1.5 million males, mostly in Northern China and Mongolia have the same Y chromosome as descendants of Giocangga, a Qing emperor who died in 1582. These men were able to father many children because of the power they had in their societies, and their sons inherited both their Y chromosome and their power and authority. Because of their authority, they were able to command better resources in terms of food and shelter for their offspring, so improving their breeding success.

It was not necessary to use military power to dominate and exterminate neighbouring peoples to achieve the resulting reduction in genetic diversity in the Y chromosome.

Both these examples are cited in this paper.

This is the explanation proposed by a team of researchers from the French Centre national de la recherche scientifique (CNRS), the Muséum national d'Histoire naturelle (MNHN) and the Université Paris Cité, who have published their research findings, open access, in the journal Nature Communications. It is explained in a brief CNRS news item:

Creationism in Crisis - How Ancient Symbiotic Relationships Drive Evolution - Naturally

Selection of lichens
symbiosis between cyanobacteria and fungi

Symbiotic relationship between clown fish and anemone.

Species living closely together in symbiosis is far older and way more common than you might think

Biologically, symbiotic relationships are alliances of genes that give the lie to creationist claims that 'selfish' genes are genes for selfishness. In fact, if it's in the interests of genes, and it usually is, genes form alliances that put the two species in the partnership on an evolutionary trajectory in which both species benefit from the evolution of one or the other in a process known as co-evolution.

When you understand this, you can find examples almost everywhere you look - think how many wild jungle fowl there would be today if they hadn't formed an alliance with humans to become the commonest bird on Earth - the domestic hen. The same goes for sheep, pigs, cattle, horses, cats and dogs. The 'selfish' genes are of course, unconcerned about the ultimate fate of their carriers, hence the term 'selfish'; the only thing that matters is how many of them there are in the world, and there are unarguably now more human and more of our domestic animals’ genes in the world than when they were wild animals and we were hunter-gatherers.

And, when you look inside a complex cell, you see more examples of symbiosis - several cell organelles such as mitochondria and (in plants) chloroplasts, are really bacteria in symbiotic association with the cell.

Our gut microbes, and the often-unique gut microbes of other species such as cockroaches, are locked in a symbiotic co-evolution from which neither can escape because to do so would lose the benefit of mutuality.

In the following article, reprinted from The Conversation under a Creative Commons licence, Gregory Moore, Senior Research Associate, School of Ecosystem and Forest Sciences, The University of Melbourne, explains how symbiotic relationships are commonplace in nature and have shaped evolution. His article has been reformatted for stylistic consistency:

Unintelligent Design - Rotten Tomato For The Bumbling Designer - Or How To Create Unnecessary Complexity

Left three images: close-ups of tomato trichomes where acylsugars are produced. These sticky chemicals act as natural flypaper for potential pests. On the right: a close-up of tomato plant roots covered in small hairs.

Credit: Rachel Kerwin

Uncovering a ‘parallel universe’ in tomato genetics

Creationism's intelligent [sic] designer, unlike a normal intelligent designer worthy of the name, seems to have a moto:

"If a thing's worth doing, it's worth doing twice, in two different ways".

However, even for someone familiar with all the different ways creationism's putative designer has designed for doing the same thing - flight, swimming, body-plan, respiratory systems and eyes, to name but a few - and the regularity with which its 'designs' turn out to be the opposite of what an intelligent designer would design, it will come as no surprise that it has managed to surpass itself with the design of two different metabolic pathways for doing the same thing in the same plant!

Scientists at Michigan State University, Robert Last, have discovered that tomato plant roots produce defensive sugars - acylsugars - by two different metabolic pathways.

And, as an added embarrassment for the creation cult, they have shown that these two pathways came about as a result of new genetic information arising by accidental gene duplication almost 17 million years before they believe Earth existed.

Acylsugars are a class of very sticky sugars produced in specialized cells in the tip of the tricomes of plants of the tomato (Solanaceae) family, which includes aubergines, potatoes, nightshades, peppers and tobacco. Their purpose appears to be to act as a sort of natural flypaper. However, they are also found in the roots of tomato plants, but the root acylsugars are different enough from the tricome acylsugars to almost warrant a separate class of sugars.

It was while investigating the reason for this difference that the Michigan State University team discovered what they termed a 'parallel universe' of metabolic pathways and the genes that control them. They discovered that if you knock out the genes for making root acylsugars, this doesn't affect their production in the tricomes and if you knock out the genes that control the tricome production, acysugars are still produced in the roots.
The team’s findings are the subject of an open access paper published recently in Science Advances. They also explain the background to the study in a Michigan State University news release:

Unintelligent Design - Has Creationism's Divine Malevolence Taken Leave Of Its Senses?

An amoeba cell infected by Naegleriavirus. The fluorescence microscopy image shows the viral factory and newly produced virus particles (in blue) within the amoeba cell (pink).

Patrick Arthofer and Florian Panhölzl.

Illustration of Naegleriavirus based on electron microscopy. A section through a virus particle with the star-shaped stargate is shown.

Credit: Stefan Pommer / photopic.at (CC BY-NC-SA 4.0)

Giant Viruses Infect Deadly Parasite

Judging by the findings of scientists led by Patrick Arthofer and Matthias Horn from the University of Vienna's Center for Microbiology and Environmental Systems Science (CeMESS), creationism's divine malevolence may have gone entirely round the twist and got carried away with its success with parasites.

Not only has it created parasites, apparently to increase the suffering in the world, but it's now creating parasites for those parasites! Kindly creationists who have realised blaming another creator such as 'Sin' for parasites is a blasphemy, might be tempted to credit their beloved pestilential malevolence with trying to combat the parasites like the single-celled organism, Naegleria fowleri, that are causing such misery by attacking them with another parasite. But that makes no sense in terms of an omniscient, omnipotent creator god who, if such a god existed, could simply destroy Naegleria fowleri and have done with it.

The only thing that makes sense, if you believe the childish notion of intelligent design by a magic invisible man is that it has become obsessed with creating parasites for the sake of creating parasites.

What the Vienna team have discovered is that the serious pathogen, Naegleria fowleri, is parasitised by a giant virus, named Naegleriavirus. Giant viruses are unusually large viruses with a complex genome.

Naegleria fowleri is an especially nasty little amoeba that I described in my illustrated book, The Malevolent Designer: Why Nature's God is not Good:

Unintelligent Design - The Brilliant Way Bacteria Evade Our Immune System - Malevolent Design or Incompetent Designer?

Burkholderia thailandensis (purple) uses cellular components (yellow) to form membrane protrusions from one host cell to another (green).

Burkholderia pseudomallei, a Gram-negative rod, straight or slightly curved, with bipolar staining

The enemy within: How pathogens spread unrecognized in the body - Biozentrum

Here's a conundrum for intelligent [sic] design creationists. Scientists working at Biozentrum, University of Basel, Switzerland with colleagues in the Department of Biochemistry, National University of Singapore, have discovered how the bacterium, Burkholderia pseudomallei that causes the serious tropical disease, melioidosis, manages to evade our immune systems to make us sick.

What information do you have on the origins of the bacterium Burkholderia pseudomallei and what it causes in humans? Burkholderia pseudomallei is a Gram-negative bacterium that causes melioidosis, a potentially fatal infectious disease primarily found in Southeast Asia and Northern Australia. The bacterium is commonly found in soil and water in endemic regions. It was first identified by Alfred Whitmore and C.S. Krishnaswami in 1912 in Rangoon, Burma (now Yangon, Myanmar). The name "melioidosis" is derived from the Greek word "melis," meaning "distemper of asses," as the disease was initially identified in horses. B. pseudomallei can infect humans and a wide range of animals through various routes, including inhalation, ingestion, or through breaks in the skin. In humans, it can cause a spectrum of symptoms ranging from localized skin abscesses and fever to more severe forms of pneumonia, septicemia (bloodstream infection), and multiple organ abscesses. Melioidosis can be challenging to diagnose due to its diverse clinical manifestations and can mimic other diseases, making it important for clinicians in endemic areas to consider it when evaluating patients with febrile illnesses. Treatment of melioidosis typically involves prolonged antibiotic therapy with drugs such as ceftazidime, meropenem, or imipenem, followed by oral antibiotics such as trimethoprim-sulfamethoxazole to prevent relapse. However, antibiotic resistance in B. pseudomallei is a growing concern, particularly in regions where the disease is endemic. Prevention strategies include avoiding contact with contaminated soil and water, wearing protective clothing during outdoor activities, and practicing good wound care.

The conundrum is, was this malevolently designed or is it the result if incompetent design?

The problem for creationists is that they believe the human immune system was intelligently designed to protect us from the bacteria and other organisms their putative designer god had designed to make us sick, and yet not only does it not work as intended but many of the harmful parasites from which we suffer seem to have been designed to avoid our immune system, some of them by ingenious ways, like the bacterium in question, B. pseudomallei.

It's hard to reconcile the difference between a designer who can't design a functional immune system and one who is genius enough to design some of the extremely clever and sophisticated mechanisms for evading our immune system. The idea that these could be one and the same entity is almost laughable unless the answer is that the inadequate immune system and the ingeniously designed parasites are all part of the same malevolent plan to make us sick.

What B. pseudomallei does to avoid being detected by the immune system, once it gets inside a cell, is cause the cell to make special tubes connected to other cells, through which it can pass without going outside the cell again, where it would be recognised as a pathogen. In this way it spreads throughout a tissue without the victim's immune system even being aware of it.

The research team have published their findings, in the open access, online Cell Press journal, Cell Host & Microbe and explain it in a press release from The University of Basel, Biozentrum: