Creationism in Crisis - 275 Million New Human Genetic Variants in USA Alone - Why So Many?

275 Million New Genetic Variants Identified in NIH Precision Medicine Data | All of Us Research Program | NIH

Researchers at the American NIH have identified 275 million previously unknown genetic variants in samples from 250,000 representative American adults who participated in their All of Us research program. Half the participants were of non-European ancestry. Nearly 4 million of these newly discovered variants are from areas of the genome tied to known disease risks.

Let's consider that from the point of view of someone who believes in intelligent [sic] design:

Why on Earth would an intelligent designer design so many variations on the same theme? An intelligent designer, especially one endowed with the foresight of omniscience and unlimited powers and who is omnibenevolent and perfect, would design the perfect solution to every problem, and stick with it, not design lots of different solutions to the same problem. And every iteration through the cycle of replication would produce an exact copy of that perfect design, so there is no logical way all those variations could be the result of random mutations which all happened to be equally good at whatever they did, so there was no element of selection involved.

Quite simply, lots of variations on the same theme are evidence not of intelligent design, but of utilitarian, mindless 'design' working without a plan and with no conception of the ideal or perfection. Variation is kept because it works; maybe not exactly as well as other alleles, but well enough for the carrier to survive and reproduce. Even if the differences are too small to play a significant part in evolution by natural selection, unless they are serious deleterious, genetic drift can account for them being a significant part of the species genome.

Creationism in Crisis - The Inner Ear Of A 6 Million-Year-Old Hominoid Fossil Gives A Clue To The Evolution Of Bipedalism In Humans

Reconstruction of the locomotor behavior and paleoenvironment of Lufengpithecus

Illustration by Xiaocong Guo;
image courtesy of Xijun Ni,
Institute of Vertebrate Paleontology and Paleoanthropology,
Chinese Academy of Sciences.

InformedHealth.org How does our sense of balance work?

How Did Humans Learn to Walk? New Evolutionary Study Offers an Earful

To walk upright successfully needs a fully functioning balance organ in the inner ear, as anyone suffering from Ménière's disease will testify, so the study of the origins of bipedalism in the remote ancestors of humans needs to take into account changes in the inner ear that would facilitate it.

Humans and our closest relatives, the great apes and the simians, display a range of locomotion but only humans are normally fully bipedal, although chimpanzees can use bipedal locomotion when carrying a load for example.

The monkeys normally run along branches on all fours, balanced on top of them and jumping from branch to branch; the apes hang beneath the branches in locomotion known as brachiation, but humans are ungainly in trees and prefer bipedal locomotion on the ground. The question is, when did this ability evolve in our ancestry?

We can be sure our hominin ancestors the Australopithecines, were fully bipedal because we have a record of their footprints in volcanic ash at Laetoli, and their lower limbs and feet were almost indistinguishable from those of Homo sapiens. 'Lucy' (Au afarensis) was probably mostly bipedal but may have taken to trees for safety and possibly to sleep on constructed platforms like chimpanzees do. The evidence of injuries to her fossilised skeletal remains suggests she may have died by falling out of a tree.

To investigate this stage in our evolution a group of researchers, led by Professor Xijun Ni, which included Yinan Zhang, a doctoral student, both of the Institute of Vertebrate Paleontology and Paleoanthropology of the Chinese Academy of Sciences (IVPP), and Terry Harrison, a New York University anthropologist, used 3-dimensional CT scanning to examine the inner ear of a 6-million-year-old fossil ape, Lufengpithecus, unearthed in China’s Yunnan Province in the early 1980s, and compared it to the inner ear of other living and fossil apes and humans from Asia, Europe, and Africa.

The formation the fossil was found in has been previously dated magnetobiostratigraphically to about 6 million years. This technique depends on the record of periodic changes in Earth's polarity trapped in magnetic particles in sedimentary rocks and by recording the microfossils such as pollen associated with these changes:

Unintelligent Design - How A Design Blunder Causes Inflammatory Diseases, Especially In Later Life

Endosomes (magenta) collect around mitochondria (blue) after infection with virus HSV-1, which attacks mtDNA (green) and causes its release.

Credit: Salk Institute

Faulty DNA disposal system causes inflammation - Salk Institute for Biological Studies

In another example of the ramshackle Heath Robinson design process that created humans, scientists today published their findings that show how when a cell process goes wrong, as it frequently does, the result can be a serious health condition, causing suffering and unhappiness.

And of course, it’s another example of how we can tell humans weren't intelligently designed by an omnibenevolent god who wants to minimise the suffering in the world, but by a mindless, amoral natural process that has no option but to settle for the sub-optimal as long as it’s better than nothing.

The discovery, by researchers at the Salk Institute and their colleagues at UC San Diego , is the way when mitochondrial DNA (mtDNA) goes wrong and the cell tried to dispose of it, some of it leaks out into the cell, the cell’s immune system treats it like the DNA of a parasitic organism and sets up an immune response which caused inflammation.

Given the origin of mitochondria in our Heath Robinson contraptions we call cells, this is hardly surprising since mitochondria started out, probably as the free-living bacterial prey of another prokaryote, possibly an archaeon. They then became symbiotic, providing the cell with free ATP in return for protection and nutrients in the form of sugar, water and oxygen. Because they need to provide a handful of enzymes to do this with, and they are self-replicating, they retained a small amount of their original DNA while giving up most of it to the host cell's nucleus.

Unintelligent Design - How Scientists Are Overcoming The "Designer's" Incompetence

Credit: Dingzeyu Li via Unsplash

Systemic lupus erythematosus

World-first discovery may enable an effective long-term lupus treatment - Monash University

Readers may recall my recent article on Lupus and why women are nine times more likely to suffer from it than men, because the epigenetic process for switching off genes on their X-chromosome sometimes goes wrong and produces proteins that induce an immune response to their own tissues.

From a creationist perspective, this can only be for one of two reasons: either the designer was incompetent, or this was by design. The choice being either incompetence, or malevolence and misogyny.

Now a team of researchers at Monash University, Clayton, VIC, Australia, have reported success in finding a way to overcome this design defect - which begs the question: if scientists can do it, why couldn't an omnipotent intelligent designer? Could the answer be that the human immune system was not designed by an omnipotent, intelligent designer, but is the result of a mindless, utilitarian process that inevitably produces sub-optimal 'designs' that can't be scrapped and redesigned?

But that is the kind of thought that would cause panic in the mind of most creationists because it would raise the terrible spectre of wondering if they could be wrong.
The Australian team have just published their results, open access, in Nature Communications. They are also explained in a Monash University news release:

Unintelligent Design News - A Newly-Discovered Virus-Like Particle That Doesn't Appear to Do Anything Other Than Replicate Itself

Streptococcus sanguinis bacteria, which live in the mouth, may host replicators named obelisks

UK Health Security Agency/
Science Photo Library

Figure 2.

Obelisks encode putatively well-folded proteins
a) Obelisk open reading frame 1 (Oblin-1) is predicted (total mean-pLDDT ± SD = 83.8 ± 13.4, see methods) to fold into a stereotyped N-terminal “globule” formed of a three alpha helix (orange) bundle partially wrapping around an orthogonal four helix bundle, capped with a beta sheet “clasp” (blue, globule mean-pLDDT = 90.1 ± 8.7), joined by an intervening region harbouring the conserved domain-A (magenta) with no predicted tertiary structure, to an arbitrarily placed C-terminal alpha helix. “Globule” emphasised on the right. b) a to-scale (secondary structure) topological representation of Oblin-1 with the “globule” shaded in grey, and the domain-A emphasised with this bit-score sequence logo (see methods). c) Obelisk Oblin-2 is confidently predicted (mean-pLDDT = 97.1 ± 4.6 ) to fold into an alpha helix which appears to be a leucine zipper. Sequence logo of an “i+7” leucine spacing emphasised in red, with hydrophobic “d” position residues emphasised in yellow (expanded in Supplementary Figure 4b). d) homo-multimer predictions of Obelisk-alpha Oblin-2. top: dimer (mean-pLDDT = 94.6 ± 0.6), bottom: trimer (mean-pLDDT = 93.6 ± 0.6). Side-on representations of homomultimers shown with numbers of inter-helix salt-bridges (see Supplementary Figure 5).

A new virus-like entity has just been discovered – ‘obelisks’ explained

At least with most of creationism's putative 'intelligent' designer, there is something that they appear to be for, other than simply reproducing themselves - even if it is, in the case of viruses and bacteria, increasing the suffering in the world by making other organisms sick.

But scientists have just discovered a small particle that seems to be in the edge of life, less so even than a virus, which doesn’t appear to do anything other than replicate, although it seems to need bacteria in which to do this. It’s not clear what harm it does to its bacterial host or even if it has some symbiotic function. But it appears to be almost everywhere, especially in our mouths and gut, where it appears to have speciated into several different forms. The team have named it 'obelisk' because it forms a rod-like shape.

It was discovered by a team of Stanford University researchers led by Andrew Z. Fire, a previous recipient of the 2006 Nobel Prize for Physiology or Medicine who have reported to have 'identified 29,959 Obelisks (clustered at 90% nucleotide identity), with examples from all seven continents and in diverse ecological niches'. Their report has been provided with free access ahead of peer-reviewed publication, in the preprint server, bioRxiv.

The question remains, what do these particles do exactly and are they potentially harmful, or are they beneficial in some way? At least one of their hosts in which they replicate is one of the bacteria responsible for the plaque on our teeth that is responsible for dental caries and gum disease that can result in lost teeth, Streptococcus sanguinis.
Like most viruses, obelisks are a single, circular strand of RNA, but unlike viruses, they don't have a protein coat. They have one and maybe two genes which code for proteins named 'oblins' which are unrelated to any other known proteins. In this respect they differ from other recently (1970) discovered free-living strands of RNA called viroids, which don't have any recognisable genes but are known to cause serious diseases in plants.

In the following article, reprinted from The Conversation under a Creative Commons license, Professor Ed Feil, Professor of Microbial Evolution at The Milner Centre for Evolution, University of Bath, explains the significance of this discovery. His article is reformatted for stylistic consistency:

Unintelligent Design - How Scientists Are Learning to Do What Creationism's 'Intelligent' Designer Found Too Difficult - Or Didn't Want To Do!

The proteins needed to create limb progenitor cells are marked with different colors under a microscope.

Images: Yuji Atsuta/Tabin lab

The proteins needed to create limb progenitor cells are marked with different colors under a microscope.

Images: Yuji Atsuta/Tabin lab

The Surprisingly Simple Recipe for Starting to Grow a Limb | Harvard Medical School

Visit any site of a supposed Marian miracle, such as Lourdes, now selling 'miracle cures' that almost never work and those that do can be attributed to the medication the pilgrim was receiving prior to the visit, or to spontaneous regression, the placebo effect or a psychosomatic condition, and you may find lots of crutches supposedly left there as testament to the cure of mobility disorders, but what you will never find is the artificial limb discarded by someone who had a spontaneous regeneration of an amputated limb.

Or visit any of the lucrative travelling, carefully stage-managed 'faith healing circuses' where people appear to be 'cured' of all manner of ailments at the touch of a 'healer', who, for perhaps obvious reasons, never works in a hospital, and you will never witness the regeneration of a limb, or even part of a limb. Not even a finger or toe.

And before some-one cites, the 'Miracle of Calanda', this is such an obvious hoax that it's a miracle anyone believes it.

Despite having allegedly created a universe from nothing and all living things from dirt, creationism's god appears to be incapable, even with the help of his miracle-working mother, to be able to regrow a human limb.

The problem is one of the designer's own making (if you believe creationists) because it would involve the epigenetic resetting of the cells at the end of the stump, so they become stem cells again, capable of making all the different specialist cells in a limb, like bone, muscle, skin, nerves and blood vessels and growing to the right shape in the right place. That was a once-only ability in the developing embryo.

Epigenetics, as I have written about many times, is necessary because the cells of a multicellular organism replicate the same way our single-celled ancestors did - by replicating the entire genome every time in every daughter cell. But the benefit of multicellularity is that cells are specialised so only need a few genes, not the entire genome and having the wrong genes active in a specialist cell would be detrimental, so most of them need to be switched off by the epigenetic system. A problem which could have been avoided by any omniscient, omnipotent designer by just replicating those genes that were going to be needed by the specialist cells, but not something a mindless, natural process with no foresight, no reverse gear and no means of scrapping a bad design and starting again, could have avoided.

And yet medical scientists investigating the problem believe they have discovered the basic principles involved, which turn out to be "surprisingly simple", so well within the capabilities of even creationism's rather limited god.

The scientists, led by Harvard Medical School geneticists, have published their findings in an open access paper in a Cell Press journal, Developmental Cell and explain it in a Harvard Medical School news release by Stephanie Dutchen:

Unintelligent Design News - Why Women Are More Prone To Lupus Than Men - Evolution, Or Does Creationism's God Just Hate Women More?

The classic 'butterfly rash' of systemic lupus erythematosus (SLE)

Lupus and other autoimmune diseases strike far more women than men. Now there's a clue why

In my days as an operational paramedic, I once had to move a 26 your old women to hospital because lupus had made her so ill her blood pressure was below the safe level to maintain her renal function.

It was so low I couldn't even sit her up to carry her down stairs without her losing consciousness, so I had to run a couple of units of IV fluid into her to bring it up enough to make it safe to move her. She really was profoundly ill and at death's door. But such was the nature of the profession that, having delivered her safely to hospital and handed her over to the care of doctors and nurses, that was the end of my role in her care, so I never heard the outcome.

The autoimmune condition, lupus erythematosus, is caused by a malfunction of the immune system in which something triggers it to turn against the sufferer's own body instead of the invasive pathogens from which it has evolved to protect us. Although, of course, a creationist would hotly dispute the idea that a system like our immune system evolved at all, and would insist that it was intelligently [sic] designed by their favourite, evidence-free, supernatural deity without whom nothing can be created, presumably because they believe chemistry and physics don't know how to behave without a magic god telling them.

But an intelligently-designed immune system would only malfunction and turn against the person it is supposedly designed to protect if it were either incompetently designed or malevolently designed and is doing what it was designed to do - randomly increasing the suffering in the world. The evidence is that lupus is far more common in women than in men by a ratio of 9:1, which begs the question, does the designer just hate women more than men or was he more diligent when designing men's immune system then when designing women's?

The answer, as anyone who understands anatomy and physiology and particularly, evolution, will tell you, is that as an evolved system, we can expect compromises and a lack of perfection because evolution is a utilitarian process with no foresight and no reverse gear, so we are stuck with a sub-optimal immune system that evolved in an ancient ancestor, maybe even a pre-vertebrate ancestor. Certainly, all known vertebrates have one, and some, like that of bats, is far superior to ours.

Now a team of researchers at Stanford University School of Medicine, Stanford, CA, USA have worked out why lupus is far more common in women than men. Ther results are published, open access, in Cell and explained in a Stanford Medical news release. But first, a little AI background:

Malevolent Designer News - Creationism's Divine Malevolence Has Just Released An E. Coli Upgrade With Added Malice

Escherichia coli

New and highly infectiousE. coli strain resistant to powerful antibiotics - University of Birmingham

Escherichia coli is a pathogenic bacterium that is loved by creationists because they have been taken in by Michael J. Behe's book, Darwin's Black Box, that made him a millionaire because so many creationists bought it (though few appear to have read it) and which they love to wave around as 'proof' that the locally popular god exists.

Behe, a leading light in the Deception Institute, which was set up to try to win converts for fundamentalist, Bible literalist Christianity, by spreading disinformation about science, had argued, falsely, that the flagellum of E. coli must have been intelligently designed, since all the components need to be present for it to work (the 'irreducibly complex' fallacy) and it is too complex to have evolved in a single step because, so he claimed none of the components on their own could have given an advantage for natural selection to select for (which of course ignores genetic drift as a cause of evolution).

What Behe neglected to do was tell his readers that almost all the components of the flagellum and the proton pump that drives it, were present in a structure called the Type III Secretory system with which bacteria bind themselves to their host and kill them, and this could easily have evolved from simpler beginning over the billions of years that bacteria were evolving into their present forms.

Since its publication, Behe has been repeatedly told of the errors in it, and as a professional microbiologist, he should be aware of the growing body of research explaining how the E.coli flagellum evolved^{1,2, 3, 4, 5}, yet he refused to correct his errors in later editions and continues to promote and defend the misinformation in it, whilst pocketing the royalties from sales, in a classic case of bearing false witness.

Creationism in Crisis - How Our Need For Vitamin D Was A Bad Design That Went From Bad To Worse

Permanent Central Maxillary Incisors showing evidence of Vit. D deficiency.

Fig 3. Permanent central maxillary incisors of CL 66.
Plane form hypoplasia is exhibited on the occlusal and labial surfaces.

Archaeological evidence of seasonal vitamin D deficiency discovered | University of Otago

The human need for vitamin D to ensure proper bone growth and development and various other health-related needs, is an example of how we were not intelligently designed but are the result utilitarian evolutionary compromises that balance benefit against detriment and that balance depends on the environment in which we evolved. It shows that we evolved in sunny climates where the sun comes directly through the atmosphere as it does in the tropics, rather than obliquely, as it does in the northern and southern parts of the globe.

We do not generally get enough vitamin D from our diet, so we need to manufacture it in our skin by the action of sunlight, in particular the ultraviolet B (UVB) spectrum. However, UVB sunlight is also harmful, so our skin needs to be protected from it with the pigment, melanin, which gives our skin its varying shades of brown or black. Generally, the darker the skin, the better protection it has from UVB but the less it can produce vitamin D.

This AI explanation outlines the problem:

Creationism in Crisis - Evolution Of The Human Imune System - By Repurposing An Existing Protein

The Joining chain (J chain) that helps bind and regulate the subunits that make up antibodies was evolutionarily co-opted by the human immune system from another biological process, according to a study by researchers from Penn State, the University of Maryland and the University of Chicago. The J chain, shown here in purple, assembles and stabilizes, from left, immunoglobin A (IgA) and immunoglobin M (IgM) antibodies. It is also required to move IgA and IgM across the mucus-producing tissue lining body structures with external exposure, like the intestine, nasal cavity and lungs.

Credit: Ttsz/Getty Images.

Evolutionary origin of mysterious immune system molecule in humans revealed | Penn State University

The human immune system is a problem for creationists who insist that their putative creator god designed humans perfectly but didn't create pathogenic parasites, which were created later by another creator called 'Sin' because of 'The Fall' after which this 'Sin' thing was free to create everything that increases the suffering in the world, so the question that throws creationists into confusion is when was the human immune system created?

If it was created before 'The Fall' then their designer god was planning for 'The Fall' all along and Adam & Eve had no choice but to comply with this god's plan for them, so there was no disobedience; just compliance with the plan.,

If, on the other hand, the creator had to upgrade its design later to protect its creation from pathogens, then it had failed to anticipate 'The Fall' so can't be omniscient.

And, since pathogens can and do get passed our immune defences, then a perfect, omnipotent creator did not design the immune system because it fails to work as designed, or 'Sin' can outwit it.

And now creationists have another problem, especially those who have been fooled into believing there is evidence of intelligent design to be found in 'irreducibly complex' structures and processes, because the simple biological explanation for such structures and processes is that they are composed of elements that originally evolved for other purposes and were later exapted for a novel function as part of the 'irreducibly complex' structure. For example, almost all the elements of the bacterial flagellum are to be found in the Type III secretion system (T3SS) which bacteria used to bind themselves to their potential host, but motility was such an advantage that the T3SS was repurposed for a flagellum with a few additional proteins and a slight modification of others to improve its efficiency.

Two of the components of the immune system are protein complexes which are the antibodies produced in response to infection by pathogens. These are the immunoglobin M (IgM) and immunoglobin A (IgA). Both these are stabilised by a Joining chain (a short length of protein) called the J chain. And this is the component that was co-opted from an entirely unrelated biological process, as a team of researchers at Penn State University, which included Kazuhiko Kawasaki, associate research professor of anthropology, discovered.

Their research was published a few days ago in Proceeding of the National Academy of Science (PNAS) and is explained in a Penn State University news release:

Malevolent Designer News - How The SARS-CoV-2 Virus Has Been Redesigned to Have Another Go

The emergence of JN.1 is an evolutionary ‘step change’ in the COVID pandemic. Why is this significant?

To anyone but a reality-denying creationist, the SARS-CoV-2 virus that causes COVID-19, is a classic example of evolution by natural selection, as it continually mutates and those mutations that make it more successful are retained, so it continually improves in its ability to infect and be passed on to another victim, so producing more offspring in the virus gene pool than rival versions.

The latest version to gain predominance, JN.1, currently spreading across the world, is yet another variation on the omicron version, which itself ousted delta as the predominant variety. This new improved version may prove to be so different to omicron that is should be given a new Greek letter designation.

One point that shouldn't go unnoticed is that because, unlike the original, the virus now exists in an environment in which most of its potential victims have a degree of immunity to it, either by vaccination or by previous infection. Because that immunity usually means the ability to produce antibodies to the 'spike' proteins on the surface of the virus, most of the mutations of progressively more successful variants are in the genes that code for those proteins - making it more difficult for antibodies to bind to them.

To a creationist, the SARS-CoV-2 virus, like all the other pathological viruses, presents the paradox of trying to believe their putative designer god is the supreme ruler of and creator of everything in, the universe and is the only entity capable of creating biological organisms, but, because it is omnibenevolent, it would not have designed SARS-CoV-2 and would not be responsible for continually redesigning it to continue making us sick, by evading the immune system it supposedly also designed to protect us from viruses and other pathogens.

Curiously, creationists who continually present what they think is evidence of design as evidence for their magic creator on the grounds that it is the only entity capable of biological design, never use evidence of malevolent design as evidence for the same magic creator. That has to be ascribed to another entity with even greater powers than their supposedly supreme-in-all-things god and with the ability to outwit it, even though that claim is blasphemous within their own religious beliefs. They need to hold those two diametrically opposite views of 'creation' simultaneously to continue to deny the evidence for evolution by natural selection of which the SARS-CoV-2 virus is a perfect example.

And those creationists who do actually believe the religion they purport to believe and who won't contemplate blasphemy, have no recourse but to believe that the SARS-CoV-2 virus was not only designed by their putative designer god but that it also regularly updates it to continue making us sick despite the efforts of biomedical scientists, because the alternative it to accept the unthinkable and ascribe it all the a god-free natural process of evolution by natural selection, just as science claims.

The following article by Suman Majumdar, Associate Professor and Chief Health Officer - COVID and Health Emergencies, Burnet Institute; Brendan Crabb, Director and CEO, Burnet Institute; Emma Pakula, Senior Research and Policy Officer, Burnet Institute; and Stuart Turville, Associate Professor, Immunovirology and Pathogenesis Program, Kirby Institute, University of New South Wales, Australia, explains why the emergence of the JN.1 variant of SARS-CoV-2 is a significant evolutionary step change. It is reprinted from The Conversation under a Creative Commons licence, reformatted for stylistic consistency:

Unintelligent Design - How Ovulation Goes Wrong Because It Wasn't Intelligently Designed

[left caption]

[Right caption/credit]

Gene expression atlas captures where ovulation can go awry | Cornell Chronicle

Back in the late 1960s and early 1970, in what seems like a different lifetime now, I was a senior research assistant in the Oxford University/MRC Neuroendocrinology Research Unit, researching the hormonal control of ovulation in guinea pigs. Two of our tools were radioimmunoassays I had adapted for measuring extremely low levels of a hormone in guinea pig anterior pituitary glands known as luteinizing hormone (LH), and another similar assay for measuring the level of the steroid progesterone in guinea pig blood.

Sadly, having worked for close on two years towards producing a research paper with hundreds of assay results, thousands of microscope slides, hundreds of electron micrographs and a freezer full of samples waiting to be assayed, the government pulled the rug from under our feet by withdrawing our research funding, and I was made redundant, so my work was never published. Disillusioned and with a young family to support, I left research and perused a career in the NHS Ambulance Service instead - but that's a different story, and not relevant to the subject of this blogpost, which illustrates how much science has progressed in the last 50-60 years.

Researchers are no longer researching the hormonal control of ovulation but the fine details of the genetic control of the process of ovulation at the cell level, and what they've found is that the process is far from intelligently designed by anything resembling a perfect, omniscient, omnipotent designer. It is a process that is so complex that it can, and does, go wrong. An intelligent designer who didn't want random women to be unable to shed viable eggs, could have designed a less complicated process, but you can depend on creationism's putative intelligent[sic] designer to never do something simple when there is a far more complicated and wasteful way to achieve the same result.

The research, published a few days ago in Proceedings of the National Academy of Sciences, was led by Iwijn De Vlaminck, associate professor of biomedical engineering in Cornell Engineering, and Yi Athena Ren, assistant professor of animal science in the College of Agriculture and Life Sciences. The paper’s lead author is Madhav Mantri, Ph.D., now a postdoctoral researcher at Stanford University.

The team used a form of RNA tagging to map the gene expressions that occur during ovarian follicle maturation and ovulation in mice.

This spatial transcriptomics map depicts the cell types of a mouse ovary undergoing hormone-induced ovulation

The research is explained in a Cornell University Press release:

Malevolent Designer News - How To Keep Ahead In The COVID Game Against Creationism's Divine Malevolence - Keep Being Boosted

How long does immunity last after a COVID infection?

Creationists stuck with the evidence of parasites and viruses that appear to be designed for two purposes only - making more copies of themselves and increasing the suffering in the world by making us sick and die - traditionally try to ride two horses. They blame something else, like 'The Fall' or 'Sin' for them, whilst still arguing that their putative designer god is supreme in all things and the only entity capable of creating complex organisms.

They also get in a terrible muddle when asked whether their 'designer' god included an immune system to protect us from these parasites when it designed us before 'The Fall', in which case it was planning for it all along, or whether there was a subsequent upgrade to V.1.2, in which case it couldn't have been omniscient and had to redo its design to account for the unforeseen.

But whatever rationalisation creationists can think up for these mutually contradictory beliefs, we are left with the fact that viruses like the SARS-CoV-2 virus and our immune system are locked in an arms race, in which human medical science has had to get involved because the immune system isn't fit for purpose, and the protection it gives us is only temporary.

Meanwhile, medical scientists, aware of the fact that evolution by natural selection is going to continually produce new variants of the virus and that these viruses may become better at evading our defences, continue to apply that knowledge and develop new vaccines against the latest variants.

The following article by Lara Herrero, Research Leader in Virology and Infectious Disease, and Wesley Freppel, Research Fellow, Institute for Glycomics, both of Griffith University, Australia explains why regular vaccination with boosters to keep out immune system primed for the latest iteration of the arms race with a latest version of the virus. The article is reproduced from The Conversation under a Creative Commons licence, reformatted for stylistic consistency:

Malevolent Designer News - How Bacterial Pathogens Are Cleverly Designed to Invade Their Victim's Body

The exceptional secretion mechanism of Tc Toxins.

MPI MOPH

Functional model for Yen-Tc toxicity. Following ingestion of the Tc, it is likely that the surface-bound chitinases bind to and/or degrade the chitin-rich peritrophic membrane of the insect midgut. Cell surface recognition is likely facilitated by motifs within the A subunits prior to internalization. Similarities to the well characterized bacterial binary toxin systems (e.g., anthrax, cholera, diphtheria) suggest a mechanism involving receptor-mediated endocytosis followed by pore formation and translocation of the B and/or C components into the cytosol (I), although alternative mechanisms (e.g., II, III) cannot be ruled out.

Landsberg, MJ., Jones, SA., Rothnagel R., et al (2011)

24-01-18 | Max Planck Institute of Molecular Physiology

Imagine you're in charge of an invading army laying siege to your enemy's outer defences. How do you neutralise them?

One way would be to send a small group of soldiers, packed with high explosives and deadly toxins on a kamikaze mission into the defences, with instructions to detonate their explosives and so spread the toxins when inside to destroy the defences and kill the defenders. You could improve on that by removing any temptation the suicide bombers might have to not detonate their defences by automating the trigger to fire as soon as they encountered the defender.

That's exactly what a team at the Max Planck Institute for Molecular Physiology (MPI MOPH), Dortmund, Germany, have found bacteria use to gain access to their victim’s body and make their hosts sick and die. The team, led by Stefan Raunser, Director of MPI MOPH, have published their findings, open access, in Nature Microbiology. Their work is described in a MPI MOPH press release:

Malevolent Design - How The Divine Sadist Makes One in Three Infected Babies' Future Lives Difficult Even If They Recover From Bacterial Meningitis

Photo: Getty Images

Bacterial meningitis damages one in three children for life | Karolinska Institutet Nyheter

Left untreated, bacterial meningitis is usually fatal, but even if it is treated with antibiotics and the patient recovers, creationism's divine sadist who designed the bacteria, ensures one in three of them will be lefts with varying degrees of disability, including mental impairment, blindness, deafness or loss of motor control that will be with them for life.

This is the conclusion of a new study published two days ago in JAMA Network Open. It was conducted by a team under the leadership of Federico Iovino, associate professor in Medical Microbiology at the Department of Neuroscience, Karolinska Institutet.

The team compiled data on 3,500 people who contracted bacterial meningitis as children between 1987 and 2021 and compared them to just over 32,000 matched controls from the general population. The average follow-up time was 23 years.

As the news release from the Karolinska Institutet explains:

Malevolent Design - No Fun For Creationists As The Candida Family of Fungi Are Evolving To Keep Infecting Us

A Candida albicans cell forming a hyphal extension

Candida auris causes multidrug-resistant infections that can result in organ failure

Credit: Kateryna Kon/Science Photo Library

Candida evolution disclosed: new insights into fungal infections | IRB Barcelona

The Candida genus of fungi are related to yeasts (i.e., single-celled fungi) but are specialists at living in or on our bodies and are common infections in body cavities such as the mouth, anus, vagina and urethra and the genito-urinary and respiratory tract, and other moist areas like armpits, inner surfaces of joints like the elbow and knee, groins and fold beneath breasts and buttocks.

They can also become systemic infections causing organ failure and death, especially in people who are immune compromised for any reason. So, they are a threat to people who are in generally poor health, who have had transplants and need to take immunosuppressive drugs, or people receiving chemotherapy for cancer.

And, like some bacterial pathogens, they are good at evolving immunity to anti-fungal medication.

One species, Candida auris, has evolved multiple drug resistance and is now a serious threat to people in hospital for other conditions.

Now, a research group from the Institute for Research in Biomedicine (IRB Barcelona) and the Barcelona Supercomputing Center - Centro Nacional de Supercomputación (BSC-CNS), led by the ICREA researcher Dr. Toni Gabaldón, has identified hundreds of genes subject to recent, clinically-relevant selection in six species of the fungal pathogen Candida. In other words, the genes that have given Candida species their clinically-relevant drug resistance.

First a little AI background to the Candida genus:

Unintelligent Design - How Creationism's Heath-Robinson Designer's 'Design' Causes Cancer

Pit Head (c. 1930) William Heath Robinson

Deregulation of Alternative RNA Splicing Promotes Pancreatic Cancer Pr | Moffitt

William Heath-Robinson was an English eccentric illustrator of ridiculously over-complicated solutions for (mostly) imaginary problems. His 'labour-saving' devices often took more people to operate them than the labour they saved.

His designs usually incorporated the most unlikely of objects, such as pianos or stacks of books to stand on, bent sticks to hold things up, pulleys and levers, held together with pieces of string, which never failed to have a knot in them because they had been made from shorter lengths tied together. And the amazing thing was, when you looked at them, it looked though they really would work, and if you took any component away, the whole thing would fail.

What he probably didn't appreciate at the time, was how closely his 'intelligent' designs resembled the designs of creationism's putative designer, but they are almost perfect metaphors for the detail beneath the superficial appearance of design in living organisms, especially the processes and mechanisms that look irreducibly complex.

Take, for example, a consequence of the failure of a 'Heath-Robinson' mechanism for correcting a problem with how RNA is built using templates in DNA which are scattered over several sections of DNA instead of being in a single, contiguous lengths. The different fragments of RNA that this initially produces must then be spliced together (just like William Heath-Robinson's pieces of string).

And of course, being a 'Heath-Robinson' machine, even this little section of the process of protein production is not simple. Splicing is a complex process involving the protein, RBFOX2, and when this fails in pancreatic cells, the resulting faulty RNA molecules can lead to cancer and metastasis of those cancer cells is itself facilitated by reduced RBFOX2.

How the failure of this correction mechanism causes pancreatic cancer was discovered by an international team of researchers led by Assistant Professor, Karen Mann, Ph.D., of the Department of Molecular Oncology, Moffitt Cancer Center, Tampa, FL, 33612, USA, with colleagues from The Tisch Cancer Institute; St. Jude Children’s Research Hospital; the Agency for Science, Technology and Research in Singapore; and the University of Otago in New Zealand.

Of course, the real problem here isn't with the designer but the mindless design process that produces these over-complicated, utilitarian 'Heath-Robinson' solutions to problems. DNA is RNA's data store and, so long as it works better than what went before it, there is no pressure to sort out and 'defrag' the DNA, so the irreducibly complex 'Heath-Robinson' machine might fail and cause pancreatic cancer occasionally, but the proteins the pancreas produces are worth the occasional failures, and mindless evolution has no concern for the suffering caused.

Here is how the team described their findings in Nature:

Malevolent Designer News - The Brilliance of Creationism's Divine Sadist

Scanning electron micrograph of Salmonella typhimurium invading a human epithelial cell.

New insights into what helps Salmonella cause infections | Carl R. Woese Institute for Genomic Biology

Salmonella

The brilliance of creationism's favourite sadist was on display again recently, when researchers from the Department of Microbiology, University of Illinois at Urbana Champaign, Urbana, Illinois, USA, showed how the pathogen, Salmonella, is designed to not only survive being engulfed by the macrophages in our blood that are supposedly designed to protect us, but positively thrives and multiplies inside them. Although rarely fatal, Salmonella infection can be distressing and unpleasant with vomiting and diarrhoea, as I can attest from my childhood in rural Oxfordshire at a time when food and water hygiene left much to be desired.

So, it looks like creationism’s intelligent [sic] designer won that particular arms race with itself, in favour of the nasty pathogen designed to increase the suffering in the world. At least, that's the sort of nonsense creationists needs to believe to retain the childish belief that living things are made by a magic man in the sky.

The fact that salmonella can live happily inside a macrophage supposedly designed to kill pathogens has been known for some time, but what the University of Illinois researchers have discovered is just how it manages the trick. It's all down to the structure and function of the bacterium's surface membrane which detects and adjusts to the conditions in which the organism finds itself.
First, a little AI background on the pathogen:

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

Bronze Age Genes.

Credit: SayoStudio

Life in Bronze Age Britain (artist's impression)

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

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

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

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

As the University of Cambridge News release explains:

Unintelligent Design - How Creationism's Incompetent Designer Tries To Fix It's Bad Design

New Study Reveals Crucial 'Housekeeping' Genetic Elements and Their Potent Role to Fight Cancer｜THE INSTITUTE OF MEDICAL SCIENCE, THE UNIVERSITY OF TOKYO

The thing about Creationism's putative intelligent [sic] designer is that it isn't just your common or garden variety of jobbing designer; it is allegedly omniscient, omnipotent and perfect, so anything it designs should be perfectly designed to do exactly what it does, nothing more and nothing less. Creationists need to ignore that aspect of its designs when it comes to the problem of all the parasites that live on and in the animals and plants it supposedly created or they need to perform some double-think mental gymnastics and blame something else which, even though their putative intelligent designer is the only entity capable of designing anything living, also designs things.

Creationists also need to ignore the fact that good design is minimally complex and pretend it’s a hallmark of good design. But imagine a manufacturing process that is so badly designed that it needs whole layers of sub-processes to correct the mistakes, and then those sub-processes need more sub-processes to correct their mistakes!

Presumably, a creationist would look at that system with its vast array of monitoring and error corrections as evidence of intelligent design, regardless of the waste and inefficiency built into the system. In reality, of course, any competent process designer would get it right first time, or would scrap a bad design and start over, learning the lessons of earlier failures, so designing the perfect system with minimal complexity and minimal waste should not be beyond the wit of a perfect, omnipotent omniscient designer, should it?

Alas, what we see in nature is nothing like perfectly designed processes; instead, we see muddle, waste and inefficiency with layer upon layer of sub-processes simply to cope with the errors in the processes.

An example of just this situation inside the cells of our allegedly intelligently design bodies was discovered recently by a team of researchers from the Laboratory of Functional Analysis in silico (Nakai-lab) at The Institute of Medical Science, The University of Tokyo, Japan, led by Professor Kenta Nakai, head of the laboratory, and Dr. Martin Loza, Assistant Professor, in collaboration with Dr. Alexis Vandenbon, Associate Professor, from the Institute of Life and Medical Sciences, Kyoto University, Japan. Their work was published, open access, in Nucleic Acids Research on December 12, 2023.

The team found as many as 11,000 gene regulators, all needed for basic 'housekeeping' and error corrections within the cell. These are known as housekeeping cis-regulatory elements (HK-CREs). These elements are vital in maintaining cellular stability beyond conventional gene regulation, influencing diverse cellular functions across healthy cell types. Moreover, a subset of these housekeeping elements, particularly those related to zinc finger genes, was found to have reduced activity in diverse cancers, suggesting their role as potential housekeeping tumor suppressors.

These HK-CREs were believed to be simple on/off switches that regulated the activity of housekeeping genes, but that was far too simple for whatever designed this complex process, of course. The Japanese team found that these switches aren't only important for the enhancement of specific genes but are crucial for the basic functions that keep our cells healthy. In other words, they are needed to clean up and correct the mistakes in the basic cell functions.

Given the significant association between cancer and mutations in epigenetic components, every small insight we gain could be key in the ongoing battle against this disease, which has tragically claimed innumerable lives. Through extensive bioinformatics analyses, we aimed to emphasize HK-CREs profound impact on fundamental cellular processes, including their potential as essential housekeeping tumor suppressors.

Assistant professor Dr. Martin Loza, lead author
The Institute of Medical Science
The University of Tokyo, Japan

To summarise at this point then, the housekeeping genes (HKRs) are needed to clean up the errors and mess of a badly designed process, but then they need more genes (HK-CREs) to regulate their activity!

But it gets worse!