Rosa Rubicondior

Sunday, 11 February 2024

Creationism in Crisis - Social Learning Is Part of Beaked Whale Culture - Just Like Humans

Surprising Behavior in One of the Least Studied Mammals in the World - SDU

Continuing where I left off with the account of how orcas (killer whales) form distinct cultures based on food, hunting strategies, location and dialect, which parallel human cultures in many way, we now have evidence that at least one of the 24 known species of the beaked whales, Baird's beaked whale, form cultural groups, and that another 'human' trait - social learning - is involved in the formation of these cultures.

Creationists, of course, continue to insist that only humans form cultures and have the social ethics that hold them together because they were specially created in a way that makes them materially different to all other animals, and by the circular reason that often typifies creationist arguments, this proves they were specially created by a god who holds them in the highest esteem.

s But as we are learning, almost all the traits creationists try to claim are uniquely human and therefore proof of our special creation, are turning out to be common to many other species, especially mammals, and so are evidence for common ancestry and evolution by descent with modification.

The little-known beaked whale, a relative of orcas and dolphins, has recently been observed changing its habitat and hunting strategy by a process of social learning. This is the same process by which growing children adopt the social norms and customs of their culture and how people from other cultures can assimilate into unfamiliar cultures. Essentially it means observing others and memorizing what they do in any given situation.

This observation was made by researchers from the University of Southern Denmark (SDU) led by Olga Filatova, a whale expert and postdoc at Department of Biology and SDU Climate Cluster. She led the study which showed that some pods of orcas in the Pacific have occupied the same area since the last Ice Age glacial maximum, 20,000 years ago when they occupied warmer refugia and adopted them as permanent territories. The same study showed how orcas form distinct 'ecotypes' which are genetically isolated from other ecotypes by cultural barriers to interbreeding.

For the beaked whale study, the team observed a population of Baird's beaked whales, which has unexpectedly been found near the coast and in shallower waters than previously observed.

Their work has been published, open access, in the journal Animal Behaviour and is explained in a SDU press release by Birgitte Svennevig:

Fossil shell of Pithocerithium rubiginosum (height is 1.5 cm) from the Miocene sediments of Nexing in Austria (left) and isolated reddish polyene pigments on calcium fluoride disc (diameter of disc is 2 cm) (right).

Photo: Klaus Wolkenstein

Information for the Media: Surprisingly vibrant colour of 12-million-year-old snail shells - Georg-August-Universität Göttingen

Another terrible week for creationists is continuing today with news that a team of researchers from the University of Göttingen and the Natural History Museum Vienna (NHMW) have shown that the red pigment frequently found associated with the shells of fossilised snails from the Middle Miocene is the pigment that would have been present in the living shells, and not, as had been suggested, the product of later reactions.

This makes these pigments, from the chemical group of polyenes which includes the carotenes that give the colour to the plumage of some birds and to carrots, the oldest known pigments ever discovered. The fossil snails, Pithocerithium rubiginosum, so named from the 'rusty red' pigment they often contain, are from the Middle Miocene deposits in the geologically important Vienna Basin:

Creationism in Crisis - How Killer Whales Were Evolving Cultural Groups - 20,000 Years Before 'Creation Week'

Researchers find 20,000 years old refugium for orcas in the northern Pacific - SDU

The northern Pacific near Japan and Russia is home for several different groups of orcas. They have no contact with each other, do not seek the same food, do not speak the same dialect, and do not mate with each other. Some are the descendants of a pod that moved there during the last Ice Age.

Any study of whales, such as dolphins and they larger cousins, the orca's or killer whales will quickly dispel one of the myths creationists use to try to justify their absurd belief that humans are somehow materially different to the rest of life on Earth in a way which isn't just because we are a variation on the general mammalian theme with enough distance between us and related species to justify a separate taxon, because we were specially created - humans form cultures and have languages and traditions, etc.

Of course, it's not just the whales that have cultures and languages; chimpanzees and bonobos and other primates also have distinct cultural groups that differ significantly from one another, but this article deals specifically with orcas and the research which has shown that they moved into Ice Age refugia at the last glacial maximum, some 20,000 years ago, and some have slayed there ever since.

The article also illustrates a problem of modern taxonomy in how to define a species with hard and fast rules when the distinction in reality is fuzzy. Some of the pods studied form isolated cultural groups that seek different foods to the others, which speak a different dialect, move in a specific area, and never interbreed. This cultural barrier to hybridization is as much a barrier as is the different plumage and mating rituals that are the pre-zygotic barriers to interbreeding that justify classifying many related birds as distinct species because the barriers ensure an isolated gene pool in species that could successfully interbreed and do so in captivity. Killer whales exist in many pods with cultural barriers to interbreeding and so form isolated gene pools, yet they are regarded as a single species.

To overcome this problem, biologists have classified the different killer whale pods into 'ecotype', but it is this genetic isolation that enables genetic analysis to determine how long the pod has been isolated.

A research team led by whale biologist, Olga Filatova, of the University of Southern Denmark recently published an open access paper in the journal Marine Mammal Science showing how environmentally stable marine regions may have preserved refugial populations of the killer whale that retained historical genetic and cultural diversity. These whales are believed to have moved into the warmer refugia during the last Ice Age.

The team's work is explained in a University of Southern Demark (SDU) press release by Birgitte Svennevig:

Ethics Ratings of Nearly All Professions Down in U.S.

According to the latest Gallup Poll, trust in the ethical standards of almost all identified professional groups in the USA has declined in the four years up to 2023 with trust in the clergy reaching an all-time low at 32 percent of those polled rating their trust in them as very high or high. The clergy now rank alongside chiropractors and psychiatrists in the public perception of their ethical trustworthiness.

All the 5 major professions in the USA fell steadily between 1976 when polling began but the profession which fell furthest and fastest was that of clergy. in 1977, 61 percent of adult Americans polled, gave their trust in clergy as very high or high; this has now fallen to 32 percent, a 29 percentage points decline to almost half what it was in 1977.

And this downward trend has accelerated since 2012, declining by an average of slightly over 1.8 percentage points per year, against an average of just over 0.38 percentage points between 1977 and 2012. This represents about a four-fold increase in the rate of decline which, projected forward, if this rate continues, no-one in America will rate the ethical trustworthiness of clergy as very high or high by mid-2032.

Unintelligent Design - The Heath Robinson Way Legumes Get Nitrates

Mechanism of Plants Obtain Nitrogen by Supplying Iron to Symbiotic Bacteria | Research News - University of Tsukuba

Creationism's 'intelligent' designer is nothing if not inventive. In fact, it's so inventive that it keeps on reinventing things it's already invented and designing new ways to do things it's already designed a way to do. It's almost exactly like it has no way of remembering what it did yesterday and using those designs and inventions today - a bit like a motor-car manufacturer who reinvents the wheel, or the steering mechanism every time it designs a new model.

Take, for example, the way most plants obtain the essential nitrates they need to make proteins. Nitrogen is abundant in the atmosphere (about 79%) where it exists as diatomic molecules N₂, in which form plants can't assimilate it. Instead they depend on soil bacteria, the 'nitrogen-fixing' bacteria such as Azotobacter and Clostridium which convert N₂, into ammonium (NH₄⁺ which forms salts with other minerals in the soil, in which form it can be taken in through the roots of plants. Apparently, it was too simple to give plants the same metabolic pathways that the nitrogen-fixing bacteria have so they could make their own ammonium, so a more complex and less energy-efficient way to get nitrates into plants had to be invented.

A small amount of ammonia (NH₃ is also produced by the action of lightening on atmospheric nitrogen and this, together with nitrates produced by industrial pollution is dissolved in rainwater and finds its way into the soil. Other bacteria, fungi and other soil organisms also release nitrates from decaying plant and animal matter in the soil.

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.

Creationism in Crisis - A New Endogenous Retrovirus Caught In The Act Of Invading a Genome

A rare recent case of retrovirus integration: An infectious gibbon ape leukemia virus is colonising a rodent’s genome in New Guinea - Leibniz Institute for Zoo and Wildlife Research

Researchers have discovered that a retrovirus is currently in the process of invading the genome of a rodent in New Guinea. This will add to the extensive list of known endogenous retroviruses. The virus, which appear to be harmless to the rodent - a mosaic tailed rat of the Melomys genus - is an infectious virus that causes leukemia in gibbons.

A retrovirus is an RNA virus that 'hides' in its host's DNA by inserting the DNA template for its RNA, using the enzyme reverse transcriptase that is coded for in its RNA. Once inserted it is replicated by every daughter cell. If it is inserted into the DNA of a germline cell, it can be passed on to the next generation.

Endogenous retroviruses (ERVs) are common in the genomes of all multicellular organisms and even some single-celled organisms, and as such constitute a large proportion of the non-coding or 'junk' DNA. A few may have been exapted for other purposes, but most are simply strands of viral DNA with a few mutations that broke them and rendered them harmless way back in our evolutionary history.

ERV's provide some of the most compelling evidence for common descent, especially since they appear at the same locus in the genomes of almost all members of a clade such as the vertebrates, including fish ancestors or the terrestrial vertebrates. The probability of the same ERV with the same mutations in in the same genetic locus to make it look like they form nested hierarchies, is vanishingly small, yet they do it over and over again.

The fact that they are present in all members of the same major clade tells us they must have been present in the last common ancestor of that clade, so they are a double embarrassment for creationists. They are both evidence of descent with modification and that there was no intelligence in the design of our genomes, because an intelligent designer would have no reason to include broken viral DNA which adds nothing by way of functionality yet must be replicated in every cell.

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

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:

Skeleton of the new pterosaur Ceoptera evansae from the Middle Jurassic of the Isle of Skye.

Trustees of the Natural History Museum London

3D models of skeleton.

Natural History Museum London

February : New species of Jurassic pterosaur discovered | News and features | University of Bristol

In another of those casual refutations of the creation myth in the Bible, archaeologists have discovered a new species of pterosaur that flew in the skies of what if now the Isle of Skye, Scotland, about 165 million years before creationism's fabled god decided to magic up out of nothing, a small flat planet with a dome over it in the Middle East.

They are thought to have lived for some 5 million years between the late Early Jurassic up to the Late Jurassic.

The fossilised skeleton fills another of those gaps in the fossil record so beloved of creationist, where the scarcity of fossils meant that the evolution of pterosaurs was poorly understood. This fossil shows that all the main clades of pterosaurs had evolved before the end of the Early Jurassic and earlier than previously thought.

The team from the University of Bristol Natural History Museum, the University of Leicester, and the University of Liverpool have named the new species, Ceoptera evansae: Ceoptera from the Scots Gaelic word Cheò, meaning mist (a reference to the Gaelic name for the Isle of Skye, Eilean a’ Cheò, or Isle of Mist - Scots Gaelic is still widely spoken on Skye), and the Latin -ptera, meaning wing. Evansae honours Professor Susan E. Evans, for her years of anatomical and palaeontological research, in particular on the Isle of Skye.

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

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:

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:

Creationism in Crisis - Scientists Are Understanding More About How Plants Evolve and Diversify - No God-Magic Required

Ecological Diversification in an Adaptive Radiation of Plants: The Role of De Novo Mutation and Introgression | Molecular Biology and Evolution | Oxford Academic

An effective way to refute the counter-factual claims of a wackaddodle cult like creationism is simply to reveal the facts and show how different they are to the cult beliefs. Sadly, this approach won't convince many creationists of course, especially those too arrogant to think their beliefs can be contradicted with mere facts, because part of being a creationist is to hold the self-idolatrous belief that your beliefs are inerrant, so trump anything science can produce, but one can but try.

In fact, researchers in biomedical sciences don't even try, they have more important things to do than try to convince fools who reject evidence before they see it and who are proud of the fact that nothing can make them change their minds. Scientists just discover the facts and add to the mountain of evidence that creationists have been conditioned to ignore or dismiss as lies or otherwise relegate to the realm of the unimportant.

For example, this week’s edition of Oxford University Press' journal Molecular Biology & Evolution has 10 different open access papers dealing with the minutia of evolution and not one of them shows any sign that the scientists are abandoning the Theory of Evolution as not fit for purpose and adopting instead, creationism's childish superstition complete with magic and unproven supernatural entities, as creationist cult leaders regularly tell their dupes.

None of these papers mention creationism or point out how the research findings refute it, of course, because they are written for people who understand the science, so don't need that to be pointed out to them. These are:

Creationism in Crisis - A Strange Shaped Tree 360 Million Years Before 'Creation Week'.

Enigmatic fossil plants with three-dimensional, arborescent-growth architecture from the earliest Carboniferous of New Brunswick, Canada: Current Biology

Creationism's designer is not known for creating a design then sticking to it. If you believe creationists, it has designed something like 500,000 beetles, for example, and, although they all do basically the same thing, hundreds of different trees.

And, if you believe creationist mythology, it created almost everything on Earth, hundred, even thousands of millions of years before it created the small flat planet with a dome over it, centred on the Middles East. Sadly, the Bronze Age story-tellers who wrote about it were oblivious of what had been living 360 million years earlier in the Tournaisian age in what is now New Brunswick, Canada, so said nothing about it in their tales. They said nothing about Canada either for that matter, because they were ignorant of anywhere outside their small area of the Middle East, as can be seen from the naive way they describe their world as they imagined it.

Had they been better informed though, they might have mentioned one of the more bizarre tree designs which consisted of a straight trunk about 15 feet tall, with long thin leaves radiating out from the top third and measuring about 18 feet in length, the whole thing resembling a giant green bottle brush. It doesn't appear to have had any branches.

Fossils of this tree have been described by an international team led by Robert Gastaldo of Colby College in Waterville, Maine, USA in collaboration with Matthew Stimson and Olivia King of the New Brunswick Museum, Saint John, and Saint Mary's University in Halifax, Nova Scotia, Canada, and others.

Their work is published, open access, in Current Biology and described in a Cell Press article reprinted in Science Daily:

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:

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

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:

Neanderthals and humans lived side by side in Northern Europe 45,000 years ago | Berkeley

35 thousand years before creationism's god decided to create a small flat Earth centred on the Middle East and put a dome over it to keep the water above the sky out, anatomically modern humans were living alongside Neanderthals in Northern Europe.

The problem was that the Bronze Age people who wrote the creation myth, which they assumed all happened in their small part of the planet, were completely unaware of Northern Europe, the people living there, or that it had a history of a different species of humans living there for half a million years. If they had been, they might have invented a different tale to compensate for what they didn't know, but being human, and humans always want a story, they made one up with what little knowledge and understanding they had, and hardly surprisingly, got it spectacularly and laughably wrong, as we now know.

We know this because science is finding out what really happened and it's turning out to be nothing like the story the Bronze Age story-tellers made up.

That Neanderthals and modern humans met, co-existed and occasionally interbred has been known to science for some time now, but there was uncertainty about how long ago they first came into contact and where. Now a large team of archaeologists which included researchers from the Max Planck Institute for Evolutionary Anthropology, Leipzig, Germany, have discovered evidence that they coexisted in Northern Europe, 45,000 years ago and lived together for several thousand years before Neanderthals became extinct.

The evidence of this is the finding of bone fragments which DNA analysis shows to be modern human DNA, dated to at least 40,000 years old, at a site in Germany at Ranis. Their finding also suggests that it was an invasion of Europe and Asian by modern humans that drove the Neanderthals to extinction, having lived in Europe for about 500,000 years. Although there is a school of thought that says Neanderthals, who existed in low population density, never became extinct so much as merged with the much larger population of modern humans. There is now probably more Neanderthal DNA in modern humans (who carry 1-3% Neanderthal DNA) then ever existed prior to the two species coming into contact.

The work of the team who made this discovery is the subject of three papers, two in Nature Ecology & Evolution and one in Nature. It is also the subject of an article by Robert Sanders in Berkely News:

Creationism in Crisis - Scientists Have Shown How The Evolution Of Bird Flight Was Connected To Growth in The Brain's Cerebellum

An artist's conception shows Archaeopteryx, a creature that had the wings of a bird but the tail and teeth of a dinosaur.

John Sibbick / NHM

Scientists Pinpoint Growth of Brain’s Cerebellum as Key to Evolution of Bird Flight | Johns Hopkins Medicine

Powered flight has evolved three times in vertebrates, the long-extinct Triassic pterosaurs, in a Jurassic dinosaur lineage that would become birds and in the Early Cenozoic ancestors of today's bats.

Of those, the easiest to study the evolution of flight in is the dinosaur lineage that became birds, because there is a large and available group of birds and a rich fossil record to study.

Now a team of Evolutionary biologists at Johns Hopkins Medicine, including assistant professor of functional anatomy and evolution, Amy Balanoff, Ph.D. have combined PET scans of modern pigeons with studies of fossil dinosaurs to answer one of the enduring questions in evolutionary biology - how did powered flight evolve in birds?

Having established the role of the cerebellum in flight with the PET scans on pigeons, they then found that there was a progressing increase in the size and complexity of the cerebellum in the ancestral dinosaurs as they evolved into flying birds.

Their results are published in Proceedings of the Royal Society B.

As the Johns Hopkins Medicine news release explains:

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:

Creationism in Crisis - The Universe Is Much Bigger Than Our Prophets Said...

NASA’s Webb Depicts Staggering Structure in 19 Nearby Spiral Galaxies - NASA Science

How is it that hardly any major religion has looked at science and concluded, “This is better than we thought! The Universe is much bigger than our prophets said, grander, more subtle, more elegant?” Instead they say, “No, no, no! My god is a little god, and I want him to stay that way.” A religion, old or new, that stressed the magnificence of the Universe as revealed by modern science might be able to draw forth reserves of reverence and awe hardly tapped by the conventional faiths.

Carl Sagan, Pale Blue Dot: A Vision of the Human Future in Space

Face-on spiral galaxy, NGC 628, is split diagonally in this image: The James Webb Space Telescope’s observations appear at top left, and the Hubble Space Telescope’s on bottom right. Webb and Hubble’s images show a striking contrast, an inverse of darkness and light. Why? Webb’s observations combine near- and mid-infrared light and Hubble’s showcase visible light. Dust absorbs ultraviolet and visible light, and then re-emits it in the infrared. In Webb's images, we see dust glowing in infrared light. In Hubble’s images, dark regions are where starlight is absorbed by dust.

NASA, ESA, CSA, STScI, Janice Lee (STScI), Thomas Williams (Oxford), and the PHANGS team

Continuing with the theme of how different the universe really is compared to the laughably naive description of it in the Bible where the sun, moon and stars were stuck to a dome over Earth above which there was just water. And the stars could even be shaken loose by earthquakes when they would fall to Earth and could be trampled on by goats.

By contrast, here are the latest clutch of images from NASA's James Webb Space Telescope (JWST). They are all of face-on spiral galaxies taken in the infra-red spectrum. Compare them to the description in Genesis where the entire Universe has a small, flat Earth at the centre of it.

Creationism in Crisis - The Billion-Year Evolutionary History of Plants On Earth

Since the first plants appeared, they have diversified into a vast range of forms, and sizes from pond scum to massive trees.

How did plants first evolve into all different shapes and sizes? We mapped a billion years of plant history to find out

Plants come in all manner of shapes and sizes, varying in complexity from simple single-celled algae, through mosses, liverworts and ferns to flowering plants and massive trees.

But how did they get this way?

A team of scientists led by Philip C J Donoghue, Professor of Palaeobiology, University of Bristol, James Clark, Research Associate, School of Biological Sciences, University of Bristol and Sandy Hetherington, Plant Evolutionary Biologist, The University of Edinburgh, set out to answer this question by looking at certain traits in each major plant group. The traits ranged from fundamentals like the presence of roots, leaves or flowers to the fine details such as the surface topography of pollen grains. All in all, the team collected data on 548 traits from more than 400 living and fossil plants, amounting to more than 130,000 individual observations.

They then used this data to plot the positions of plants, living and extinct in a 'design space', i.e., the theoretical range of possible forms for each major group.

What they found was that there tended to be a burst of diversification soon after the evolution of a major new trait, with the new lineage then tending to settle down to improve on what they had, rather than to innovate - until the next major innovation.

This what we would expect from the way a major new trait, such as the evolution of pollen as the male reproductive cell which could be transferred to the female by wind, insects, etc., so freeing the plants from the need to live in water or damp conditions so the motile male cells could 'swim' to the female, as it still does with the gametophytes - mosses, liverworts and ferns.

This innovation meant plants were not free to diversify into the dryer land between rivers, lakes and coastal margins and so colonise much more of the planet.

The same phenomenon is seen in animals where, for example, terrestrial living freed the early amphibians from dependence on water, except to breed, and the evolution of eggs, freed them even from that dependence; the evolution of flight freed the birds and bats to diversify into the new niches now open to them.

The team's work was published, open access in Nature Plants and is the subject of an article in The Conversation by the three lead authors. Their article is reprinted here under a Creative |Commons license, reformatted for stylistic consistency:

Banksia spinosa inflorescence

Credit: Nadiatalent via Wikipedia (CC BY-SA 3.0)

Banksias are iconic Australian plants, but their ancestors actually came from North Africa

No real scientists these days sets out to refute creationism as such, but most do anyway, because creationism is so counter-factual that almost any scientific facts, especially in the fields of biology, cosmology, archaeology, geology and palaeontology refute it. It takes a resolute and determined ignoramus to not be aware of that. The problem creationists have is that they get all their beliefs from an ancient text that is demonstrably wrong, even when explained away as allegorical or metaphorical. It is neither. It is quite simply wrong on every level.

So, creationists are left desperately trying to defend the childishly absurd claim that the entire Universe, including Earth and all living things on it, were all created out of nothing in a few days, about 10,000 years ago, by a magic man also made of nothing who designed himself before he existed then self-assembled according to that plan, with all the complexity and information needed to create and micromanage an entire Universe.

This, despite the fact that there are fossil remains of plants and animals from hundred, even thousands of millions of years before then and despite the fact that all the evidence points to a long, slow, evolutionary process of divergence from a common ancestor that lived well over a billion years ago, which was itself the result of a symbiotic associations of much earlier organisms.

One such paper, which casually and incidentally refutes creationism, recently published in Perspectives in Plant Ecology, Evolution and Systematics by three Australian botanists and plant ecologists and a South African Professor of botany, traces the origin of the family of iconic Australian plants, the Banksias, to North West Africa, 132 million years ago.

The story of this migration meshes in with the sciences of plate tectonics and oceanography allowing the plants to migrate across then contiguous land masses from what is now North West Africa to what is now Australia via South America and Antarctica, as land-masses split and diverged and sea-levels rose and fell to reveal land bridges where there is now ocean.

How they discovered this is the subject of an article in The Conversation by the four scientists. Their article is reprinted here under a Creative Commons licence, reformatted for stylistic consistency:

OSU-CHS student discovers new dinosaur species, publishes findings | Oklahoma State University

Between about 67 and 66 million years ago, during a period that geologists call the Maastrichtian, there was a thriving ecosystem of dinosaurs in what is now the Hell Creek formation which spans parts of Montana, Wyoming, and North and South Dakota. We know this because their remains are frequently found in this fossil-rich formation known as the Hell Creek Formation.

The great thing about this formation is the way, as the layers built up, nearby volcanoes periodically spread a layer of ash (or tufa) over it forming neat bands that can be accurately dated using one of the most accurate radiometric dating methods - Uranium-Lead (U-Pb) in zircons. This gives a maximum and minimum age of the fossils found between these layers of tufa.

I wrote about U-Pb dating in a recent blogpost, but for the sake of creationists who are about to squawk "Radiometric dating is false!", I'll expand on what I said here:

Unintelligent Design - How A Virus Saved The Unintelligent Designer's Blushes Early In Multicellular History

A virus that infected animals hundreds of millions of years ago has become essential for the development of the embryo

I've remarked before how similar biological systems are to the machines the late William Heath Robinson designed for solving simple, everyday problems. Simple solutions were eschewed for more complicated ones and unlikely items were used in ways they weren't intended for, such as a grandfather clock standing on a piano to support a platform balanced on top. Everything was held together by pieces of knotted string and labour-saving devices took far more people than would have been needed to do the job more simply.

And yet, the whole contraption worked, or at least looked as though it would if were ever made, but take any part away and the whole thing would fail, in an example of what creationists call 'irreducible complexity'.

So, let's pretend that creationism's, 'intelligent'[sic] designer really is behind the design of living organisms and see how closely Heath Robinson unwittingly parodied it:
Just such an example of a Heath Robinson machine in biology was revealed a few days ago in an open access paper published in Science Advances, explaining how a virus which became incorporated in the genome of an early multicellular organism provided a solution to a problem of the designer's own making. The problem it solves was how to overcome the problem created by choosing the same method of cell replication in multicellular organisms that single-celled organisms use, where the entire genome needs to be replicated at each division.

The entire 'point' of multicellularity, and what gave it its success over single-celled organisms is division of labour, in other words, specialisation, so the organisms can be divided into tissues and organs that perform a specialised task. This means that every cell has to have the potential to carry out every function, in the genes it inherits from its parent cell, yet only a few genes are need for its particular specialty.

The process by which this is achieved is the complicated epigenetic system which turns off unneeded genes as the cells differentiate into different cell lines in the developing embryo, and these settings can't normally be reversed.

However, the sperm and egg which then fused to form the zygote from which a new embryo develops, are themselves specialised cells with all the epigenetic settings of their parent cells with an additional few of their own, and these are inherited by the zygote, so to make cell differentiation possible again, the zygote is quickly (within minutes of fertilisation) reset to a state of totipotency.

So, to overcome the epigenetic settings problem that is a problem of the designer's own making, the zygote needs to be epigenetically reprogrammed and this happens in two stages: first to produce a 'totipotent' cell with the potential to produce all the different cells in the embryo as well as the placenta, umbilical cord, and amniotic sack in which the embryo will develop, and then, soon after cell division begins, 'pluripotent' cells from which the different stem cells for the required specialised cell lines will develop.

How this was helped by a virus is the subject of the paper by researchers from the Spanish National Cancer Research Centre (CNIO), Madrid, Spain. First, a little AI background:

Creationism in Crisis - A Multicellular Organism 1.63 Billion Years Before 'Creation Week'

Fig. 1. Transmitted-light (TL) photomicrographs of Q. magnifica from the Chuanlinggou Formation.
(A to D and K) Filaments with cells of varying length and width. (E) Four-celled filament with hemispherical terminal cell. (F and G) Filament with notably decreasing cell width toward one end. Note that (F) and (G) represent the same specimen; (F) lost the narrowest part of the filament as shown in (G). (H to J) Filaments displaying more uniformity of cell dimensions. (L) Two-celled filament with ovoid terminal cell. All specimens were handpicked from organic residues of acid maceration and photographed in wet mounts, except for (K), which was photographed from a permanent strew mount. Solid and empty gray triangles in (A), (C), and (K) indicate the longest and the shortest cells, respectively, within single filaments. tb, transverse band (interpreted as cross wall); tr, transverse ring (interpreted as partially preserved cross wall). Scale bar, 50 μm [(A) to (E), (I), (J), and (L)] and 100 μm [(F) to (H) and (K)].

Fossils from North China indicate eukaryotes first acquired multicellularity by at 1.63 billion years ago---- Nanjing Institute of Geology and Palaeontology Chinese Academy of Sciences

As though the abundant evidence of life on earth before about 10,000 years ago wasn't bad enough for creationists who believe the Universe and everything in it were was magicked out of nothing in 6 days around about then, a team of scientists led by led by Professor ZHU Maoyan from the Nanjing Institute of Geology and Palaeontology, Chinese Academy of Sciences (NGIPAS), has now pushed the date of oldest-known multicellular, eukaryote organism back another 70 million years to a whapping 1.63 billion years before the supposed 'Creation Week'.

This would mean, if their superstition had any merit that creationists believe Earth has been around for just the last 0.0006% of the time that multicellular eukaryotes have existed on it.

And they wonder why people laugh!

The fossils were discovered in the Yanshan area of North China in the late Paleoproterozoic Chuanlinggou shale Formation which is about 1,635 million years old. The age of the fossils is constrained by a layer of volcanic ash ~40 m above the fossil horizon in the Kuancheng area, which has yielded a U-Pb zircon age of 1634.8 ± 6.9 Ma (23).

All complex life on Earth, including diverse animals, land plants, macroscopic fungi and seaweeds, are multicellular eukaryotes. Therefore, multicellularity is key for eukaryotes to acquire organismal complexity and large size, and often regarded as one major transition in Earth’s life history by scientists. However, it is still poorly understood when eukaryotes first evolved this innovation in their deep evolutionary history.

Fossil records with convincing evidence show that eukaryotes with simple multicellularity already appeared at 1.05 billion years ago, including red and green algae, and putative fungi. Older records claimed to be multicellular eukaryotes, but most of them are controversial due to their simple morphology and lack of cellular structure.

Subscribe to: Posts ( Atom )

Please note:

The "Rosa Rubicondior" Blog by Bill Hounslow is licensed under a Creative Commons Attribution-NonCommercial-NoDerivatives 4.0 International License.

As an Amazon Associate I earn from qualifying purchases. All commission earned from Amazon for the sale of books, etc. advertised here, will be donated to Oxfam.

Hopefully, religious and other offensive advertising content has now been blocked from this site. Please let me know if you see any.

Note: This is my only blog. Others purporting to be by me or bearing my ident will contain plagiarised and deliberately altered material from this site or material presented as being by me. They will usually be run and maintained by a well-know unemployable Internet abuser, fraud and expelled Catholic seminarian who appears to have developed an obsessive fascination with me, bordering on the psychotic. You can read about him and what caused his psychosis here.

Sunday, 11 February 2024

Saturday, 10 February 2024

Friday, 9 February 2024

Thursday, 8 February 2024

Wednesday, 7 February 2024

Tuesday, 6 February 2024

Monday, 5 February 2024

Sunday, 4 February 2024

Saturday, 3 February 2024

Friday, 2 February 2024

Thursday, 1 February 2024

Wednesday, 31 January 2024

Tuesday, 30 January 2024

Monday, 29 January 2024

Sunday, 28 January 2024

Saturday, 27 January 2024