F Rosa Rubicondior: April 2024

Tuesday 30 April 2024

Creationism in Crisis - Yeast Evolution - Not Whether But How

Electron micrograph of budding yeast cells
Photo: Ira Herskowitz and E. Schabtach
Bioinformatics professor discovers surprising evolutionary pattern in landmark yeast study | Inside UNC Charlotte | UNC Charlotte

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

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

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

Meanwhile real scientists do real science and science moves on.

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

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

Monday 29 April 2024

Creationism in Crisis - How Order Emerges From Chaos - Naturally


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

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

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

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

Sunday 28 April 2024

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

Structural model at atomic resolution of bacteriophage T4

Study details a common bacterial defense against viral infection

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

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

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

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

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

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

Unintelligent Design - How the Periodic Cicadas Evolved

13-year cicada, Magicada tridecima
Billions of cicadas are about to emerge from underground in a rare double-brood convergence

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

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

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

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

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

Saturday 27 April 2024

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

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

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

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

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

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

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

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

Both these examples are cited in this paper.

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

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

Symbiotic relationship between clown fish and anemone.
Species living closely together in symbiosis is far older and way more common than you might think

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

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

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

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

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

Friday 26 April 2024

Malevolent Design News - The Superbug, Clostridium Difficile (C. Diff), May Be Developing Resistance to Vancomycin - Design or Evolution?

Treatment for Deadly Superbug C. diff May Be Weakening - University of Houston

The latest rabbit hole Michael J Behe has driven the creation cult into is the daft notion of 'Genetic Entropy'. This was introduced following the failure of the Discovery Institute to trick the courts in the USA into declaring that 'Intelligent [sic] Design' is real science and so should be foist on impressionable children in science class at taxpayers’ expense.

The notion of 'Genetic Entropy' plays on what used to be presented as an anti-evolution argument - the Second Law of Thermodynamics, which says that a closed system tends to disorder (increased entropy), so evolution can't increase order and complexity. This ignores the fact that Earth is not a closed system, of course, and relies on the scientific illiteracy of its target marks. And it looks nice and sciencey - something that creationists all crave while purporting to reject science.

So, Genetic Entropy starts off with the assumption that every species was created perfect and then, because Adam and Eve allowed 'Sin' to enter the world, these 'perfect' genes have been getting progressively less perfect. Now, this isn't Bible literalism, obviously, because that would make 'Genetic Entropy' religion, not science! Got it!

I posted this in an Evolution Vs Creation Facebook group. Creationists appear to be pretending not to have seen it.

The problem then is, how can increasing 'entropy' lead to greater fitness in a given environment? It can't of course because unlike the random process of mutation, there is no selective element which can produce more descendants from a worse genome, and unless it is getting worse, in what possible sense of the word can it be getting less perfect?

So, faced with something like increasing bacterial resistance to antibiotics, creationists in Michael J Behe's latest rabbit hole have only two ways to go. They can't argue that increased entropy is leading to an improved genome (from the perspective of the bacterium) because that would mean 'genetic entropy' is leading towards greater perfection. That then leaves them with the unenviable choice of design or evolution, and for design, read 'malevolence' because increasing antibiotic resistance increases the ability of the bacterium to make us sick, and any omniscient designer would know that.

IOW, Michael J Behe's attempt to resuscitate the Discovery Institute's flagging 'Wedge Strategy' has resulted in his fundamentalist cult having to choose between the twin 'evils' of blasphemy or evolution!

The latest twist in the evolutionary arms race between bacteria and human medical science is in the increasing weakness of the antibiotic of choice for Clostridium difficile (C. diff), vancomycin, against which C. diff appears to be developing resistance. This was discovered by researchers at the University of Houston College of Pharmacy, Texas, USA, who have just published their findings in the Journal Clinical Infectious Diseases, sadly behind a paywall with only the abstract available. However, their work is described in a University of Houston news release:

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

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

Credit: Rachel Kerwin
Uncovering a ‘parallel universe’ in tomato genetics

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

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

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

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

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

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

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

Thursday 25 April 2024

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

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

Credit: Stefan Pommer / photopic.at (CC BY-NC-SA 4.0)
Giant Viruses Infect Deadly Parasite

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

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

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

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

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

Creationism in Crisis - Earth's Magnetic Field 3.5 Billion Years Before 'Creation Week'.

Illustration of the dynamo mechanism that generates the Earth's magnetic field: convection currents of fluid metal in the Earth's outer core, driven by heat flow from the inner core, organized into rolls by the Coriolis force, generate circulating electric currents, which supports the magnetic field.

Researchers find oldest undisputed evidence of Earth’s magnetic field | University of Oxford

The problem with trying to sustain a belief that Earth is just a few thousand years old, is that scientists keep finding evidence that it is very much older. Here, for example, is a recent paper by Oxford University and Massachusetts Institute of Technology scientists that shows not only the Earth had a magnetic field 3.5 billion years ago, but that it was not hugely dissimilar in strength to the present magnetic field.

To add insult to injury, Earth's magnetic field, and the way it deflects harmful solar radiation away from the surface if often cited by creationists as evidence for their absurd claim that Earth is fine tuned for life, so a god must have fine-tuned it. If that were true, it was fine tuned for life almost 3.5 billion years before creationists believe there was any, and before there was even a universe, let alone solar radiation and Earth.

But then what did the primitive Bronze Age hill farmers who described the universe as a small, flat planet with a dome over it centred on the Middle East in the Bible, know about solar radiation, magnetic fields or the history of the planet? Well, nothing at all, obviously!

Wednesday 24 April 2024

Catholic Sex Abuse - Spain To Compensate Victims of Predatory Catholic Priests

Cardinal Juan Jose Omella
President of the Spanish Conference of Bishops
Spain approves plan to compensate victims of Catholic Church sex abuse. Church will be asked to pay | AP News

After years of ignoring the issue and long after many other European countries had launched enquiries into the systematic sexual abuse of minors by Spain's Catholic clergy and its cover-up and facilitation by senior figures in the Catholic Church, in 2022, the Spanish government finally caved in and commissioned an enquiry by ombudsman Ángel Gabilondo.

The government was forced to act by public outrage following allegations in the newspaper, El País, that more than 1,200 people had been sexually abused by Catholic priests.

A Madrid-based law firm is conducting a parallel inquiry ordered by the Spanish Episcopal Conference, which for years rejected the idea of taking a comprehensive approach to investigating sex abuse.

That commission has now concluded that some 440,000 individuals were sexually abused by people linked to the church, half of whom were clergy. It has recommended that the victims be compensated, and that this compensation should be financed by the Catholic Church.

However, Spain’s Bishops Conference has rejected the plan on the disingenuous grounds that it doesn't compensate victims 'outside the church circle'. In other words, because it doesn't compensate people who were abused by people not connected with the church.

This is the same Bishop's Conference that resisted the idea of an enquiry and refused to launch its own, unlike Churches in many other countries. Now they have suddenly discovered a concern for all victims of sexual abuse, not just their own clergy's victims.

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

Burkholderia pseudomallei, a Gram-negative rod, straight or slightly curved, with bipolar staining
The enemy within: How pathogens spread unrecognized in the body - Biozentrum

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

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

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

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

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

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

Tuesday 23 April 2024

Unintelligent Designer - How Creationism's Idiot Designer Competes With Itself To Overcome The Problems It Designs

Ornate Bella moth, Utetheisa ornatrix
Bella moths use poison to attract mates. Scientists are closer to finding out how – Research News

Imagine a man in your street who designs a brilliant defensive structure to put around your property to keep intruders out, and then invents a brilliant protective suit the intruder can wear so he or she can get through your defensive structure. He then designs an improvement in the defences that overcome the protection the suit provides, and, in a final display of madness, he brilliantly designs a remote control the intruder can use to switch off that improvement and so still burgle your property. He or she then uses the proceeds of the burglary to buy more suits and remote controls to give to friends and acquaintances so they can parasitise you too.

This is exactly the sort of mad inventor that creationists believe designs living organisms and the parasites that predate on them or, in the case of plants, eat their leaves, flowers and seeds. The plant gets given defensive chemicals that deter herbivores from eating them and even kills them if the deterrent doesn't work, and then it redesigns one of the organisms to eat the toxic plant not only with complete impunity, but to help it breed more successfully to produce more organisms to eat the toxic plant.

And it goes one step more and designs the organism so it uses the toxins to defend itself and even attract a mate! All very clever, but you can't help wondering what it’s doing it all for, exactly, and who's side is it on in these wasteful arms races of increasing complexity, like running up a down escalator in order to stand still.

An incomprehensible example of this (incomprehensible in terms of intelligent design; perfectly rational in terms of evolution by natural selection) was revealed a few days ago by researchers from the Department of Biophysics, University of Texas Southwestern Medical Center, Dallas, TX, USA together with colleagues from the Department of Biology, University of Pennsylvania, Philadelphia, PA, USA and the McGuire Center for Lepidoptera and Biodiversity, Florida Museum of Natural History, University of Florida, Gainesville, FL, USA, who have shown how the Ornate Bella moth, Utetheisa ornatrix, detoxifies the deadly toxins, Pyrrolizidine alkaloids, used as a defence against being eaten by the rattlebox plant amongst others.

And, as a further example of idiot design, the rattlebox plant concentrates its toxin in the seeds - which makes them especially attractive to the bella moth caterpillars. A 'deterrent' that encourages predators to eat its seeds!

Monday 22 April 2024

Religion In The USA -The Decline Gathers Pace - Two-Thirds Of Baltimore Catholic Parishes To Close

Baltimore Archdiocese's Proposal Could Cut City Parish Locations by Two-Thirds - The Tablet

In contrast to the view we in Europe sometime have of the USA where fundamentalist religion and far-right Christian nationalism seem to be growing, especially in their political influence, the reality is that religion in the USA is following Europe's lead and losing its grip on the population.

Symptomatic of this decline is the recent announcement that the Catholic diocese of Baltimore, Maryland, is to close about two-thirds of its parishes and amalgamate them with others, because the numbers attending church services has declined too far to make them economic to keep open, with their own priest.

They are now facing a similar problem to that experienced in the UK, and elsewhere in Europe. The biggest problem for the Anglican Church in the UK is what to do with all its unused and boarded-up churches? Many of these are listed buildings, having special historic or architectural significance and the burial grounds are protected by law, so the owners (the C of E) have a legal duty to maintain the buildings that can't be demolished, sitting on land that can't be built on.

In Baltimore, the problem has been getting increasingly acute for several years now. As the Catholic online news magazine, The Tablet, reported on 18 April 2024:

Malevolent Designer News - How Creationism's 'Intelligent Designer' COULD Have Designed Us To Survive A Heart Attack - But Chose Not To

Zebra fish, Danio rerio
Why can zebrafish regenerate damaged heart tissue, while other fish species cannot? – @theU

If you're foolish enough to believe the claims of creationist frauds that we were intelligently designed by an omniscient, omnibenevolent god, then the work of four researchers at Utah University, USA, should be a cause for concern.

They have shown how the zebra fish is 'designed' to survive a heart attack by repairing the damaged cardiac muscle unlike humans and other mammals who replace the damaged muscle with non-functional scar tissue, which can cause several life-limiting problems for those who survive the initial attack.

Just to recap; a heart attack is caused when an artery supplying blood to the heart muscle becomes blocked, so depriving the muscle of oxygen. Unless cleared very quickly, the muscle will die and will be replaced with scar tissue which lacks the contractile ability of cardiac muscle. How much this affects the functioning of the heart will depend on how much muscle was damaged.
How the zebra fish heart is able to repair itself is the subject of an open access paper in the journal Biology Open and of a news release from Utah University:

Sunday 21 April 2024

Malevolent Designer News - How The Monkeypox Virus (MPVX) Was Redesigned To Make It More Contagious

Monkeypox virus (MPXV)
New Research Defines Specific Genomic Changes Associated with the Transmissibility of the Monkeypox Virus | Mount Sinai - New York

Why did the monkeypox virus (MPXV) suddenly become much more contagious in 2022 to transform it from a relatively harmless, low-level infection of humans and other animals into a potential pandemic virus?

Scientists from Mount Sinai, New York, USA, in collaboration with researchers from the Carlos III Health Institute (ISCIII) in Madrid, Spain believe they have worked out the answer to this puzzle - a substantive change in the DNA virus' genome.

Creationists will reject the idea that this change was an evolutionary change driven by environmental selectors, despite the obvious explanation of the observed facts that this explanation offers because their cult dogma states that changes in genomes only happen if caused by their putative intelligent [sic] designer, although, to be fair to creationists, some of them will betray the religious nature of creationism by blaming viruses and these sorts of changes in their genomes on another creator, called 'Sin' to make it compliant with fundamentalist beliefs in a literal Bible.

But these apologists are continually undermined by those fundamentalists who generally, in their kind, caring and compassionate way, greet every new epidemic as their god's punishment for something they don't like. This will usually be some far-right political hobbyhorse in the USA, the way HIV was greeted with great jubilation by Christians as a 'Gay Plague', sent to punish homosexuals, and COVID-19 was declared to be God's punishment on New Yorkers for voting for Democrats.

However, those few creationists intelligent enough to realise they should be supporting the Discovery Institutes efforts to disguise creationism as science, will avoid these excuse, but they are then left with either evolution by natural selection, or intelligent [sic] design, so let's go with those who claim to see their god's hand in these viruses, so at least have managed to avoid the blasphemy of believing in two or more creators, while presenting their allegedly loving god as a pestilential malevolence.

Saturday 20 April 2024

Abiogenesis News - RNA's Hidden Potential & Role In Early Cells

RNA's Hidden Potential: New Study Unveils Its Role in Early Life and Future Bioengineering | Tokyo University of Science

In a recent open access paper in the online journal, Life, a Tokyo University of Science team led by Professor Koji Tamura of the Department of Biological Science and Technology, has given support to the 'RNA World' hypothesis that explains the beginnings of self-replicating organisms as self-catalysing RNA assemblies known as 'ribozymes'.

Ribozymes have the ability to catalyse the production of new ribozymes, so overcoming the 'problem' for abiogenesis that proteins are needed to catalyse the assembly of DNA but DNA is needed to create proteins, leading to a classic 'chicken and egg' paradox. Since ribozymes don't need proteins, this solves the problem.

How Professor Tamura' team did this is the subject of a Tokyo University of Science news release:

Friday 19 April 2024

Creationism in Crisis - How A Small Mutation Made Us Human - And Shows Our Common Origin With Other Apes

A regulatory variant impacting TXB1 expression contributes to the morphology at the base of the skull. (SNP = single nucleotide polymorphisms).
Genetic Variant Identified that Shaped the Human Skull Base|Tokyo Medical and Dental University, National University Corporation

Creationists like Michael J Behe try to fool their fellow cultists that all mutations are 'devolutionary' and move the organism away from some notional idea of created perfection, although perfection for what is never stated. It is left to the parochial ignorance of the reader to fill the gap and conclude that the religious superstition of 'The Fall' must be true, so he can claim his absurd notion is not really Christian fundamentalism in a lab coat like his 'intelligent design' notion, but real science.

The same parochial, ignorant religious fundamentalists will also assume that somehow humans represent the supreme created perfection (how could it be otherwise for those who, with the 'humility' of a religious fundamentalist, see themselves as the perfect creations of a perfect creator?).

So how does that square with the many examples of mutations being what makes humans different to other species, as shown by any comparison of our genome with that of apes such as chimpanzees or bonobos?

Of course, it's biological nonsense to talk of perfection without reference to the environment and how a mutation affects fitness in that environment, and fitness is what the process of natural selection produces. There is no perfect pattern against which to compare what evolution produces, so both Homo sapiens and Pan troglodytes (common chimpanzee) are perfect at being human or common chimpanzee respectively, as is are African elephants, a cabbages, or a bacteria, perfect at being what they are.

And this was demonstrated a few days ago with publication of a paper by a team from Tokyo Medical Dental University (TMDU), the University of Helsinki, and the University of Barcelona who have analysed the genetics of the shape of the base of the human skull and found it to be due to a mutation in a single gene called TBX1. The mutation is a single nucleotide polymorphism (SNP), which means a change in a single letter in the DNA 'code' for a single amino acid. The SNP (“rs41298798”) is in the DNA involved in the regulation of TXB1.

This single mutation allowed the base of our skull to change shape as our brain enlarged as we became more intelligent and more dependent on technology and the cognitive abilities that enabled us to become Homo sapiens.

The team have published their findings, open access, in the Cell Press, American Journal of Human Genetics, the journal of the American Society for Human Genetics, and explain it in a TMDU News release:

Creationism in Crisis - How Interspecies Rivalry Gave Rise To Multiple Hominin Species

Australopithecus sediba
Interspecies competition led to even more forms of ancient human – defying evolutionary trends in vertebrates | University of Cambridge

The gulf between science and creationism continues to widen with the publication of an open access research paper in Nature Ecology & Evolution in which the two authors argue that early hominins speciates as a result of inter-species competition, but not like most vertebrates through competition for niches, but because the evolution of technology enabled species to evolve quickly into new niches with what amounts to memetic evolution, i.e., evolution of cultures which, in an intelligent species can occur much more quickly than the slow, genetic evolution in other species.

In this respect the pattern of early hominin evolution was more like that of beetles evolving on an island.

Creationists, by contrast, as still stuck desperately looking for evidence that all humans are descended from a single pair of humans who were magically made from dirt just a few thousand years ago.

The researchers, Laura A. van Holstein and Robert A. Foley of the Leverhulme Centre for Human Evolutionary Studies, Department of Archaeology, University of Cambridge, Cambridge, UK, explain their research in a Cambridge University new release:

Thursday 18 April 2024

Creationism in Crisis - How People Lived In Caves in Arabia Before, During And After Creationism's Mythical Genocidal Flood

The entrance to Umm Jirsan Cave.
Credit: Green Arabia Project
First evidence of human occupation in lava tube cave in Saudi Arabia – Griffith News

In a stunning, if incidental and unintentional, rebuttal of creationist mythology, a team of palaeontologists led by scientists from Grifith University' Australian Research Centre for Human Evolution (ARCHE), have uncovered evidence of human occupation of caves in Saudia Arabia about 10,000 - 3,500 years ago.

This, of course, as any creationist will pretend isn’t significant, means that humans were living in these caves from before 'Creation Week' right through the mythical global genocidal flood, and beyond, and were completely undisturbed by any of it.

How Science Works - Darwin's Wonderful Worms Revisited

How a little-known clergyman studying worms by candlelight in the 1700s inspired Charles Darwin – but didn’t get the credit he deserved

Almost exactly 10 years ago today, I wrote an article in praise of the last work Charles Darwin wrote about, in 1881, where he showed how earthworms were not the garden pests they had been assumed to be, but how they were essential for creating the soil and how their activity had transformed the landscape. He showed how they were responsible for burying very much of history, transforming the budding science of archaeology.

He also showed how the planet is not a static place, unchanged since its 'creation' like the Christian dogma taught, but a dynamic and changing place where the present has been shaped by natural forces which were also responsible for the history that archaeology and geology were revealing.

So, it's rewarding to write about how Darwin did this research and particularly how he built on the knowledge of those who had gone before him, in the best traditions of science, where knowledge is accumulative and build on the known to discover the unknown and so advance the sum total of human knowledge. The sad thing is that either deliberately, or through forgetfulness in his advanced years, Darwin neglected to give due credit to Rev. Gilbert White.

This is the subject of an article by Kevin Richard Butt, a Reader in Ecology, University of Central Lancashire, UK, published in The Conversation. His article is reprinted under a Creative Commons license, reformatted for stylistic consistency:

Wednesday 17 April 2024

Creationism in Crisis - How Plant Leaves Were Evolving 201 Million Years Before 'Creation Week'

Fossil leaves of Furcula granulifer from the Late Triassic, Greenland, scale bar = 5cm.

© Mario Coiro, Leyla Seyfullah
Seed ferns: Plants experimented with reticulated leaf venation 201 million years ago

Check any plan leaf and it will normally be one of two types - the monocotyledons with parallel leaf veins and the dicotyledons with a network of veins organised around a central vein with regular branches.

But this has not always been so. As a team of researchers at Vienna University, in collaboration with colleagues from the National Museum of Natural History in Stockholm and the Hebrew University in Jerusalem, have discovered, plants seem to have evolved the network pattern of leaf several times over the course of their evolution with most of them becoming extinct fairly quickly on an evolutionary timescale.

Their findings are published, open access, in the journal New Phytologist and explained in a University of Vienna news release:

Creationism in Crisis - How Copy & Paste Errors Created New Genetic Information - 700 Million Years Before 'Creation Week'

Examples of bilaterans
Centre for Genomic Regulation Website

Contrary to creationists dogma that no new genetic information can arise in a genome without god-magic because of some half-baked notion that the Third Law of Thermodynamics, which applies to energy, somehow applies to genetic information, researchers at the Centre for Genomic Regulation (CRG) in Barcelona, Catalunya, Spain, have shown how errors in replication in DNA some 700 million years ago eventually resulted in a vast supergroup of animals (the bilaterans, i.e. animals with bilateral symmetry) including vertebrates (fish, amphibians, reptiles, birds, and mammals), and invertebrates (insects, arthropods, molluscs, worms, echinoderms and many more).

These errors where whole genomes and genes were duplicated, created the condition where the original genes could continue to function while copies of them were free to mutate and produce new genes with new functions, under the control of natural selection which retains anything which is better than what preceded it and quickly eliminate anything which is worse.

Bilaterians are animals that exhibit bilateral symmetry, meaning they can be divided into two equal halves along a single plane. The vast majority of animals on Earth are bilaterians, including many familiar groups such as:
  1. Mammals: Humans, dogs, cats, elephants, and dolphins are all examples of bilaterians within the mammalian group.
  2. Birds: Birds, like sparrows, eagles, penguins, and ostriches, are also bilaterians.
  3. Reptiles: Snakes, lizards, turtles, and crocodiles exhibit bilateral symmetry.
  4. Amphibians: Frogs, toads, salamanders, and newts are examples of bilaterians within the amphibian class.
  5. Fish: Most fish species, including tuna, salmon, sharks, and goldfish, are bilaterians.
  6. Insects: Butterflies, ants, bees, beetles, and flies are bilaterians within the vast group of insects.
  7. Arachnids: Spiders, scorpions, ticks, and mites are bilaterians within the arachnid class.
  8. Mollusks: Snails, slugs, octopuses, and squids exhibit bilateral symmetry.
  9. Annelids: Earthworms, leeches, and marine worms are examples of bilaterians within the annelid phylum.
  10. Echinoderms: While not as obvious due to their radial symmetry as adults, echinoderms like sea stars and sea urchins exhibit bilateral symmetry during their larval stages.
These are just a few examples, but bilaterians encompass an incredibly diverse range of animal life on Earth.
The researchers have published their findings in Nature Ecology & Evolution and have explained it in a news release from the Centre for Genomic Regulation (CRG):

Monday 15 April 2024

Creationism in Crisis - Jumping Jehosaphat! It's Giant Kangaroos 30,000 Years Before 'Creation Week'!

Impression of South-eastern South Australia during the Pleistocene
(~500 thousand years ago)
Peter Schouten
We found three new species of extinct giant kangaroo – and we don’t know why they died out when their cousins survived

Archaeologists have re-assesses the fossils of giant kangaroos that lived in the Pleistocene along with other megafauna such as giant goannas (an Australian lizard) or Megalania, Varanus priscus, that grew to 4 meters (about 13 feet) long and went extinct about 40,000 years ago along with much of the megafauna. One of these kangaroos, the short-faced kangaroo Procoptodon goliah grew to three metres (9.5 feet) and probably weighed over 250 kilograms (about 550 lbs).

Why these large animals went extinct and what part if any the arrival of Homo sapiens played any part in it is a matter of debate, but what is not a matter for debate is whether or not they existed and when. Their discovery is explained by Isaac A. R. Kerr, a Research Assistant in the Palaeontology Laboratory, Flinders University, Australia in an open access article in The Conversation. His article is reprinted here, reformatted for stylistic consistency, under a Creative Commons license:

How Science Works - Tracking How Great Tits In An Oxfordshire Wood Are Responding To Climate Change

Early morning, Wytham Wood
The great tits in this Oxford wood are adapting their breeding times as climate changes – here’s how

This article caught my eye because it concerns the birds in a wood which is local to me - Wytham Wood, near Oxford, to which I have licensed access. This is reputedly the most intensively studied area of woodland in the world, belonging, as it does, to Oxford University.

Wytham Woods form an iconic location that has been the subject of continuous ecological research programmes, many dating back to the 1940s. The estate has been owned and maintained by the University of Oxford since 1942. The Woods are often quoted as being one of the most researched pieces of woodland in the world, and their 1000 acres are designated as a Site of Special Scientific Interest.

The wooded parts of the Wytham Estate comprise ancient semi-natural woodland (dating to the last Ice Age), secondary woodland (dating to the seventeenth century), and modern plantations (1950s and 60s). The fourth key habitat is the limestone grassland found at the top of the hill. Other smaller habitats include a valley-side mire and a series of ponds.

The site is exceptionally rich in flora and fauna, with over 500 species of plants, a wealth of woodland habitats, and 800 species of butterflies and moths.

Through intensive observation over successive years, researchers are able to measure changes in behaviour of species such as the Great Tit, Parus major with some of the best examples of observational biology in the form of research papers. For example, a few years ago a team of researchers showed that the British race of Great tits were diverging from their European relatives with changes in the beaks probably reflecting the fact that we in Britain provide feeding stations for birds to sustain them through the winter much more frequently than other Europeans, so the British Great tits are evolving so they can get the food in the bird feeders in British gardens.

In the following article, ecologist, David López Idiáquez, a Postdoctoral Research Associate in Behavioural and Evolutionary Ecology, University of Oxford, explains how their research is measuring how Great tits are responding to climate change. His article is reprinted here from The Conversation under a Creative Commons license, reformatted for stylistic consistency, with photographs from Internet sources:

Creationism in Crisis - When Earth Was Flooded, According To Creationist Mythology, Australian Aboriginal People Were Making Pots And Campfires And Sailing To Pacific Islands

View across excavation to Blue Lagoon and reef flat.
Photograph: Ian J. McNiven.
Aboriginal people made pottery and sailed to distant offshore islands thousands of years before Europeans arrived

Sometimes you wonder whether creationists ever stop to think whether what they believe is rational, then you realise that most of them are from America where parochial ignorance and cultural chauvinism are the norm. They can believe, for example, that a global flood which left ancient cultures intact and their artifacts just where they left them, and which failed to lay down the predictable global layer of sediment full of jumbled fossils was still a global flood because er... Grand Canyon.

So, news that Australian archaeologists have unearthed potshards from 6,500 years ago in a shell midden which can be accurately dated (unlike potshards), will almost certainly pass unnoticed by the majority of American creationists.

But for those few who are interested in the truth, here is an article by Sean Ulm Sean Ulm, Director, ARC Centre of Excellence for Indigenous and Environmental Histories and Futures, James Cook University, Ian J. McNiven, Professor of Indigenous Archaeology; Chief Investigator, ARC Centre of Excellence for Australian Biodiversity & Heritage, Monash University and Kenneth McLean, Director, Walmbaar Aboriginal Corporation, Indigenous Knowledge describing how they found this evidence. Their article is reprinted here under a Creative Commons license, reformatted for stylistic consistency:

Saturday 13 April 2024

Creationism in Crisis - How Multicellularity Evolved - With New Genetic Information

Green Alaga, Stigeoclonium sp.

Macroalgal deep genomics illuminate multiple paths to aquatic, photosynthetic multicellularity: Molecular Plant

What are the main types of algae and how do they differ? Algae are classified into several main groups based on their characteristics, including pigmentation, cellular structure, and mode of reproduction. The main types of algae include:
  1. Diatoms (Bacillariophyta):
    • Diatoms are single-celled algae characterized by their unique glass-like silica cell walls called frustules.
    • They are typically found in freshwater and marine environments.
    • Diatoms are important primary producers and play a significant role in the global carbon cycle.
  2. Green Algae (Chlorophyta):
    • Green algae encompass a diverse group of algae that are mostly freshwater but also found in marine and terrestrial environments.
    • They contain chlorophyll a and b, giving them a green color, similar to land plants.
    • Green algae can be unicellular, colonial, filamentous, or multicellular, with a wide range of morphologies.
  3. Red Algae (Rhodophyta):
    • Red algae are predominantly marine algae, although some species can also be found in freshwater.
    • They contain pigments like chlorophyll a and various accessory pigments, including phycobiliproteins, giving them shades of red, pink, or purple.
    • Red algae often have complex multicellular structures and are important contributors to coral reef ecosystems.
  4. Brown Algae (Phaeophyta):
    • Brown algae are primarily marine algae, commonly found in cold-water habitats.
    • They contain chlorophyll a and c, along with fucoxanthin, which gives them their characteristic brown color.
    • Brown algae can range from small filamentous forms to large, complex seaweeds like kelps.
  5. Blue-Green Algae (Cyanobacteria or Cyanophyta):
    • Despite being called algae, cyanobacteria are actually prokaryotic organisms, classified within the domain Bacteria.
    • They are photosynthetic and often form colonies or filaments.
    • Cyanobacteria can be found in diverse habitats, including freshwater, marine environments, soil, and even extreme environments like hot springs.
    • Some cyanobacteria can produce toxins under certain conditions, leading to harmful algal blooms (HABs) and posing risks to aquatic life and human health.
These main types of algae differ in their pigmentation, cellular structure, habitat preferences, and ecological roles. While some are beneficial and essential for ecosystem health, others can become problematic under certain conditions, such as nutrient pollution or climate change. Understanding the characteristics and ecological functions of different types of algae is crucial for managing and conserving aquatic ecosystems.
Today’s refutation of creationists dogma comes in the form of an open access paper just published in the Cell Press journal, Molecular Plant. Research biologists have revealed how multicellularity evolved several times independently in algae, and how many of the new genes were acquired initially by viruses.

This gives the lie to creationist claims that new information can't arise in the genome because of some half-baked confusion of information with energy and a nonsensical assumption that new genetic information would need to come from nothing.

And of course, like about 99.99% of the history of life on Earth, it all happened in that very long period of pre-'Creation Week' history between Earth forming in an accretion disc around the sun and creationism's little god creating a small flat planet with a dome over it in the Middle East out of nothing, according to creationist mythology

In information provided by Cell Press ahead of publication, the scientists at New York Abu Dhabi University and Technology Innovation Institute, United Arab Emirates, said:
A deep dive into macroalgae genetics has uncovered the genetic underpinnings that enabled macroalgae, or "seaweed," to evolve multicellularity. Three lineages of macroalgae developed multicellularity independently and during very different time periods by acquiring genes that enable cell adhesion, extracellular matrix formation, and cell differentiation, researchers report April 12 in the journal Molecular Plant. Surprisingly, many of these multicellular-enabling genes had viral origins. The study, which increased the total number of sequenced macroalgal genomes from 14 to 124, is the first to investigate macroalgal evolution through the lens of genomics.

This is a big genomic resource that will open the door for many more studies. Macroalgae play an important role in global climate regulation and ecosystems, and they have numerous commercial and ecoengineering applications, but until now, there wasn't a lot of information about their genomes.

Alexandra Mystikou, co-first author
Division of Science and Math
New York University Abu Dhabi, Abu Dhabi, UAE.
Macroalgae live in both fresh and seawater and are complex multicellular organisms with distinct organs and tissues, in contrast to microalgae, which are microscopic and unicellular.

There are three main groups of macroalgae -- red (Rhodophyta), green (Chlorophyta), and brown (Ochrophyta) -- that independently evolved multicellularity at very different times and in very different environmental conditions.

Rhodophytes and Chlorophytes both evolved multicellularity over a billion years ago, while Ochrophytes only became multicellular in the past 200,000 years.

To investigate the evolution of macroalgal multicellularity, the researchers sequenced 110 new macroalgal genomes from 105 different species originating from fresh and saltwater habitats in diverse geographies and climates.

The researchers identified several metabolic pathways that distinguish macroalgae from microalgae, some of which may be responsible for the success of invasive macroalgal species.

Many of these metabolic genes appear to have been donated by algae-infecting viruses, and genes with a viral origin were especially prevalent in the more recently evolved brown algae.

They found that macroalgae acquired many new genes that are not present in microalgae on their road to multicellularity.

For all three lineages, key acquisitions included genes involved in cell adhesion (which enables cells to stick together), cell differentiation (which allows different cells to develop specialized functions), cell communication, and inter-cellular transport.

Many brown algal genes associated with multicellular functions had signature motifs that were only otherwise present in the viruses that infect them. It's kind of a wild theory that's only been hinted at in the past, but from our data it looks like these horizontally transferred genes were critical factors for evolving multicellularity in the brown algae.

David Nelson, co-first author
Division of Science and Math
New York University Abu Dhabi, Abu Dhabi, UAE.
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