F Rosa Rubicondior: Evolution
Showing posts with label Evolution. Show all posts
Showing posts with label Evolution. Show all posts

Tuesday 12 March 2024

Malevolent Design - How The Malaria Parasite is 'Designed' To Evolve And Outwit Medical Science


The malaria parasite generates genetic diversity using an evolutionary ‘copy-paste’ tactic | EMBL

Devotees of creationism’s divine malevolence would be conflicted by this news if they understood it, because it shows the creative genius of any intelligent designer who could come up with this system, but, it looks like it did so (if you believe it couldn't happen naturally) by setting up an evolutionary process that creationists are obliged by dogma to believe doesn't work.

The news is that the organisms that causes malaria, Plasmodium falciparum, is 'designed' to quickly find a way to overcome the anti-malarial drugs medical science has developed to cure people suffering from it and to prevent others from getting malaria, by evolving very quickly.

The discovery was by researchers at European Molecular Biology Laboratory's (EMBL’s) European Bioinformatics Institute who have identified a mechanism of ‘copy-paste’ genetics that increases the genetic diversity of the parasite at accelerated time scales. This helps solve a long-standing mystery regarding why the parasite displays hotspots of genetic diversity in an otherwise unremarkable genetic landscape. Copy-paste' is a way of doing something creationists insist is impossible without the aid of god-magic of increasing the genetic information in a genome and making it available for evolution by mutation and selection without any loss of function in the original copied genes.

The team have recently published their finding in the open access journal PLOS Biology and describe it in an EMBL news item:

Unintelligent Malevolence - Pathogens 'Designed' to Beat Medical Science In Two Different Ways


Acinetobacter baumannii seen under a scanning electron-microscope

Escherichia coli
What makes a pathogen antibiotic-resistant? | Sanford Burnham Prebys

One of todays examples of the stupidity of creationism is something of a novelty. Usually, by applying the central tenets of creationism, any putative designer of living things like parasites either appears malevolent (and sometime it has to be said, malevolent at a near genius level in the ways it finds to make us and other animals sick) or it looks incompetent in that its 'solutions' are often to problems of its own making and more often than not to solutions it designed for one side of an arms race which it now trets as problems for the other side.

But today's example can only be described as an example of incompetent malevolennce, as creationism's putative designer, faced with the same 'problem' of medical science developing antibiotics effective against two different species of pathogen, set about designign two completely different 'solutions' to this problem. - Talk about re-inventing the wheel!

The pathogens are: Escherichia coli and Acinetobacter baumannii.

Creationists will probably be familiar with Escherichia coli (E. coli) because they believe their guru, Michael J Behe, 'proved' their god exists by claiming (falsely) that E. coli's flagellum must have been intelligently designed because he didn't know it evolved out of a pre-exiting structure and couldn't think how else it could have evolved. But then such is the standard of creationist apologetics!

What Behe had unwitting done was destroy the traditional excuse creationists use to explain pathogens like E. coli by blaming them on another 'designer' called 'Sin' which somehow creates living organisms although the creationit designer god is the only entitiy capable of designing livign things, so any example of 'intelligent design, real or imaginary, if 'proof' of this designer god's existance.

So, what creationists are now left with is an E.coli with a flegellum designed by their god to make it better at making us sick, and now resitant to antibiotics to help it win against medical science trying to prevent it makign us sick!

But what creationists are less likely to be familiar with is the pathogen, Acinetobacter baumannii, so here is a little background:

Monday 11 March 2024

Unintelligent Design - RuBisCO Is Slowly Evolving - And Becoming Even More Embarrassing For Any Creationist Who Understands It


The world’s most prolific CO2-fixing enzyme is slowly getting better | University of Oxford

The world’s worst enzyme, ribulose-1,5-bisphosphate carboxylase/oxygenase, or RuBisCo as it is known, has featured in these blog posts several times and it described in my book, The Unintelligent Designer: Refuting the Intelligent Design Hoax as an example of the lack of intelligence in biological systems, and, as such, why it would be a major embarrassment to creationists - if they understood it.

Briefly, RuBisCo is one of the most ancient enzymes known and became an essential component of photosynthesis early on in the history of life on Earth when the first cyanobacteria evolved the ability to use the energy from sunlight to fix the carbon in atmospheric carbon dioxide (CO2) to build the sugar glucose. Eventually, these photosynthesising cyanobacteria became incorporated into plant cells as the chloroplasts to produce the green plants at the base of most food chains. Because it is so inefficient, it quickly became probably the most abundant enzyme on Earth, making up with quantity what it lacked in quality.

But, evolution, unlike good intelligent design, is a one-way, utilitarian process in which whatever works better than preceded it will be retained and will provide the next basis for further evolution, because evolution has no mechanism to scrap a bad design and start again as any backward step will inevitably be worse, so will be quickly eliminated.
Tell me all about RuBisCo and why it's so inefficient. RuBisCo, or ribulose-1,5-bisphosphate carboxylase/oxygenase, is an enzyme crucial for the process of carbon fixation in plants, algae, and some bacteria. It catalyzes the first major step of the Calvin cycle, which is the primary pathway for carbon dioxide fixation in photosynthesis. Despite its importance, RuBisCo is often considered inefficient for several reasons:

Malevolent Design - How a Bacterium Carries a Virus That Selectively Kills Male Insects And Only Allows Infected Females To Breed


How does a virus hijack insect sperm to control disease vectors and pests? | Penn State University

Wolbachia are a genus of bacteria that form a symbiotic relationship with about 50% of arthropod species, including insects and spiders but they can also manipulate the species for their own ends (in terms of breeding success). They are aided in this by a virus which is incorporated in their genome which has been shown to join forces with Wolbachia to ensure their own reproductive success in the form of females infected with the virus-bearing Wolbachia.

So completely have Wolbachia integrated with insects that one species of fruit fly has the entire Wolbachia genome incorporated into its own genome, making it, biologically, both bacterium and fruit fly.

One way Wolbachia ensure their own survival at the expense of the species of insect they infect is by making the sperm and egg incompatible if the female is not also a carrier of the right species of Wolbachia. And, to be on the safe side, two proteins produced by the virus break the sperm's DNA so any resulting embryo will be defective and will fail to develop. This ensures that only the females carrying the infection can breed, so increasing the Wolbachia and its virus in the gene pool.

The team who discovered this nasty little virus and how it acts selfishly, was co-led by Professor Seth R. Bordenstein, of the One Health Microbiome Center at Pennsylvania State University. They have published their findings in Science and described it in a Penn State News item.

But first, a little background on Wolbachia:

Sunday 10 March 2024

Covidiot News - Just Because You Haven't Had COVID-19 Yet, Doesn't Mean You Won't!


Haven't had COVID yet? It could be more than just luck

There are some scary questions for creationists at the end of this article. They follow on naturally from what's being discussed, so creationists should probably avoid reading too far, unless they have a responsible adult with them.

This article from The Conversation is from May 2022, when we were into the second year of the COVID-19 pandemic and most vulnerable people had had the two-step vaccinations and many would have had the spring booster. At that point neither me nor my partner had had COVID-19, which we put down to rigorously following the recommendations regarding mask-wearing, social distancing, hand washing, etc. and had tried to reduce our vulnerability to the sever forms of it by losing about 3 stone in weight and, in my case, getting my blood pressure under control with medication. We also tried to ensure our immune systems were healthy by taking vitamin D3, vitamin C, zinc and iron supplements.

In the early days of the pandemic, even before the official restrictions on social contact, we had observed the basic rules of hygiene and everyone who came into the house used hand-cleanser at the front door. I had even managed to obtain a supply of face-masks and plastic gloves online, which we wore at all times outside the house. Every package that was delivered to the house was left for several hours before we touched it, and all our weekly shopping was delivered or bought with click and collect. Delivered bags were left for four hours before unpacking. And we took weekly tests just in case we had it asymptomatically. All that might seem a little over the top now, but we were vindicated as events were to prove.

We put the fact that we hadn't caught it by mid-2022 down to our preventative measures, not to luck or genetics - a view that was vindicated last year when we both came back from a two-week vacation in France with a mild form of COVID-19, despite having had all the boosters on offer. We probably picked it up in a crowded airport or on the plane, where all the social distancing measures had been forgotten and even face masks were no longer worn. We both felt like we had a mild case of flu for a couple of days and after a week we were testing negative. Had we contracted it in Spring 2020, the outcome would probably have been very different as we had no immunity, and both had three of the risk-factors - overweight, high BP and over 70. In addition, my partner had had a mastectomy and was receiving treatment for breast cancer.

One reason you can't ever be sure that you won't catch COVID-19 is because the virus keeps mutating to produce new variants so, even if you were fortunate enough to have natural or acquired immunity to the variants so far, it is quite possible that the next or subsequent variants will have evolved a way round it. The following chart from the UK NHS, shows the rise and fall of the main variants over the course of the pandemic:
But still, a few people managed to stay free from the virus. In the following article, reprinted from The Conversation under a Creative Commons license, Lindsay Broadbent, Research Fellow, School of Medicine, Dentistry and Biomedical Sciences, Queen's University Belfast, explains why. Her article has been reformatted for stylistic consistency:

Saturday 9 March 2024

Creationism in Crisis - Geobiologists Discover The Cause of Earth's First Mass Extinctions Event - 550 Million Years Before 'Creation Week'


Impressions of the Ediacaran fossils Dickinsonia (at center) with the smaller anchor shaped Parvancorina (left) in sandstone of the Ediacara Member from the Nilpena Ediacara National Park in South Australia.
Photo: Scott Evans.
Geobiologists shine new light on Earth’s first known mass extinction event 550 million years ago | VTx | Virginia Tech

A big problem for Creationists, especially those who believe the Bible was written by an infallible creator god, so think Earth is just a few thousand years old, is that science keeps finding evidence that Earth is billions of years old, and finding fossils of the life-forms that were around then.

As though that wasn't refutation enough, a team of scientists from Virginia Tech have now explained the mass extinction that wiped out most of these early life forms several billion years ago - giving the lie that they were intelligently designed by a god with the ability of foresight. Such a god would have known about the future mass extinctions and either prevented it, designed his creations to survive it or at least waited till it was safe to create things. Creating things to go extinct is not the act of an intelligent or sane creator.

This mass extinction appears not to have been a sudden event, such as that that resulted in the extinction of the non-avian dinosaurs and large marine reptile predators, but to have occurred in two phases that resulted in a loss of about 80% of species and separated by about 10 million years.

But before creationists get over-excited, this does not mean all the Ediacarans were extinct at the Cambrian 'explosion' so the Cambrian biota had no ancestors. It means that there were still about 20% of the Ediacaran biota to evolve over the 6 million years of the Cambrian 'explosion' into the Cambrian biota.

The Ediacaran mass extinction was probably caused by falling Oxygen levels as Ediacarans that had evolved large mass to surface-area ratios suffered from a loss of oxygen more so than those which had retained a smaller mass to surface area ratio.

How this mass extinction was identified and related to changes in global oxygen levels was the subject of an open access paper in PNAS and a Virginal Tech News item:

Creationism in Crisis - Earth's Oldest Forest Was In Present-Day Dorset, UK - 390 Million Years Before Creationism's 'Creation Week'


Cliffs of the Hangman Sandstone Formation, where many of the fossils were found.
Credit: Neil Davies
Earth’s earliest forest revealed in Somerset fossils

Archaeologists have found what are believed to be the remains of the earliest forest so far discovered in Devonian sandstone rocks dated to 390 million years ago, which makes them 4 million years older than the previous record found in New York State, and means they were living almost 390 million years before creationism's 'Creation Week' when their god decided to create a small flat planet with a dome over it, centered on the Middle East.

The fossils were discovered in coastal cliffs near Minehead, Dorset, England in what is known as the Eifelian Hangman Sandstone Formation and consist of primitive trees which were ancestral to today's trees but looked more like palm trees. The discovery is the subject of a paper in the Journal of the Geological Society and a news release from the University of Cambridge, UK.

First a little about this rock formation:

Creationism in Crisis - How Genomic Imprinting Evolved - Unintelligently


Revealing the evolutionary origin of genomic imprinting 
Caenorhabditis elegans

Genomic imprinting is the process by which genes are suppressed by epigenetic settings that differ depending on whether the genes come from the father or the mother in a sexually-reproducing species.

This is an example of the sort of Heath Robinson machine which a natural, mindless evolutionary process can and does produce and which distinguishes evolved systems from intelligently designed processes. It comes from the fact that multicellular organism uses the same method to replicate their cells as their single-celled ancestors used, yet only need a small selection of the genes depending on how specialised the particular cells are.

But the reason for genomic imprinting involves something even more embarrassing to any creationists who understand it - it probably evolved out of an arms race not between the organism and a foreign parasite but between the organism and one of its genes that had gone rogue and turned into a 'jumping' gene or 'selfish genetic element':
What exactly are 'selfish genetic elements' and what do they do? Selfish genetic elements are DNA sequences that have evolved to enhance their own transmission to the next generation, often at the expense of the organism's overall fitness. These elements can manipulate various cellular and reproductive processes to increase their own propagation within a population, sometimes even if it is detrimental to the host organism.

One well-known example of selfish genetic elements is transposable elements, also known as jumping genes. These DNA sequences have the ability to move or copy themselves within the genome, potentially disrupting genes or regulatory sequences in the process. While transposable elements can sometimes contribute to genetic variation and evolution, they can also cause harmful mutations or genomic instability.

Another example of selfish genetic elements is meiotic drive elements. These elements bias their own transmission during meiosis, the process by which gametes (sperm and eggs) are formed. Meiotic drive can result in the preferential transmission of one allele (variant of a gene) over another, leading to distortions in genetic inheritance patterns within a population.

Selfish genetic elements can have significant implications for evolutionary processes, population genetics, and genome stability. They can influence patterns of genetic diversity, contribute to speciation, and even drive the evolution of complex biological systems. However, they can also pose challenges for organisms by causing genetic disorders or reducing overall reproductive success.
In the case of the nematode, Caenorhabditis elegans, this arms race has produced a truly bizarre result, and something only an unintelligent, mindless designer, or a malevolent designer, could come up with, known as toxic ascaris, or TAs:

Friday 8 March 2024

Creationism in Crisis - Like Humans, Bumblebees Learn Through Social Interaction And May Have Cumulative Culture


Buff-tailed Bumblebee, Bombus terrestris
Source: Wikipedia.
Bees master complex tasks through social interaction - Queen Mary University of London

A sacred Tenet of creationism is that we humans are a special creation by the creator of the universe who made everything just for us. They point to the many 'unique' traits and abilities of humans as evidence of this - the ability to teach and learn, to form cultures, even walking upright are frequently cited as examples. It's also a sacred Tenet of creationism that anything which might refute the sacred tenets of creationism must be ignore, hand-waved aside or misrepresented but never, ever acknowledged for what it is - a refutation of creationism.

So, we can expect one or more of those tactics for handling the cognitive dissonance that news that bumble bees can teach and learn and so have at least the basis for forming cumulative cultures. The news itself comes in the form of an open access research paper in Nature by a team Led by Dr Alice Bridges and Lars Chittka, Professor of Sensory and Behavioural Ecology at Queen Mary University of London.

The team showed that a complex, two-step task, which needed to be performed to receive a reward in the form of a sweet liquid could be learned by bees who were allowed to watch a trained 'demonstrator' perform the task. The bees not only learned how to perform the steps involved but that there was a reward to be had for doing so.

The 'demonstrators' had previously been trained by giving intermediate rewards as each stage was completed successfully, which were eventually withdrawn, leaving only the final reward. The experiment and its significance are explained in a Queen Mary University news release:

Unintelligent Design - New Species Of Deep-Ocean Worm - But What Is It For, Exactly?


New Deep-Sea Worm Discovered at Methane Seep off Costa Rica | Scripps Institution of Oceanography

Fig 1. Pectinereis strickrotti gen. nov., sp. nov. in life.

A, B, D. Several epitokous males swimming near methane seeps of Mound 12 (~1,000 m depth) of the Costa Rica margin and videoed via the submersible DSV Alvin. A. A frame grab from a video taken on Alvin dive 4503 on Feb. 4, 2009. B and D. Frame grabs from video taken on Alvin dive 4987 on Nov. 2, 2018. C. A fragment of an atokous infaunal female was collected at the same depth and locality via sediment pushcore on Alvin dive 4984 on Oct. 30, 2018. A white egg ~350 μm in diameter is visible on the exterior. Scalebar 1 mm. E. An epitokous male swimming near methane seeps of Parrita Scar (~1,000 m depth) of the Costa Rica margin. The specimen was initially caught via slurp with the ROV SuBastian (dive S0218, Jan. 11, 2019) but escaped.

Images A, B, D, courtesy of Woods Hole Oceanographic Institute. E, courtesy of Schmidt Ocean Institute.
One of the hallmarks of good intelligent design is that the designed object must be designed for a purpose. No intelligent designer is going to waste time making something that doesn't have any use. Even a decorative use is a function. As the designer William Morris said, "Have nothing in your house that you do not know to be useful, or believe to be beautiful.", but creationism's designer seems to just design things for the sake of it - half a million different beetles, for example. And now we have the example of a deep-ocean worm that appears to have no other purpose than to make more deep-ocean worms.

It's almost exactly like these different organisms are being designed by a mindless, natural process without a plan and no sense of purpose!

According to creationist superstitions in Genesis, every living thing on Earth was created for the benefit of mankind, and, incidentally, named by Adam (as though Adam would have had enough time to name every living species!). So, a challenge to creationists is to tell us what these deep-ocean worms are for in terms of their utility value for humans, and how did Adam dive that deep to name them?

Its discovery if the subject of an open access paper in PLOS ONE and is described in a Scripps Institute for Oceanography news release:

Thursday 7 March 2024

Creationism in Crisis - Evolution of Porcini Fungus


A tale of terroir: Porcinis evolved to the local environment – @theU
Structure of Fungi
This illustration is a little misleading because mycelia are often much larger than any of their mushrooms that appear on the surface of the soil or tree stumps. Fungi can grow up to a half a mile of the thread-like hyphae a day. In fact, the largest known organism on the planet is the Humongous Fungus (Armillaria ostoyae) in The Malheur National Forest, Oregon, measuring 2,385 acres (3.72 square miles) in area. It is estimated to be between 1900 and 8650 years old.
Photo credit: FoodPrint.org
The edible porcine fungus (Boletus edulis) also known as the boletus or penny bun is highly prized culinary delicacy throughout much of Europe. However, there is something strange about it evolution, especially in North America, according to a new report in the journal New Phytologist.

Creationists should note here that the scientists who produced the report see this 'problem' entirely within the Theory of Evolution by Natural Selection (TOE). The strangeness is not a problem for the theory but an example of how a fundamental principle of the theory - environmental selection - operates in North America.

The 'problem' is that while Boletus edulis exists in North America as a number of different varieties and genetically distinct populations, probably caused not so much by geographical isolation as environmental adaptation, albeit with regular ingress from surrounding populations, In Eurasia, a single genetic lineage dominates from Spain to Georgia to Scandinavia, so the interesting question is why does is the species genetically continuous in Eurasia but fragmented in North America; what is the difference between the two landmasses that causes this difference.

The Eurasian and North American populations are believed to have become separated during a period of climatic change and the onset of glaciation, 1.62–2.66 years ago. Attempts to segregate populations of Boletus edulis into distinct species based on phenotype have foundered on the genetic evidence, illustrating how small genetic differences can give large phenotypic differences and how a species in the process of speciating passes through a stage at which the diverging populations have not diverged sufficiently to qualify as new taxons because the practice of taxonomy tries to fit a continuous process into a series of distinct events.

The 'problem' is the subject of a free access paper in the journal New Phytologist by Keaton Tremble and Bryn T. M. Dentinger from Utah University, Utah, USA. together with J. I. Hoffman from Bielefeld University, Germany, and was described in a University of Utah press release:

Creationism in Crisis - 500 Million Year-Old Fossils Reveal the Answer to an Evolutionary Riddle


500 million year-old fossils reveal answer to evolutionary riddle | EurekAlert!

It must be galling to the leaders of the Creationist cults when science closes yet another gap and casually refutes the misleading claims they have fooled their cult followers with. It's much easier for the frauds to play to the parochial ignorance and childish thinking of their followers who will always assume that if science can't explain something, the locally popular god must have done it, ignoring the false dichotomy fallacy underpinning that deception.

Some of the gaps are artificial, obviously, being created by Creationists from misrepresentations of the actual science, such as claiming there are no transitional fossils showing, for example, a half chimpanzee - half human, but some of them are genuine gaps in the fossil record, although these tend to be ignored by creationist frauds because it would require a detailed knowledge of the evidence to appreciate where the real gaps are, and a detailed knowledge of the evidence is something no Creationist can afford to have.

One such gap, until now, was the early evolution of skeletal animals. The first fossils of skeletal animals appeared in the fossil record 550-520 million years ago during the so-called the Cambrian Explosion, which must be one of the slowest explosions on record, occurring over several tens of millions of years, but nevertheless a period of rapid evolution and diversification into different body-plans in the early history of multicellular organisms.

Many of these early fossils are simple hollow tubes ranging from a few millimetres to many centimetres in length. However, what sort of animals made these skeletons was almost completely unknown, because they lack preservation of the soft parts needed to identify them as belonging to major groups of animals that are still alive today.

Now though, a team of palaeontologist led by Dr Luke A. Parry of the Department of Earth Sciences, University of Oxford, Oxford, UK, Dr Xiaoya Ma and PhD student Guangxu Zhang, of the Institute of Palaeontology, Yunnan University, Kunming, People's Republic of China, and Dr Jakob Vinther from the Schools of Earth Sciences and Biological Sciences, University of Bristol, UK have analysed a collection of exceptionally well preserved fossils from 514 million years ago that include four specimens of Gangtoucunia aspera with soft tissues still intact.

Just to clarify that , soft-tissue term, before Creationist quote miners misrepresent it: fossilised soft tissue is not soft. It simply means the soft tissue was preserved long enough for it to become mineralised, just as bones, shells and teeth become mineralised in fossils of hard tissue. It is not evidence that these fossils are just a few thousand years old, like Creationist fraud claim dinosaur soft tissue fossils are (they are not soft either, by the way).

Before long, we can expect Creationists to either be claiming these 'soft tissues' have been carbon-dated and found to be recent, or that they haven't been carbon-dated because the scientists were afraid they would be found to be recent!

As the Oxford University News release explains:

Wednesday 6 March 2024

Creationism in Crisis - Earliest Toothless Bird From 120 Million Years Ago


Imparavis attenboroughi, a 'strange bird' named after Sir David Attenborough, British broadcaster and naturalist
Fossil named “Attenborough’s strange bird” was the first of its kind without teeth - Field Museum

It seems every week is a bad week for creationists, yet the wackadoodle cult staggers on, albeit with dwindling numbers, managing as always to ignore anything that shows their childish superstition to be wrong.

On top of the recently-reported predatory marine lizard, from 66 million years ago, we now have the earliest bird without the teeth of its enantiornithine ancestors. The enantiornithines were a diverse class of avian dinosaurs that went extinct 66 million years ago following the meteor impact that killed most of the dinosaurs. Only the ornithuromorphs survived, for reasons not completely understood, and they gave rise to all modern birds.

Creationism in Crisis - Giant Sea Lizards From 66 Million Years Before 'Creation Week'


Fossil skull of Khinjaria acuta
Reconstruction of the skull of Khinjaria acuta
Dr. Nicholas R. Longrich
Fossils of giant sea lizard show how our oceans have fundamentally changed since the dinosaur era

Creationists only have themselves to blame. By insisting that Earth is only 6-10 thousand years old, they are consigning the vast majority of Earth’s 3.8-billion-year history to the pre-'Creation Week' period, before they believe Earth Existed.

So, they then need to perform the most ludicrous of intellectual gymnastics to avoid dealing with all the evidence that they are wrong about the age of Earth and wrong about their denial of what else that evidence shows. For example, there is no way a 66-million-year-old fossil of a marine lizard could be assimilated into creationist superstition, so their only recourse is to devise a way to dismiss it. Favorite tactics are straight denial; bear false witness against the scientists by impugning their honesty and professional integrity; claim, without any evidence to support it, that the dating methods were so flawed they somehow made 10,000 or less look like 66 million.

But the fact remains, no matter that creationists stamp their feet and cover their eyes and ears and demand the Universe changes to conform to their requirements, there were orca-sized marine lizards in the seas 66 million years ago.

This is explained in a recent paper by researchers from the University of Bath in the UK, the Marrakech Museum of Natural History, Morocco, the Museum National d’ Histoire Naturelle (NMNH) in Paris, France, Southern Methodist University in Texas, USA, and the University of the Basque Country, Bilbao, Spain. Their paper is published in Cretaceous Research and explained in a Bath University news release.

First, a little background on the dating of the phosphate deposits in Morocco where the fossils were found:

Tuesday 5 March 2024

Abiogenesis News - New Evidence For The 'RNA World' Hypothesis


Stylized rendering of the full-length hammerhead ribozyme RNA molecule
Source: Wikipedia
Modeling the origins of life: New evidence for an “RNA World” - Salk Institute for Biological Studies

On way of looking at cellular life is that it is based on RNA, not DNA. In that model, DNA is RNA's data store. All the functional processes that DNA codes for are first transcribed into RNA and short lengths of RNA still regulate some of the cell processes. RNA can even act as a catalyst playing the role normally performed by protein enzymes - proteins that are themselves transcriptions of RNA triplet codes for amino acid sequences.

On that model, early self-replicating systems were based on RNA, and DNA was late to the game.

Now three researchers at the Salk Institute for Biological Studies, La Jolla, California, USA, have shown how such a system could have bootstrapped from simple, self-catalysing lengths of RNA which not only self-replicate but can continue to do so even when there are variations stemming from faulty replications. This system would have created the variation needed for Darwinian evolution by natural selection as some variant performed better in terms of competing for resources and ultimately making more copies, so coming to predominate in the pool of RNA-based organisms.

How the scientists discovered this is the subject of a research paper in PNAS which sadly is behind a paywall with only the abstract and statement of significance freely available. It is also the subject of a news release from the Salk Institute.

Since the team refer to an RNA structure known as the 'hammerhead ribozyme', it might help to understand a little about it first:

Creationism in Crisis - A Mystery In Plant Evolution - 125 Million Years In The Making In That Long Pre-'Creation Week' History Of Life On Earth



A 'Ginormous' tomato produced by an unregulated CLV3 gene.

An evolutionary mystery 125 million years in the making | Cold Spring Harbor Laboratory

In an example of one of those lovely gaps in the record of the evolution of a species into which creationists try to shoehorn their ever-shrinking and increasingly homeless little god, there is something about the evolution of tomatoes and Arabidopsis thaliana that scientists can't yet explain.

But the problem for creationists is that this gap is somewhere in the evolutionary history of these plants that occurred almost 125 million years before creationism’s god decided to create a small flat planet with a dome over it to keep the water above the sky out, centred on the Middle East, in what creationists like to call 'Creation Week'.

The problem comes from the fact that what creationists think is a science and history text book was written by ignorant people who knew nothing of the world outside their small part of it and who had no idea about the history of the planet or of life on it, so they wrote an imaginative story to fill the gap in their knowledge and understanding, and, quite understandably, got almost every aspect of it complete wrong.

And of course, they would never have imagined that one day someone almost as ignorant as they were, would gather their tales into a book and declare it to be the inerrant word of a god - an idea that would be hilarious if it wasn't taken seriously by adults who can become dangerously violent when their superstition is questions.

The mystery that Cold Spring Harbor Laboratory (CSHL) biologists have uncovered is that sometime during the last 125 million years, tomatoes and Arabidopsis thaliana plants experienced an extreme genetic makeover. Just what happened remains unclear. But the mystery surrounds CLV3, a gene key to healthy plant growth and development.

CLV3 controls the growth of fruit in these plants and, if uncontrolled will result in large, even gigantic, fruits, so there is an evolutionary trade-off between a few large fruits and lots of smaller fruits. The mystery is just how and why this balance was achieved differently in two distantly-related plants.

As the CSHL press release explains:

Saturday 2 March 2024

Unintelligent Design - The Heath-Robinson Workaround For A Design Fault In The Immune System


The “switch” that keeps the immune system from attacking the body - EPFL

A Machine for Testing Golf Drivers - William Heath-Robinson
A characteristic of designs by creationism's putative intelligent designer, is the needless complexity which often arises because earlier solutions were suboptimal and either didn't work very well or tended to cause problems that needed to be mitigated with another layer of (often suboptimal) complexity.

This is also a characteristic of systems 'designed' by a mindless natural process with no power or mechanism for scrapping a suboptimal design and starting again and no ability to predict the future and design for problems which will arise later.

In fact, what creationists think is evidence of a supreme intelligence, more often seems to resemble the designs of the British cartoonist and eccentric designer, William Heath-Robinson, who was famous for his machines designed to solve every-day problem, which were invariably far more complex than they need have been, and which incorporated everyday objects such as umbrellas, full coal-scuttles for counter-weights, lengths of knotted string and stepladders balanced on upright pianos to give them enough height. Take away any of these unlikely components and the whole machine would fail, in an almost perfect metaphor for how evolution can exapt pre-exiting structures from other processes and structures for novel functions, to give the appearance of irreducible complexity.

And yet they work, or at least look as though they would if anyone ever made one.

An example of a Heath-Robinson machine in mammalian 'design' was revealed by a scientists working at the Swiss École polytechnique fédérale de Lausanne (EPFL), who have discovered how the body prevents the immune system from attacking itself.

But, as the very many auto-immune diseases show, this system is far from perfect and frequently fails, sometime with serious, even fatal, consequences.

But the whole immune system is only needed because something designed pathogens such as bacteria, viruses and other parasites, apparently to attack us and make us sick in the first place. Parasites are a source of conflict for creationists who have to believe both that the putative designer god is the only entity capable of designing living things, and that something else created parasites because their god wouldn't do such a thing, and both that their god is omnipotent, but powerless against that other designer.

So, what is this mechanism the EPFL researchers have discovered?

Their findings are the subject of an open access paper in Nature and is explained in an EPFL news release:

How Science Works - A Fossil Whale Is Not What Was Thought - But It Still Refutes Creationism!


Size comparison of a modern blue whale (Balaenoptera musculus) and the extinct Perucetus colossus, known from a fossil discovered in Peru.

Image by Cullen Townsend (https://www.cullentownsenddesign.com/)
Slimming Down a Colossal Fossil Whale | UC Davis

Scientists may have got it wrong when they thought they had the fossilised remains of the heaviest thing that ever lived, in the form of a 39 million-year-old fossil whale from the Peruvian Middle Eocene, which they called Perucetus colossus.

But, before creationists get over-excited, thinking it's the 30 million years they got wrong, they need to read on; it isn't the age they got wrong, but the estimated mass.

A new analysis by palaeontologist at the University of California Davis has put Perucetus colossus back into the same range as modern whales and lighter than the blue whale, which retains its position as the largest and heaviest organism ever to exist on Earth, dwarfing even the largest dinosaurs.

How they went about it is the subject of an open access paper in PeerJ and a news release from UC Davis:

Friday 1 March 2024

Malevolent Designer News - How Creationism's Divine Malevolence Is Adapting The Avian Flu Virus to Kill Marine Mammals


Avian Influenza Virus Is Adapting to Spread to Marine Mammals | UC Davis

Elephant seals lie dead on a beach in Argentina following an outbreak of avian influenza in the region.
Photo: Maxi Jonas.
As an example of creationist double-think and intellectual bankruptcy, their attitude toward parasites like viruses is a classic:
  • "Only God is capable of designing organisms, so "Look at the trees!" and "What about irreducible complexity?"
  • "Something else created parasites like bacteria, worms and viruses, because God wouldn't do something like that!"

Simultaneously committing blasphemy and refuting their own argument from teleology!

I wonder then how that rarest of animals, the intellectually honest creationist copes with the news that the creator of the avian flu virus, H5N1, is in the process of adapting it to kill marine mammals such as elephant seals, just as it adapted the SARS-CoV-2 virus from a bat virus to one that could kill humans and cause economic collapse.

Evidence that it is doing so, if you believe viruses are created and don't evolve naturally, which dogma forbids a creationist from believing, comes in the form of a study by scientists from University of California, Davis, and the National Institute of Agricultural Technology (INTA) in Argentina. The study, the first genomic characterization of H5N1 in marine wildlife on the Atlantic shore of South America, is published in the journal Emerging Infectious Diseases and is described in a UC Davis news release:

Thursday 29 February 2024

Malevolent Designer News - Creationism's Divine Malevolence Is Still Victimising Frogs


Foothill yellow-legged frog, Rana boylii

Photo: Rebecca Fabbri/USFWS
Scientists assemble a richer picture of the plight and resilience of the foothill yellow-legged frog | The Current

Almost unnoticed by the general public and noticed only by biologists and wildlife conservationists, is a pandemic far more deadly than the Covid-19 pandemic, or even the Medieval Black Death.

It kills a very high percentage of its victims, has already exterminated whole populations of frogs and other amphibians, and has contributed significantly to the global mass extinction currently underway.

It is, of course, the chytrid fungus Batrachochytrium dendrobatidis, which, along with a closely-related fungus, B. salamandrivorans, causes the fatal disease, chytridiomycosis, in frogs and other amphibians.

As an example of the work of creationism's divine malevolence, it takes some beating for its sheer malevolent nastiness. It infects the skin of these amphibians, through which they breath, and causes it to thicken and fail as a respiratory organ, leading to suffocation, multiple organ failure and death. Here is how I described it in my illustrated book, The Malevolent Designer: Why Nature's God is not Good:
Exterminating Frogs with a Fungus.

Most of the examples I’ve talked about so far have been organisms and viruses that affect humans, but we are far from being the only species that Creationism’s putative intelligent designer seems to have taken an intense dislike to. For example, the world’s frogs and other amphibians are currently being decimated by chytridiomycosis, caused by a couple of related Chytrid fungi, Batrachochytrium dendrobatidis and B. salamandrivorans. It has been estimated that over 500 different species have been severely reduced in number by this fungal plague, with over 90 extinctions.

These fungi seem to have originated in an area of Southeast Asia by modification of a common, harmless, soil fungus. In that part of the world, the local population of amphibians seems to be resistant to the pathogenic forms of the fungi, suggesting that these fungi frequently become pathogenic and the local population have built up resistance to it.

According to research carried out by a team from the Fenner School of Environment and Society, Australian National University, ACT, Australia, it was resistance in the local population which probably kept the disease from spreading more widely, until human agency intervened to change the environment. They have related the increased trade in amphibian species to the spread of the fungi all over the world where they found species with no evolved resistance (42).

Figure 5 Frog Victims of Chytrid Fungus

Illustration: Catherine Webber-Hounslow
Recently, another team found that one of the factors that could have made these fungi so successful is that the frog’s immune response seems to have worked against it. Researchers from the University of Central Florida and the Smithsonian Conservation Biology Institute (SCBI) found that, in the frog Rana yavapaiensis, a species known to vary in its ability to survive attack by these fungi, those which showed an elevated immune response had a worse outcome that those with a lower response (43). Somehow, the frog’s ‘designed’ immune system was working against it and the fungi had been ‘designed’ to exploit this.

ID advocates would have us believe that, for reasons unknown, their putative intelligent designer has deliberately redesigned a soil fungus so it can overcome the immune system it designed to protect frogs from infections, and so exterminate over 90 species of amphibians that it designed earlier and severely endanger some 500 species in what has been described as the biggest single loss of biodiversity, albeit, aided and abetted by humans in this endeavour. Creationism’s intelligent designer must really hate the frogs it designed. Maybe a private definition of the word ‘intelligent’ is being employed here.
Now a team of researchers from multiple American wildlife and conservation agencies have looked in detail at the spread of this fungus in one particular frog which has declined so rapidly it is now an endangered species - the foothill yellow-legged frog, Rana boylii. This small frog's range once extended from Oregon to Baja California.

They have shown that human agency is implicated in the spread of this fungus by not only spreading it around the world in trade, as the earlier Australian study found (42), but with regard to the foothill yellow-legged frog specifically, by global warming, climate change and habitat destruction as more land is converted to agriculture. They have published their work, open access, in Royal Society Open Science. It is also explained in a University of California Santa Barbara, news release:

Up to only a few inches in length, with a lemon-hued belly, the foothill yellow-legged frog may seem unassuming. But its range once stretched from central Oregon to Baja California. In 2023, it was listed under the federal Endangered Species Act. Its rapidly decreasing range is due in part to a fungal pathogen called Batrachochytrium dendrobatidis, or Bd, that has devastated amphibians around the world.

A team of researchers, including UC Santa Barbara’s Andrea Adams, has conducted the most comprehensive study to date of disease dynamics in foothill yellow-legged frogs. The team’s data — sourced from both wild frogs and specimens in museum collections — enabled them to track patterns of infection across a large geographic range. In a study published in Royal Society Open Science, the researchers reveal that drought, rising temperatures and the increasing conversion of land for agriculture appear to be the largest factors driving Bd infection in this species.

The researchers aimed to assemble as much data as they could, both in space and time. They surveyed in the creeks and rivers of California and Oregon, where they swabbed wild yellow-legged frogs for the presence of Bd. It also led them into fluorescent-lit museum collections to sample specimens from as far back as the 1890s.

The team leveraged a large network of people and institutions to amass this wealth of samples.

Many foothill yellow-legged frog field researchers had data that they weren’t actively analyzing, and so we were able to bring all of this data together and get it into a usable format that we could use to paint a much bigger picture of what is, and was, going on with Bd in this species.

Andrea J. Adams, co-author.
Earth Research Institute
University of California, Santa Barbara, CA, USA.
The researchers swabbed each frog’s skin to determine if the animal was infected. To test for Bd, they used a PCR test, similar to some tests for COVID. By searching for Bd DNA from thousands of samples, the researchers were able to identify infection rates and severity. Co-lead author Ryan Peek ran this information through statistical models, which accounted for climatic, geographic, biologic and land use variables. This enabled the team to track disease patterns across a large geographic range over roughly 120 years.

The team discovered that disease patterns of Bd aligned with historical frog declines. The pathogen began to spread in the 1940s from the southern coast of California, moving northward and eventually affecting nearly the entire region. The biggest factors driving infection seem to be drought, increasing temperatures and the use of ever more land for agriculture.

Bd is a fungus that is spread through spores in the water, but that spread may occur differently in foothill yellow-legged frogs in different regions and climates, the researchers found. In some places, drought increased infection, while in others, it did not, possibly because of the presence or absence of other species that can carry Bd and share the same water, such as American bullfrogs, a species introduced from eastern North America.

If you combine the fact that there are bullfrogs building up the number of spores that these frogs are exposed to, and then they’re all kind of stuck in these small pools together, that explains why drought matters. They are suddenly getting hit with a really large number of spores and getting sick and dying.

These findings open more questions about what was stopping transmission and what allowed it to happen later.

Dr. Anat M. Belasen, co-first author
Department of Integrative Biology
University of Texas at Austin, Austin, TX, USA
And Department of Ecology and Evolutionary Biology,
Cornell University, Ithaca, NY, USA.
What’s more, foothill yellow-legged frogs live exclusively in streams and rivers, not ponds and lakes. So the species is already stressed when these waterways shrink into isolated pools.

The progression of Bd in the foothill yellow-legged frog also differed from its course in other western amphibians. In many other species, the disease radiated from urban centers, rather than this clear south-to-north trend. What’s more, the disease showed up later in the foothill yellow-legged frog than in other species in its range.

Frogs switch from herbivores as tadpoles to carnivores as adults, which means they connect different nutrient cycles together in the food web. Their position at the center of the food chain also influences the ecosystem.

When you remove frogs from an ecosystem, what you get is less control of insects, things that the frogs would eat. There is also less food for things that eat the frogs, like snakes, birds and small mammals. It really throws things off and makes the ecosystem less stable and less functional.

“There are areas that have wet soils that would be alongside suitable habitat. In areas where more of those lands have been converted to agriculture, we see a higher risk of frogs being infected with the fungus.

Dr. Anat M. Belasen.
Co-author Jamie Bettaso swabs a wild foothill yellow-legged frog to test for fungal infection.

Photo Credit: Jamie Bettaso
The conversion of land for agriculture was another major factor influencing the spread of Bd. for these frogs.

In addition to disease hotspots, the team also identified a number of cold spots — areas where the pathogen is present but less influential. The existence of so many cold spots in different areas is a good sign, as it may mean that many areas have conditions suitable for keeping disease rates low, even as climate change increases temperatures and patterns of drought.

The authors are curious what might explain this clustering, especially when cold spots appear in unexpected locations: for example, places with similar habitat, land-use and climatic impacts as hotspots. It suggests there may be some genetic basis for the differences, whether on the pathogen side or the host side. Adams is currently researching the feasibility of reintroducing foothill yellow-legged frogs to Southern California.

The results of this paper shed a lot of light on the dynamics of where Bd occurs, what drives its spread and how the pathogen and frog may interact in the future.

We took a big snapshot of this species’ disease relationship through time. Earlier studies provided the researchers with glimpses into disease patterns in smaller geographic regions, “but now we have a much larger dataset that further confirms many of these patterns, and expands on them.

Andrea J. Adams.
More detail is given in the team's open access paper in Royal Society Open Science:
Abstract

Species with extensive geographical ranges pose special challenges to assessing drivers of wildlife disease, necessitating collaborative and large-scale analyses. The imperilled foothill yellow-legged frog (Rana boylii) inhabits a wide geographical range and variable conditions in rivers of California and Oregon (USA), and is considered threatened by the pathogen Batrachochytrium dendrobatidis (Bd). To assess drivers of Bd infections over time and space, we compiled over 2000 datapoints from R. boylii museum specimens (collected 1897–2005) and field samples (2005–2021) spanning 9° of latitude. We observed a south-to-north spread of Bd detections beginning in the 1940s and increase in prevalence from the 1940s to 1970s, coinciding with extirpation from southern latitudes. We detected eight high-prevalence geographical clusters through time that span the species' geographical range. Field-sampled male R. boylii exhibited the highest prevalence, and juveniles sampled in autumn exhibited the highest loads. Bd infection risk was highest in lower elevation rain-dominated watersheds, and with cool temperatures and low stream-flow conditions at the end of the dry season. Through a holistic assessment of relationships between infection risk, geographical context and time, we identify the locations and time periods where Bd mitigation and monitoring will be critical for conservation of this imperilled species.

1. Introduction

Threatened species with large geographical ranges often require unique, regional conservation strategies to combat stressors such as infectious disease. Pathogen surveys and reporting have become standard for North American wildlife diseases [1,2]; however, relative risk across a landscape and among populations within species remains difficult to anticipate, especially when data are collected by separate research groups [3]. Central reporting databases [4], synthetic analyses and retrospective surveys can help assess disease threats and identify high-risk populations.

Among the most significant wildlife diseases, amphibian chytridiomycosis caused by the fungal pathogen Batrachochytrium dendrobatidis (Bd) has contributed to declines of hundreds of species worldwide [5]; but see [6]. In North America, notable Bd-associated declines have occurred across the west including the southern Rocky Mountains [7,8], Arizona and New Mexico [9,10], Nevada [11] and California [1214]. In several of these cases, infection outcomes varied widely among populations due to host-related and environmental factors including genetics, prior Bd exposure and abiotic conditions [1517].

For the stream-dwelling foothill yellow-legged frog, Rana boylii, Bd's role in the species' changing abundance across its endemic range (California and Oregon, USA) is not well-understood. The species has declined for at least the last half-century, with extirpations reported from xeric lower latitudes [18], at the wetter northern range limit [19] and downstream of large dams range-wide [20]. A mix of abiotic and biotic factors influence Bd infection risk and disease dynamics in many systems, including elevation, latitude, climate, habitat quality and host characteristics [21]. The relative importance of these factors remains unclear in rivers with winter flood/summer drought flow regimes typical across R. boylii's geographical range. Bd is considered a significant potential threat to R. boylii [22] because it is implicated in the species' disappearance from rivers of California's South Coast [23] and in recent autumn die-offs of R. boylii in Central Coast streams [24,25]. A large-scale assessment of Bd infections is needed to clarify how infections relate to historical declines in some regions' rivers and persistence in others, identify clusters of increased infection risk across the species’ range, and evaluate how infection incidence and severity changes with the seasonality of the Mediterranean climate and across the diverse ecoregions that R. boylii occupies.

Here, we leverage data from over 2000 field and museum samples covering 124 years to synthesize knowledge and evaluate patterns of Bd infections in R. boylii. We use a combination of modelling approaches and spatial scan statistics to ask: (i) how are Bd detections in R. boylii are distributed over space and time, (ii) whether watersheds with high versus low Bd infection risk clustered historically and today, and (iii) how Bd infections are related to biotic and abiotic factors. Our results highlight priority populations for Bd mitigation, regions that are data-deficient and warrant further sampling and monitoring, and remaining gaps in our knowledge about Bd susceptibility in R. boylii. Our study serves as a resource for wildlife managers implementing disease mitigation and species recovery projects, such as re-introductions, and as an example of collaborative research to address conservation challenges in wide-ranging imperilled species.

Figure 1.
Distribution of R. boylii samples assayed for Bd infection. Diamonds show museum samples (collected 1897–2005), circles show field samples (2005–2021). Filled symbols indicate Bd-positive samples. (a) Sampling locations across California and Oregon, USA. Symbols overlap in some localities; see inset barplots for sample sizes. Rana boylii clades are outlined and labelled, with California Endangered Species Act status abbreviated in parentheses: SSC = Species of Special Concern, TH = Threatened, EN = Endangered. (b) Spatio-temporal spread of Bd detections. Symbol size indicates sample size at the HUC-12 (sub-watershed) level. Generalized additive model (GAM) of latitude∼capture year + sample size in Bd-positive samples is shown with black curved line (R2 = 0.133).

Photo of R. boylii in Napa County, CA by Marina De León.
It must be thrilling for devotees of the putative divine malevolence to see the stunning success it is having exterminating so many species of frog, but one can't help but wonder what the ancestral frog did to incur this wrath. Did it maybe eat a forbidden mosquito or spawn out of wedlock?

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The Unintelligent Designer: Refuting The Intelligent Design Hoax

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

Available in Hardcover, Paperback or ebook for Kindle


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

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

Illustrated by Catherine Webber-Hounslow.

Available in Hardcover, Paperback or ebook for Kindle


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