Tiny circles of DNA (small rings) upend conventional genetic principles that govern inheritance of genes on chromosomes (oblongs). The large blue circles are cell nuclei.
Paul Mischel lab
Extrachromosomal DNA (ecDNA), DNA circles carrying cancer-associated genes, play a critical role in cancer development, according to new research led by Stanford Medicine. These DNA circles can be found in precancerous cells, and their presence accelerates the transformation to a cancerous state. This discovery paves the way for potential early diagnosis and intervention methods in cancer treatment.
Here's a conundrum for creationists to avoid or blame on 'The Fall' - so showing creationism is Christian fundamentalism, not science.
It's the finding by scientists at Stanford Medical Centre, that errors in DNA replication can cause small circles of extrachromosomal DNA (ecDNA) to form and that these can lead to the formation of cancers. ecDNAs have been found before and the suggestion was that they are produced by cancerous cells as the DNA replication becomes increasingly botched, but this new study shows they can arise in pre-cancerous cells and may well be the cause of the cell becoming cancerous.
The ecDNA contains genes that deliver a super-charged growth signal that can override a cell’s natural programming. They also contain genes likely to dampen the immune system’s response to a nascent cancer.
Creationists, of course, insist that the process of DNA replication was designed by their putative intelligent [sic] omniscient designer. An intelligent, omniscient designer will know in advance exactly what it's design will do, so this raises several questions:
If this was the work of an intelligent designer, why should it not be regarded as malevolent and responsible for designing a process that deliberately causes cancers and so increases the suffering in the world?
If this was not the intended outcome, why should the designer not be regarded an incompetent?
If it was incompetent, why didn't it change its design once it realised what the outcome was? Is it either ignorant of what its design does, or doesn't it care?
Anyway, those are problems for advocates of the childish notion of design by a magic, supernatural magician, believed by those who want easy answers and the pretense of superior knowledge to that of scientists, while avoiding the bother of learning.
The problem for science is how to use this knowledge to reduce the pain and suffering in the world, because medical science, unlike creationism's supposed god is actually moral and seeks to reduce the pain and suffering in the world, and so fights a continuous battle with whatever force is tending to increase it - in this case, as any intelligent person can understand, the force is that of evolutionary arms races and the self-interest of mindless genes.
So, how did the Stanford Medical School scientists make this discovery? The Stanford Medical news release by Krista Conger, explains:
Rapid Evolution of Codfish Caused by Human Predation
Codfish drying in Lofoten, Norway, illustrating the region's classical long-term fishing tradition. Scientists collected historical and contemporary genetic samples at Lofoten for a study on evolutionary changes in codfish.
Just as the theory of evolution predicts, codfish have evolved under the selection pressure of human predation, and this evolution has occurred over the second half of the 20th century when the policy had been to only take cod over an agreed size to allow stocks to replenish from younger fish.
So, codfish have responded to this selection pressure by becoming sexually mature earlier before reaching the size at which they would previously have become sexually mature. Under this intense selection pressure, evolution that would normally be expected to take hundreds of thousands or millions of years, has occurred in a few decades.
This discovery was made by Brendan N. Reid, and Malin L. Pinsky of the Department of Ecology, Evolution, and Natural Resources, Rutgers University, NJ, USA, and Bastiaan Star of the Center for Ecological and Evolutionary Synthesis, Department of Biosciences, University of Oslo, Norway, using new techniques that enabled them to extract DNA from codfish caught more than 110 years ago, and analyse it with sufficient sensitivity to detect subtle changes over time when compared with that of recent samples.
It transpired that the evolution involved changed to multiple genes, and these changes were seen in fish from both sides of the Atlantic.
When a mass extinction some 200 million years ago wiped out related species along with very many others, there was some reason why the common ancestor of the sturgeon and the paddle fish survived and went on to diverge into the 28 species of sturgeon (Acipenseridae) and the 2 extant and 6 extinct species of paddlefish (Acipenseridae).
Now reserchers led by Professor Aoife McLysaght and Dr Anthony Redmond from Trinity College Dublin’s School of Genetics and Microbiology, believe they have found the reason.
It was probably all due to whole genome duplication, followed by rediploidation, which gave the common ancestor an advantage in being able to evolve rapidly in the rapidly changing conditions. Genome duplication provides a spare copy of a gene which is then free to mutate without any loss of the function of the original gene. This is a natural way in which new information can arise in a genome. Gene duplication is a common feature of the evolutionary history of most species but whole genome duplication is unusual.
Recent new findings illustrate the way a species will evolve by diverging into related species that may still be able to interbreed even though other indicators show that they should be regarded as a distinct species. It also shows how a single species can diverge into populations as the precursor to evolving into subspecies and then species.
How are dingoes unique?
Dingoes possess several unique characteristics that distinguish them from domestic dogs and wolves. These characteristics include:
Size and Body Proportions: Dingoes are typically smaller than wolves and many domestic dog breeds. They exhibit a lean and agile body structure with a head that is broader and flatter than that of domestic dogs.
Coat Color and Texture: Dingoes commonly have a sandy or reddish-brown coat color, although variations can occur. Their coat is usually short, dense, and well-adapted to the Australian climate. Some dingoes have a white chest and facial markings.
Cranial Features: Dingoes often have a skull shape that is different from both domestic dogs and wolves. Their skull is generally longer and less domed than that of most dogs, with a narrower zygomatic arch (cheekbone) region.
Dentition: Dingoes possess a unique set of teeth, including relatively large canine teeth and sharp carnassial teeth adapted for cutting flesh. Compared to domestic dogs, their teeth are generally larger and exhibit less size variation.
Behavior and Social Structure: Dingoes are highly adaptable and display behavior suited to their semi-arid and arid habitats. They are generally more independent and less social than domestic dogs. Dingoes often live in small packs or as solitary individuals, whereas wolves form larger, more structured packs.
Reproduction and Breeding: Dingoes typically have a different breeding cycle than domestic dogs, with a once-a-year breeding season. They also exhibit different mating behaviors and have fewer puppies per litter compared to many domestic dog breeds.
It's important to note that while these characteristics are typical of dingoes, there can be variations among individuals and populations. Additionally, some of these traits may be influenced by interbreeding between dingoes and domestic dogs, which can introduce genetic diversity into the dingo population.
ChatGPT3 "What are the unique characteristics that distinguish dingoes from domestic dogs and wolves?" [Response to user question]
Retrieved from https://chat.openai.com/
It also shows how, as science refines and improves its techniques, new information brings about a change of consensus in a classic example of scientific opinion changing when the information changes, unlike religion which needs to find reasons not to change its collective mind despite new information, or risk another fragmentation into mutually hostile sects.
The study is a re-examination and re-evaluation of the status of the Australian dingo, Canis dingo, in view of improved DNA testing. Using earlier techniques which involved comparing just 23 DNA markers, geneticists had concluded that there were very few pure-bred dingoes left as most had DNA derived from hybridization with feral domestic dogs, Canis familiaris. On that basis, the dingo was reclassified as a wild dog and an invasive pest, and several eradication programs were implemented.
But a new study, using newer techniques which enable the scientists to compare not just 23 but 195,000 DNA markers has revealed a very different picture. This shows not only that ingression of familiaris DNA has been very limited in some areas, but that the dingo species can be regarded as four distinct populations. In other words, not only is the dingo still a species distinct from feral dogs but the dingo species is showing early signs of speciating.
It is now accepted that dingoes have not evolved directly from wolves so are not a subspecies of Canis lupus but are descended from the Southeast Asian domestic dog, meaning they were taken to Australia by humans and have evolved to adapt to the Australian environment. They have also been there so long that they have become an important part of the Australian ecosystem as apex predators, so can't now be regarded as an alien species, unlike rabbits, rats, European foxes, mice, cane toads and domestic cats.
The new study, by geneticists from the University of New South Wales and Sydney University, NSW, Australia, with colleagues in the National Human Genome Research Institute, National Institutes of Health, Bethesda, Maryland, USA, is published, open access, in the journal Molecular Ecology.
Three of the scientists, Kylie M Cairns, Research fellow, UNSW Sydney, Mathew Crowther, Associate professor, University of Sydney and Professor Mike Letnic, Evolution and Ecology Research Centre, UNSW Sydney have explained their research and its significance for dingo conservation in an article in The Conversation. Their article is reprinted here under a Creative Commons license, reformatted for stylistic consistency.
How the Biblical Origin Myths Failed the 'Chosen People'
The toilet seat from the estate at Armon ha-Natziv. The site, excavated in 2019, probably dates from the days of King Manasseh, a client king for the Assyrians who ruled for fifty years in the mid-7th century.
Any caring, omni-benevolent, omniscient god would have warned his chosen people about the need for good hygiene in the form of sanitation and the importance of hand-washing, because it would have told them about germ theory and how to avoid catching the parasites it had designed to cause, amongst other things, debilitating diarrhoea.
But not so the god of the Old Testament.
The evidence just discovered by scientists working at Cambridge University, in collaboration with colleagues at Tel Aviv University, with the cooperation of the Israel Antiquities Authority, is that a particularly nasty parasite, Giardia duodenalis, which causes an intractable form of dysentery, was rife in Iron Age Judah.
There is, of course, no mention of this in the Bible, not any hint about how to avoid it with good hygiene and sanitation. It's just like the authors of the Bible were as ignorant as the Late Bronze age/Early Iron age people who lived in Judea at the time. There are extra-biblical Babylonian references to diarrhoea affecting the populations of what is now the Near and Middle East. One example reads: “If a person eats bread and drinks beer and subsequently his stomach is colicky, he has cramps and has a flowing of the bowels, setu has gotten him". The cuneiform word often used in these texts to describe diarrhoea was sà si-sá.
Some texts also included recommended incantations to increase the chances of recovery, showing that they believed magic spells would help control the cause.
But if we listen to the childish fantasies of creationists, we should conclude that this was deliberate, because an omniscient creator would know precisely what the microorganisms it designs will do and creates them for that purpose. Leaving humans ignorant was all part of the plan to allow the parasites to make them suffer, apparently.
How did the Cambridge-led scientists make this discovery? A press release gives the details:
Another Mystery of Abiogenesis May Have Been Solved
Image by Triff/Shutterstock
Chirality in a generic amino acid (-NH 2 : amine,-COOH: caboxyl,-R: rest of the molecule). (a) Left-handed (LH) enantiomer: with thumb along the C→H axis, it takes the left hand for the fingers to point from COOH to NH 2 through R. (b) Righthanded (RH) enantiomer: with thumb along the C→H axis, it takes the right hand for the fingers to point from COOH to NH 2 through R.
One of the enduring problems in biology is explaining why just about all organic molecules in biological organisms have the same chirality. Creationists often latch onto this problem as evidence of something that science "can't explain", as though not (yet) being able to explain something renders the entire body of science wrong, so their "God did it!" superstition wins by default.
Of course, creationism can't explain it either other than by declaring it to be one of their creator god's mysteries.
But, properly understood, chirality is evidence of common descent since the earliest molecules from which self-replicating organisms evolved had one particular chirality - a property which has been inherited by all its descendants. The mystery is why one chirality came to dominate so completely to the exclusion of the other.
Chirality arises because an atom of carbon can form a molecule with four different groups which can be in one of two stereo-spacial arrangements, a levo (L) and a dextro (D) form, known as enantiomers. All amino acids from which proteins are built, and all fatty acids, are L-enantiomers.
Chiral molecules also display 'optical isomerism' in that the different enantiomers rotate the plane of polarisation in polarised light in opposite directions. 'L' enantiomers rotate it to the right 'd' (dextro rotation) and 'D' enantiomers rotate it to the left 'l' ( levorotation).
Genetic information is stored as long, complex sequences of the four different bases in DNA: adenine (A), thymine (T), guanine (G) and cytosine (C). Triplets of these bases are interpreted by the genetic machinery as instructions to add a certain amino acid to a protein.
Alfred Pasieka/Science Photo Library/Getty Images Plus
By way of an introduction to this article on abiogenesis, I'm going to try to dispel the common, but evidence-free claim from creationists that the genetic code is so complex that it must have been designed by an intelligent designer.
This is, of course, nothing but the usual argument from ignorant incredulity and a false dichotomy fallacy - I don't know enough, I can't be bothered to learn, and I can't imagine how something could have arisen naturally, so God did it - and of course it must be the locally popular god because there are only two possibilities; the current science or the local god. It's an argument that demonstrates better than most the scientific illiteracy, intellectual bankruptcy and cultural chauvinism of creationism.
First, I look at the genetic codes and how it could have evolved naturally, without a supernatural magician making chemistry and physics do things they couldn't do without it, or making the highly improbable happen - as though the notion of an undetectable entity existing outside space and time but able to influence things inside space and time makes any sense.
The first anatomically modern Homo sapiens to migrate out of Africa were almost certainly hunter-gatherers. This much can be deduced from the fact that agriculturalists tend to be relatively sedentary and tied to the land. Our early ancestors, however, were migrants who spread relatively rapidly and one of the best habitats for hunter-gatherers is the coast where food in the form of shell-fish is abundant.
It is often assumed that these migrants travelled up the Nile or the Red Sea coast to the Middle East, and dispersed from there, but there is an alternative coastal route once they arrived at the Horn of Africa.
It is a short sea journey from there to what is now Yemen in Arabia and from there either up the Hijaz to the Middle East or along the south-east coat to what is now Oman. From Oman it is again a short sea-crossing at the Gulf of Hormuz, or even up the Arabian Gulf coast, into what is now Iran. From there, the whole of south and south-east Asia is accessible by coastal spread, as is Mesopotamia and then Central Asia either by going round the Black Sea coast, or the more difficult rout through the Caucasus mountains between the Black Se and the Caspian Sea.
Even Australia could be reached via land at a time when sea-levels were much lower than today at glacial maxima.
And now, a team of Australian researchers led by Raymond Tobler and Yassine Souilmi, of the Australian Centre for Ancient DNA, The University of Adelaide, Adelaide, South Australia, Australia, have found genetic evidence of a 30,000 year period of evolutionary adaptation to a colder environment, probably in Arabia of the immediate area, prior to a rapid dispersal across Eurasia as far as Australia. Functional targets in the genome include multiple interacting loci involved in fat storage, neural development, skin physiology, and cilia function, with associations with multiple modern Western diseases.
The team’s findings were published recently in PNAS, sadly behind a paywall, although the Abstract is published open access.
Three of the team have also written about their research and findings in an article in The Conversation. There article is reprinted here under a Creative Commons license, reformatted for stylistic consistency:
Fig. 5: Hypothesis of the elaboration of the PAFF to paired fins.
Simplified evolutionary scenario of vertebrates showing the presence of a PAFF and subsequent modifications leading to paired fins. Dashed lines and dagger symbols indicate extinct lineages, and solid lines indicate extant lineages. PM-derived fins and fin folds are in cyan, while LPM-derived fins are in pink. Larval PAFF is hatched. Black arrows indicate the position of the anus.
The thing about the Theory of Evolution is that it is confirmed by every discovery in archaeology and palaeontology since it predicts what the 'transitional forms' and structures will look like, being intermediate between two knowns.
Creationism, on the other hand, beyond childish hand-waving denialism, can't even offer an explanation for intermediate forms, since it claims all species were created as they are today, without ancestors, so there should be no evidence of progression through a gradual series of change, and an omniscient, omnipotent creator would not need to constantly revise and refine its creation, nor create species destined to become extinct and replaced by new ones.
That's just one reason, amongst many, why the archaeological and palaeontological record refutes the childish notion of special creation, without ancestry, by an omniscient creator making chemistry and physics do something they couldn't do without it.
So, when an international collaboration of scientists fills a gap in our knowledge, with new clues about the origin of paired appendages – a major evolutionary step that remains unresolved and highly debated, we can be confident it fits neatly into an evolutionary framework and completes a segment of the evolutionary picture of terrestrial tetrapods evolving from lobe-finned fish. It also, quite incidentally and without intent, refutes creationism yet again.
The scientists who have just produced this additional confirmation included scientists from the University of Colorado School of Medicine. Their findings have just been published, open access, in the journal Nature.
Their research and its significance are explained in a University of Colorado press release:
I've just been shown an article from Ken Ham's deception site, answersingenesis.com, which the posted claimed proved the Bible contains accurate science.
Evidently the dupe hadn't got the courage or the ability to check the claimed '10 Best Evidences [sic] from Science That Confirm a Young Earth.
The article starts of in typical Creationist style with circular reasoning arguing that the Bible must be true because it says so in the Bible. He then launches into an attack on dating methods which he claims can't be proven because no-one was there to witness it (apart from his God, obviously.
This has the same intellectual merit as arguing that you can't be sure your great grandparents met and has sex, because no-one recorded seeing them doing it, so their children being born by magic is at least as good an explanation as that they had them the normal way.
Or, more subtly, it you met a friend in one town one day then in a different town a month later, you can't prove he/she travelled from the first town to the second in the intervening month unless you saw them on the journey, so a rational explanation is that he/she magically teleports from one place to another.
Despite this wealth of evidence, it is important to understand that, from the perspective of observational science, no one can prove absolutely how young (or old) the universe is. Only one dating method is absolutely reliable—a witness who doesn’t lie, who has all evidence, and who can reveal to us when the universe began!
And we do have such a witness—the God of the Bible! He has given us a specific history, beginning with the six days of Creation and followed by detailed genealogies that allow us to determine when the universe began. Based on this history, the beginning was only about six thousand years ago (about four thousand years from Creation to Christ).
And Ham doesn't even understand the science he's attacking: The evidence is that Earth is 4.54 billion years old, not the 3 billion he's attacking. But this is only a minor aspect of his profound ignorance and/or intellectual bankruptcy, as we will see.
There then follow several Bible references which are supposed to prove that the Bible is the word of God - because it says so in the Bible. And believe it or not, this site appears to be aimed at adults, although Ham shows his contempt for his dupes by treating them like toddlers and being incapable of basic logic.
But let's move swiftly on to the 10 evidences [sic]:
How A Fossil Sabre-Toothed Predator Adjusted to Environmental Change, 250 Million Years Ago
New top predator in town (at least, temporarily): giant gorgonopsian Inostrancevia with its dicynodont prey, scaring off the much smaller African species Cyonosaurus
Evidence published a few days ago in Current Biology illustrates how major environmental change can cause major evolutionary events as vacated niches due to extinction are occupied by other species adjusting to the new conditions.
This is illustrated by the migration over some 7000 miles of a top predator in Eastern Eurasia, a tiger-sized, saber-toothed creature called Inostrancevia, to South Africa where it replaced an earlier top predator which had recently gone extinct. At the time of the migration, there was only one large super-continent, Pangea.
The discovery was made by Christian F. Kammerer of the North Carolina Museum of Natural Sciences, Raleigh, NC, USA working with Pia A. Viglietti and Jennifer Botha, of the Evolutionary Studies Institute, University of the Witwatersrand, Johannesburg, South Africa, and Elize Butler of the National Museum, Bloemfontein, South Africa, who identified the fossil of a large predator found in South Africa’s Karoo Basin, as that of Inostrancevia, previously only known from fossils found in Russia.
Their discovery is explained in a press release from the Field Museum, Chicago:
More evidence today that creationism is a fallacy. Scientists at Lund University, Sweden, have shown that what creationists proclaim to be the unique ability of humans, thus proving special design by their putative designer god - the ability to empathise - may have its origins, not even in ancestral mammals, but in common ancestors of both mammals and birds, i.e., dinosaurs.
Creationists normally get themselves in a terrible muddle over empathy, preferring to ignore it as an evolved source of morality in favour of their supposedly God-given morals, and yet their holy book, in which they claim their designer god wrote down these morals includes an assumption that empathy is a human trait.
So in everything, do to others what you would have them do to you, for this sums up the Law and the Prophets.
Matthew 7:12
Do to others as you would have them do to you.
Luke 6:31
But creationists, while arguing that humans have this unique ability, argue that they, like a sociopath, can't work out how their actions might affect others, so need a handbook to look it up in.
The evidence that this trait first arose in a common ancestor of birds and mammals comes in the form of a paper in Science Advances by three researchers from Lund University, Sweden.
A Lund University press release explains the research:
Creationism's divine malevolence excelled itself with the SARS-CoV-2 virus that caused the COVID-19 pandemic, killing millions, making hundreds of millions more sick either in the short term with the initial infection, or long-term with the long-lasting aftereffects experienced by some victims with 'long-COVID'. It managed to achieve a stunning over three-quarters of a billion cases worldwide with nearly 7 million deaths, as of 18 May 2023, not to mention the bankrupted business and ruined national economies.
But human science having hit back with a vaccine produced in record time, it then had to go into an arms race of new, resistant variants to keep it ahead of science. The most successful of those, Omicron, resulted in unprecedented peaks of cases although deaths were relatively low due to the vaccines.
And now, not to be outdone by humans, it has produced the latest variant, a version of Omicron (Omicron XBB.1.16) that epidemiologists have named Arcturus.
Should we be concerned, that Arcturus can evade the immunity conveyed by vaccines, regular booster vaccines and natural immunity due to previous infections? Here is how Manal Mohammed, a Senior Lecturer and Medical Microbiology at the University of Westminster, UK sees it. Her article is reprinted from The Conversation under a Creative Commons licence, reformatted for stylistic consistency:
Arcturus: what to know about the new COVID variant, omicron XBB.1.16
A new COVID variant XBB.1.16, or “Arcturus”, has now been identified in at least 34 countries including the UK.
Arcturus is a subvariant of omicron and was first detected in India in January 2023.
As of April 17, the latest date up to which the UK Health Security Agency (UKHSA) has reported data on this variant in the UK, 105 cases of Arcturus had been sequenced across England. Five Britons who tested positive for Arcturus have died.
It’s important to note that only a small portion of COVID infections undergo genetic sequencing, so it’s likely there are many more cases of Arcturus. The UKHSA recently reported that the variant is making up 2.3% of sequences in the UK.
Meanwhile, Arcturus has been steadily rising in the US in recent weeks, accounting for more than 10% of new confirmed COVID cases as of the end of April.
But the variant has been most dominant in India, which had recorded 61% of global sequences of Arcturus as of mid-April. It has driven a huge increase in cases in India over the past month. The country was recording more than 10,000 COVID cases each day with Arcturus making up about two-thirds of all cases. Fortunately this wave now appears to be on the decline.
Nonetheless, Arcturus has been classified as a variant of interest by the World Health Organization. So what do we know about this variant, and should we be worried?
XBB.1.16 is a descendant of XBB, a recombinant omicron strain, meaning it contains genetic material from two different variants. Specifically, XBB is a mixture of two BA.2 sublineages: BA.2.10.1 and BA.2.75.
XBB has shown increased transmissibility relative to earlier variants, probably because it appears to be better at evading existing immunity from vaccination and prior infections.
Arcturus is very closely related to XBB.1.5, also known as Kraken.
Compared with its parent strain XBB, Arcturus has three additional mutations in the spike protein: E180V, F486P and K478R. This is a protein on the surface of SARS-CoV-2 (the virus that causes COVID) which allows it to bind to and infect our cells.
Arcturus is understood to be the most contagious subvariant yet, and these additional mutations might explain why.
The typical symptoms of COVID include fever, cough, runny nose and loss of sense of taste or smell. However, doctors in India have reported conjunctivitis symptoms in children infected with Arcturus, which has not generally been seen in earlier COVID waves.
What about vaccine protection?
COVID vaccines target the spike protein of SARS-CoV-2. As such, mutations in the spike protein may affect how well the vaccines work.
There is no data yet on vaccine efficacy against Arcturus. However, a recent study found that among people who had been vaccinated or previously infected, the antibody responses generated against closely related strains XBB and XBB.1 were significantly lower than against other variants.
So XBB subvariants could threaten current COVID vaccines and therapeutics. But importantly, it’s likely vaccines still offer good protection against severe disease.
While further studies are needed to confirm how Arcturus responds to vaccines, scientists are continuing work on new vaccines that could offer stronger protection against emerging variants.
The continued evolution of omicron
Although omicron was first detected in late 2021 it continues to evolve resulting in new subvariants. Arcturus is one of some 600 detected to date.
This is to be expected in a highly vaccinated population. New variants naturally evolve to evade existing defences. Those strains with a competitive advantage – namely greater transmissibility and capacity to escape our immune response – will dominate. Arcturus may yet fuel a rise in cases in the UK and elsewhere.
However, there is no great cause for concern. While scientists will continue to monitor Arcturus, there’s no evidence at this stage to suggest it’s more severe than previous variants. In addition, we have good protection now from vaccines and natural infection.
That said, the continued evolution of COVID and the emergence of new strains such as Arcturus is a reminder that the virus is still with us. For those eligible for further boosters, it’s important to keep these up to date.
Manal Mohammed, Senior Lecturer, Medical Microbiology, University of Westminster
Published by The Conversation. Open access. (CC BY 4.0)
I'm still waiting for an intelligent reply explaining why creationists would rather we thought of their putative designer god as a pestilential malevolence forever designer new and better ways to make its creation suffer, than have people accept that the theory of evolution explains the origins of parasites like the SARS-CoV-2 coronavirus as a natural process, without the intervention of a supernatural deity - which would let their favourite genocidal monster off the hook.
Bear in mind that Creationists believe all parts of the human body, indeed all parts of every living organism, were intelligently designed by an omniscience and omnipotent god. With omniscience comes inerrant foresight of the consequences of any particular design, so, whatever the design does, must be the intended outcome of the design, or else the designer is not omniscient and needs to wait to find out what its design does.
In that case it can't be described as omniscience, but still being intelligent, it should be capable of discarding a design that doesn't do what it wants and starting again. In other words, it should be capable of ensuring that anything it designs does exactly what it wanted it to do, and should do it efficiently, with minimal waste and with the minimal complexity.
In other words, omniscient or not, its designs should comply with the basic principles of intelligent design - minimal waste, minimal complexity and maximal fitness for a clear purpose and endurance over time.
Sadly, for creationists that's not what we see; instead, we see evidence of utilitarianism. Whatever conveys a short-term benefit in terms of producing more offspring that go on to reproduce, is retained, regardless of any long-term detriment, provided the short-term benefits outweigh the long-term detriments. However, the result is often suboptimal compared to what it would have been had there been no detrimental effects, or had the design been more efficient at what it does.
One of the pieces of evidence for utilitarian design is the replication of the entire genome in every cell in multicellular species, when only a small portion of it is needed in specialised cells, and a characteristic of multicellularity is cell specialisations. This ludicrously wasteful method of cell reproduction, retained because it was the method used in the ancestral single-celled species, has meant that a complex system of epigenetics is needed to turn off the unwanted genes and to ensure just the right genes are active when needed. It also requires another complex mechanism for detecting and repairing the frequent mistakes that replicating billions of base pairs of DNA inevitably produce, because the method of replication is far from perfectly designed.
The result is two of the hallmarks of bad design - prolific waste and unnecessary complexity. And now, as shown by this piece of research by Harvard Medical School scientists, harmful consequences. As though the risks of developing a cancer due to run-away replication of cells, as sometimes happens when cell replication goes wrong, the scientists have discovered that one of the types of one of the commonest cancers, breast cancer, is caused when the sex hormone, oestragen, needed for reproduction, enhances the probability of things going wrong and producing a cancer.
Traditionally, creationists faced with this sort of evidence against intelligent design, resort to religious mumbo-jumbo and start gibbering about 'The Fall' allowing 'sin' to enter the world, as though there is some other intelligence, empowered by 'sin' against which their supposedly omnipotent god is powerless, or this thing called 'sin' is itself capable of intelligently creating things. But what of these problems - the result of cell replication going wrong because of the sex hormone that in needed for reproduction in women, did their putative designer not design? Cell reproduction or sexual reproduction?
The research and its significance are explained in a Harvard Medical School press release by Ekaterina Pesheva:
In a tacit acknowledgement that religions promulgate hate and division, and spread disinformation, The National Religious Broadcasters (NRB), an association of Christian media outlets, is joining a coalition opposing a Californian law that would require social media operators such as Facebook and Twitter to publish their policies for removing hate speech from their platforms.
In effect, NRB's president and chief executive officer, Troy Miller, is campaigning for the right of Christians to retain the special privileges of spreading hate and misinformation with impunity when he declared in a statement:
In an environment where much religious viewpoint expression is considered ‘controversial’ speech, NRB is acting to stop the weaponization of new laws against Christian communicators.
It's been a while since I wrote about the paedophile ring known as the Catholic Church, because the stories have become so commonplace that they had dropped out of the mainstream new.
Many people assume the much-vaunted reforms supposedly implemented by the Catholic Church at the behest of Pope Francis to protect potential abuse victims from their priests, have been successful and put a stop to the routine sexual abuse of minors by priests and nuns that had become the norm throughout the Catholic world.
However, not all senior Catholic clerics have signed up to these reforms. It seems that the instinct of some, such as Archbishop Salvatore Cordileone, of San Francisco, is to protect the paedohiles and facilitate their abuse of minors for recreational sex.
One of the more hilarious arguments against science that I have had levelled at me by a Creationist is that you can't prove reality exists, and yet the whole of science claims to be a description of reality and the scientific method is an examination of it based on materialist principles.
The conversation was ended abruptly with the traditional condescending insult when I pointed out that he was trying to persuade me that reality doesn't exist in order to justify his belief in a creator of it!
Whether or not reality exists as we see and experience it, or whether what we see is an optical illusion or an emergent product of the underlying structural chaos of spacetime is irrelevant to our everyday lives, or course. If you're shot to death by a gun, or hit and killed by a bus, you're just as dead, whether or not the gun or bus actually exists.
The Zoonomia Consortium was formed in 2015 by a group of scientists from several institutions, including the University of California, Davis, the University of California, Berkeley, the University of California, Santa Cruz, and the Broad Institute of MIT and Harvard. The goal of the consortium was to develop a comprehensive database of animal genomes that could be used to study and compare the genetic basis of traits across different species.
In 2020, the Zoonomia Consortium published a paper in the journal Nature describing the results of their work. The paper, entitled "Zoonomia Consortium, A comparative genomics multitool for scientific discovery and conservation," provides an overview of the consortium's approach and the tools they developed.
The Zoonomia database includes genomic data from over 100 species of animals, including mammals, birds, reptiles, and fish. The database is freely available to researchers and includes a variety of tools for analyzing and comparing genomic data, such as genome browsers, alignment tools, and gene expression analysis tools.
The Zoonomia Consortium's work has significant implications for conservation biology, as it allows researchers to compare the genetic basis of traits across different species and identify genetic factors that may be important for species survival. For example, researchers could use the Zoonomia database to identify genes that are associated with disease resistance or tolerance to environmental stressors, which could inform conservation efforts.
Reference:
Lewin, H.A., Robinson, G.E., Kress, W.J. et al. Zoonomia Consortium, A comparative genomics multitool for scientific discovery and conservation. Nature 587, 240–245 (2020). https://doi.org/10.1038/s41586-020-2876-6
chatGPT3 "Tell me about the Zoonomia Consortium, with references." [Response to user question]
Retrieved from: https://chat.openai.com/
Yet more evidence of mammalian common origins and the lack of intelligence in design, or, if we assume design, then evidence of malevolence, has emerged from the Zonomia Consortium this week.
Researchers at the University of Southern California (USC) Keck School of Medicine have used their database of the genomes of 240 different mammal species, to work out why humans suffer from diseases despite being the end-point of millions of years of evolution that might have been expected to weed out predisposition to diseases.
It turns out that most of the genes that lead to diseases are in a group of highly conserved genes that are common to all mammals. These genes appear to be highly constrained in evolutionary terms, meaning that any mutations would have been seriously deleterious so making their carriers less successful in competition with carriers of the normal allele.
As the USC Keck School of Medicine news release explains:
“Why do humans have disease if they went through millions of years of evolution?” It’s a question Steven Gazal, PhD, assistant professor of population and public health sciences at the Keck School of Medicine of USC, hopes to answer.
Gazal is part of an international team of researchers who have become the first to precisely identify base pairs of the human genome that remained consistent over millions of years of mammalian evolution, and which play a crucial role in human disease. The findings were published in a special Zoonomia edition of Science.
Gazal and his team analyzed the genomes of 240 mammals, including humans, zooming in with unprecedented resolution to compare DNA. They were able to identify base pairs that were “constrained” – meaning they remained generally consistent – across mammal species over the course of evolution. Individuals born with mutations on these genes may not have been as successful within their species or were otherwise not likely to pass down the genetic variation. “We were able to identify where gene mutations are not tolerated in evolution, and we demonstrated that these mutations are significant when it comes to disease,” explains Gazal.
The team found that 3.3% of bases in the human genome are “significantly constrained,” including 57.6% of the coding bases that determine amino acid position, meaning these bases had unusually few variants across species in the dataset. The most constrained base pairs in mammals were over seven times more likely to be causal for human disease and complex trait, and over 11 times more likely when researchers looked at the most constrained base pairs in primates alone.
The dataset was provided by the Zoonomia consortium, which according to the project website, “is applying advances in DNA sequencing technologies to understand how genomes generate the tremendous wealth of animal diversity.” Gazal gives credit to Zoonomia for making this type of data available to researchers and anticipates it will be widely used by human geneticists. “It’s a cheap resource to generate, as opposed to datasets generated in human genetic studies,” says Gazal.
His team’s findings are a significant step forward, as Gazal notes, “we do not understand 99% of the human genome, so it is fundamental to understand which part has been constrained by evolution and is likely to have an impact on human phenotypes.” Their discoveries and methods could become crucial tools for further research.
The next step for Gazal and his team is to repeat the process with a primate-only dataset. By restricting the subjects, they hope to focus on functions of DNA that appeared more recently in human evolution. “We expect this to be even more useful in determining information on human disease,” says Gazal.
Thousands of genetic variants have been associated with human diseases and traits through genome-wide association studies (GWASs). Translating these discoveries into improved therapeutics requires discerning which variants among hundreds of candidates are causally related to disease risk. To date, only a handful of causal variants have been confirmed. Here, we leverage 100 million years of mammalian evolution to address this major challenge.
RATIONALE
We compared genomes from hundreds of mammals and identified bases with unusually few variants (evolutionarily constrained). Constraint is a measure of functional importance that is agnostic to cell type or developmental stage. It can be applied to investigate any heritable disease or trait and is complementary to resources using cell type– and time point–specific functional assays like Encyclopedia of DNA Elements (ENCODE) and Genotype-Tissue Expression (GTEx).
RESULTS
Using constraint calculated across placental mammals, 3.3% of bases in the human genome are significantly constrained, including 57.6% of coding bases. Most constrained bases (80.7%) are noncoding. Common variants (allele frequency ≥ 5%) and low-frequency variants (0.5% ≤ allele frequency < 5%) are depleted for constrained bases (1.85 versus 3.26% expected by chance, P < 2.2 × 10−308). Pathogenic ClinVar variants are more constrained than benign variants (P < 2.2 × 10−16).
The most constrained common variants are more enriched for disease single-nucleotide polymorphism (SNP)–heritability in 63 independent GWASs. The enrichment of SNP-heritability in constrained regions is greater (7.8-fold) than previously reported in mammals and is even higher in primates (11.1-fold). It exceeds the enrichment of SNP-heritability in nonsynonymous coding variants (7.2-fold) and fine-mapped expression quantitative trait loci (eQTL)–SNPs (4.8-fold). The enrichment peaks near constrained bases, with a log-linear decrease of SNP-heritability enrichment as a function of the distance to a constrained base.
Zoonomia constraint scores improve functionally informed fine-mapping. Variants at sites constrained in mammals and primates have greater posterior inclusion probabilities and higher per-SNP contributions. In addition, using both constraint and functional annotations improves polygenic risk score accuracy across a range of traits. Finally, incorporating constraint information into the analysis of noncoding somatic variants in medulloblastomas identifies new candidate driver genes.
CONCLUSION
Genome-wide measures of evolutionary constraint can help discern which variants are functionally important. This information may accelerate the translation of genomic discoveries into the biological, clinical, and therapeutic knowledge that is required to understand and treat human disease.
Using evolutionary constraint in genomic studies of human diseases.
(A) Constraint was calculated across 240 mammal species, including 43 primates (teal line). (B) Pathogenic ClinVar variants (N = 73,885) are more constrained across mammals than benign variants (N = 231,642; P < 2.2 × 10−16). (C) More-constrained bases are more enriched for trait-associated variants (63 GWASs). (D) Enrichment of heritability is higher in constrained regions than in functional annotations (left), even in a joint model with 106 annotations (right). (E) Fine-mapping (PolyFun) using a model that includes constraint scores identifies an experimentally validated association at rs1421085. Error bars represent 95% confidence intervals. BMI, body mass index; LF, low frequency; PIP, posterior inclusion probability.
Abstract
Thousands of genomic regions have been associated with heritable human diseases, but attempts to elucidate biological mechanisms are impeded by an inability to discern which genomic positions are functionally important. Evolutionary constraint is a powerful predictor of function, agnostic to cell type or disease mechanism. Single-base phyloP scores from 240 mammals identified 3.3% of the human genome as significantly constrained and likely functional. We compared phyloP scores to genome annotation, association studies, copy-number variation, clinical genetics findings, and cancer data. Constrained positions are enriched for variants that explain common disease heritability more than other functional annotations. Our results improve variant annotation but also highlight that the regulatory landscape of the human genome still needs to be further explored and linked to disease.
The significant points, that creationist will avoid like the plague, are:
The evidence of common ancestry of the mammals in the study.
The lack of any evidence that the scientists were rejecting the TOE as an explanation for the observed facts.
The inevitable conclusion that if a magic designer designed genes to cause diseases, then the designer can only be described as malevolent; it this was an accident, then incompetence is the only explanation.
Even if, as 'theistic evolutionists' argue, an invisible supernatural deity was guiding human evolution, it was either incompetent, or malevolent, in allowing genes that caused diseases to be conserved in the evolving human genome.
But those who want to feel important, as the conscious creation of a mighty god who made everything just for them, are hardly likely to allow little considerations like those to make them feel they might be less important than they want to feel.
A transient change in expression of one gene (Shh) can produce a cascade of developmental events leading to the formation of feathers instead of scales
Lurk a while in any Evolution vs Creationism group in the social media and you can guarantee a creationist will try to argue that a given example of evolution which they have probably just demanded be provided, and which conforms to the scientific definition of evolution - any change in allele frequency over time - is not real evolution because it wasn't 'macro-evolution' which they will define as a change in 'kind' or the evolution of a new species, even the evolution of new structures - whichever definition they think stands the best chance of winning.
I've been at this for long enough to remember how, when the early internet 'bulletin boards' on CompuServe had morphed into thriving debate 'forums', creationists would simply argue that there was no such thing as evolution, full stop! It simply never happened; not in the slightest. No Way! Everything was created exactly as it is today during 'Creation Week' a few thousand years ago! Any evidence to the contrary was a forgery by evil scientists or had been planted by Satan.
Then, in the face of so much evidence, particularly the very large number of living and extinct species and the impossibility of them all being collected together in a few days, herded onto a wooden boat and surviving for a year, they began to concede that there had indeed been evolution, but only limited to evolution withing species, and evolution moreover at a phenomenal rate, far exceeding anthing proposed by biologists, so as to produce the millions of species from a few 'kinds' that survived the genocidal flood their putative creator had inflicted on its creation, just a few thousand years ago.
What creationists are doing is moving the goal-posts by redefining a well-understood scientific term to place it beyond what science actually claims, so they can demand evidence of something that no evolutionary biologist ever claimed - that a single mutation produced a new species or that one species gave birth to another in a single event, ignoring the fact that evolutionary biologists understand that evolution is normally a slow process which takes place in the species gene pool, with the instances of new species arising by, for example, hybridization, being rare exceptions, but nevertheless, natural processes, not requiring supernatural entities to explain.
So, ask a creationist now wedded to the notion that real evolution needs to be 'macro-evolution' to define a reptile 'kind' and a bird 'kind' and they will normally define a reptile 'kind' as having scales and a bird 'kind' as having feathers, ignoring the fact that paleontologists have discovered several feathered dinosaurs (reptiles).
Now, present a creationist with an example such as the one in this research paper, where changes to a small number of genes resulted in what they would define as 'macro-evolution', i.e., a change in 'kind' because that change in chickens results in them growing feathers where they normally grow scales, showing the feathers are simply evolved scales.
