Unintelligent Designer News - Correcting the Incompetent Designer's Blunders

Unintelligent Designer News

Correcting the Incompetent Designer's Blunders

Credit: Phospho Biomedical Animation

What are these 'cancer vaccines' I'm hearing about? And what similarities do they share with COVID vaccines?

Creationists would have us believe that cancers are caused by 'Sin' in some magical process that makes chemistry and physics do something they wouldn't do on their own. This also makes Creationists feel smug because they've blamed cancer victims for their own condition, and absolved their putative creator god of any responsibility.

That idea arose in the fearful infancy of our species when we lived in what seemed to be a demon-haunted, magical world in which there was a simple, teleological answer to every mystery - God did it if it was a good thing, or, if it was a bad thing, an evil demon did it. Cancer, like mental illness, was a symptom of moral weakness for allowing the demon to take over, so the sufferer deserved it.

But we are grown up and know better now.

For instance, we know that cancers almost always have one of four causes:

1. Viruses. For example liver cancer can be caused by hepatitis B and cervical cancer can be caused by the human papillomavirus.
2. Inherited genetics. Rare because there is strong selection pressure to eliminate lethal genes from the gene pool.
3. Mutagenic substances such as tars in cigarette smoke, benzene and asbestos fibres.
4. Errors in DNA replication during cell division for growth, repair and replacement. Some of these may include a genetic predisposition.

The fourth of these is by far the most common, especially now cigarette smoking has been reduced to low levels, and tends to occur more frequently as we age.

So why do these errors arise?

This involves something that I have yet to see a Creationist give a satisfactory explanation for in terms of the putative intelligent [sic] designer.

The errors arise primarily because the mechanism for replicating the DNA during cell division is imperfect, resulting in one or both daughter cells having errors in its DNA. This is so common that there is a correction mechanism for repairing DNA - which should not be necessary if the process had been designed to work properly in the first place. Normally, if this error is serious and the DNA can't be repaired, the cell will self-destruct in a process known as apoptosis. This process itself is imperfect and sometime fails, particularly if the person has a genetic mutation that prevents it happening, so predisposing them to these sorts of cancers.

But why is this complex process necessary in the first place

In evolutionary biology terms this is perfectly understandable since evolution is unplanned and necessarily utilitarian - whatever works to give an advantage is retained and built upon, no matter how suboptimal.

The process for cell replication that evolved when multicellular organisms evolved out of single-celled organisms was the same one that had been used for single-celled organisms when the entire genome had to be copied into the daughter cells. But the big advantage of multicellularity is cell specialisation and division of labour. This means that specialised cells only need the genes to carry out their speciality and don't need all the others, which are replicated needlessly in every one of the tens of trillions of cells that make up a human body and most have to be switched off by a complex process of epigenetics.

Meanwhile, all that unnecessary DNA replication not only wastes resources but increasesd the risk of the defect tha causes cancer.

In intelligent [sic] terms, it makes no sense since a perfect, intelligent, omniscient designer would not settle for a utilitarian suboptimal process. It would have designed a cell replication process which replicated only the genes needed by a specialised cell for example. And it would have designed a DNA replication process that didn't require correcting.

In brief then, if you believe in intelligent [sic] design, you must agree that cancers are either caused by viruses that are designed for the purpose, or because of the imcompetence of the designer.

But human medical science is making progress in correcting these problems with vaccines against the viruses and more recently, bespoke vaccines against the specific cancers caused by errors in cell replication, using a similar mRNA vaccine technology to that used to create the CAVID vaccines that have transformed the pandemic.

In the following article, reproduced from The Conversation, Sathana Dushyanthen, an academic specialist & lecturer in cancer sciences & digital health at The University of Melbourne, explains what these vaccines are and what similarities they have with the COVID vaccines. The article has been reformatted for stylistic consistency. The original can be read here.

Published: March 6, 2023 7.03pm GMT

What are these ‘cancer vaccines’ I’m hearing about? And what similarities do they share with COVID vaccines?

Shutterstock

Sathana Dushyanthen, The University of Melbourne

Barely a month goes by without headlines announcing yet another advancement in cancer vaccines.

Just last month, the United States Food and Drug Administration (FDA) granted breakthrough therapy designation to Moderna and Merck’s skin cancer vaccine. This allows expedited development and review of drugs intended to treat serious conditions.

We already have a vaccine to prevent human papillomavirus (HPV), which causes cervical and other cancers. We also have a vaccine to protect against the hepatitis B virus, which can cause liver cancer.

But you may have heard of new types of cancer vaccines being developed using technology similar to that used for COVID vaccines. Decades before COVID vaccines, scientists had been working on messenger ribonucleic acid (mRNA) vaccines targeting cancer.

Rather than preventing disease, these vaccines are a personalised treatment for cancer, to combat disease.

How do they work?

Science in Motion.

Traditionally, vaccines inject part or all of a weakened virus (or other pathogen) into the body to provoke an immune response.

mRNA works by injecting only the genetic instructions and allowing the body’s cells to make part of the cancer protein (antigen) itself. This trains the immune system to develop antibodies against the protein.

When these same proteins are present on an invading tumour cell, the immune system stimulates an immune response against it.

While COVID mRNA vaccines respond to one antigen – the spike protein on the outside of coronavirus – cancer vaccines act on several antigens present on the tumour surface.

The mRNA cancer vaccines train the patient’s immune system to fight their own cancer. Most trials are manufacturing vaccines for individual patients based on the specific antigens present on their tumours.

It takes around two months to produce a vaccine.

The vaccine stimulates an immune response against cancer cells.

Shutterstock

How are they made?

To make these vaccines, a sample of the patient’s tumour and healthy tissue is taken. These samples are DNA-sequenced to compare differences between the DNA in the cancerous cells and the healthy cells.

Scientists identify problem mutations driving disease. These can then be used as antigen targets in the mRNA vaccine.

Bespoke approaches allow scientists to target a wider range of cancer antigens. Targeting multiple antigens decreases the odds that cancer cells will mutate and become resistant to vaccines, because the immune system attacks on multiple fronts.

Personalised medicines are extremely expensive because they are bespoke products. Manufacturing costs for bespoke treatments remain high. However, with rapidly falling costs of different aspects such as genome sequencing (some companies are now offering genome sequencing for just US$100), sequencing the entire genome is becoming more viable.

As large-scale manufacturing increases in future for off-the-shelf vaccines, there will be resource efficiencies that reduce cost.

What vaccines are in development?

In December 2022, Moderna and Merck (known outside the United States and Canada as MSD) published the results of its early phase (2b) clinical trial. The trial was investigating a combination therapy of an mRNA vaccine and immunotherapy (a drug that stimulates an immune response) in advanced stage melanoma patients.

After one year of treatment in 157 patients, they found the combination reduced the risk of cancer recurrence or death by 44%.

2/x Their cancer vaccine is personalised and called called mRNA-4157/V940. What's that? It means that it targets mutations or abnormalities only seen for that cancer. This actives your immune system 🦀 . Good video here 👇 https://t.co/Q3k88Jyksy

— Dr Lennard Lee (Oxford University) (@drlennardlee) February 27, 2023

Now, Moderna and Merck plan to follow up their initial trial with a phase 3 trial for advanced melanoma in 2023. Phase 3 trials test for safety and efficacy in larger groups of patients.

Moderna's experimental cancer vaccine treats but doesn't prevent melanoma – a biochemist explains how it works

BioNTech has several mRNA cancer candidates in the works, including for advanced melanoma, ovarian cancer and non-small cell lung cancer. It will release results from its own phase 2 melanoma trial (of 131 patients) using immunotherapy and an mRNA vaccine combination later this year. Its primary aim is to measure cancer progression and survival over 24 months in previously untreated patients.

A third company called CureVac is also developing mRNA vaccines targeting a range of cancers including ovarian, colorectal, head and neck, lung and pancreatic.

CureVac has a deal with Tesla, the electric car manufacturer, to develop small, portable mRNA bioprinters to automate the process of producing patient mRNA. These can be shipped to remote locations where they are able to churn out vaccine candidates based on the DNA template (recipe) fed into the machine.

A lot of these vaccines, including those targeting cancer, are in pre-clinical to phase 1 stages of development, to test the effects and side effects in the laboratory, animal models or small groups of patients.

When will they become available?

Overseas, Moderna and Merck’s mRNA cancer vaccine was fast-tracked for review by the US FDA in February 2023.

Australia’s Therapeutic Goods Administration has not approved the use of mRNAs for use either alone or with other cancer treatments yet.

World's first cancer vaccine one step closer to reality: Given 'breakthrough' status by FDA https://t.co/3zMRzM4pRx

— Daily Mail Online (@MailOnline) February 24, 2023

In January 2023, the United Kingdom’s National Health Service partnered with BioNTech to fast-track the development of mRNA cancer vaccines over the next seven years. Eligible UK cancer patients will get early access to clinical trials from late 2023 onwards. By 2030, these mRNA vaccines will be made clinically available to around 10,000 cancer patients.

Cancer vaccine trials could start in the autumn – UK signs deal with BioNTech

In Australia, BioNTech is establishing its Asia-Pacific mRNA clinical research and development centre in Melbourne, in partnership with the Victorian government. This would develop mRNA vaccines for research and clinical trials, including personalised cancer treatments.

Meanwhile, Moderna will develop Australia’s first large-scale mRNA vaccine facility at Monash University by 2024, in partnership with the state and federal government. This will give Australians priority access to mRNA vaccines made locally.

What else could the technology be used for?

Aside from cancer, there is huge potential to use mRNA technologies across many gene therapies.

There are studies underway testing mRNA vaccines for various diseases such as evolving COVID strains, seasonal influenza, malaria, HIV, cystic fibrosis and even allergies, giving new hope for many previously incurable diseases.

3 mRNA vaccines researchers are working on (that aren't COVID)

Sathana Dushyanthen, Academic Specialist & Lecturer in Cancer Sciences & Digital Health| Superstar of STEM| Science Communicator, The University of Melbourne

This article is republished from The Conversation under a Creative Commons license. Read the original article.

Published by The Conversation.
Open access. (CC BY 4.0)

Human medical science is making good progress at coping with the problems caused by incompetent, unintelligent design because we now understand that there are no magic demons involved in the diseases they result in, and no magic designer who can be appeased in the right way to make the demons go away or improve its shoddy designs.

What I've yet to see is a Creationist give a grown-up answer to this glaring evidence of incompetence in design with its needless complexity, prolific waste and failure to plan, without resorting to religious superstition and demonstrating why Creationism is not science.

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Thank you for sharing!

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Malevolent Designer News - It Didn't Take Creationism's Divine Malevolence Long to Design Parasites

Malevolent Designer News

It Didn't Take Creationism's Divine Malevolence Long to Design Parasites

Reconstruction shows the dense aggregations of monotypic Neobolus wulongqingensis forming benthic ‘meadows’ on the soft sediment with their associated obligate encrusting kleptoparasitic tube-dwelling organisms.

Artist: Rebecca Gelernter of Near Bird Studios.
Source: Zhang, Z., et al.(2020)

Neobolus wulongqingensis with encrusting kleptoparastic tubes.

Source: Zhang, Z., et al.(2020)

Incredible fossil find is the oldest known parasite | Ars Technica

As we can see from the very many parasites that exist in nature, Creationism's putative designer likes nothing more than to create organisms that harm other organisms - if you subscribe to the intelligent [sic] design hoax, that is.

The existence of parasites refute any notion that the designer god is also the supposedly all-loving god of the Christian Bible because, if anything fits the adjective 'evil' it's parasites that cause sickness, disability and death or otherwise take from their host, giving nothing in return.

Now, according to a 2020 paper in Nature, it seems that parasitism has been around for almost as long as multicellular life, and in all probability, well before that. The evidence is in the form of fossil brachiopods encrusted with kleptoparasitic tube worms. These worms are aligned to match the feeding currents of the brachiopods, making it clear that they took a share of the food in the water currents the sedentary brachiopods generated to bring them food.

The authors, a team of palaeontologists from the Northwest University, Xi’an, China, point out that there are no convincing examples of parasite-host relationships in the Ediacaran biota, so these parasites appear to have arisen early in the Cambrian and so would have played an important role in the Cambrian radiation.

Creationism in Crisis - New Science Poses a Massive Threat to Creationist Superstitions

Creationism in Crisis

New Science Poses a Massive Threat to Creationist Superstitions

A skull of a new hominin species named Homo naledi, which was alive sometime between 335 and 236 thousand years ago.

Photograph: Xinhua/Alamy

Homo naledi.

Source

New analysis of ancient human protein could unlock secrets of evolution | Evolution | The Guardian

If they understood its implications, news that the UK is setting up two centres to study the potential of the new technique of proteomics should give Creationist frauds a sinking feeling on a par with what the captain of the Titanic must have felt. This assumes that they ever allow mere facts to influence them, other than creating a need to explain them away to their credulous cult followers, that is.

Basically, proteomics is the study of residues of ancient proteins sometimes found on ancient fossils in which all useful trace of DNA has disappeared. If these proteins can be recovered and analysed, the hope is that they can be used to deduced some of the DNA of the fossil’s original individual, so pushing the DNA record back much further than currently possible, and with it, constructing the evolutionary trees of, for example, ancient hominins.

The problem this would overcome is that DNA is relatively fragile and is only preserved in useful detail in colder climes, meaning that the African hominin fossils have lost any useful DNA, leaving palaeontologists with having to work out relationships based on anatomical data alone. Proteins, particularly structural proteins, on the other hand, are more stable and are often preserved in, for example, the enamel of teeth.

Australopithecus sediba

Source

If successful, this technique could settle debates about when and where the common ancestor of Home sapiens and Neanderthals lived, for example. It might also be possible to fit the ancient South African hominin, H. naledi, in it correct place in the hominin family tree. This enigmatic hominin combines features of both the chimpanzee with its small brain and human lower limbs and arms - basically, a chimpanzee head on a human body. Despite its relatively small brain there is evidence that H. naledi ritually buried its dead, suggesting a sophisticated culture and sense of mortality. It is also in the 'wrong' place to be a direct ancestor of H. sapiens, which is believed to have evolved in East Africa. H. naledi was also contemporaneous with other African hominins, living about 300,000 years ago.

Creationism in Crisis - Chinese Culture From 30,000 Years Before Creationists Believe Earth Was Created!

Creationism in Crisis

Chinese Culture From 30,000 Years Before Creationists Believe Earth Was Created!

Archaeologists excavating the well-preserved surface at the Xiamabei site, northern China, showing stone tools, fossils, ochre and red pigments.

© Fa-Gang Wang

Location of Xiamabei in the Nihewan Basin

Creationism in Crisis - The Bad News Continues With More on Ancient European Hominins

Creationism in Crisis

The Bad News Continues With More on European Hominin Lineage

Part of the tibia of an early human believed to be Homo heidelbergensis discovered at the Boxgrove archaeological site in West Sussex.

Image © The Trustees of the Natural History Museum, London

Reconstruction of Homo heidelbergensis

Source

Earliest human fossils in the UK reveal how ancient Europeans were connected | Natural History Museum

Although there is still debate about how exactly they relate to one another and exactly which species some of them are, there is no comfort to be had from that for Creationists, because what is not in any doubt is that there were species of Homo alive and well 430,000 years ago - some 420,000 years before Creationist superstition says Earth was created, and, although there as yet are no fossils, evidence of tools shows that there were humans or proto-humans living in Britain up to 700,000 years ago.

In fact, there is even less comfort to be had for creationists from the doubts about in which exact taxon the different specimens should be placed, because as one species transitions over time into a descendant species, there is never a point in time where the next generation is a different species to its parents - that only happens in the rare cases of a new species arising by hybridization, or in childish Creationist parodies of the process. As I've said before, to determine the exact point of transition is like trying to determine the exact point at which green becomes yellow or blue becomes green in the following colour continuum.

And this gets even more complex because not all features evolve in lockstep, so, for example, modern Homo sapiens teeth could have been present in a hominin with an ancestral tibia - exactly what we would expect from an evolutionary process.

That problem is the essence of a study published last November, which somehow I missed at the time. It concerns the exact position of the 'Boxgrove' fossil in relation to other archaic European hominins, using the large sample of about 29 individuals from the Sima de los Huesos (Pit of Bones) site at Atapuerca, Spain. The fossil found at Boxgrove in Suffolk, UK, is normally placed in the H. heidelbergensis taxon, as indeed are many other fossils, simply because they are not, H. erectus, H. neanderthalensis or H. sapiens.

However, a comparison with the Sima de los Huesos fossils, which were also initially assigned to H. heidelbergensis but have since been reclassified on the basis of DNA analysis as early H. neanderthalensis, shows that 'Boxgrove' has many features in common with them. For example, the Boxgrove incisors fit within the range found at Sima de los Huesos, but the tibia has distinct features which suggests it belongs in a separate taxon.

The study is published, open access, in the Journal of Human Evolution. The research, by an international team of paleoanthropologists which included Professor Chris Stringer an expert in human evolution the Natural History Museum, London, and its significance is explained in the Natural History Museum's new release by Emma Caton:

Creationism in Crisis - 30 Thousand Years of European Hominin History

Creationism in Crisis

30 Thousand Years of Continuous European Human History

Depiction of the people of the Ice Age.

Credit: Esteban De Armas/Shutterstock

Artist's impression of life in a Gravettian camp

Source

We thought the first hunter-gatherers in Europe went missing during the last ice age. Now, ancient DNA analysis says otherwise

It's another bad day for Creationism. Close on the news that scientists have reconstructed the last 100 million years of the history of Earth's surface, comes news that a different group of scientists have revealed the last 30,000 years of the history of Homo sapiens in Europe.

Since Creationists are capable of holding to the belief that Earth is only 10,000 years old because ancient Bronze Age nomads who knew no better thought so, despite the fact that the last 100 million years of its history is known in detail, they should have little difficulty in ignoring the evidence that Europeans have a known history stretching back three times longer than they believe Earth has existed. After all, what is a mere 30,000 years when 100 million years can be ignored?

In fact, we know from fossil evidence that early modern human hunter-gatherers spread out of Africa and across Eurasia beginning about 45,000 years ago. The mystery was what happened to them during period between 25,000 and 19,000 years ago when the last Ice Age was at its maximum and much of Europe was under vast ice sheets like that covering Greenland today.

Some authorities believed that European Homo sapiens disappeared during that time, but this recent research shows that they hung on in France and the Iberian Peninsula, to repopulate Europe as the ice sheets retreated north. The evidence is in the traces of their DNA now found in modern Europeans. The scientists who made this discovery have published their work in two papers, one in Nature and the other in Nature, Ecology & Evolution

One of the authors of these papers, Adam B. Rohrlach of the Department of Archaeogenetics, Max Planck Institute for Evolutionary Anthropology, Leipzig, Germany and the School of Mathematical Sciences, University of Adelaide, Adelaide, South Australia, Australia, has written about the team's research in The Conversation. His article is reprinted here under a Creative Commons licence, reformatted for stylistic consistency. The original article can be read here.

Creationism in Crisis - Scientists Reveal 100 Million Years of Earth's History

Creationism in Crisis

Scientists Reveal 100 Million Years of Earth's History

Credit: ttsz / Getty Images

Scientists just revealed the most detailed geological model of Earth's past 100 million years.

By Map:USGS Description:Scott Nash
This file was derived from: Tectonic plates.png, Public Domain, Link

When your holy book tells you Earth is only about 10 thousand years old, but the evidence tells you there is a continuous history of the last 100 million years, it takes a special form of self-deception and denialism, amounting to a mental disorder, to cling to the tales in your holy book and continue to believe it's a text book of history and science and not really a book of stories made up by people with little science so knew no better.

So, with their tradition of science denial and rejection of any evidence they don't want to be true, it probably won't come as a surprise to Creationists that Australian scientists working with colleagues in the École Normale Supérieure (ENS), Paris, France, the Université Lyon, Villeurbanne, France, and Université Grenoble-Alpes, Grenoble, France, have published a detailed model of the changes to Earth's surface over the past 100 million years. Their model is published in the journal, Science.

The research is explained in an article in The Conversation, by lead author, Tristan Salles, Senior Lecturer, University of Sydney, Australian, reprinted here under a Creative Commons license and reformatted for stylistic consistency. The original article can be read here:

Malevolen Designer News - How Creationism's Putative Designer COULD Have Given us Immunity to COVID-19 But Chose Not To

Malevolen Designer News

How Creationism's Putative Designer COULD Have Given us Immunity to COVID-19 But Chose Not To

Photo: wildpixel/iStock/Getty Images Plus

Genetics might explain why some people have never had COVID – but we shouldn't be too focused on finding out

Early in January, 2020, when stories of a potentially dangerous infection in China were beginning to emerge in the world's news media, my partner and I had a daytrip to London to see the Lucian Freud exhibition at the National Gallery. We drove to the Westgate Centre in Shepherd's Bush where we left the car to avoid congestion charges, then took a London Underground train to central London. It was a popular exhibition, so the gallery was crowded, as were the underground trains on our return journey during rush hour, when commuters pack like sardines into the trains.

The following day, my partner developed a cough and a fever and was quite ill for several days with what we thought then was a nasty cold. Two weeks later, I developed the same symptoms and was quite ill for about 48 hours.

Had we had those symptoms today, we would assume we had COVID-19! That was three months before Britain went into full lock down. Since then both of us have had every vaccination offered and always observed the precautions like wearing face masks, regularly using hand cleanser, avoiding crowds, regular testing, even leaving anything delivered to the house for several hours before touching it, and we haven't had so much as a cold.

Did we have COVID-19, in January 2020? There is now no way of knowing, of course, but it is very unlikely that we both have a genetic immunity to the SARS-CoV-2 virus - the explanation now being offered for why some people have never been infected, despite the prevalence of the virus in the environment. The probability is that we either caught it early on and were immune during the first major wave, then had immunity from vaccinations, or we had it asymptomatically - as a high, but indeterminate number are now believed to have had.

Creationism in Crisis - Scientists Discover Flamingos Have Personalities Too

Creationism in Crisis

Scientists Discover Flamingos Have Personalities Too

The partner of one Caribbean flamingo helps it out in an argument with another pair

Caribbean flamingo, Phoenicopterus ruber

Credit: Paul Rose

1 of 6

Caribbean flamingos with chicks

© Claudio Contreras Koob/naturepl.com

2 of 6

Nesting flamingos

© Claudio Contreras Koob/naturepl.com

3 of 6

Flamingos bathing

© Claudio Contreras Koob/naturepl.com

4 of 6

Flamingos bathing

Klaus Nigg, National Geographic Image Colection

5 of 6

Flamingo chick

© Claudio Contreras Koob/naturepl.com

6 of 6

Chick being fed

© Claudio Contreras Koob/naturepl.com

Flamingos form cliques with like-minded pals - News

According to Creationist superstition, humans are specially created as a different form of life from the rest of creation and so are the only species capable of experiencing 'higher' emotions such as love and friendship, or of being able to empathise with other members of the same species. This superstition is vigorously maintained, probably because the cult leaders understand that it makes their dupes feel special enough, so they stick with the cult and reject any idea which seems to reduce their over-inflated sense of self-importance.

The superstition is maintained despite the growing number of examples of other species having these 'human' emotions, such as this example of flamingos forming friendship and mutual support groups depending on their personality. Flamingos with similar personalities prefer to associate together and will even defend one another if attacked by a member of another group.

Flamingos are highly gregarious and can be seen in groups ranging from a half dozen to many thousands. I have seen small flocks of maybe a dozen in Andalucia, Spain and in Kuwait, larger flocks of several thousand in the Camargue, France and probably tens of thousands on the Limasol Salt Lake, Akrotiri, Cyprus.

The research in question was carried out on a captive population of Caribbean flamingos at the Wildfowl & Wetlands Trust, Slimbridge, Gloucestershire, UK, by two scientists from Exeter University.

The research is explained in an Exeter University news release:

Creationism in Crisis - Scientists Find New Clues to How Hummingbird Diversity Evolved

Creationism in Crisis

Scientists Find New Clues to How Hummingbirds Evolved Coloured Feathers

Pink-throated Brilliant, Heliodoxa gularis

© Carlos Calle Quispe
16 April 2017

Pink + pink = gold: hybrid hummingbird’s feathers don’t match its parents | Field Museum

The gold-throated hybrid, center, with its parent species H. branickii (left) and H. gularis (right).

© Kate Golembiewski, Field Museum

When scientists from the Field Museum of Natural History, Chicago, Illinois, USA, discovered a hummingbird with an iridescent gold throat, they thought they had discovered a new species, but DNA evidence revealed that it was a hybrid between two closely related species - the Pink-throated Brilliant, Heliodoxa gularis and the Rufous-webbed Brilliant, H. branickii.

The problem was that the two parent species both had pink throats, so you might expect a hybrid to have a pink throat also, not glittering gold.

Creationism in Crisis - How Malaria is Evolving in Humans and Our Closest Ape Relatives

Creationism in Crisis

How Malaria is Evolving in Humans and Our Closest Ape Relatives

Bonobo, Pan paniscus

Photo: Sean M. Lee

Bonobo gently cradling a young mongoose

Malaria infection harms wild African apes - The Source - Washington University in St. Louis

The embarrassing lack of scientific research support for Creationism continues with the publication of yet another paper that utterly refutes it and exposes the fraudulent nature of the cult's claims.

Researchers led by assistant professor Emily, E. Wroblewski of Washington University in St Louis, MO, USA, have found that the closest relative of humans, the bonobo, Pan paniscus, not only suffers from malaria parasites closely related to the that infect humans - Plasmodium falciparum - but that the pattern of immunity is related to the prevalence of infections, similar to the pattern found in humans. This shows that infections can be severe enough in bonobos to reduce fitness to survive and reproduce. Natural selection, as in humans, has led to an increase in genes for immunity in bonobo populations subject to parasitism by the organisms.

The scientists have discovered that bonobo populations differ in a key immune trait depending on the presence of malaria infection. Infected populations have a higher frequency of an immune variant that protects against developing severe disease, a pattern that mirrors what is observed among human populations.

Because of the difficulty in monitoring wild bonobos and particularly in obtaining blood samples to analyse for malaria parasites and bonobo DNA, the team used the ingenious method o c collecting fecal samples which contain both the parasite and bonobo DNA.

The research and its significance is explained in a Washington University in St Louis news release:

Conservation News - Why 'Extinct In The Wild' is Not Always a Death Sentence

Conservation News

Why 'Extinct In The Wild' is Not Always a Death Sentence

The Socorro Dove, Zenaida graysoni

© Josep del Hoyo
Macaulay Library

1754 painting of a passenger pigeon.
(Plate 23 in Volume 1 of The Natural History of Carolina, Florida and Bahamas)

By Mark Catesby, George Edwards - The Natural History of Carolina, Florida and Bahamas V. 1 (1754) A version by Seligmann 1749, Public Domain, Link

The animals and plants that only exist in captivity – and why time is running out to restore them to the wild

In southern Ontario, Canada, in 1866, a flock of migrating passenger pigeons, was estimated to be 1.5 Km (.93 miles) wide and 500 Km (310 miles) long. It took 14 hours to pass and contained an estimated 3.5 billion birds. The passenger pigeon was then probably the most abundant species of bird on Earth and certainly in North America.

On September 1, 1914, at Cincinnati Zoo, less than 50 years later, 'Martha' the last known passenger pigeon died and the species became extinct. The species had been functionally extinct when the last male died some years earlier. Its death went unrecorded. The last wild passenger pigeon is believed to have been shot in 1901.

The extinction of this species was due entirely to human intervention, including hunting for cheap meat on a massive scale, deforestation and habitat destruction. Because of its habit of migrating in closely-packed flocks, a single shot could bring down several birds.

Why passenger pigeons went extinct a century ago - Eric Guiry, The Conversation

A passenger pigeon flock being hunted in Louisiana. From the ‘Illustrated Shooting and Dramatic News’, 1875.

Credit: (Wikimedia/Smith Bennett), CC BY-NC-ND

A gene line that had taken 3.5 billion years to evolve was ended.

Malevolent Designer News - How The Intelligent [sic] Designer Could Have Been Kinder, But Chose Not To Be

Malevolent Designer News

How The Intelligent [sic] Designer Could Have Been Kinder, But Chose Not To Be

White-tailed deer, Odocoileus virginianus

Photo: Shutterstock

White-tailed deer, Odocoileus virginianus

Image: Pixabay

Deer protected from deadly disease by newly discovered genetic differences | College of Agricultural, Consumer and Environmental Sciences | UIUC.

An open access paper published a couple of weeks ago in the journal Genes should have set alarm bells ringing in Creationists circles, assuming anyone in Creationist circles reads peer-reviewed science and risks having their cherished superstitions spoilt with facts.

The paper was a report on the findings of a team of researchers from the University of Illinois at Urbana-Champaign, Illinois, USA into why, during a summer 2022 outbreak of the highly infectious viral disease of white-tailed deer, Odocoileus virginianus, some deer remained unaffected while scores of others died within days of infection.

The disease, epizootic haemorrhagic disease (EHD), is caused by a double-stranded RNA virus, spread by a midge. There are outbreaks of this disease every 3-5 years.

The team sequenced the entire genome of the white-tailed deer for the first time and found variations in one particular gene associated with apparent immunity to EHD.

So, why should this concern Creationists?

Bearing in mind that Creationists insist their supposed intelligent [sic] designer is omniscient and so knows exactly what its designs will do when it designs them, if we buy into this evidence-free superstition, we have to believe:

1. Creationist's intelligent [sic] designer designed the virus that causes EHD to kill white-tailed deer, and designed the midge to act as the vector for the disease to ensure the virus gets spread to kill new victims.
2. It then gave some deer a modified gene which protects it from the virus it designed to kill them.
3. It could have given all white-tailed deer this protective gene, but chose not to.
4. Therefore the only conclusion is that it wanted most deer to be susceptible to the fatal disease it had designed to make them suffer and die.

As though that evidence of malevolence wasn't enough, what we have here is a simple example of how a mutant alle can give carriers of that mutation a significant advantage over carriers of the non-advantageous alle. It would take an exceptional degree of denialism to conclude that killing carriers of the non-protective allele while allowing carriers of the protective mutation to survive is not going to lead to an increase in the copies of that protective allele in the population gene pool over time.

In other words, what we have here is a perfect example of evolution by mutation and natural selection - the very same process that created the viral parasite in the first place. Evolution being defined by biological science as change in allele frequency in a population over time, not the childish Creationist parody of one species magically turning into another, unrelated species, in a single event.

Creationists need to explain why the patently obvious isn't true and why malevolent intent is a better explanation for these deer being killed by a virus, and Creationism's putative designer's apparent malevolent intent in creating the disease in the first place.

The research team's work was explained in a University of Illinois news release. As you read this, bear in mind that what the article is describing is what Creationists believe was created deliberately by their allegedly omniscient, omni-benevolent deity:

URBANA, Ill. – It was the height of summer 2022 when the calls started coming in. Scores of dead deer suddenly littered rural properties and park preserves, alarming the public and inconveniencing landowners. According to officials at the Urbana Park District, it was Epizootic Hemorrhagic Disease (EHD), a midge-borne viral illness that pops up in white-tailed deer populations around the state every few years. And when susceptible deer are infected, they die within days.

Now, University of Illinois scientists have found gene variants in deer associated with the animals’ susceptibility to EHD.

This is the first time this gene has been sequenced completely in white-tailed deer. This is important because without the sequences, there's no starting point to do any kind of research.

Professor Alfred Roca, c-author
Department of Animal Sciences
College of Agricultural, Consumer and Environmental Sciences (ACES)
University of Illinois, Urbana-Champaign, USA.

The team sequenced the gene for Toll-Like Receptor 3 (TLR3), a protein that spans membranes of intracellular organelles in immune cells and helps recognize double-stranded RNA (dsRNA) viruses. When a dsRNA virus, such as the one that causes EHD, enters the cell, TLR3 activates the host’s first immune defenses, triggering inflammation and priming the rest of the immune system.

When the team sequenced TLR3 from EHD-infected and uninfected deer, they found dozens of variable sites in the DNA known as single-nucleotide polymorphisms (SNPs). Two of the SNPs were significantly more common in uninfected deer.

Because we found mutations in TLR3 more frequently in EHD-negative animals, we think deer with these mutations are less susceptible to EHD.

Yasuko Ishida, co-author
Department of Animal Sciences
University of Illinois, Urbana-Champaign, USA.

That conclusion is rooted in the probability that many white-tailed deer in Illinois are exposed to EHD in their lifetimes, but only some will die from the disease.

In many areas, outbreaks occur every 3-5 years, when environmental conditions favor the life cycle of midges that carry the virus. The midges spend their larval stages in mud under ponds and puddles where deer drink during drought conditions. As those water sources dry up, usually during late summer, the midges’ muddy habitat is exposed and the adult flies emerge to bite and infect deer. The cycle can be interrupted locally by a soaking rain or a cold snap, which is why outbreaks don’t happen every year.

The researchers emphasize that EHD is not transmissible to humans or pets through midge bites or consumption of infected deer meat.

Although there’s not much wildlife managers can do to disrupt the cycle and prevent outbreaks in natural habitats, the team says it’s still helpful to understand the genetic underpinnings of the disease. Theoretically, deer in captive herds could be sampled to characterize the level of vulnerability to EHD, and wild herds could be sampled during the hunting and EHD-outbreak seasons, informing managers and the public of future risk.

The value of this research is that it helps inform the public about EHD. It helps them to understand not only what the disease will look like, but potentially the severity of an outbreak in a particular area. Sometimes there's value in knowing what to expect.

Nohra Mateus-Pinilla, co-author
Wildlife veterinary epidemiologist
Illinois Natural History Survey
And the Department of Animal Sciences
The Department of Natural Resources and Environmental Sciences in ACES
And the Department of Pathobiology
University of Illinois, Urbana-Champaign, USA.

It’s very complicated to respond to an outbreak of EHD because there are often large numbers of deer found dead near water. People don’t know what to do when that happens, but we encourage the public to report potential EHD outbreaks to their local IDNR wildlife biologist for the surveillance and future study of the disease.

Jacob Wessels, first author
Now a conservation police officer with the Illinois Department of Natural Resources

Considering the disease’s episodic nature, it’s not likely to present as a severe outbreak again in Urbana parks anytime soon. But it is an increasing threat to the state’s northern regions, including Chicagoland. Another recent study by Mateus-Pinilla, Roca, and others shows the disease has been slowly but steadily moving northward in Illinois. The researchers don’t know whether that’s due to climate change or greater reporting, but it’s clear EHD isn’t restricted to rural parts of Illinois.

The article, “The Impact of Variation in the Toll-like Receptor 3 Gene on Epizootic Hemorrhagic Disease in Illinois Wild White-tailed Deer (Odocoileus virginianus),” is published in Genes [DOI: 10.3390/genes14020426].

Copyright: © 2023 The authors.
Published by MDPI, Basel, Switzerland. Open access. (CC BY 4.0)

More detail is provided in the team's open access paper in Genes:

Abstract

Epizootic hemorrhagic disease (EHD) leads to high mortality in white-tailed deer (Odocoileus virginianus) and is caused by a double-stranded RNA (dsRNA) virus. Toll-like receptor 3 (TLR3) plays a role in host immune detection and response to dsRNA viruses. We, therefore, examined the role of genetic variation within the TLR3 gene in EHD among 84 Illinois wild white-tailed deer (26 EHD-positive deer and 58 EHD-negative controls). The entire coding region of the TLR3 gene was sequenced: 2715 base pairs encoding 904 amino acids. We identified 85 haplotypes with 77 single nucleotide polymorphisms (SNPs), of which 45 were synonymous mutations and 32 were non-synonymous. Two non-synonymous SNPs differed significantly in frequency between EHD-positive and EHD-negative deer. In the EHD-positive deer, phenylalanine was relatively less likely to be encoded at codon positions 59 and 116, whereas leucine and serine (respectively) were detected less frequently in EHD-negative deer. Both amino acid substitutions were predicted to impact protein structure or function. Understanding associations between TLR3 polymorphisms and EHD provides insights into the role of host genetics in outbreaks of EHD in deer, which may allow wildlife agencies to better understand the severity of outbreaks.

Wessels JE, Ishida Y, Rivera NA, Stirewalt SL, Brown WM, Novakofski JE, Roca AL, Mateus-Pinilla NE.
The Impact of Variation in the Toll-like Receptor 3 Gene on Epizootic Hemorrhagic Disease in Illinois Wild White-Tailed Deer (Odocoileus virginianus).
Genes. 2023; 14(2):426. https://doi.org/10.3390/genes14020426

Copyright: © 2023 The authors.
Published by MDPI, Basel, Switzerland. Open access
Reprinted under a Creative Commons Attribution 4.0 International license (CC BY 4.0)

These examples of how the childish Creationist notion of intelligent [sic] design simply makes no sense at all, are almost daily occurrences in biological science, as are the examples of evolution in progress that we see in this example of natural selection favouring immunity to a viral parasite. The basic problem with Creationism and Creationists is that facts and deductive logic are irrelevant, otherwise there wouldn’t be Creationism and Creationists.

The psychology needed to maintain a superstition despite the overwhelming evidence against it must amount to a mental disorder that can only be accounted for by intensive mental abuse in childhood that gives rise to a mind-numbing acute anxiety disorder, or psychotic theophobia. Creationism and the wilful ignorance and science denial that it requires are not normal psychological states.

To inflict this mental disorder on the vulnerable minds of children, reinforced by threats of eternal torture, is a form of coercive child abuse. As someone once said, there are good people who do good things and bad people who do bad thing, but with religion, good people can do bad things believing them to be good. Inflicting Creationism on children is a case in point.

Creationism in Crisis - How Did Birds Get Their Wings? They Evolved of Course!

Creationism in Crisis

How Did Birds Get Their Wings? They Evolved of Course!

Fossilised propatagium, labeled ppt in image

©2023 Yurika Uno and Tatsuya Hirasawa CC-BY

Musculoskeletal system of the avian left wing in ventral view. A, B, Propatagium (A) and forelimb muscles (B). C, D, Synchronous actions between the elbow and wrist joints, at an extension via the function of the musculus (m.) propatagialis (C) and at a flexion via the interlocking wing-folding system (D)

Uno, Y., Hirasawa, T. (2023)

How birds got their wings | The University of Tokyo

Another gap was slammed shut by science recently and, once again, no gods were found.

The gap was in our knowledge of how exactly birds wings evolved; now two Japanese scientists from the Department of Earth and Planetary Science, Tokyo University's Graduate School of Science, Yurika Uno & Tatsuya Hirasawa, have shown that the key structure, known as the propatagium, evolved out of an analogous structure in non-avian dinosaurs.

Creationists hoping to find evidence that the Theory of Evolution is being increasingly rejected by mainstream scientists will be disappointed to find not a scrap of evidence in this paper that the TOE is other than alive and well and providing an explanation for the observable facts as well as predicting what the scientists would find and informing their research. This paper is not about whether birds’ wings evolved, but how and from what starting point.

The Tokyo University news release explains the research and its significance:

Unintelligent Designer News - The Hopeless Muddle When the Intelligent [sic] Designer Doesn't Have a Plan

Unintelligent Designer News

The Hopeless Muddle When the Intelligent [sic] Designer Doesn't Have a Plan

European Spruce bark beetle, Ips typographus

Source: Wikipedia
By Gilles San Martin - Flickr - Ips typographus
(CC BY-SA 2.0), Link

Bark Beetle galleries in wood.

Photo: Deborah Bell, Smithsonian Institution.

Symbiotic fungi transform terpenes from spruce resin into attractants for bark beetles | Max Planck Institute for Chemical Ecology

Whatever designed the symbiotic relationship between the European spruce bark beetle Ips typographus, the various fungi it depends on and Spruce trees, is either incompetent, severely amnesiac, or deliberately malevolent.

Briefly, the beetle grubs depend on the fungus to kill and breakdown the tissues of the spruce tree in which they live and develop into mature adults and the fungus gets carried to new trees by the beetles when they disperse. For this relationship to work, the adult beetles need to be directed to suitable new host spruces. This is achieved by the fungus producing attractive chemical known as terpenes which are detected by the beetles with a special olfactory organ. Not only that but research has shown that the fungi also produce chemicals that stimulate the beetles to burrow into the bark of the spruce hosts, so starting the infection and killing process.

All very brilliant and a triumph of 'designed', as no doubt the average Creationist will claim, even claiming that this system must have been created as a whole system, which is nonsensical, of course, as every component could have evolved gradually over time with each generation improving on the previous one, either in the sensitivity of the beetles' olfactory organ, the attractiveness of the chemicals the fungi produce or the dependence on each other for feeding and dispersal.

However, where the incompetence or malevolence of the 'designer' created by comes in is in the way the attractive chemicals are created by the fungus. A recent piece of research led by scientists at the Max Planck Institute for Chemical Ecology, Jena, Germany, has shown that the fungus uses a substance produced by the spruce tree to defend itself against fungal attack!

And it gets even more complicated because some species fungi are harmful to the beetles, so the beetles have evolved the ability to distinguish between the chemicals produced by symbiont species and ignore those produced by harmful species.

Let's just run through the logic of Creationist claims of intelligent [sic] design shown here: