Sunday, 12 March 2023

Creationism in Crisis - Jewel Beetles Evolved by Gene Duplication

Creationism in Crisis

Jewel Beetles Evolved by Gene Duplication

Jewel Beetle, Chrysochroa raja


Jewel beetles evolve to see new colors by duplicating their genes | University of Minnesota

Jewel beetle, Chrysochroa rajah
Jewel Beetle, Chrysochroa rajah.

Credit: Nathan Lord, Louisiana State University
The beautiful Jewel beetle is about as devastating to Creationism as it would be if Michael J Behe announced that he was a secret evolutionary biologist all along, taking part in an elaborate experiment to test how gullible the average American fundamentalist is.

Recent research has shown that these beetles get their color from gene duplication. This is the process where a mistake in the duplication of DNA leads to genes being duplicated, creating a second, spare, copy. This copy is then free to mutate without any loss of function because the original is still functioning, creating new genetic information by mutation.

This is a problem for Creationists for two reasons:

Saturday, 11 March 2023

Icons of Feminism - Mary Woolstencraft and Rejection of Religious Doctrine

Icons of Feminism

Mary Wollstonecraft and Rejection of Religious Doctrine.

Mary Wollstonecraft by John Opie, c. 1797
Source: Wikipedia

Mary Wollstonecraft, by John Keenan, 1787
Mary Wollstonecraft, by John Keenan, 1787
Mary Wollstonecraft: an introduction to the mother of first-wave feminism

Reading this account of the life of Mary Wollstonecraft, one of the first 'radical' feminists, by Bridget Cotter, Lecturer in Social Sciences, University of Westminster, UK, one of the things that stands out most vividly is the religious inspiration for the repression and subjugation of women in Victorian England, and how much of that religion is now seen as wrong and antisocial by the vast majority of decent people.

Far from providing society with a fixed moral framework, religion has served to hold back moral development as society evolves, only to have to reluctantly acceded to the new standards when the tension becomes irresistible.

One of the great crimes of religion, or rather the clerics who control it, is the theft of control of social ethics by a clique who knew they would lose control if they allowed the people too much freedom to think for themselves.

If we give all men the vote, where will it all end? Women demanding the same?!"

"If we give way on feminism, where will it all end? Women priests?!"

"If we give way on contraception, where will it all end? Sexually liberated women?!"

“If we give way on same-sex marriage, or allow gays to become priests, Where will it all end?

… Etc, etc, etc.

Because she challenged these imposed social norms and questioned the authority of those who sought to impose them on us, Mary Wollstonecraft was considered a dangerous revolutionary. Ironically she was opposed most vigorously by the same church that proudly, but wrongly, proclaims its founder as a dangerous revolutionary who challenged authority and the prevailing social norms and cultural ethics.

And today, much of what Mary Wollstonecraft campaigned for is taken for granted as right and proper in most civilised countries.

Bridget Cotter's article in The Conversation is reprinted here under a Creative Commons license. The original can be read here.

Creationism in Crisis - Not All Science Has to be Done in a Laboratory

Creationism in Crisis

Not All Science Has to be Done in a Laboratory

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How we discovered flamingos form cliques, just like humans

A few days ago I wrote about a paper which incidentally refutes the notion that humans are a special creation with unique characteristics that distinguish us from other animals in a way over and above those handful of characteristics that distinguish any distinct species from others.

One of these, so Creationists would have us believe, is having higher emotions and cognition which enable us to form close friendships and empathise with other people, for instance. The paper showed how Caribbean flamingos forms 'cliques' or friendship groups with other flamingos with similar personalities, just like humans do.

Another piece of disinformation that the cult leaders feed their dupes, in order to attack and undermine the science behind the Theory of Evolution (TOE), is the nonsensical claim that a scientific theory must be verified with experiments in a laboratory or else it isn't real science but an unproven hypothesis which is no more valid than a belief in magic. This trick enables Creationists to present their evidence-free superstition as a theory which should carry equal weight to the TOE and so should be taken seriously as an alternative to the science.

Curiously, Creationists who despise science and try to undermine and misrepresent it at every opportunity, would like nothing more than Creationism being regarded as serious science.

Thursday, 9 March 2023

Creationism in Crisis - Scientists Have Discovered How Our Sense of Smell Has Evolved

Creationism in Crisis

Scientists Have Discovered How Our Sense of Smell Has Evolved
Neanderthal hunter.
How good was their sense of smell?
Reconstruction of a Neanderthal woman
Reconstruction of a Neanderthal woman.
Bacon Cph, CC BY 2.5, via Wikimedia Commons
Study offers new insight on what ancient noses smelled | UAF news and information.

Inadvertently exposing laughable Creationists claims that the Theory of Evolution is a theory in crisis about to be overthrown in the scientific consensus by Creationist superstition, including magic done by unproven supernatural entities, a study led by University of Alaska Fairbanks biological anthropologist Kara C. Hoover and Universite Paris-Saclay biochemist Claire de March, shows how our sense of smell evolved as an adaption to new environments, in classic example of evolution by natural selection.

The research involved a comparative genetic analysis of the genomes of modern humans, Neanderthals and Denisovans.

The research is explained in a University of Alaska Fairbanks (UAF) news release:
It sounds a little like Stone Age standup: A Denisovan and a human walk past a bees’ nest heavy with honeycomb. What happens next? According to a study led by University of Alaska Fairbanks biological anthropologist Kara C. Hoover and Universite Paris-Saclay biochemist Claire de March, the Denisovan, with the species’ greater sensitivity to sweet smells, may have immediately homed in on the scent and beat the human to a high-energy meal.

This research has allowed us to draw some larger conclusions about the sense of smell in our closest genetic relatives and understand the role that smell played in adapting to new environments and foods during our migrations out of Africa.

[Smell is integral to the human story.] Such a strongly overlapping olfactory repertoire suggests that our generalist approach to smelling has enabled us to find new foods when migrating to new places — not just us but our cousins who left Africa much earlier than us!

Profesor Kara C. Hoover
Department of Anthropology
University of Alaska Fairbanks, Alaska, USA
A paper on the research, recently published in iScience, was written by collaborators from UAF, Duke University, Universite Paris-Saclay, Tokyo University of Agriculture and Technology, and the University of Manchester. The study investigated whether humans share a sense of smell with their now-extinct Denisovan and Neanderthal cousins, who left Africa about 750,000 years ago. Contemporary humans left Africa about 65,000 years ago.

To recreate the noses of our extinct genetic relatives and compare them to those of present-day people, the research team used publicly available genome sequences from multiple Neanderthals, one Denisovan and one ancient human. They used data from the 1000 Genomes project to represent modern humans.

They then compared 30 olfactory receptor genes from each group. The team found that 11 of the receptors had some novel mutations present only in extinct lineages. In the largest study of its kind to date, the team created laboratory versions of those 11 olfactory receptors and then exposed them to hundreds of odors at different concentrations.

When the receptors detected an odor, they literally lit up. The speed and brightness of the luminescence told the scientists whether, how soon and to what degree each “nose” could smell the odors. While the receptors could detect the same things as modern humans, they differed in sensitivity to many of the odors.

We literally reproduced an event that hadn’t happened since the extinction of Denisova and Neanderthal 30,000 years ago: an extinct odorant receptor responding to an odor in cells on a lab bench. This took us closer to understanding how Neanderthal and Denisova perceived and interacted with their olfactory environment.

Claire A. de March, lead author
Institut de Chimie des Substances Naturelles
Université Paris-Saclay, Gif-sur-Yvette, France And Department of Molecular Genetics and Microbiology
Duke University Medical Center, Durham, NC, USA

This is the most exciting research I have ever been involved in. It shows how we can use genetics to peer back into the sensory world of our long-lost relatives, giving us insight into how they will have perceived their environment and, perhaps, how they were able to survive.

Matthew Cobb, co-author
Faculty of Life Sciences
The University of Manchester, Manchester, UK
Neanderthals, who lived in Eurasia between 430,000 and 40,000 years ago, had the poorest sense of smell. For example, the Neanderthal from the Chagyrskaya Cave couldn’t detect the sex steroid androstadienone, which smells something like sweat and urine. That may have been useful, Hoover said, given that they were trapped in close quarters in caves during glacial maximums, when the ice sheets from the poles expanded southward and made many areas uninhabitable.

Each species must evolve olfactory receptors to maximize their fitness for finding foodX. In humans, it's more complicated because we eat a lot of things. We're not really specialized.

Professor Hiroaki Matsunami, co-author
Department of Molecular Genetics and Microbiology
Duke University Medical Center, Durham, USA
Denisovans have left behind less physical evidence than Neanderthals. They are known mostly from modern-day Siberia, where remains in the Denisova Cave were dated to between 76,200 and 51,600 years ago. Denisovans were generally more sensitive to odors than humans and much more sensitive than Neanderthals. They were most responsive to sweet and spicy smells like honey, vanilla, cloves and herbs. That trait could have helped them find high-calorie food.

Present-day humans fell somewhere in the middle.

In many species, olfactory receptors have been linked to their ecological and dietary needs.
The same research is also the subject of a press release from Duke University, the university to which several of the team, are affiliated and where the lead author, Claire A. de March, completed her PhD:
If you had the grooming habits of a Neanderthal, perhaps it’s a good thing your nose wasn’t as sensitive to urine and sweat as a modern human’s.

And if you lived the hunting and gathering lifestyle of a Denisovan on the Asian steppes, your strong nose for energy-rich honey was almost certainly an advantage.

Though we can’t really know what these two extinct human species perceived or preferred to eat, a new study from Duke University scientists has figured out a bit more about what they might have been able to smell.

Using a technique they developed that allows researchers to test smell sensitivity on odor receptors grown in a lab dish, researchers Claire de March of CNRS Paris Saclay University and Hiroaki Matsunami of Duke University were able to compare the scents-abilities of three kinds of humans. Their work appeared Dec. 28 in the open access journal iScience.

Drawing from published databases of genomes, including ancient DNA collections amassed by 2022 Nobel Prize winner Svante Pääbo, the researchers were able to characterize the receptors of each of the three human species by looking at the relevant genes.

It is very difficult to predict a behavior just from the genomic sequence. We had the odorant receptor genomes from Neanderthal and Denisovan individuals and we could compare them with today’s humans and determine if they resulted in a different protein.

The Neanderthal odorant receptors are mostly the same as contemporary humans, and the few that were different were no more responsive/

Claire A. de March
So then they tested the responses of 30 lab-grown olfactory receptors from each hominin against a battery of smells to measure how sensitive each kind of receptor was to a particular fragrance.

The laboratory tests showed the modern and ancient human receptors were essentially detecting the same odors, but their sensitivities differed.

We don’t know what Denisovans ate, but there some reasons why this receptor has to be sensitive

[Neanderthals] may exhibit different sensitivity, but the selectivity remains the same.

Each species must evolve olfactory receptors to maximize their fitness for finding food. In humans, it’s more complicated because we eat a lot of things. We’re not really specialized.

Some people can smell certain chemicals, but others can’t. That can be explained by functional changes.

Professor Hiroaki Matsunami
The Denisovans, who lived 30,000 to 50,000 years ago, were shown to be less sensitive to the odors that present-day humans perceive as floral, but four times better at sensing sulfur and three times better at balsamic. And they were very attuned to honey.

Contemporary hunter-gatherers such as the Hadza of Tanzania are famous for their love of honey, an essential high-calorie fuel.

Neanderthals, who were still around up to 40,000 years ago and who apparently swapped a few genes with modern humans, were three times less responsive to green, floral and spicy scents, using pretty much the same receptors we have today.

Odor receptors have been linked to ecological and dietary needs in many species and presumably evolve as a species changes ranges and diets.
The team's findings were published open access last December in the journal iScience:
Graphical abstract
Graphical anstract
Highlights
  • Neanderthal and Denisovan ORs vary less than human ORs but our repertoires are similar
  • OR variation may have helped humans adapt to new environments
  • There are limited functional differences in odor specificity across lineages
  • Neanderthals are less sensitive to odors than humans, and Denisovans more sensitive

Summary

Humans, Neanderthals, and Denisovans independently adapted to a wide range of geographic environments and their associated food odors. Using ancient DNA sequences, we explored the in vitro function of thirty odorant receptor genes in the genus Homo. Our extinct relatives had highly conserved olfactory receptor sequence, but humans did not. Variations in odorant receptor protein sequence and structure may have produced variation in odor detection and perception. Variants led to minimal changes in specificity but had more influence on functional sensitivity. The few Neanderthal variants disturbed function, whereas Denisovan variants increased sensitivity to sweet and sulfur odors. Geographic adaptations may have produced greater functional variation in our lineage, increasing our olfactory repertoire and expanding our adaptive capacity. Our survey of olfactory genes and odorant receptors suggests that our genus has a shared repertoire with possible local ecological adaptations.

The researchers are in no doubt whatsoever, that natural selection drove these differences in the olfactory sensitivity of these three closely rated hominins, as each adapted to their particular environment, cultural preferences for particular food and social habits. Nowhere have they had to invoke magic or supernatural deities in their explanation for the observable evidence.

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Tuesday, 7 March 2023

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.



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

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.
Doctor checks patient's mole
The vaccine stimulates an immune response against cancer cells.

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%.
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.
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.
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.
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.
The Conversation 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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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)

<i>Neobolus wulongqingensis<i></i></i> with encrusting kleptoparastic tubes
Neobolus wulongqingensis with encrusting kleptoparastic tubes.

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.

Monday, 6 March 2023

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
Homo naledi.
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.

 skull of Au. sediba
Australopithecus sediba
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

Map of China showing the location of Xiamabei in the Nihewan Basin
Location of Xiamabei in the Nihewan Basin
An innovative 40,000-year-old culture in China | Max-Planck-Gesellschaft

It's probably difficult to embarrass a Creationist, who will have a well-rehearsed routine for dismissing any evidence he/she doesn't want to be true, but if anything should, it's evidence that there is a continuous Chinese history dating back 30,000 years before Creationists believe Earth and the Universe were created. This culture has continued uninterrupted up to modern times, with no evidence anywhere of a genocidal global flood followed by repopulation with people from the Middle East some 4-6,000 years ago - another central belief of Creationism.

In fact, scientists have now found evidence that there was a rapid diversification of culture in China about 40,000 years ago, possibly spurred by cultural and genetic hybridization, when early Homo sapiens who had migrated out of Africa were encountering the Denisovans and Neanderthals. The Denisovans are believed to have been descended from an earlier dispersal out of Africa, probably by H. erectus - H. erectus being the probable parent or grandparent species of both Neanderthals and Denisovans, and probably at least one more species of archaic Eurasian hominin whose existence has been inferred from DNA evidence.

The evidence of this cultural diversification is being found at the Xiamabei archaeological site in the Nihewan Basin of northern China. It is described in a recent paper published in Nature by an international team of paleoanthropologists including scientists from Hebei Provincial Institute of Cultural Relics and Archeology, Shijiazhuang, China, the Chinese Academy of Sciences, Beijing, China, the Institut Català de Palaeoecologia Humana i Evolució Social (IPHES-CERCA), Tarragona, Spain, the Universitat de València, Valencia, Spain, and the Max Planck Institute for the Science of Human History, Jena, Germany.

The findings and their significance are explained in a Max Planck Insitute press release:
When did populations of Homo sapiens first arrive in China and what happened when they encountered the Denisovans or Neanderthals who lived there? A new study by an international team of researchers opens a window into hunter-gatherer lifestyles 40,000 years ago. Archaeological excavations at the site of Xiamabei in the Nihewan Basin of northern China have revealed the presence of innovative behaviors and unique toolkits.

The discovery of a new culture suggests processes of innovation and cultural diversification occurring in Eastern Asia during a period of genetic and cultural hybridization. Although previous studies have established that Homo sapiens arrived in northern Asia by about 40,000 years ago, much about the lives and cultural adaptations of these early peoples, and their possible interactions with archaic groups, remains unknown. In the search for answers, the Nihewan Basin in northern China, with a wealth of archaeological sites ranging in age from 2 million to 10,000 years ago, provides one of the best opportunities for understanding the evolution of cultural behavior in northeastern Asia.

A new study describes a unique 40,000-year-old culture at the site of Xiamabei in the Nihewan Basin. With the earliest known evidence of ochre processing in Eastern Asia and a set of distinct blade-like stone tools, Xiamabei contains cultural expressions and features that are unique or exceedingly rare in northeastern Asia. Through the collaboration of an international team of scholars, analysis of the finds offers important new insights into cultural innovation during the expansion of Homo sapiens populations.

Xiamabei stands apart from any other known archaeological site in China, as it possesses a novel set of cultural characteristics at an early date.

Fa-Gang Wang, co-lead author
Hebei Provincial Institute of Cultural Relics and Archaeology
Shijiazhuang, China.
cultural artifacts
Ochre pieces and stone processing equipment laying on a red-stained pigment patch.
© Fa-Gang Wang, Francesco d’Errico / Wang et al. (2022)
Cultural adaptations at Xiamabei

The ability of hominins to live in northern latitudes, with cold and highly seasonal environments, was likely facilitated by the evolution of culture in the form of economic, social and symbolic adaptations. The finds at Xiamabei are helping us to understand these adaptations and their potential role in human migration.

Shixia Yang, co-lead author
Chinese Academy of Sciences, Beijing, China And the Max Planck Institute for the Science of Human History
Jena, Germany.
One of the significant cultural features found at Xiamabei is the extensive use of ochre, as shown by artefacts used to process large quantities of pigment. The artefacts include two pieces of ochre with different mineral compositions and an elongated limestone slab with smoothed areas bearing ochre stains, all on a surface of red-stained sediment. Analysis by researchers from the University of Bordeaux, led by Francesco d’Errico, indicates that different types of ochre were brought to Xiamabei and processed through pounding and abrasion to produce powders of different color and consistency, the use of which impregnated the habitation floor. Ochre production at Xiamabei represents the earliest known example of this practice in Eastern Asia.

Stone tools
Extraordinarily well preserved bladelet showingmicroscopic evidence of a bone handle, plant fibres used for binding, and plant polish produced by whittling action.
© Andreu Oll  / Wang et al. (2022)
The stone tools at Xiamabei represent a novel cultural adaptation for northern China 40,000 years ago. Because little is known about stone tool industries in Eastern Asia until microblades became the dominant technology about 29,000 years ago, the Xiamabei finds provide important insights into toolmaking industries during a key transition period. The blade-like stone tools at Xiamabei were unique for the region, with the large majority of tools being miniaturized, more than half measuring less than 20 millimeters. Seven of the stone tools showed clear evidence of hafting to a handle, and functional and residue analysis suggests tools were used for boring, hide scraping, whittling plant material and cutting soft animal matter. The site inhabitants made hafted and multipurpose tools, demonstrative of a complex technical system for transforming raw materials not seen at older or slightly younger sites.

Our findings show that current evolutionary scenarios are too simple, and that modern humans, and our culture, emerged through repeated but differing episodes of genetic and social exchanges over large geographic areas, rather than as a single, rapid dispersal wave across Asia.

Michael Petraglia, co-corresponding author
Max Planck Institute
Jena, Germany
A complex history of innovation

The record emerging from Eastern Asia shows that a variety of adaptations were taking place as modern humans entered the region roughly 40,000 years ago. Although no hominin remains were found at Xiamabei, the presence of modern human fossils at the contemporary site of Tianyuandong and the slightly younger sites of Salkhit and Zhoukoudian Upper Cave, suggests that the visitors to Xiamabei were Homo sapiens. A varied lithic technology and the presence of some innovations, such as hafted tools and ochre processing, but not other innovations, such as formal bone tools or ornaments, may reflect an early colonization attempt by modern humans. This colonization period may have included genetic and cultural exchanges with archaic groups, such as the Denisovans, before ultimately being replaced by later waves of Homo sapiens using microblade technologies.

Given the unique nature of Xiamabei, the authors of the new paper argue that the archaeological record does not fit with the idea of continuous cultural innovation, or of a fully formed set of adaptations which enabled early humans to expand out of Africa and around the world. Instead, the authors argue that we should expect to find a mosaic of innovation patterns, with the spread of earlier innovations, the persistence of local traditions, and the local invention of new practices all taking place in a transitional phase.
In other words, not a single founding couple or even a single founding species a few thousand years ago, let alone a culture derived from a small area of the Middle East, as Creationist dogma dictates their cult members believe, but a species and culture derived from hybrids and cross fertilisation of species that had been in existence for well over the 40,000 before they came into contact in China.

As usual with science, the revealed facts flatly contradict and refute Creationism.

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Sunday, 5 March 2023

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

Homo heidelbergensis
Reconstruction of Homo heidelbergensis
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:

Saturday, 4 March 2023

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
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.

Tectonic plate boundaries
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:

Friday, 3 March 2023

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

SARS-CoV-2 Viruses and human respiratory system
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:

Wednesday, 1 March 2023

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.

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