Thursday, 19 May 2022

Evolution News - Tracing Our Cousins the Denisovans

Views of the TNH2-1 specimen.
a. Occlusal, b. inferior, c. mesial, d. distal, e. buccal and f. lingual
Ancient tooth suggests Denisovans ventured far beyond Siberia.

Until recently, the archaic humans, the Denisovans, cousins of the Neanderthals and probably cousins to modern humans, were known only from a few fragments of bone and teeth from a single site - the Denisova Cave in Siberia. One fragment turned out to be from a girl who was the child of a Denisovan father and a Neanderthal mother, showing that the two species co-existed and interbred, at least in Siberia.

Since then, there has been increasing acceptance that, because up to 5% of the genome of many people from South East Asian and Oceania, including Native Australians and people from Papua-New Guinea, is Denisovan DNA, Denisovans probably occupied South East Asia and interbred with modern Homo sapiens as they migrated to and through it.

There was also the intriguing discovery that the genes that help the inhabitants of the Tibetan Plateau live at high altitude were from Denisovans. The initial assumption was that they must have been acquired from people from lower altitudes because Denisovans would probably not have lived on the Tibetan Plateau. This would have meant that the Denisovans must have evolved these genes for a different purpose, possibly related to prolonged physical exertion, and that modern humans exapted them for high altitude survival.

The Xiahe mandible, only represented by its right half, was found in 1980 in Baishiya Karst Cave.
© Dongju Zhang, Lanzhou University
That view was challenged in 2019, when a jawbone, discovered in 1980, proved to be Denisovan on analysis of the proteins extracted from it. Proteins can be reverse engineered to reveal the DNA template that coded for them and that turned out to be Denisovan. The mandible had been discovered in a cave on the Tibetan Plateau, the Baishiya Karst Cave, Xiahe, Gansu, China, showing that Denisovans occupied the site about 160,000 years ago, way before H. sapiens arrived on the scene. Sadly, the paper describing this find, published in Nature lies behind a paywall. In the abstract, the authors say:

The Xiahe specimen provides direct evidence of the Denisovans outside the Altai Mountains and its analysis unique insights into Denisovan mandibular and dental morphology. Our results indicate that archaic hominins occupied the Tibetan Plateau in the Middle Pleistocene epoch and successfully adapted to high-altitude hypoxic environments long before the regional arrival of modern Homo sapiens.

These Denisovan 'high altitude' genes gave the founder population of Han Chinese who migrated to the plateau and interbred with the Denisovans, such an advantage that they would have spread rapidly through the population, especially since one of the effects of altitude sickness that non-carriers of these Denisovan genes experience, is a high proportion of failed pregnancies.

We’ve always assumed that Denisovans were in this part of the world, but we’ve never had the physical evidence. This is one little piece of evidence that they were really there.

Laura Shackelford, Co-author
Department of Anthropology
University of Illinois at Urbana-Champaign, Urbana, IL, USA
And now, more detail has been added to the Denisovan story by the discovery of a single tooth, a deciduous tooth of a child - probably a female - in the Tam Ngu Hao 2 (Cobra Cave), a limestone cave in the Annamite Mountains, Laos, dated to 164,000-131,000 years old - a date range which includes the Xiahe specimen’s age. This tooth shows a 'close morphological affinity' with the teeth in the Xiahe jaw, so the researchers are almost certain it is from the same taxon, i.e., that it is Denisovan. If DNA or protein analysis confirm that this is indeed the tooth of a Denisovan child, it will confirm that Denisovans were a widespread and very adaptable species, being present in the tropical forests of Loas in the Middle Pleistocene at the same time they were also present on the high Tibet plateau and the cold northern tundra of Siberia.

It surely can't be much longer before Denisovans are given a respectable binomial scientific name - Homo altai or Homo denisovensis, perhaps?

Copyright: © 2022 The authors.
Published by Springer Nature. Open access. (CC BY 4.0)
The paper describing the Tam Ngu Hao 2 tooth is published, open access, in Nature Communications:
The Pleistocene presence of the genus Homo in continental Southeast Asia is primarily evidenced by a sparse stone tool record and rare human remains. Here we report a Middle Pleistocene hominin specimen from Laos, with the discovery of a molar from the Tam Ngu Hao 2 (Cobra Cave) limestone cave in the Annamite Mountains. The age of the fossil-bearing breccia ranges between 164–131 kyr, based on the Bayesian modelling of luminescence dating of the sedimentary matrix from which it was recovered, U-series dating of an overlying flowstone, and U-series–ESR dating of associated faunal teeth. Analyses of the internal structure of the molar in tandem with palaeoproteomic analyses of the enamel indicate that the tooth derives from a young, likely female, Homo individual. The close morphological affinities with the Xiahe specimen from China indicate that they belong to the same taxon and that Tam Ngu Hao 2 most likely represents a Denisovan.

Evidence then of a second archaic hominin in addition to Neanderthals, probably evolving from an earlier migration out of Africa of a common ancestor (probably H. erectus) to both them and H. sapiens, which had not diversified so far as to prevent interbreeding between all three species, although not sufficiently well to justify them being regarded as subspecies or regional variants, judging by the few genes of either that have been retained by modern H. sapiens.

In fact, for much of our shared history, hominins have behaved very much like a ring species, undergoing speciation across a wide geographical range. A snapshot of speciation in progress and entirely inconsistent with the popular Bronze Age origin myth that require a founder couple magically arising out of dirt without ancestry, as though such a thing was even remotely possible. Not a founder couple and not even a founder species, but at least three ancestral species contributing to the modern H. sapiens genome and sharing at least one common ancestor that evolved in Africa, where the genetic evidence shows periods of isolation and partial speciation followed by contact and remixing of the genomes, even before migration up into Eurasia.

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Tuesday, 17 May 2022

Malevolent Designer News - Why Creationism's Beloved Malevolence Has Its Work Cut Out

Even as the structure of SARS-CoV-2 changes with different variants of the virus (gray), the J08 antibody (blue) can still bind it, Scripps researchers showed.
Credit: Scripps Research
Scripps Research scientists explain what makes COVID-19 antibody “J08” so potent | Scripps Research

Creationist mode:

Creationism’s beloved malevolence is going to have its work cut out it it is to outdo bio-medical science in their search for a definitive cure for the COVID-19 virus it created to cause the current COVID-19 Pandemic. So far, it has come up with several variants, the latest being the Omicron variant that is much more contagious than earlier variants, but, at least in a population where a large proportion of the people have been vaccinated, is mostly, though not always, a relatively mild infection.

Nevertheless, it has managed to achieve nearly 6.3 million deaths worldwide, 1 million of them in the USA where, due to the incompetence and narcissistic Dunning-Kruger stupidity of the president when the pandemic started and was most dangerous in 2020, and because of the opposition to measures to control it by fundamentalist Christians and the super spreader events they insisted on holding in their churches, deaths were far in excess of anything seen in most other advanced economies.

But now, a collaborative effort between scientists at the Scripps Institute and scientists in Italy and France may have found an antibody to the SARS-CoV-2 virus that not only treats and prevents known variants of COVID-19 but will probably be effective against future variants. The antibody is currently undergoing stage II/III clinical trials in Italy. The antibody, known as J08 was isolated from the blood of people who had recovered from COVID19 by scientists at the Scripps Institute and Toscana Life Sciences.

The question creationist devotees of the magic, pestilential sky man whom they believe designs these things, is just how is it going to find a way round this new prevention/treatment so it can continue the chaos and suffering it created? Only time will tell.

Creationist mode:

Even though we can’t predict what variants of COVID-19 will emerge next, understanding the details of J08 reveals what works against the virus, and perhaps how we can engineer antibodies to be even more potent.

Professor Andrew Ward, PhD, senior author
Professor of Integrative Structural and Computational Biology
Scripps Research, La Jolla, CA, USA
Their research is published, open access, in the journal Proceedings of the National Academy of Sciences (PNAS), where the researchers claim that, because of it's flexibility it will likely remain effective against future variants.

As the Scripps news release explains:
When a person is exposed to a virus like SARS-CoV-2, their body generates a variety of antibodies that bind to different sections of the virus to clear it from the body. Scientists designing vaccines and treatments against COVID-19 are interested in what makes some of these naturally produced antibodies—like J08—more effective than others. In the months after Ward and his collaborators first identified J08, it became clear that the antibody, unlike many others, was potent against a variety of COVID-19 variants.

With variants other than Omicron, this antibody binds quickly and doesn’t come off for hours and hours. With Omicron, we were initially happy to find that it still binds, but it falls off very quickly. We identified the two structural changes that cause this.

I think we’re pretty confident that future variants won’t necessarily have both of these two critical mutations at the same time like Omicron, so that makes us hopeful that J08 will continue being very effective.

Gabriel Ozorowski, co-first author
Senior staff scientist
Professor Ward’s Laboratory
Scripps Research, La Jolla, CA, USA.
In the new work, the researchers determined the three-dimensional structure of J08 as it bound to the spike protein of SARS-CoV-2. They confirmed that J08 successfully attached to the Alpha, Beta, Gamma and Delta variants and neutralized the viruses—preventing them from replicating. However, J08 attached to the Omicron variant about 7 times more slowly, and then rapidly came off. About 4,000 times more J08 was needed to fully neutralize Omicron SARS-CoV-2 compared to the other variants.

This small, flexible footprint is part of why J08 is able to withstand so many mutations—they don’t impact the antibody binding unless they happen to be in this one very small part of the virus.

Jonathan Torres, co-first author
Lab manager
Professor Ward’s Laboratory
Scripps Research, La Jolla, CA, USA.
The team showed that, for all the variants, J08 binds to a very small section of the virus—a section that generally stays the same even as the virus mutates. Moreover, J08 could attach in two completely different orientations, like a key that manages to unlock a door whether it is right side up or upside down.

The Omicron variant of SARS-CoV-2, however, had two mutations (known as E484A and Q493H) that changed the small area of the virus that directly interfaces with J08, anchoring it in place. Ward and his collaborators found that if just one of these mutations is present, J08 still manages to bind and neutralize the virus strongly, but mutations in both are what make it less effective against the Omicron variant.
The team have published their results in the journal Proceedings of the National Academy of Sciences (PNAS):
Clinical candidate monoclonal antibody J08 binds the severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) S-protein independent of known escape mutations and is able to potently neutralize most variants of concern (VoCs). Here, we explore these properties using cell-based assays and structural studies. A relatively small epitope footprint high on the receptor binding domain (RBD) ridge and the ability to bind multiple conformational states of the S-protein contribute to strong neutralization across several variants.
As the coronavirus disease 2019 (COVID-19) pandemic continues, there is a strong need for highly potent monoclonal antibodies (mAbs) that are resistant against severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) variants of concern (VoCs). Here, we evaluate the potency of the previously described mAb J08 against these variants using cell-based assays and delve into the molecular details of the binding interaction using cryoelectron microscopy (cryo-EM) and X-ray crystallography. We show that mAb J08 has low nanomolar affinity against most VoCs and binds high on the receptor binding domain (RBD) ridge, away from many VoC mutations. These findings further validate the phase II/III human clinical trial underway using mAb J08 as a monoclonal therapy.
If this antibody proves as effective as early indications seem to show, and if it can be produced in sufficient quantities, and if it can be made available world-wide regardless of national wealth, then it might be possible to irradicate this nasty little virus in the human population altogether.

However, in the past, the process which produces new variants has proved to be amazingly creative. With a world-wide population of the virus probably numbering in the trillions or quadrillions, the probability of a novel combination of mutations arising by chance alone is a virtual certainty. And of course, as with any zoonotic species of parasite, the potential for breeding a novel variant in some other species can't be ruled out.

The likelihood is that science will always be playing catchup until a generic vaccine against all coronaviruses is found and measures to get it into the arms of everyone aren't hampered by the same superstitious, credulous fools who believe in magic designers, because people who study only the fantasies of Bronze Age hill farmers told them it was real science, and threatened them with eternal torture if they didn't believe it.

Evolution News - Ecology Before the 'Cambrian Explosion'

A group of Ediacaran specimens of Fractofusus and Plumeropriscum from the “E” surface, Mistaken Point Ecological Reserve, Newfoundland, Canada.
Credit: Charlotte G. Kenchington (CC BY 4.0)
Creationists are fascinated by the so-called Cambrian Explosion, believing it to have happened over a very short time span and claiming it to be evidence of spontaneous creation of a wide variety of body plans. Of course, it took place over tens of millions of years and was preceded by the Ediacaran biota in which a number of novel body plans evolved in the second major wave of multicellular evolution.

Now, According to a study by Rebecca Eden, Andrea Manica1 and Emily G Mitchell of the Zoology Department, Cambridge University, UK, published today in the open access online journal, PLOS Biology, these early animals formed complex ecological communities more than 550 million years ago, setting the evolutionary stage for the Cambrian explosion.

The Ediacaran period is itself divided into three periods of evolutionary radiation, named after the locations where representative fossils have been found: the Avalon, White Sea and Nama radiation. The Avalon (575-565 million years ago), shows relatively limited ecological and morphological diversity, unlike the White Sea radiation which shows a large increase in morphological diversity, including probable bilateralism and with it an increase in ecological diversity and environmental influence. Some this was followed by a mass extinction leading to a loss of taxonomic diversity but the evolution of biomineralization, such as shells, in the third, Nama, radiation.

Biomineralization implies the need for protection and that implies the prior evolution of motility and predation and the beginnings of evolutionary arms races between predator and prey, and with that would have come environmental pressure to evolve sensory organs such as eyes. Predation also requires digestive and excretory systems.

According to information supplied by PLOS ahead of publication:

Evolution News - How the Environment Made a Difference with Penduline Tits

Eurasian penduline tit, Remiz pendulinus
Chinese penduline tit buries eggs to prevent them from blowin’ in the wind | Science Linx News | Science LinX | University of Groningen

First off, if you came here attracted by the title, hoping to see something about large busty substances, you're in the wrong place. This is about a couple of closely related birds known as the Eurasian and Chinese penduline tits and about how subtle differences in their environments can cause differences in behaviour that act as barriers to hybridisation and so reinforce the evolving divergence into different species. If you're so shallow as to be looking for the former on line, you're probably too shallow to be interested in the latter.

The Eurasian penduline tit, Remiz pendulinus, is so called because males build a relatively large, dangling (penduline) nest on the end of thin willow branches or reeds, often over water. He then tries to attract a female to use the nest and, if she approves, he mates with her, and she begins to lay a batch of eggs over the next 14 days but won't permit the male to enter the nest. This choice of location is probably to make it difficult for predators to reach the nest.

The strange thing is each day she covers the eggs in the bottom of the nest before going off to feed herself. This is thought to be due to inter-sex rivalry because either one or the other parent is going to take responsibility for the incubation of the eggs and rearing the chicks and the female needs the male to hang around to mate with her and the male needs her to stay and use his nest so his offspring are in the eggs she lays.

When the batch of eggs is complete, the female, more often than not, incubates them and the male leaves to find another mate, but frequently, it's the female who leaves the male to do the incubation and rearing. Very occasionally, neither parent takes responsibility, and the nest and eggs are abandoned. But the male won't start to incubate the eggs until the batch is complete. Burying the eggs is thought to be an evolved strategy for keeping the male interested until the batch is complete.

Chinese penduline tit, Remiz consobrinus
However, a closely related species, the Chinese penduline tit, Remiz consobrinus, has a different pattern of behaviour. The make builds the next in the same way and in a similar position to his Eurasian cousin, and attracts a female to use it. However, she doesn't exclude him from the nest but they both roost in it together at night, and both sexes share responsibility for incubation and rearing the chicks. But, like her Eurasian cousin, the female Chinese penduline tit still assiduously buries her eggs every day. The question is, if this isn't due to inter-sex rivalry as with the Eurasian species, what is it due to? The answer has turned out to be due to subtle environmental differences.

To investigate this difference and the lack of aggression between the sexes by which the Eurasian female keeps the male from entering the nest while she is laying her batch of eggs, Jia Zheng, who had completed her master’s degree under Professor Zhengwang Zhang, from Beijing Normal University, and was now completing her PhD at the University of Groningen, conducted a number of experiment to test out various hypotheses.

The Groningen University News release explains how she went about it:

Monday, 16 May 2022

Malevolent Designer News - Creationism's Favourite Malevolence Suffers Another Blow From Science

Congenital melanocytic nevus.
These can be very large and often involve the head, face or genitalia.
Skin drug treatments may regress dangerous birthmarks and prevent melanoma

Creationist mode:

The malevolent designer that creationists worship must be getting really pissed off with modern bio-medical scientist, the way they keep finding ways to combat the nasty things it designs to increase the suffering in the world, and all because someone scrumped one of its apples, allegedly.

Fresh from science's partial victory over the SARS-CoV-2 virus with which the divine malevolence caused a major pandemic, killing millions, ruining economies and businesses and making even the survivors suffer long-term complications, we have news that scientists led by investigators at Massachusetts General Hospital (MGH), MA, USA may have come up with a treatment for a rare form of melanoma that about 20,000 babies a year are born with.

The congenital melanoma is usually in the form of a large mole or 'giant nevus' that covers part of the face, head or other parts of the body and carries a very high risk of becoming malignant. Because of the high risk of malignancy, the treatment up to now had been surgical removal, which was not always successful in that the melanoma could recur, and which often left a large, permanent scar. Congenital giant nevi are normally caused by a mutation in the gene NRAS, which, as any intelligent [sic] design creationist will tell you, only happens by design.

Sunday, 15 May 2022

QAnon/COVID Conspiracy News - The Flights of Fancy Go Stratospheric

Dr Bryan Ardis, Chiropractor and acupuncturist.
"Covid-19 is not a virus, it's snake venom" [sic]
The King Cobra Venom Pandemic: Stew Peters Unveils a New COVID-19 Conspiracy Theory | Right Wing Watch

It's amazing how, the more QAnon's ludicrous conspiracy theories are debunked, the more risible they became in trying to justify them, like toddlers caught with their hands in the cookie jar, rather than admit the game's up and they've been rumbled.

The even more amazing thing is that adults, even adults holding responsible positions, like Representative Marjorie Taylor-Green (R-GA 13) and Senator Doug Mastriano (R-PA 33) continue to fall for these tactics.

One example of how far into the stratosphere QAnon conspiracists have gone in the justification for opposing measures to mitigate the COVID-19 pandemic, which is about to achieved its millionth American death, on the grounds that it's all a plot, somehow linked to a Satanic, cannibalistic paedophile, deep state conspiracy run by Hillary Clinton, Barak Obama and the Pope, and including Bill Gates, Andrew Faucci and others, is the so-called 'explosive report' by medical quackticioner, Dr. Bryan Ardis.

His 'explosive' report which he revealed on the far right Stew Peters Show, is that the SARS-CoV-2 virus that causes COVID-19 is not a virus at all but a modified snake venom which is passed on deliberately in drinking water. Seriously!

Here is how he arrived at that conclusion, not by analysis of drinking water, or by subjecting samples of the virus to biochemical analysis, but by a form of logic of which any self-respecting toddler might be proud, until they grew up enough to cringe in embarrassment at their childish thinking.

Here is his 'reasoning':

SCOTUS Now Represents Only a Small Minority of American Religious Extremists.

Attitude towards abortion by religiosity and political leanings. States set to make abortion illegal in all circumstances will be complying with the opinion of Americans who attend church every week, especially Republicans.
Personal Religiosity and Attitudes Toward Abortion

The evidence from Gallop is that, if SCOTUS as expected overturns the 1973 ruling in Roe v Wade and allows the criminalisation of abortions in all or most cases, they will be empowering states to impose the views of a small minority of religious extremists on the rest of America, as the following charts show.

SCOTUS, whose prime purpose is to uphold the Constitutional constraints on government action, will be explicitly endorsing a flagrant imposition of Conservative Christian dogma by incorporating it into state laws.

On every measure, the opinion that abortions should be illegal in all circumstances - including where pregnancy is the result of rape or incest or the woman is very young, and even when there is severe foetal abnormality such that independent life will be impossible or there is a serious risk to the woman's life - is an opinion not shared by most Americans. It's not even the majority opinion of those Americans who go to church every week.

Saturday, 14 May 2022

YEC/Creationism - Notions in Crisis

A spatiotemporal interpretation of population differentiation in SW Asia and Europe based on our model and the geographic distribution of the genomes.
Colored shaded areas indicate approximate putative distributions of populations at different time points. The letters (A) to (H) indicate the chronological order of events; see main text for a detailed description. Note that warmer periods (Bølling and Allerød interstadials, Holocene) correspond to population range expansions while colder periods (LGM, Older Dryas) are associated with contractions. See also Figure S4 for additional f-statistics analyses supporting alternative connections between the Levant and the Aegean/Greece area.

Ancient DNA maps ‘dawn of farming’

The flood of evidence that YECism and Creationism are notions (I won't grace them with the scientific term, 'theories') in crisis continues with news that two of the largest assemblages of ancient human genomes have revealed that the origins of European farmers was in Turkey, but that population originated many thousands of years earlier from diverse hunter-gatherer populations in Europe and Asia.

Of course, there is absolutely no evidence that all humans are descended from a single founder couple who lived just a few thousand years ago in the Middle East, as creationism's favourite myths claim.

The advances in recovering high quality genomes from ancient remains would be terrifying creationist cult leaders if they weren't safe in the knowledge that their dupes would never dream of checking facts or reading scientific publications in case they had to admit they could be wrong, so articles in science magazine such as Nature or New Scientist will go unnoticed and ignored.

The evidence in question was published in two open access papers in Cell and BioRxiv a few days ago. These works build on the 2016 findings by Lazaridis, Iosif, et al, who showed that:
…the earliest populations of the Near East derived around half their ancestry from a ‘Basal Eurasian’ lineage that had little if any Neanderthal admixture and that separated from other non-African lineages before their separation from each other. The first farmers of the southern Levant (Israel and Jordan) and Zagros Mountains (Iran) were strongly genetically differentiated, and each descended from local hunter–gatherers. By the time of the Bronze Age, these two populations and Anatolian-related farmers had mixed with each other and with the hunter–gatherers of Europe to greatly reduce genetic differentiation. The impact of the Near Eastern farmers extended beyond the Near East: farmers related to those of Anatolia spread westward into Europe; farmers related to those of the Levant spread southward into East Africa; farmers related to those of Iran spread northward into the Eurasian steppe; and people related to both the early farmers of Iran and to the pastoralists of the Eurasian steppe spread eastward into South Asia.
Copyright: © 2022 The authors.
Published by Published by Elsevier Inc. Open access (CC BY 4.0)
So, in contrast to the YEC/Creationist myth, the people of Israel and Jordan did not arise in situ, without ancestry, but evolved locally from earlier hunter-gatherer people to form genetically distinct populations which later merged and mixed with other hunter-gatherer people in what is now modern Turkey and then spread westwards into Europe.

These new papers flesh out the bbare bones of that finding by exploring the origins of the populations who merged with the indigenous people to become the original farmers of Anatolia who then spread westwards.

A team co-led by population geneticist, Laurent Excoffier, from the University of Bern, sequenced the genomes of 15 individuals from archaeological sites in Western Anatolia and along the Danube River - one of the main migration routes into Europe. The genomes were of sufficient quality to enable analysis of, for example, major changes in population size. Excoffier's team found that the ancient Anatolian farmers were descended from repeated mixing between populations from Europe and the Middle East who had split about 25,000 years earlier at the height of the last Ice Age. The European population had almost died out at one point but bounced back when the climate warmed. The spread of these farmers into Europe began about 8,000 years ago. The migrants would have encountered and replaced the indigenous hunter-gatherers although they don't appear to have interbred extensively with them. This team's findings are published inCell:
Graphical abstract

  • European HGs diverged from SW Asian HGs during the LGM
  • Low genetic diversity of European HGs is due to a strong LGM demographic bottleneck
  • Ancestors of western early farmers emerged after repeated post-LGM admixtures
  • EFs strongly diverged from SW Asians during their expansion through Anatolia


The precise genetic origins of the first Neolithic farming populations in Europe and Southwest Asia, as well as the processes and the timing of their differentiation, remain largely unknown. Demogenomic modeling of high-quality ancient genomes reveals that the early farmers of Anatolia and Europe emerged from a multiphase mixing of a Southwest Asian population with a strongly bottlenecked western hunter-gatherer population after the last glacial maximum. Moreover, the ancestors of the first farmers of Europe and Anatolia went through a period of extreme genetic drift during their westward range expansion, contributing highly to their genetic distinctiveness. This modeling elucidates the demographic processes at the root of the Neolithic transition and leads to a spatial interpretation of the population history of Southwest Asia and Europe during the late Pleistocene and early Holocene.

These findings are supported by the work of a second team, co-led by palaeogeneticist Eske Willerslev at the University of Copenhagen, who obtained genomes from 317 early farmers and hunter gatherers from across Eurasia. Their findings also show an early split between eastern and western hunter-gatherers and dates the arrival of early farmers in the Balkans to about 8,000 years ago. Their findings are published in BioRxiv:
Copyright: © 2022 The authors.
Published by Published by bioRxiv. Open access (CC BY 4.0)
The transitions from foraging to farming and later to pastoralism in Stone Age Eurasia (c. 11-3 thousand years before present, BP) represent some of the most dramatic lifestyle changes in human evolution. We sequenced 317 genomes of primarily Mesolithic and Neolithic individuals from across Eurasia combined with radiocarbon dates, stable isotope data, and pollen records. Genome imputation and co-analysis with previously published shotgun sequencing data resulted in >1600 complete ancient genome sequences offering fine-grained resolution into the Stone Age populations. We observe that:
  1. Hunter-gatherer groups were more genetically diverse than previously known, and deeply divergent between western and eastern Eurasia.
  2. We identify hitherto genetically undescribed hunter-gatherers from the Middle Don region that contributed ancestry to the later Yamnaya steppe pastoralists.
  3. The genetic impact of the Neolithic transition was highly distinct, east and west of a boundary zone extending from the Black Sea to the Baltic. Large-scale shifts in genetic ancestry occurred to the west of this “Great Divide”, including an almost complete replacement of hunter-gatherers in Denmark, while no substantial ancestry shifts took place during the same period to the east. This difference is also reflected in genetic relatedness within the populations, decreasing substantially in the west but not in the east where it remained high until c. 4,000 BP.
  4. The second major genetic transformation around 5,000 BP happened at a much faster pace with Steppe-related ancestry reaching most parts of Europe within 1,000-years. Local Neolithic farmers admixed with incoming pastoralists in eastern, western, and southern Europe whereas Scandinavia experienced another near-complete population replacement. Similar dramatic turnover-patterns are evident in western Siberia.
  5. Extensive regional differences in the ancestry components involved in these early events remain visible to this day, even within countries. Neolithic farmer ancestry is highest in southern and eastern England while Steppe-related ancestry is highest in the Celtic populations of Scotland, Wales, and Cornwall (this research has been conducted using the UK Biobank resource).
  6. Shifts in diet, lifestyle and environment introduced new selection pressures involving at least 21 genomic regions. Most such variants were not universally selected across populations but were only advantageous in particular ancestral backgrounds. Contrary to previous claims, we find that selection on the FADS regions, associated with fatty acid metabolism, began before the Neolithisation of Europe. Similarly, the lactase persistence allele started increasing in frequency before the expansion of Steppe-related groups into Europe and has continued to increase up to the present.
Along the genetic cline separating Mesolithic hunter-gatherers from Neolithic farmers, we find significant correlations with trait associations related to skin disorders, diet and lifestyle and mental health status, suggesting marked phenotypic differences between these groups with very different lifestyles. This work provides new insights into major transformations in recent human evolution, elucidating the complex interplay between selection and admixture that shaped patterns of genetic variation in modern populations. [My formatting for added clarity].

Allentoft, Morten E.; Sikora, Martin; Refoyo-Martínez, Alba; Irving-Pease, Evan K., et al
Population Genomics of Stone Age Eurasia
bioRxiv 2022; DOI:10.1101/2022.05.04.490594

Copyright: © 2022 The authors. Published by bioRxiv.
Open access
Reprinted under a Creative Commons Attribution 4.0 International license (CC BY 4.0)
Two papers that both tell the same story: not spontaneous generation in the Middle East a few thousand years ago, but a history going back at least 250,000 years by which time the Eurasian populations had already diverged and become genetically distinct, just as the Theory of Evolution predicts isolated populations will, and these were the people who populated the Middle East to form the Bronze Age farmers who invented the origin myths in the Bible - the same people who believed Earth was small, flat, ran on magic and had a dome over it to keep the water above the sky out and as somewhere to hang the sun, moon and stars.

Creationists hold that this is the best description of geological and human history, far surpassing for accuracy anything that science can produce, such as the above genetic evidence that the myths are nothing more than childish fantasies, made up by people who knew no better. The human story is far too fascinating and wonderful to be dismissed by childish fools who require the narrative to be simple enough for a toddler to understand.

Lying Christians News - David Barton Just Can't Stop

David Barton, pseudo-historian and Talibangelical liar
David Barton Falsely Claims Voter Turnout 'Was 100 Percent' in Early America Because 'Churches Ran the Communities' | Right Wing Watch

How can you tell when pseudo-historian and Talibangelical Christian extremist David Barton is lying again?

Well, I'll leave you to fill in the obvious punchline, but Barton epitomises the old adage that when you show the world you know you need to lie for your faith, you show the world you know your faith needs fools to believe falsehoods. As Mark Twain said, "Lying is trying to fool someone into believing something you know ain’t so!"

The question is, why does David Barton and his extremist Christian supporters need Americans to believe something they know ain’t so? The answer is because they don't want them believing things they know are so, of course.

Friday, 13 May 2022

Abiogenesis News - Closing in to Fill Creationism's Favourite Gap - No God Found.

a, tRNA structure showing selected ribose and nucleobase modifications. The 3′-amino acid-acylated adenosine is located at the CCA 3′ end in contemporary tRNAs. 5-Methylaminomethyl uridine, mnm5U, is found in the wobble position 34. The amino acid-modified carbamoyl adenosine, (m6)aa6A (aa, amino acid), is present at position 37 in certain tRNAs. b, General RNA–peptide synthesis cycle based on mnm5U and m6aa6A. The structures of oligonucleotides are simplified and only terminal nucleobases are drawn.
The origin of life: a paradigm shift - LMU Munich

It doesn't seem to have dawned on creationists who forlornly claim, despite the daily torrent of evidence to the contrary, that the Theory of Evolution is a theory in crisis. Far from the TOE being a 'theory in crisis', the reality is that it's the childish notion of creationism that's in crisis and which is being increasingly rejected even by religious people as a valid explanation for how life diverged. It's only by creative misrepresentation of the data, or by dismissing it out of hand, that creationist frauds are still able to pull the wool over the eyes of their credulous dupes, to maintain their cult’s superstitions.

One of their mainstays as an 'argument' which they invariably fall back on when confronted with unarguable evidence for evolution by natural selection and other mechanisms, is that none of the mechanisms explain the origin of 'life' itself (abiogenesis, life from non-life'), and without that, evolution would have nothing to work on. It is, of course, irrelevant to the mechanisms by which life diversified once replicators did get going, but, as usual with childish notions, the relevance of using the false dichotomy fallacy is lost on creationists who lack the critical thinking skills to spot the trick, and few if any of them could define the term 'life' in a scientifically meaningful way, anyway, so assume it means some magic ingredient that separates organic' molecules from inorganic ones. It is one of the last remaining gaps which they insist must contain their god and their belief is that, of all the gaps closed by science, this will be the one where a god is found. Their ever-shrinking little god has degenerated to the size of this one remaining gap. The magician that magicked 'life' from non-life and made them 'speshul'.

There are, of course, many possible alternative explanations for how a simple replicator could have got going and, indeed, there doesn't even need to be a single explanation since two or more replicators could have got together early on. If the result had given them an advantage over remaining separate, then this symbiosis would have been almost inevitable.

One of the more popular hypotheses amongst biologists is the 'RNA world hypothesis' that says, because RNA is still the functional unit of biological activity and it is simpler than DNA, it probably came first and DNA followed on as an evolved improvement, acting as RNA's data store and so became the functional organ of inheritance of genetic data.

This is the idea currently being expanded by a team at the Ludwig-Maximilians-Universität München, Germany. Their work has just been published, open access in Nature. They believe they have solved one of the outstanding problems with the theory - how RNA began catalysing the production of chains of amino acids to form peptides and short proteins without the peptides it codes for - a classic chicken and egg conundrum.

Like all chicken and egg conundrums, if this scenario is correct, it turns out that neither of them came first; they both emerged simultaneously and part of a developing complex out of simple pre-existing precursors.

As the Ludwig-Maximilians-Universität news release explains:

Thursday, 12 May 2022

Malevolent Designer News - Creationism's Divine Malevolence Excels Itself With Toxoplasmosis

Toxoplasma gondii
I thought devotees of creationism's malevolent designer might like to read about an astonishingly successful organism it allegedly created. It is the organism known to medical science and biology as Toxoplasma gondii, the organism responsible for the disease, toxoplasmosis.

According to the WHO over 1 million people in the European area alone become infected by it and, according to Professor Justine R. Smith, Professor of Eye & Vision Health, Flinders University, Australia and Assistant professor João M. Furtado, Assistant professor of Ophthalmology, Universidade de São Paulo, Brazil, writing in The Conversation, 30%-50% of the world's population could be infected by it, making it the most successful pathological organism known. Once infected a person carries it for life and it is one of the most zoonotic organisms, capable of infected almost any animal or bird.

Wednesday, 11 May 2022

Unintelligent Designer News - More on the Blunder That is RuBisCo

The enzyme rubisco is found in all plants and other photosynthesizing organisms. It plays a key role in fixing carbon from the air and has helped shape life on Earth.
Credit: Getty Images
Photosynthesis unaffected by increasing carbon dioxide channels in plant membranes | RIPE

Readers may recall how I wrote recently about the enzyme RuBisCo, and how, if they understood its significance, it would be a major embarrassment for devotees of creationism's putative intelligent [sic] designer. To give it it's full chemical name, ribulose-1,5-bisphosphate carboxylase/oxygenase is probably the least efficient enzyme in all biology and yet is absolutely essential for the energy almost all living things ultimately depend on.

It is responsible for 'fixing' the inorganic carbon in atmospheric carbon dioxide (CO2) as the first stage in building the carbon chain that is the backbone of the organic sugar, glucose, which is the end product of photosynthesis, along with free Oxygen (O2) as a by-product.

Indeed, so inefficient is RuBisCo that it is the reason there is so much green in the world, wherever there are growing plants. RuBisCo manages about 4 reactions a second against the hundreds or thousands of reactions that most other enzymes are capable of, and, because it frequently mistakes a molecule of O2 for one of CO2, it frequently wrecks the process and causes a loss of carbon. It can also go wrong and produce xylulose-1,5-bisphosphate which actually poisons it!

Because of this inefficiency, there is great pressure on scientists to come up with an alternative, or to develop an improved version, in order to increase food production, and, to that end, multiple universities and research institutes have established the RIPE Project, led by the University of Illinois, USA in partnership with The Australian National University, Chinese Academy of Sciences, Commonwealth Scientific and Industrial Research Organisation, Lancaster University, UK, Louisiana State University, USA, University of California, Berkeley, USA, University of Cambridge, UK, University of Essex, UK, and U.S. Department of Agriculture, Agricultural Research Service.

But one of the programs run by RIPE has just reported a failure. The researchers at the Division of Plant Sciences, Research School of Biology, The Australian National University, Acton, ACT, Australia, had been hoped that, if they could improve the supply of CO2 to RuBisCo, they could improve its efficiency. However, they discovered that the limitation was not the availability of CO2 itself but the ability of RuBisCo to utilise it that was the bottleneck in the process.

As the RIPE news release explains:

Our research targeted the membranes in leaf cells; we wanted to know if we could make CO2 transfer more efficient by adding extra channels for CO2 diffusion into cell membranes

Dr Tory Clarke
Australian National University
Modifying photosynthesis has increasingly been a research target to improve crop yields to feed a growing global population in the face of climate change and other environmental factors. In a recent study, published in the Journal of Experimental Botany, a team from the Australian National University (ANU) investigated the effects of increasing the amount of carbon dioxide channels in plant membranes, but could not detect any impact on photosynthesis in model tobacco plants.

Photosynthesis relies on a supply of carbon dioxide (CO2) to the chloroplasts within leaf cells, where it is fixed into sugars by the enzyme Rubisco. To get to the chloroplast, CO2 must diffuse into the leaf and through the leaf mesophyll cells, crossing barriers such as cell walls and membranes. Increasing CO2 diffusion through mesophyll cells into the chloroplast (termed mesophyll conductance) will improve photosynthesis–boosting yields in crops while also improving water-use efficiency.

Copyright: © 2022 The authors. Published by Published by Oxford University Press on behalf of the Society for Experimental Biology.
Open access
The team have published their work in the Journal of Experimental Botany:

In plants with C3 photosynthesis, increasing the diffusion conductance for CO2 from the substomatal cavity to chloroplast stroma (mesophyll conductance) can improve the efficiencies of both CO2 assimilation and photosynthetic water use. In the diffusion pathway from substomatal cavity to chloroplast stroma, the plasmalemma and chloroplast envelope membranes impose a considerable barrier to CO2 diffusion, limiting photosynthetic efficiency. In an attempt to improve membrane permeability to CO2, and increase photosynthesis in tobacco, we generated transgenic lines in Nicotiana tabacum L. cv Petite Havana carrying either the Arabidopsis PIP1;2 (AtPIP1;2) or PIP1;4 (AtPIP1;4) gene driven by the constitutive dual 2x35S CMV promoter. From a collection of independent T0 transgenics, two T2 lines from each gene were characterized, with western blots confirming increased total aquaporin protein abundance in the AtPIP1;2 tobacco lines. Transient expression of AtPIP1;2-mGFP6 and AtPIP1;4-mGFP6 fusions in Nicotiana benthamiana identified that both AtPIP1;2 and AtPIP1;4 localize to the plasmalemma. Despite achieving ectopic production and correct localization, gas exchange measurements combined with carbon isotope discrimination measurements detected no increase in mesophyll conductance or CO2 assimilation rate in the tobacco lines expressing AtPIP. We discuss the complexities associated with trying to enhance gm through modified aquaporin activity.

Imagine a production line where a critical part of the production process is performed by a machine which is so slow at the task that it slows the whole production line down to its very slow pace, and then frequently fits the wrong component and wrecks the product so the next stages in the process can't be performed, and it all has to be dismantled and started again. In the case of this study, the scientists tried increasing the supply of the components the machine need in case it wasn’t being supplied quickly enough. But that wasn't the problem. The problem is that the machine is so badly designed it just can't go any faster.

Creationists believe the equivalent of this machine was designed by a supremely intelligent production line engineer who didn't realise what a bad job it was doing so saw no reason to start again with a new design, and now modern factory managers are trying to find a way to make it more efficient, so they can continue to supply the demand for the product.

As the product of a utilitarian, near enough is good enough, evolutionary process that occurred early in the evolution of living organism and in an oxygen-free atmosphere, this is perfectly understandable. It is not understandable in terms of intelligent design by a supremely intelligent, omniscient designer who would have known in advance what problems lots of the by-product in the atmosphere - free oxygen - was going to cause.

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Evolution News - Why North American Fossils from 95 Million Years Ago Look Like Tropical Fossils

Cretaceous oysters of the genus Pycnodonte investigated in the new study. These specimens were collected in San Miguel County, Colorado (top left), Kane County, Utah (top right), Big Horn County, Wyoming (bottom left), and Natrona County, Wyoming (bottom right), with a penny for scale.
Image credit: Matt Jones
Bali-like temperatures in Wyoming? Fossils reveal tropically hot North America 95 million years ago | University of Michigan News

Gullible fools who have been conned into believing, despite all the evidence showing otherwise, that planet Earth is just a few thousand years old, for no better reason than their mummy and daddy had been fooled into believing it, will need to ignore this evidence as well.

It is evidence that not only were fossils of highly evolved species being laid down in Wyoming, USA, 95 million years ago, but that the climate there at that time was more like that in tropical regions of Earth today.

The new study, by researchers from the University of Michigan shows that much of western North America, 95 million years ago, was covered by a shallow sea as warm as today’s tropics. The existence of this sea coincided with the "Cretaceous Thermal Maximum", one of Earth's hottest periods in the past 100 million years.

According to information supplied by the University of Michigan:

Malevolent Designer News - How Creationism's Divine Malevolence Made a Parasite Better at Killing Children

The Kissing bug, Triatom infestans,
The main vector for Trypanosoma cruzi, the parasite that causes Chagas disease.
Hybrid strains make insidious parasite more dangerous | Karolinska Institutet Nyheter

Creationist mode:

If you’re a divine malevolence and have gone to all the trouble to design a blood-born parasite like the trypanosome, Trypanosoma cruzi, especially for making people sick and die, and have even created a special means of passing it from one person to another to make sure as many people suffer as possible, such as the 'kissing bug', Triatom infestans, you're not going to just stand by and allow a potential victim's immune system (that you designed to protect them from your parasites), stop the trypanosome from doing its job and making them sick, are you?

Of course not!

Trypanosoma cruzi, the organism that causes Chagas disease

Credit: CDC/Dr. Myron G. Schultz
As we have seen before, most of these nasty little organisms that creationists believe were created by their favourite god, have been designed to evade or even suppress their host's immune system so they can make life as miserable, or as short, as possible.

A good example of this, and an example of the inventive genius of anything that designed it, is in fact Trypanosoma cruzi, the microorganism that causes Chagas disease, which affects millions of people in Central and South America, causing thousands of deaths every year. Researchers at the Karolinska Institutet, Sweden, have discovered just how brilliantly this parasite has been designed so it can continue to do what it was designed to do. They have shown that it can form new variants from hybrids of different strains that are often better at circumventing the immune system and causing disease.

As the Karolinska Institutet news item announcing the team's publication of their findings in the online journal, eLife, explains:

Tuesday, 10 May 2022

Malevolent Designer News - How a Mutation Made Us More Susceptible to Cancer

A single genetic mutation made humans more susceptible to cancer | New Scientist

Creationist mode:

Creationism’s favourite divine malevolence could have given humans the same protection from cancer that it gave to elephants, but it chose not to.

Instead, it gave us a mutated version of a gene that makes us more likely to develop life-threatening cancers when the replication mechanism it designed for our cells, goes wrong and the faulty DNA doesn't get repaired. This replication mechanism, where the entire genome is replicated even though most cells will use only a small fraction of it, is necessary because the designer used the same method for us multicellular animals that it created for single-celled organisms, so being massively wasteful and increasing the danger of something going wrong, of course, but that's a slightly different issue.

I have more to say on this phenomenon in my popular, illustrated book, The Malevolent Designer: Why Nature's God is not Good

What scientists have recently discovered is that the gene, BRCA2, which plays a key role in repairing the DNA when it isn't replicated properly, has been modified in humans to make it less effective at doing what it was designed to do in other mammals, including chimpanzees. This repair mechanism was already far less efficient than that in elephants which get multiple copies of these repairing genes, so, although they have very many more cells than us and so very many more cell replications as they grow, they very rarely get cancers.

Even in our closest relative, the other great apes, cancers are relatively rare. Between 1901 and 1932, of the 971 non-human primates that died in Philadelphia Zoo, only 8 were found to have tumours on autopsy. so there is no doubt that humans, supposedly the favourite creation of creationism's favourite creator, are designed to get cancers more than most mammals and the decision to design us that way was a choice.

Creationist must believe, because they are obliged to, that this change in the BRCA2 gene can't have been accidental because nothing happens in nature without the intention and involvement of their magic creator, so we can only assume it wants us to get cancer.

Creationist mode:

Now to the science, which, unlike creationism and the childish notion of intelligent design, makes sense of the facts:

Unintelligent Designer News - Another Arms Race between Bats and Owls is Another Problem for Batty Creationists

Greater mouse-eared bat, Myotis myotis
Bats mimic the sound of bees and hornets to scare away predators | New Scientist

Italian scientists have recently discovered a fascinating example of Batesian mimicry, using sound rather than colour and shape, to deter predators.

Batesian mimicry is where a species comes to resemble a harmful or distasteful species although being harmless and edible itself. Examples are the beetles and butterflies that resemble wasps, or the eyes on a butterfly's wings that resemble the eyes of a predatory animal. These often result in arms races where the predator evolves to be able to tell the difference, but the prey then evolves to improve the mimicry.

The phenomenon of arms races is a subject most intelligent [sic] design creationists understandably steer well clear of. They are almost invariably features of host-parasite and prey-predator relationships. A prey species will benefit from any changes that improve its ability to avoid being prey and a predator will benefit from any changes that improve its ability to catch its prey, so arms races are major drivers in evolution.

It's difficult to see how a single designer switching back and forth between two species, seeing every solution it has just designed for one species as a problem to be overcome for the other species, can possibly be regarded as the behaviour of an intelligent designer. Creationists, by the dogma of the religion they invariably subscribe to, are forbidden from explaining this as the acts of two or more competing creators, of course, so are obliged to continue to present their favourite god as, frankly, a rather stupid amnesiac, not knowing from one day to the next what it is supposed to be achieving and forgetting what the solution it designed yesterday was all for.

I cover these evolutionary arms races and the problem they present for intelligent [sic] design advocates in my popular book, The Unintelligent Designer: Refuting the Intelligent Design Hoax.

But enough of the problems creationists have in sustaining their childish superstition and the absurd mental gymnastics they need to perform.

What the scientists have discovered is that bats, which are predated on by tawny owls (Strix aluco), can deter an attack by mimicking the buzz of harmful hymenopteran insects such as bees and hornets. The team, led by Danilo Russo of the Wildlife Research Unit, Dipartimento di Agraria, Università degli Studi di Napoli Federico II, Portici, Italy, realised that the bats they caught in mist nets would buzz like bees or hornets when they handled them. To study the phenomenon, they recorded the sounds made by the greater mouse-eared bat, Myotis myotis.

Towny owl, Strix aluco
Fooled by buzzing bats
When they modified the frequencies of the recorded sounds to resemble how an owl would hear them, they sounded even more like bees and hornets. When they played these recordings to tawny owls, along with the recorded buzzing of a western honeybee, a European hornet and a non-buzzing vocalisation of the bat, the owls moved away from all the buzzing sounds, but toward the non-buzzing bat vocalisations.

The team's findings are published in Current Biology, sadly behind an expensive paywall, however the abstract can be read here. In it the authors explain the phenomenon of mimicry, with:

Mimicry traits often reflect complex, finely tuned, and sometimes extravagant relationships among species and have evolved to deceive predators or prey. Indeed, mimicry has most often evolved to discourage predation: the ‘mimic’ exhibits phenotypic convergence towards a non-related ‘model’ organism which is inedible or harmful, so that a given predator, or ‘receiver’, will refrain from attacking or ingesting the mimic.

Monday, 9 May 2022

The Lunatics Are Now Running the US Asylum

The impending SCOTUS ruling overturning the 1973 Roe vs Wade ruling that legalised abortion in all US states is a sign that the lunatics have taken over and are now running the asylum.

As I reported yesterday, the decision was based, at least in part on the false idea that a foetus suffers during the procedure. This claim was based on a 2020 discussion paper by British scientist, Dr Stuart Derbyshire, that wrongly claimed the work of the Italian professor of neuroscience, Giandomenico Iannetti, had shown that the foetus could feel pain even before its cerebral cortex had developed at 24 weeks.

SCOTUS were not told by the Lawyers representing evangelical Christian extremists that Professor Iannetti strongly refuted Derbyshire's claim, and he was not called to testify to that fact, nor even told that his work was being (mis)used to argue against a woman’s right to abortion - something of which he is strongly in favour.

A highly selective piece of scientific 'evidence', refuted by the majority of neuroscientist, was presented as the mainstream, consensus view of relevant medical experts. SCOTUS seems to have swallowed that, hook line and sinker and failed to consult expert medical opinion which could have given them a balanced view and corrected their misapprehension. They lapped up the pap they were fed because it told them what they wanted to hear to 'confirm' their preconceptions.

Their opinion is not a scientific, evidence-based ruling, but a prejudiced, preconceived religious opinion based on falsehoods and misrepresentation of the real science. The lunatics have taken over SCOTUS.

Another lunatic who wants to be running the show is MAGA/QAnon Trumpanzee cultist, Pastor Shane Vaughn, who has recently announced that "Conservatives are always right" because they are smarter than liberals who are suffering from a "mental disease". Why does he think they are smarter than liberals? Because they are always right, of course. Why are they always right? Because they are smarter than liberals. A neatly circular, self-referencing argument, not grounded at any point in reality, typical of the mental disorder we call narcissistic personality disorder or delusions of grandeur.

Famous examples of Shane Vaughn (real name, John Vaughn) always being right are:
  • Being convicted of multiple instances of identity theft, fraud and other felonies when, as an insurance agent in Baton Rouge, he stole the identity of a child who had died aged 4 years, and defrauded, banks, pensioners and others. He had his licence to operate as an insurance agent revoked and was slapped with a $100,000 fine and a 3 years spell in jail. During the trial he was described as "a chameleon, changing his look and name repeatedly". In other words, a shyster and con artist - just the sort to start a megachurch and declare himself to be God's spokesperson.
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