Malevolent Designer News - How Cholera was Redesigned To Make It More Effective.

Scanning Electron Microscope photograph of Vibrio cholerae bacteria.

Credit: G. Knott, M. Blokesch, EPFL

Two DNA defense systems behind resilience of 7th cholera pandemic - EPFL

What is not generally appreciated is that the coronavirus pandemic is not the only pandemic the human population of Earth is being subjected to. We are also in the midst of a cholera pandemic - the seventh such pandemic - caused by the bacterium Vibrio cholerae, a waterborne pathogen that infects the gut of humans through contaminated water and food. When ingested, V. cholerae colonizes the gut’s inner surface, causing a watery diarrhea, that if left untreated, can lead to severe dehydration and death. The form that infects humans differs from the 'wild' form in a number of ways, one of which is the low number of plasmids they carry, but quite why remained a mystery until now.

According the World Health Organization (WHO), the ongoing seventh cholera pandemic is responsible for up to four million infections, and up to 143,000 deaths each year.

Now, three researchers at the Laboratory of Molecular Microbiology, Global Health Institute, School of Life Sciences, Ecole Polytechnique Fédérale de Lausanne (EPFL), Lausanne, Switzerland have discovered that the variant responsible for the current pandemic has been modified to make it better able to defend itself against viruses and ingression of genetic material from other bacteria via horizontal gene transfer of plasmids. Their paper was published a few days ago in Nature

According to the EPFL new release:

Horizontal gene transfer

Only a few strains of V. cholerae can cause pandemic disease, with most being harmless aquatic organisms. This is because the pandemic strains have acquired specialized “toolboxes” of genes and other genetic elements called “pathogenicity islands”, which can turn the bacterium into a pathogen.

Strains that cause cholera pandemics have acquired pathogenicity islands through a process known as “horizontal gene transfer”, by which bacteria share genes both within and across species. Horizontal gene transfer is a powerful driver of bacterial evolution because it can quickly endow bacteria with new abilities that help them adapt and survive. But it is also indiscriminate, passing on genes that are unnecessary or even harmful to their new host.

Horizontal gene transfer often involves plasmids – self-replicating circular pieces of DNA found in bacteria that can carry up to hundreds of genes. But strains of V. cholerae that are causing the currently ongoing 7^th pandemic of cholera only rarely carry plasmids while plasmids are abundant in related strains isolated from the environment instead of patients.

We wanted to find out why plasmids are so rare in the 7^th pandemic clade of V. cholerae, shedding light on how bacterial pathogens evolve.

Professor Melanie Blokesch, lead author
Laboratory of Molecular Microbiology
Global Health Institute
School of Life Sciences
Ecole Polytechnique Fédérale de Lausanne, Lausanne, Switzerland

This surprising phenomenon caught the attention of scientists at EPFL, who decided to look into it.

Mystery of the missing plasmids

First, the researchers introduced a small model plasmid into V. cholerae strains from the 6^th and 7^th pandemics, as well as non-pandemic strains isolated from different water bodies. They then t^thracked the plasmid’s stability over the course of many generations. Surprisingly, the model plasmid persisted in all strains, but was quickly eliminated from the 7^th pandemic ones.

Two DNA defense systems

Encouraged, the scientists used genetic engineering methods to identify the parts of the V. cholerae genome responsible for this loss. This approach led to the discovery of two novel defense systems that work together to eliminate plasmids, and are encoded within two distinct pathogenicity islands.

Publishing in Nature, the researchers named the systems ‘DNA defense modules’ (Ddm). The first one, DdmDE, is made up of two proteins that target and degrade small plasmids in a process helped by a second defense system, DdmABC.

This finding might explain why the recent pandemic strains mainly carry antibiotic resistance integrated in their genome and not on plasmids.

Professor Melanie Blokesch

This second system turned out to have a much broader role in bacterial defense. Not only can it enhance the elimination of small plasmids, but it can turn against the

The combined activity of these two defense systems solves the long-standing mystery of the missing plasmids in the 7^th pandemic V. cholerae strains. Furthermore, our discovery suggests that the ability of the 7^th pandemic strains to defend against mobile genetic elements has likely played a key role in their evolution and success.

host cell, degrading its DNA and triggering a form of cell suicide. Essentially, DdmABC protects bacterial population against viruses by killing infected cells before the virus has time to replicate and spread.

The team also found that DdmABC targets large plasmids that often carry huge arrays of antibiotic-resistance genes, and can persist by jumping from one bacterium to the next, spreading multidrug resistance.

In summary then, it seems that the ability to pick up plasmids left around by other bacteria and thus acquire new traits is a two-edged sword because it can also insert harmful genes into the bacterium. The pathogenic form of V. cholerae is sufficiently well adapted to living in the specialised environment in the human gut that, on balance, picking up more plasmids carries a greater risk of harm than it does of acquiring a benefit, so they have been modified to reject any such plasmids. The same mechanism also protects them against the phage viruses that abound in the human gut.

Of course, a biologist will explain this as the result of evolution, but a creationist is obliged by dogma to reject that explanation and instead attribute this to intelligent [sic] design by their favourite magic deity - which unfortunately leaves that deity looking responsible for making 4 million people sick and killing 143,000 of them every year, by designing a specialised form of V. cholerae to do it with.

For some reason, the politically motivated extremist frauds behind the creationist movement would prefer their dupes to see their putative deity as some sort of evil, pestilential genius than to accept that the scientific method is the best tool we have for discovering the truth about the world. Could this be because the scientific method is also the best tool we have for exposing the fallacies that underpin their political ambitions, so they prefer an ignorant, superstitious and above all, fearful, population?

Reference:
Jaskólska, M., Adams, D.W. & Blokesch, M.
Two defence systems eliminate plasmids from seventh pandemic Vibrio cholerae.
Nature (2022). https://doi.org/10.1038/s41586-022-04546-y

Evolution News - How Amazonian Biodiversity Arose

Population genomic structure in six codistributed Amazonian bird species groups. For each species, results of the best k value for STRUCTURE analysis of split datasets (left) and example replicates of the t-distributed stochastic neighbor embedding (t-SNE) analysis (right) are shown. Colored bars underneath the STRUCTURE plots and circles on the t-SNE plots are colored on the basis of major interfluvial regions in map 1 (top left). Map 2 (top right) shows the topography of the study region within the dark red box, where yellow contours represent the 250- to 300-m elevational zone demarcating dynamic lowland (>250 m; shaded in blue) from relatively stable upland (>300 m; shaded in red) basins. Map 3 (top right inset) shows precipitation during the driest annual quarter (76), with high precipitation in gray, low precipitation in red, and a strong cline across the middle to lower reaches of the rivers draining the Brazilian Shield (plotted using QGIS).

Study: Rivers Contribute to Amazon Rich Biodiversity | AMNH

The major driver of evolutionary diversity is environmental change because it is the environment the species finds itself in that selects for fitness to survive and reproduce in that environment. This is why species can superficially look as though they are designed to suit their particular environment.

So, it is not surprising that a group of scientists led by Dr. Lukas Musher of the American Museum of Natural History’s Richard Gilder Graduate School found that changes in the local environment in the Amazon River basin are what led to the rich biodiversity in the Amazon Rain Forest. What was surprising, however, was the fact that it was dynamic changes in the courses of the many small tributaries to the Amazon that were the major factor and that proliferating bird species were the result, despite the fact that small rivers do not present major barriers to flying birds.

The team also discovered that this dynamic system had produced several local micro-species along the banks of these rivers, which are vulnerable to extinction.

From the American Museum of Natural History press release:

One of the most contentious questions in evolutionary biology is, how did the Amazon become so rich in species?

A new study focused on birds examines how the movements of rivers in the Amazon have

Evolution News - How SARS-CoV-2 Evolved the Different Strains

Evolution of SARS-CoV-2 between February 1, 2020 and July 1, 2021 depicted by waves (i.e., successions of “mutation groups”) in UK (a), USA (b), India (c), and Global (d). Sequencing data were obtained from the GISAID database. The frequencies of nonsynonymous mutations (A) and synonymous mutations (S) reaching the frequency cutoff of 0.3 at their peaks are presented. The number of mutations is shown in the parentheses. Although a curve represents the rise and fall of a variant, each observed curve usually represents multiple curves that overlap completely. In COVID-19, there are five waves (W0 to W4). Note that the decline in each wave as the next one rises (between W1 and W2, W2 and W3, or W3 and W4) is true in both relative and absolute abundance.

Runaway Evolution of SARS-CoV-2 Leading to the Highly Evolved Delta Strain | Molecular Biology and Evolution | Oxford Academic

Since the Coronavirus pandemic first took off in early 2020, the world has experienced several waves of new, more infectious variants. This presents creationists with two possibilities:

1. Either their preferred 'intelligent [sic] designer' is intentionally modifying its original design to overcome human efforts to contain and control the pandemic.
2. Or, the SARS-CoV-2 virus is evolving naturally under environmental pressure in exactly the way scientists explain how evolution works.

Now, to make matters worse for creationists, a team of Chinese scientists have shown how the waves of new variants followed patterns exactly as predicted by the Theory of Evolution, not to show that creationism is wrong, but to warn the world that more such waves are to be expected unless we break the cycle of new variants leading to a population explosion, leading to new variants, and so on… Evidence that creationism is wrong is, as always, the unintended but inevitable consequence of discovering the truth.

COVID-19 News. Why Men Should Get Vaccinated

This heat map reveals significant differences in the amounts of fertility-related proteins in the semen of healthy men (control) and those who had recovered from COVID-19 (COVID-19R).

Credit: Adapted from Ghosh, et al, ACS Omega 2022, DOI: 10.1021/acsomega.1c06551

COVID-19 alters levels of fertility-related proteins in men, study suggests - American Chemical Society

With the SARS-CoV-2 pandemic far from over, new research shows why men should get vaccinated to avoid the risk of an infection seriously affecting their fertility.

The research by Indian scientists working at the Department of Biosciences and Bioengineering at the Indian Institute of Technology in Mumbai, has shown that even a mild or moderate illness could change the levels of semen proteins related to male reproductive function.

The information supplied by the Americam Chemical Society (ACS) explains more:

Many people who recover from COVID-19 experience long-term symptoms, such as brain fog or heart problems. Increasing evidence suggests that the virus can also impair fertility. Now, researchers reporting in ACS Omega have analyzed protein levels in semen of men who have recovered from COVID-19. The pilot study suggests that even mild or moderate illness could change the levels of proteins related to male reproductive function, the researchers say.

Although SARS-CoV-2 mainly affects the respiratory system, the virus — and the body’s response to it — also damages other tissues. Recent evidence indicates that COVID-19 infection can reduce male fertility, and the virus has been detected in male reproductive organs. Firuza Parikh and Rajesh Parikh at Jaslok Hospital, Sanjeeva Srivastava at the Indian Institute of Technology and colleagues wondered if COVID-19 infection could have long-term impacts on the male reproductive system. To find out, they decided to compare levels of proteins in the semen of healthy men and those who previously had mild or moderate cases of COVID-19.

The researchers analyzed semen samples from 10 healthy men and 17 men who had recently recovered from COVID-19. None of the men, who ranged in age from 20 to 45, had a prior history of infertility. The team found that the recovered men had significantly reduced sperm count and motility, and fewer normally shaped sperm, than men who hadn’t had COVID-19. When the researchers analyzed semen proteins using liquid chromatography-tandem mass spectrometry, they found 27 proteins at higher levels and 21 proteins at lower levels in COVID-19-recovered men compared with the control group. Many of the proteins were involved in reproductive function. Two of the fertility-related proteins, semenogelin 1 and prosaposin, were present at less than half their levels in the semen of the COVID-19-recovered group than in the semen of controls. These findings suggest that SARS-CoV-2 has direct or indirect effects on male reproductive health that linger after recovery, the researchers say. The work might also reveal insights into the pathophysiology of human reproduction in recovered men, they add. However, they note that larger studies should be done to confirm these findings, and a control group of men who recently recovered from other flu-like illnesses should be included to ensure that the findings are specific for COVID-19.

The team's findings were published open access yesterday in AMC Omeg:

Malevolent Designer News - How Bacteria Help Cancers Spread

Evidence in mice that bacteria in tumors help cancer cells metastasize -- ScienceDaily

Creationist mode:

Creationism's beloved malevolence is never short of ideas for making life a little (or preferably a lot) more unpleasant in it's never-ending quest to increase the amount of suffering in the world.

For instance, as a group of research scientists have shown, not content with creating cancers, it has enlisted the help of the bacteria it also created to help spread the cancers once they take hold in a body. The bacteria travel inside the cancer cells as they circulate in the blood looking for somewhere else to start a new tumour, and help defend them against the mechanical stresses they encounter in the circulation.

The findings by Shang Cai of the Westlake Laboratory of Life Sciences and Biomedicine, Westlake University, Hangzhou, Zhejiang, China and colleagues was published yesterday in the journal Cell, sadly, behind an expensive paywall. However, the abstract is available here.

Evolution News - How a Human Malarial Parasite Evolved From a Chimpanzee Parasite

Chimpanzees in Kibale National Park, Uganda.

Credit: Yannick Tylle via Getty Images

Malaria parasite puzzle solved as ape origin found | The University of Edinburgh

the An open access paper published in Nature Communications yesterday, illustrates how, contrary to creationist claims, the Theory of Evolution is not only alive and kicking, but is the fundamental theory underpinning most of biomedical research.

The paper, by an international team of scientists led by Dr. Lindsey J. Plenderleith of the Institute of Evolutionary Biology and Centre for Immunity, Infection and Evolution, University of Edinburgh, Edinburgh, Scotland, UK and including colleagues from the Department of Medicine, University of Pennsylvania, Philadelphia, PA, USA and the Recherche Translationnelle Appliquée au VIH et aux Maladies Infectieuses, Institut de Recherche pour le Développement, University of Montpellier, Montpellier, France, and others, solves the 100-year-old mystery of the origins of a species of the malaria-causing parasite, Plasmodium malariae which is distinct from the commoner, P. falciparum and P. vivax which normally cause the disease in humans. P. malariae is morphologically identical to a species found in the other African apes and was once thought to be the same species.

Creationist Bigot News - Creationists are Much More Likely to be Racist, Homophobic and Violent

Disbelief in Human Evolution Linked to Greater Prejudice and Racism | UMass Amherst

According to a paper published in the Journal of Personality and Social Psychology recently, people who reject the idea of human evolution are significantly more likely to be racist, homophobic, intolerant of other political opinions and supportive of political violence. This was true, not only of the USA, where the tendencies were especially marked, but also in Eastern Europe, Israel and Islamic countries.

Christian Liars News - More Lies from the Liar King

David Barton
Showing the world he knows his faith is a lie.

David Barton Is Constantly Unveiling New and Misleading Claims About American History | Right Wing Watch

No-one epitomises the axiom that when you show the world you know you need to lie for your faith, you show the world that you know your faith is a lie that needs fools to believe falsehoods, than pseudo-historian and right-wing Christian Talibangelical, David Barton.

David Barton relies on the guaranteed fact that his right-wing audience will be mostly ignorant of both the Bible and American history and will never fact check any of his claims. So long as he tells them what they want to hear, they will continue to give him money and support his efforts to turn the USA into a fundamentalist Christian theocracy.

Evolution by Loss of Genetic Information Sends Creationists Batty

The common vampire bat, Desmodus rotundus, feeds exclusively on the blood of other animals. Adaptations to this unique diet are due in part to the loss of genes.

Photo: Brock Fenton

Vampires with genetic defects: MPI-CBG

Sometimes, refuting Creationism is too tempting to resist. The basic problem is that Creationism relies on creationists being fooled into believing things that are, frankly, counter-factual and easily demonstrated to be so.

Take, for example, the latest attempt to make it look like science is wrong about evolution and the facts comply with a literal interpretation of the Bible - Michael J Behe's 'Devolution' nonsense, that basically argues that every mutation is a retreat from the initial perfection of creation, (with the implication that this is due to 'sin' following 'The Fall' - a popular Judeo-Christian myth from the Bronze Age). Following his failure to make any progress in the courts with his and the Deception Institute's 'Intelligent [sic] Design' ploy, he has tried to come up with an alternative that makes Bible-literalist creationism look like real science. Sadly though, the facts are once again against him.

For example, this recent open access publication in Science Advances, by scientists from the LOEWE Centre for Translational Biodiversity Genomics in Frankfurt and the Max Planck Institute for Molecular Cell Biology and Genetics in Dresden, which shows that the common vampire bat's ability to live exclusively on a diet of mammalian blood, was made possible by a loss of thirteen genes - mutations which gave them significant advantages so were selected for by natural evolution. It takes some wonderful mental gymnastics to believe that mutations which give an advantage are somehow 'devolutionary' - a meaningless term which implies a 'correct' direction for evolutionary change, so appeals to the childish, teleological thinking of creationists.

Evolution News - Science Got it Wrong, But Not The Way Creationists Like to Imagine.

The sand dollar Mellitella stokesii.

Image credit: Rich Mooi (CC BY 4.0)

Study reconsiders early evolution of sea urchins | eLife

In yet another example of how science constantly re-examines, reassesses and revises its understanding, according to an open access paper published in eLife, scientists had got the evolution of sea urchins wrong.

Now, calm down Creationists and don't get over-excited! They didn't get it wrong in the way you've been fooled into believing. There is absolutely no threat to the fundamental biological science of evolution; what they got wrong, according to this paper, is the details. The scientists are in no doubt that the processes involved on evolutionary diversification are as stated in the theory.

As the eLife press release explains:

New insight on the origins and early evolution of echinoids, a group that includes the sea urchins, the sand dollars, and their relatives, has been published today in the journal eLife.

There are still debates among scientists about when the ancestors of echinoids emerged and what role the mass extinction event that occurred between the Permian and Triassic periods may have played in their evolution. We set out to help resolve these debates by combining genomic and paleontological data to disentangle their evolutionary relationships. The extraordinary fossil record of echinoids and the ease with which these fossils can be incorporated in phylogenetic analyses make them an ideal system to explore their early evolution using this approach.

Dr Nicolás Mongiardino Koch, first author
Formerly at Yale University, New Haven, Connecticut, USA.
Now at Scripps Institution of Oceanography
UC San Diego, USA

The study suggests that modern echinoids emerged approximately 300 million years ago, survived the Permo-Triassic mass extinction event – the most severe biodiversity crisis in Earth’s history – and rapidly diversified in its aftermath. These findings help address a gap in knowledge caused by the relative lack of fossil evidence for this early diversification.

There are more than 1,000 living species of echinoids, including sea urchins, heart urchins, sand dollars and sea biscuits, which live across different ocean environments ranging from shallow waters to abysses. Throughout history, the hard spine-covered skeletons of these creatures have left an impressive number of fossils. However, despite this remarkable fossil record, their emergence is documented by few fossil specimens with unclear affinities to living groups, making their early history uncertain.

Our work greatly expands the genomic data available for echinoids and helps resolve some of the long-standing questions around their evolutionary history. Together, the results suggest that we need to re-evaluate the echinoid fossil record, with future studies of overlooked fossil remnants potentially providing further support to our findings.

Professor Greg Rouse, senior author
Professor of Marine Biology
Scripps Institution of Oceanography
UC San Diego, USA

Mongiardino Koch and the team built upon available molecular resources with 18 novel genomic datasets, creating the largest existing molecular matrix for echinoids. Using this dataset, they were able to reconstruct the phylogenetic relationships and divergence times of the major lineages of living echinoids and place their diversification within broader evolutionary history. They did so by applying a ‘molecular clock’ technique to their dataset, whereby the rate at which mutations accumulated in the echinoid genomes is translated into geological time with the use of fossil evidence, allowing researchers to determine when different lineages first diversified.

Their analyses suggest that the ancestors of modern echinoids likely emerged during the Early Permian, and rapidly diversified during the Triassic period in the aftermath of a mass extinction event, even though this evolutionary radiation does not seem to have been captured by the fossil record.

Additionally, the results suggest that sand dollars and sea biscuits likely emerged much earlier than thought, during the Cretaceous period about 40 to 50 million years before the first documented fossils of these creatures. The authors say this result is remarkable, as the tough skeleton of the sand dollars, their buried lifestyles, and their extremely distinct morphologies imply that their fossil record should faithfully reflect their true evolutionary history.

This is just another example of how the study of DNA and genetics has confirmed Darwin's basic idea and extended our understanding of how species evolved and diversified from common ancestors. Darwin knew nothing of how information was passed to the next generation but he knew that it must be and that it included small variations of which natural selection could favour or disfavour, giving rise to ever-greater adaptation and fitness to survive and reproduce in the selective environment.

The scientists explain more in the abstract to their eLife paper, as does the journal editor in the editor's evaluation:

Abstract

Echinoids are key components of modern marine ecosystems. Despite a remarkable fossil record, the emergence of their crown group is documented by few specimens of unclear affinities, rendering their early history uncertain. The origin of sand dollars, one of its most distinctive clades, is also unclear due to an unstable phylogenetic context. We employ 18 novel genomes and transcriptomes to build a phylogenomic dataset with a near-complete sampling of major lineages. With it, we revise the phylogeny and divergence times of echinoids, and place their history within the broader context of echinoderm evolution. We also introduce the concept of a chronospace – a multidimensional representation of node ages – and use it to explore methodological decisions involved in time calibrating phylogenies. We find the choice of clock model to have the strongest impact on divergence times, while the use of site-heterogeneous models and alternative node prior distributions show minimal effects. The choice of loci has an intermediate impact, affecting mostly deep Paleozoic nodes, for which clock-like genes recover dates more congruent with fossil evidence. Our results reveal that crown group echinoids originated in the Permian and diversified rapidly in the Triassic, despite the relative lack of fossil evidence for this early diversification. We also clarify the relationships between sand dollars and their close relatives and confidently date their origins to the Cretaceous, implying ghost ranges spanning approximately 50 million years, a remarkable discrepancy with their rich fossil record.

Editor's evaluation

The study by Mongiardino Koch et al., presents new phylogenomic and molecular clock analyses of echinoids. The study uses state of the art phylogenetic approaches and includes 18 newly sequenced genomes and transcriptomes, which are used to estimate the tree topology and divergence times of major groups of echinoids. The molecular clock-estimated times of origin of particular echinoid lineages predate the lineages' appearance on the fossil record by tens of millions of years, prompting re-evaluation of the early evolution of echinoid diversity.

Mongiardino Koch, Nicolás; Thompson, Jeffrey R; Hiley, Avery S; McCowin, Marina F; Armstrong, A Frances; Coppard, Simon E; Aguilera, Felipe; Bronstein, Omri; Kroh, Andreas; Mooi, Rich; Rouse, Greg W; Rokas, Antonis; Perry, George H; Irisarri, Iker
Phylogenomic analyses of echinoid diversification prompt a re-evaluation of their fossil record
eLife 2022;11:e72460. DOI: 10.7554/eLife.72460

Copyright: © 2022 The authors. Published by eLife Sciences Publications Ltd.
Open access
Reprinted under a Creative Commons Attribution 4.0 International license (CC BY 4.0)

Incidentally, if anyone is in any doubt about peer-review and imaging it's some sort of formality that waves any scientific papers through on the nod, provided they conform to some assumed dogma, like creationist articles, it is worth scrolling down to the Decision letter section, where unusually for a scientific paper the reviewers' comments appear in full, together with the authors' responses. Peer-review is not a process to ensure compliance to some assumes party line, but a constructive, critical process by experts in the field that ensure the highest standards of scientific integrity and accuracy are maintained in the articles published by scientific journals, so readers can rely on the accuracy and validity of the findings.

For examples (reviewer's comments in italics and the authors' response to them):

Reviewer #2 (Recommendations for the authors):

I found the text long in places and thus tedious to read. Particularly the introduction and the discussion. The intro could have a tighter narrative more focused on the discrepancies of the fossil record and divergence times, and on discrepancies in topology without the needed to review so much echinoid biology. The discussion appears too long. Too much effort is made on justifying the chronospace approach. This perhaps does not need to be justified at all beyond a sentence or two.

The issue of the length of the introduction and the extent to which echinoid background is developed seems to be a discrepancy between reviewers. We have decided not to modify its length, as we believe the present version is already a good compromise, as is suggested by Reviewer #1 as well. We have however reduced the length of the justification of chronospaces.

Because the clock model has such an impact, you should explore this further. PhyloBayes provides the ability to test for the various rate models using Bayes factors and you should try this. Because this analyses are computationally expensive, you can do them on a reduced amount of data. MCMCtree also allows you to test for various clock models with Bayes factors.

Given the computational burden of running a Bayes factor analysis on PhyloBayes, we had explored CorrTest instead, a different approach for selecting among competing clock models. The results of this were not reported before, but are now incorporated as Reviewer #1 also suggested this. Given that these methods did not eliminate uncertainty in terms of which clock model should be preferred, we have taken the position of exploring and reporting the sensitivity of results to all factors. All conclusions drawn in the manuscript regarding echinoderm diversification are robust even to the large effects introduced by the choice of clock models. We don’t feel the need to restrict the analyses or results to a subset of conditions when this would not modify our insights.

Additional points:

The y-axis (Δ likelihood) of panel C in Figure 2 needs to be explained in the legend. What is the benchmark likelihood?

Panel C of Figure 2 is better explained now in the caption. There is no benchmark likelihood, values larger than 0 mean support for one topology, those below 0 for the alternative.

In the figure legends, the program/models used to infer the tree and times should be indicated. From the methods it's clear that many many different methods were tested, but from the main text and the figure legends is not clear what is being summarised in the figures.

Software are now mentioned in the captions of Figures 2 and 4.

Please remove the p-value for the multivariate analysis in line 198. This is not a replicated stochastic experiment. You are simply changing priors and substitution models and hence the posterior changes. This is a deterministic mapping between data/prior and posterior.

We agree with this comment and have removed the mention to p-values.

Panel C of Figure 4: please mention in the legend the scale of the x-axis tickmarks (10 My?).

Done.

Lines 359 to 367 have little substance. There are no figures in this paper showing the correlation structure among branch lengths. For example, figure 4 shows stacked posterior distributions, like those in previous works, so isn't this work a victim of its own criticism? There is indeed a correlation structure among branches and times, which is not shown, and which is discarded in the plots shown here. To emphasise this point, here is paper's text edited: "The sensitivity of inferred ages is commonly explored by running analyses under different settings and summarizing the results in tables or by stacking chronograms in order to visualize the relative position of nodes (see for example Figure 4C here and the supplementary material figures)."

We agree with the reviewer and have removed all of the text mentioned here, as well as other parts referring to the chronospace approach. Correlation plots were shown in a previous version of the manuscript, but we agree that these sentences do not add much after these have been removed.

Why The Pandemic Is Not Over and Why You Should Get Vaccinated and Boosted

The folowing article is taken from The Conversation under a Creative Commons licence.

Most COVID patients in NZ’s Omicron outbreak are vaccinated, but that’s no reason to doubt vaccine benefits

Hannah Peters/Getty Images

Thomas Lumley, University of Auckland

New Zealand’s Omicron wave may be peaking, but we’ll continue to record thousands of new cases each day and most people who test positive or are hospitalised with COVID will have been vaccinated.

This is exactly what we should expect and it’s no reason to doubt vaccine effectiveness.

The principal reason why a lot of COVID cases are vaccinated is because most New Zealanders are now vaccinated. As of today, about 94% of people 12 years and older have had two or more vaccine doses, and even if their risk of catching COVID is significantly lower than for an unvaccinated person, they vastly outnumber those who aren’t.

Omicron is not mild. The only reason it appears mild is because we have excellent vaccines. If we didn't have the high vaccine coverage we have in NZ, we would be in a truly dire situation right now https://t.co/0tvdIaNKdk

— Michael Plank (@MichaelPlankNZ) March 14, 2022

In the week ending March 13, about 93% of the 118,000 confirmed cases 12 years and older were in people with two or more doses. But such crude proportions of cases aren’t all that good an indicator of vaccine effectiveness.

Last year, during the Delta outbreak, the proportions were misleading in the other direction. The rate of cases in people who were unvaccinated was about 20 times that in vaccinated people.

Unfortunately, some commentators talked about that ratio as if it was all a real benefit of vaccination. It wasn’t.

The outbreak in Auckland was nearly under control and was spreading among unvaccinated people partly because they had less resistance to infection, but also because they were more likely to come into contact with infected people. Social clustering leads to disease clustering.

What case numbers can tell us

For Delta, two doses of the vaccine produced very good immunity, especially in the short term. The vaccine is less effective for Omicron; two doses give only partial immunity even in the short term, and the effectiveness wears off over time.

About 60% of people 12 years and older have had a booster dose, and in the week ending March 13, only 42% of cases were in people who had been boosted. We can see that boosters help.

Updated vaccine status #covidgraph for week ending 13 March. This very clearly shows the difference boosters make: Unvaxxed are 3.6 x more likely to be in hospital than the boosted. Get your booster people! pic.twitter.com/gOXlVAWzu3

— John Hart 🦗🦗🦗 🌳🌳🌳 (@farmgeek) March 13, 2022

Counting cases remains important, because even a non-hospitalised case of COVID can be unpleasant, and because we don’t know how likely a mild case is to lead to long COVID and months or years of disability. We can’t draw strong conclusions from numbers of cases, though.

Many cases, probably most cases, are not being diagnosed at the moment. Unvaccinated people will be less likely to get tested, especially in mild cases of the disease, either because of poor access to the health system or because they don’t think COVID is important. We can’t really tell how much bias this introduces into the numbers.

Hospitalisations and deaths are much more reliably counted than cases. Results from clinical trials and careful population studies of COVID vaccines consistently show the vaccines to be more effective in preventing more serious disease, especially with the new variants. There are plausible biological explanations for this, based on different parts of our immune response.

Antibodies against the COVID virus seem to be affected more by differences between strains than T-cells are; antibodies are probably more important for preventing initial infection and less important for fighting serious disease.

More benefit in protecting from serious disease

When we look at hospitalisations and deaths, the difference between vaccinated and unvaccinated people is much more dramatic. In the week ending March 13, 65% of people over 12 hospitalised were vaccinated, compared to 94% in the population; 32% had a booster dose, compared to 60% in the population. The 5% of unvaccinated people over 12 contributed 20% of hospitalisations.

The number of deaths is, fortunately, too small for the Ministry of Health to publish detailed weekly breakdowns, but vaccinated people are a minority over the period since August.

The relatively small number of deaths in New Zealand’s Omicron wave also shows the effectiveness of the vaccine. Hong Kong had largely eliminated COVID until Omicron; they are now getting a large outbreak similar to New Zealand’s, but only in the number of cases. Over the past week, Hong Kong averaged 280 deaths per day, in a population less than twice that of New Zealand.

The vaccination rate in Hong Kong is much lower. About 71% are fully vaccinated and only 30% have had a booster. Among elderly people, who are at much greater risk from COVID, the vaccination rate is especially lower, with two-thirds of people over 80 and more than a third of those aged 70-80 having been unvaccinated when Omicron hit.

Towards fair comparisons

Comparing across whole populations this way gives some indication of the vaccine benefit, but it is very imprecise. We don’t choose randomly who gets the vaccine and who doesn’t.

In New Zealand, for example, essentially everyone over 75 has been vaccinated. Since people over 75 are much more likely to need hospital care than younger people, the higher vaccination rate in people over 75 makes the vaccine look less effective than it really is.

Statisticians call this “confounding by indication”. Auckland has always had more exposure to new outbreaks and had higher vaccination rates than the rest of the country; this again tends to make the vaccine look less effective that it really is.

More reliable comparisons require either random allocation of vaccine to people, as in the clinical trials performed before the vaccines were approved, or careful statistical matching of vaccinated and unvaccinated groups to get a fair comparison.

Omicron is too recent to have useful clinical trial data, but peer-reviewed statistical analyses of individual case data from the United Kingdom, the United States, and South Africa all agree the vaccines are beneficial.

There’s some evidence vaccination also reduces the risk and severity of long COVID, the most likely bad outcome for healthy people. But there obviously hasn’t been time to do this sort of comparison specifically for the Omicron variant.

Overall, the most reliable comparisons between vaccinated and unvaccinated people have consistently shown a benefit of vaccination. The effectiveness of the vaccines does wear off over time, and the effectiveness is lower against Omicron than it was against Delta or the original COVID strain, but it still improves your chances of avoiding infection, keeping out of hospital and making a full recovery.

Thomas Lumley, Professor of Biostatistics, University of Auckland

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

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Religious War Crimes News - How the Russian Orthodox Church Backs Putin's War on Women & Children

Patriarch Kirill and Vladimir Putin.

War on Ukraine is "an active manifestation of evangelical love for neighbours" - Patriarch Kirill

How Putin's invasion became a holy war for Russia

Fulfilling the Christian Churchs' historic roll of supporting right-wing totalitarian nationalism, the Russian Orthodox Christian Church is backing Putin's murderous and unprovoked attack on Ukraine and the territorial ambitions of Vladimir Putin.

For Putin and the Russian Orthodox Church, the war against Ukrainian democracy is wrapped in the Russian flag and shrouded in religious zeal, since Kiev is the home of Prince Vladimir the Great of Kiev, the legendary founder of the Russian Church who , in about 978 AD, was responsible for making Byzantine Christian Orthodoxy the official religion of Russia, Ukraine and Belarus.

The Hagia Sophia, Istanbul
Legend has it that Prince Vladimir the Great of Kiev was so impressed he adopted the Orthodox Christianity of Byzantium as the state religion for Russia, Ukraine and Belorus.

The legend is that he invited missionaries from Eastern (now Orthodox) Christianity, Western (now Catholic) Christianity, Judaism and Islam to persuade him to adopt their religion. He rejected Islam because of the prohibition on alcohol and pork, saying that the Rus couldn't do without alcohol and Judaism because 'God had allowed the Jews to lose Jerusalem'. He eventually settled on Eastern Christianity when his emissaries reported the magnificence of the Hagia Sophia Church in Constantinople (now Istanbul).

On Russian National Unity Day, 4th November 2016, with Patriarch Kirill, the oleaginous head of the Russian Orthodox Church, at his side, smiling and applauding enthusiastically, Putin unveiled a huge statue of Vladimir the Great outside the Kremlin. On the day that Putin ordered his troops into Ukraine, Patriarch Kirill published a grovelling and nauseatingly obsequious statement which read:

Malevolent Designer News - Another Design Blunder as a Fungus Prevents a Bacterium From Doing Its Job

UMaine study shows pathogen and drug work together to fight fungal lung infection - UMaine News - University of Maine

Scientists working at the Department of Molecular & Biomedical Sciences, University of Maine, Orono, Maine, USA, have discovered a phenomenon that, if you're gullible enough to be a creationist, which admittedly would make it unlikely that you'd be reading, let alone understanding, this blog, must look like the putative intelligent [sic] designer has lost the plot.

The discovery is that when two particular organism occur together to produce a polymicrobial disease, one of the organisms will work against the other. In the presence of an antibiotic, it will not only prevent the other organism developing resistance, but will remove it from the infection site.

The two organisms are the fungus, Candida albicans and the bacterium, Pseudomonas aeruginosa, both of which are opportunistic pathogens that can be found in similar sites of infection such as in burn wounds and most importantly in the lungs of cystic fibrosis and mechanically ventilated patients.

As the University of Maine news release explains:

Evolution News - Evolution of Evolvability

Capturing the many facets of evolvability | Science Linx News | Science LinX | University of Groningen

Imagine, if you can, being a creationists who has swallowed the absurd idea that the scientific theory of evolution is a 'theory in crisis' which is about to be overthrown by a superstition from the fearful, ignorant infancy of our species in the Bronze Age, from a time when a bunch of nomadic pastoralists and hill farmers in the Middle East though Earth was small, young, flat and had a dome over it to keep the water above the sky out. You've been waiting excitedly for most of your adult life for this momentous event - the first time an established scientific theory has been replaced by a mystical, supernatural one involving unproven entities and magic - and so proving that you know better than all those clever scientists without having bothered to learn any science!

Then along comes a bunch of those clever scientists from Groningen Institute for Evolutionary Life Sciences at the University of Groningen in the Netherlands and not only presents a detailed discussion paper on how evolution works, but on how evolvability itself evolved, with no hint whatsoever that they have any doubts about evolution being the reason for all the biodiversity.

Copyright: © 2022 The authors. Published by Elsevier Ltd.
Open access
(CC BY-NC-ND 4.0)

And to cap it all, they even explain the notion of 'punctuated equilibrium' that was invented by the evolutionary biologist, Stephen Jay Gould, to try to explain the fossil record which appears to show that many species have long periods of stasis when their morphology changes very little, followed by a burst of rapid evolution, then another period of stasis, etc.

Many creationists like to imagine this somehow refutes Darwinian evolution, although Gould never proposed a mechanism for it and other biologists have explained that Darwinian gradualism doesn't imply a constant rate of evolutionary change, especially at the phenotypic level and that what can appear to be a sudden change in phenotype in the geological columns can take tens or hundreds of thousands of years. Or the record simply shows that one species was replaced by another closely related species over that part of its range, as happened in the UK where the more robust introduced grey squirrels have replaced the slighter native red squirrels in less than a hundred years. In the geological column in, say, 10,000 years, this will look like a case of 'punctuated equilibrium' and an unexplained sudden change to a more robust form. The explanation is that newly evolved evolvability enables a species to radiate into new niches to give a relatively sudden increase in new species or to more quickly evolve in response to environmental pressures.

So, what do you do if you're a creationists and a paper like this is published?

Human Evolution News - Human Cultural and Technological Evolution in Northern China, 40,000 Years Ago

Ochre pieces and stone processing equipment laying on a red-stained pigment patch.

Fa-Gang Wang, Francesco d’Errico / Wang et al.,
Innovative ochre processing and tool-use in China 40,000 years ago.
Nature. 2022

Archaeologists Discover Innovative 40,000-Year-Old Culture in China | Max Planck Institute for the Science of Human History

Of course, they never could have guessed it, so the people who were leaving these remains 40,000 years ago would have been oblivious of the fact that their activities as discovered by modern archaeologist, have utterly refuted the ideas that were to emerge in another part of the world some 37,000 years later.

The fact is, however that this is exactly what they have done insofar as the primitive Bronze Age origins myths of a bunch of Middle Eastern nomadic pastoralists and hill farmers are concerned, because these people who made up these camp-fire tales or elaborated on earlier ones, had no inkling that there had been people much like them around in what is now Northern China, some 37,000 years earlier.

The tales these simple people had been handed down had their origins in a part of the world where people believed Earth was very small and only a couple of thousand years old and had been created just for them by magic beings who lived above the sky-dome and who directed the affairs of man.

For these people, the entire world was a circle bounded by the Eastern Mediterranean to the west, the Black Sea and the Caucasus Mountains to the north, the Arabian desert to the south and the flood plains of Mesopotamia and the Iranian Plateau to the east. These were the tales that eventually got written down and incorporated into the state religion of a desperate, increasingly autocratic, dying Roman Empire and are now, almost unbelievably, still regarded as historical truths by some number of people alive today, albeit a decreasing proportion of the developed world's people.

Sadly for these deluded people, evidence of human habitation and cultural/technological progress in Northern China 40,000 years ago, utterly refutes their primitive beliefs which include a global genocidal flood just 6000 years ago, which, had it really happened, would have swept away the archaeological evidence of this culture, as it does the notion that the entire planet has been repopulated by the descendants of a handful of survivors of this flood.

The findings by an international group of archaeologists including scientists from the Chinese Academy of Science and the Max Planck Institute for the Science of Human History, were published recently in Nature. The artifacts are from a period in Eurasian hominin history when Homo sapiens was coming into contact with the Neanderthals and Denisovans, the descendants of an earlier migration by an archaic hominin such as H. erectus, and interbreeding with them and no doubt sharing ideas and technologies.

Malevolent Designer News - How The Devine Malevolence Has Turned Our Immune System Against Us.

Roseolovirus particles emerge from an infected immune cell (above). Studying mice, researchers at Washington University School of Medicine in St. Louis have discovered that roseolovirus can trigger autoimmunity in a previously unknown way: by disrupting the process by which immune cells learn to avoid targeting their own body's cells and tissues.

Credit: Bernard Kramarsky

New way viruses trigger autoimmunity discovered – Washington University School of Medicine in St. Louis

Researchers at Washington University School of Medicine in St. Louis have discovered how a virus can probably make our immune system turn against us to create autoimmune diseases such as arthritis, lupus and type I diabetes, long after infection by the virus.

In the wackadoodle world of Creationism, this means that the viruses in question were designed specifically to produce that outcome since, being omniscient, the designer knows exactly what the outcome will be and so designs them for that exact function.

The fact that it does this to use a system it supposedly designed to protect us from the parasites like viruses and bacteria it designs to harm us with, is not seen as a reason to doubt the intelligence or sanity of this supposed designer!

Religious Greed News - Mega-Church Theft Was Definitely NOT an Insurance Scam, Honest Gov!

Multimillionaire Pastor Joel Osteen, Lakewood Mega-Church, Houston, Texas.
Definitely not an insurance scam as that would be the sin of theft!

Plumber who found money stashed in wall at Joel Osteen’s church gets $20,000 reward

Here's a heart-warming story involving mega rich televangelist Joel Osteen and his Lakewood Church in Houston, Texas.

The plumber, one Justin Cauley, who found $600,000 in cash and cheques hidden behind a panel in the church's toilet, is to receive a $20,000 reward for recovering the money, which was believed to have been stolen from a safe in the church in 2014 - a crime which remains unsolved.

I hope it's not somebody currently working in a church environment that's hiding $600,000 from the people who donated it.

Erik Scott Smith.
Co-host of the Morning Bullpen with George, Mo and Erik
Houston country radio station 100.3 The Bull.

According to this report, and from statements by a church spokesperson, reported at the time, all donations made to the megachurch are fully insured, so no money was lost as a result of the theft. Although the dates and names on the checks strongly point to the recovered money being the same as the 'stolen' money, police have not yet been able to verify that it is indeed the 'stolen' money.

Religious Stupidity News - Blundering Priest Now Trying to Save People From the Hellfire His Blunder Destined Them For

Pope Benedict XVI performing the ritual of baptism - but the words must be exact or God doesn't know it has been performed.

Priest’s new assignment: Helping those he invalidly baptized

The ludicrous tale of the Catholic priest who inadvertently condemned thousands of residents of St. Gregory Parish, Phoenix, Arizona USA, to hellfire by using a wrong word in the magic spell called baptism, took a new turn recently.

Having resigned as the parish priest, he took up a new role of baptising those he cursed, this time with the right words in the magic spell. The ritual of baptism inducts children into the Catholic Church, and so the 'one true faith', without their consent or participation. This then gives them special protection by God who casts everyone without the 'one true faith' into Hell, there to suffer an eternity of agony in hellfire.

The problem was that by using the wrong words, God was unaware that he, in the form of Jesus, for whom the priest was speaking, had baptised the children into the one true faith, so he doesn't know which ones to save and which ones to cast into the fiery pit for having the wrong faith. What Fr. Andrés Arango, should have said was "I baptise you...", instead, he said "We baptise you..." and obviously, "I" means "Jesus" in that context, and "We" doesn't, because, being specially anointed, a Catholic priest (but now any other priest, mind you!) speaks for Jesus, so God wouldn't know what was going on as he, being omniscient, doesn't understand a spell if even one word is wrong.

Evolution News - Researchers Have Constructed a Massive Human Family Tree

Map depicting the way early modern humans (Homo sapiens) are thought to have spread across the globe. It also shows the geographical spread of Homo erectus and the Neanderthals. The dates are approximations (and not 100% guaranteed)

BDI researchers create largest ever human family tree — Oxford Big Data Institute

Researchers from Oxford University's Big Data Institute (BDI) have developed a technique to help construct the entire genetic relationship amongst humans to produce a single genealogy for all of us, showing how we have all evolved from a single founder population, and incorporating the genomes of archaic hominins such as Neanderthals and Denisovans
.
This has been made possible by the enormous technical advances in being able to extract and sequence DNA but the problem was in using this vast and growing database. However, the group has now developed a new method which allows researchers to easily and quickly combine data from multiple sources and scale to accommodate millions of genome sequences. Their method was published yesterday in Science.

The press release from BDI explains further:

Evolution News - Ancient DNA Reveals How Early Africans Lived

1 of 3

Hora Rockshelter in Malawi, where recent excavations uncovered two of the individuals analyzed in a collaborative study of ancient DNA.

Photo credit: Jacob Davis.

2 of 3

Mt. Hora in Malawi, where recent excavations at Hora Rockshelter uncovered two of the individuals analyzed in a collaborative study of ancient DNA.

Photo credit: Jacob Davis.

3 of 3

Ostrich eggshell beads from Mlambalasi Rockshelter in Tanzania, where one of the individuals in the study was buried.

Photo credit: Jennifer Miller.

Ancient DNA reveals surprises about how early Africans lived, traveled and interacted | Rice News | News and Media Relations | Rice University

A new analysis by a large team of geneticists and anthropologists from several North American Universities, of remains, including DNA, recovered from a site in Malawi, Tanzania and Zambia, Africa, has revealed new details of the movements and interactions of Early Africans. The individuals whose remains were analysed lived between 18,000 and 5,000. This is more than twice the age of previously recovered human DNA from sub-Saharan Africa.

The study also reanalysed published data from 28 individuals buried at sites across the continent, generating new and improved data for 15 of them. The results are published, open access, in the journal Nature.

The Rice University press release accompanying this publication explains:

The result was an unprecedented dataset of DNA from ancient African foragers — people who hunted, gathered or fished. Their genetic legacy is difficult to reconstruct from present-day people because of the many population movements and mixtures that have occurred in the last few thousand years.

We've never been able to directly explore these proposed demographic shifts, until now," she said. “It has been difficult to reconstruct events in our deeper past using the DNA of people living today, and artifacts like stone tools and beads can’t tell us the whole story. Ancient DNA provides direct insight into the people themselves, which was the missing part of the puzzle.

Maybe it was because by that point, previously established social networks allowed for the flow of information and technologies without people having to move.

Assistant professor Elizabeth A. Sawchuk, co-author
Department of Anthropology
University of Alberta, Edmonton, Alberta, Canada And Department of Anthropology
Stony Brook University
Stony Brook, NY, USA

Thanks to this data, the researchers were able to outline major demographic shifts that took place between about 80,000 and 20,000 years ago. As far back as about 50,000 years ago, people from different regions of the continent moved and settled in other areas and developed alliances and networks over longer distances to trade, share information and even find reproductive partners. This social network helped them survive and thrive, the researchers wrote.

Our genetic study confirms an archaeological pattern of more local behavior in eastern Africa over time. At first people found reproductive partners from wide geographic and cultural pools. Later, they prioritized partners who lived closer, and who were potentially more culturally similar.

Assistant professor Jessica Thompson, co-author
Department of Anthropology and Peabody Museum of Natural History
Yale University, New Haven, CT, USA
And Institute of Human Origins
School of Human Evolution and Social Change
Arizona State University, Tempe, AZ, USA.

Elizabeth Sawchuk, an author of the study who is a Banting Postdoctoral Fellow at the University of Alberta and research assistant professor at Stony Brook University, said a dramatic cultural change took place during this timeframe, as beads, pigments and other symbolic art became common across Africa. Researchers long assumed that major changes in the archaeological record about 50,000 years ago reflected a shift in social networks and maybe even changes in population size. However, such hypotheses have remained difficult to test.

Humans began relying on each other in new ways, and this creativity and innovation might be what allowed people to thrive.

There are around 30 times more published ancient DNA sequences from Europe than from Africa. Given that Africa harbors the greatest human genetic diversity on the planet, we have much more to learn.

Assistant professor Mary E. Prendergast, co-author
Department of Genetics
Harvard Medical School, Boston, MA, USA
And Department of Anthropology
Rice University, Houston, TX, USA

Mary Prendergast, an author of the paper and associate professor of anthropology at Rice University, said there are arguments that the development and expansion of long-distance trade networks around this time helped humans weather the last Ice Age.

[…]

By associating archaeological artifacts with ancient DNA, the researchers have created a remarkable framework for exploring the prehistory of humans in Africa," said Archaeology and Archaeometry program director John Yellen of the U.S. National Science Foundation, one of the funders behind this project. "This insight is charting a new way forward to understanding humanity and our complex shared history.

John Yellen
Archaeology and Archaeometry program director
U.S. National Science Foundation

Prendergast said the study provides a better understanding of how people moved and mingled in this part of Africa. Previously, the earliest African DNA came from what is now Morocco — but the individuals in this study lived as far from there as Bangladesh is from Norway, she noted.

[…]

This work shows why it’s so important to invest in the stewardship of human remains and archaeological artifacts in African museums.

Potiphar Kaliba, co-author
Research Director
Malawi Department of Museums and Monuments
Lilongwe, Malawi

The research team included scholars from Canada, Kenya, Malawi, Tanzania, the United States, Zambia and many other countries. Critical contributions to the study came from curators and co-authors at African museums who are responsible for protecting and preserving the remains.

Potiphar Kaliba, director of research at the Malawi Department of Museums and Monuments and an author of the study, noted that some of the skeletons sampled for the study were excavated a half-century ago, yet their DNA is preserved despite hot and humid climates in the tropics.

The main conclusions from the study is that there were two highly-diverged populations before about 80-20 thousand years ago: one in East Africa, one in Southern Africa and a ubiquitous population ancestral population that is represented today by the Central African rainforest hunter-gatherers. The team's findings are published, open access, in Nature:

a, Locations of individuals analysed in this study. The shapes and colours of the symbols correspond to the PCA in b. 1, Shum Laka; 2, Mota Cave; 3, Kakapel RS (Rockshelter); 4, Nyarindi RS; 5, Jawuoyo RS; 6, White Rock Point; 7, Panga ya Saidi; 8, Makangale Cave; 9, Kuumbi Cave; 10, Gishimangeda Cave; 11, Kisese II RS; 12, Mlambalasi RS; 13, Fingira; 14, Hora 1; 15, Chencherere II; 16, Kalemba RS; 17, Ballito Bay; 18, Faraoskop RS; 19, St Helena. b, PCA results. Axes were computed using present-day groups from eastern (Dinka pastoralists), southern (Juǀ'hoansi foragers) and central Africa (Mbuti foragers). Small circles represent present-day individuals; other symbols represent ancient individuals (larger points corresponding to earlier individuals and black outlines to newly reported individuals). The lowest-coverage individual (from Mlambalasi), shown with an asterisk, has the most uncertain position. The base map in a is from Natural Earth (https://www.naturalearthdata.com). E., east.

Abstract

Multiple lines of genetic and archaeological evidence suggest that there were major demographic changes in the terminal Late Pleistocene epoch and early Holocene epoch of sub-Saharan Africa^1,2,3,4. Inferences about this period are challenging to make because demographic shifts in the past 5,000 years have obscured the structures of more ancient populations^3,5. Here we present genome-wide ancient DNA data for six individuals from eastern and south-central Africa spanning the past approximately 18,000 years (doubling the time depth of sub-Saharan African ancient DNA), increase the data quality for 15 previously published ancient individuals and analyse these alongside data from 13 other published ancient individuals. The ancestry of the individuals in our study area can be modelled as a geographically structured mixture of three highly divergent source populations, probably reflecting Pleistocene interactions around 80–20 thousand years ago, including deeply diverged eastern and southern African lineages, plus a previously unappreciated ubiquitous distribution of ancestry that occurs in highest proportion today in central African rainforest hunter-gatherers. Once established, this structure remained highly stable, with limited long-range gene flow. These results provide a new line of genetic evidence in support of hypotheses that have emerged from archaeological analyses but remain contested, suggesting increasing regionalization at the end of the Pleistocene epoch.

Lipson, Mark; Sawchuk, Elizabeth A.; Thompson, Jessica C.; Oppenheimer, Jonas; Tryon, Christian A.; Ranhorn, Kathryn L.; de Luna,Kathryn M.; Sirak, Kendra A.; Olalde, Iñigo; Ambrose, Stanley H.; Arthur, John W.; Arthur, Kathryn J. W.; Ayodo, George; Bertacchi, Alex; Cerezo-Román, Jessica I.; Culleton, Brendan J.; Curtis, Matthew C.; Davis, Jacob; Gidna, Agness O.; Hanson, Annalys; Kaliba, Potiphar; Katongo, Maggie; Kwekason, Amandus; Laird, Myra F.; Lewis, Jason; Mabulla, Audax Z. P.; Mapemba, Fredrick; Morris, Alan; Mudenda, George; Mwafulirwa, Raphael; Mwangomba, Daudi; Ndiema, Emmanuel; Ogola, Christine; Schilt, Flora; Willoughby, Pamela R.; Wright, David K.; Zipkin, Andrew; Pinhasi, Ron; Kennett, Douglas J.; Manthi, Fredrick Kyalo; Rohland, Nadin; Patterson, Nick; Reich, David; Prendergast, Mary E.
Ancient DNA and deep population structure in sub-Saharan African foragers
Nature (2022). DOI: 10.1038/s41586-022-04430-9

Copyright: © 2022 The authors. Published by Springer Nature Ltd.
Open access
Reprinted under a Creative Commons Attribution 4.0 International license (CC BY 4.0)

The picture then is of a species that spread far and wide within Africa, as well as out of Africa into Eurasia and eventually beyond, to form relatively isolated populations that diverged enough to form genetically distinct populations but within which interbreeding was frequent enough to prevent divergence into sub-species or species, to produce a genetically diverse single pan-African human species. There is probably a great deal more to learn in terms of the interchange and spread of new technologies and cultures as well as about the patterns of migration as the climate changed.

Malevolent Designer News - How the Colorado Beetle Has Been Redesigned to Resist Pesticides

The Colorado potato beetle, Leptinotarsa decemlineata’s rapid spread, hardiness, and recognizable tiger-like stripes have caught global attention since it began infesting potatoes in the 1800s.

Photo: Zach Cohen

‘Super pest’ Colorado potato beetle has the genetic resources to sidestep our attacks

Scientists led by Professor Sean Schoville, of the University of Wisconsin–Madison's Entomology Department, have discovered the design modifications that enable the Colorado potato Beetle to resist just about all the insecticides humans have developed against it. As its name implies, the Colorado potato beetle is a major pest on the potato plant and can devastate crops. In the UK, it is considered so serious that it is compulsory to notify the police if you detect the adult or larval form of the beetle.

The new research shows that the beetle has evolved a whole range of genetic adaptations that give it the capability to quickly evolve resistance in a local population. As any intelligent [sic] design advocate will tell you, this doesn't happen by natural selection selecting from chance mutations, but must be intelligently designed by a magic designer. If this were true, it would raise the question of why this putative magic designer designed this pest on an essential human food crop in the first place, and now seems to have given it the ability to resist anything we can combat it with.

The researcher's findings are published, open access, in the journal, Molecular Biology and Evolution.

According to the University of Wisconsin-Madison's press release accompanying the publication:

Covidiot News - Two More Good Reasons To Get Vaccinated

Two more studies, published today in PLOS Medicine show that the reported risks of blood clots following vaccination with anti-COVID vaccination are minuscule and have been greatly exaggerated in the antivaxx disinformation campaigns.

The first study, by William Whiteley of the University of Edinburgh, UK, and colleagues from the BHF Data Science Centre, UK., found, for those under 70, the risk was of the order of 0.9 – 3 per million (varying by age and sex) for AstraZeneca ChAdOx1-S, which is about double the risk for non-vaccinated people. There was no statistically significant increase in the rate of blood clots with Pfizer BNT162b2.

This study analysed the electronic health records of 46 million adults in England of whom 21 million were vaccinated during the study time span, December 2020 to March 2021. For people aged 70 or over, the risks of arterial and venous thrombotic events were slightly lower in the 28 days following vaccination with either the Pfizer BNT162b2 or ChAdOx1-S vaccine.

The second paper, by Steven Kerr of the University of Edinburgh, UK, and colleagues, used a dataset of 11 million adults in England, Scotland, and Wales came to a similar conclusion.

Information provided ahead of publication by PLOS, explains: