A study by researchers at the University of Virginia, Charlottesville, VA, USA, has shown why it is not only important to get vaccinated, but why it is just as important to get boosted and this is especially true for those vaccinated with Pfizer's BNT162b2 vaccine, but also for those vaccinated with either Moderna's mRNA-1273 vaccine or the single-shot Johnson & Johnson Ad26.COV2.S vaccine.
It shows that for the Pfizer vaccine, antibody levels rose more slowly than with the Moderna mRNA vaccine and fall more quickly, especially in older people. Antibody levels also fell with the Moderna vaccine, but age did not appear to make a significant difference. Peak levels were reached after about 20 days for all three vaccines, but levels for Pfizer and Moderna were some 50 times higher than with Johnson & Johnson's Ad26.COV2.S vaccine.
According to the University of Virginia news item:
Yet more evidence, if any were needed, of the efficacy and desirability of getting vaccinated against COVID-19 was provided today in a paper published by a Swiss team from the Université de Genève (UNIGE) and the Hôpitaux universitaires de Genève (HUG). The results of their study were published in Nature Medicine a few days ago.
The team have shown that vaccinations reduce the viral load and thus the infectivity of vaccinated people who are unfortunate to become infected.
The press release from the Université de Genève explains:
Layer-deflecting bright red concretion of haematitic chert (an iron-rich and silica-rich rock), which contains tubular and filamentous microfossils. This co-called jasper is in contact with a dark green volcanic rock in the top right and represent hydrothermal vent precipitates on the seafloor. Nuvvuagittuq Supracrustal Belt, Québec, Canada. Canadian quarter for scale.
Scientists from University College, London (UCL) and State Key Laboratory of Biogeology and Environmental Geology, School of Earth Sciences, China University of Geosciences, Wuhan, China, believe they may have found evidence of the earliest life on earth, from just 300 million years after its formation.
The traces of bacterial deposits were found in rocks from Quebec’s Nuvvuagittuq Supracrustal Belt which are believed to have been formed in hydrothermal vents - regarded as the most likely place for the formation of organised, self-replicating, biotic systems from inorganic sources.
The evidence is in the form of tubes, branching filaments and ellipsoids of haematite, very similar to structures formed today by chemosynthetic bacteria in hydrothermal vents such as those close to the Loihi undersea volcano near Hawaii, as well as other vent systems in the Arctic and Indian oceans. Although the scientists concede that these structures could conceivably be the result of chance chemical reactions, no structures like these that are the result of chemical reactions have ever been found.
The UCL press release which accompanied the team's open access publication in Science Advances explains the technique used to examine the microfossils:
There has been some serious forgery going on in the world of evolution!
And, despite any hopes the thought of that might raise in the deluded minds of creationists, I'm not talking about human forgeries such as the famous Piltdown skull hoax, but natural forgeries produced by the natural force of evolution by natural selection.
The forgeries in question are the way brood parasite birds' eggs mimic those of the hosts.
Cuckoo Finches and Arms Races.
The cuckoo finch or parasitic weaver, Anomalospiza imberbis of East Africa is an obligate brood parasite on other birds of the Cisticolas and Prinias families. As we have seen with the earlier brood parasites, this has resulted in the inevitable evolutionary arms race as the parasitized hosts evolve strategies to reduce the depredation and the cuckoo finch evolves ways to circumvent the defence strategies of its intended hosts.
The strategy adopted by the tawny-flanked prinia, Prinia subflava, is to change the colours of its eggs more quickly than the cuckoo finch can and to produce eggs in an array of colours with markings that the prinia recognises as its own, almost like a signature.
The red-faced cisticola, Cisticola erythrops, on the other hand, while not varying the colour of its eggs has evolved to be better at spotting the cuckoo finch’s eggs and removing them. Another species, the rattling cisticola, Cisticola chiniana which might be expected to be an ideal host for the cuckoo finch appears to have won the arms race and is not parasitized at all (89).
Now one of the zoologists I cited in that section of my book, Professor Claire Spottiswoode from the Department of Zoology, Cambridge University, England, UK and the FitzPatrick Institute of African Ornithology, University of Cape Town, South Africa, along with Professor Michael Sorenson of the Department of Biology, Boston University, Boston, MA, USA, and others, has published an open access paper in PNAS which addresses the following questions:
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.
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 7th 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 7th 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 6th and 7th pandemics, as well as non-pandemic strains isolated from different water bodies. They then tthracked the plasmid’s stability over the course of many generations. Surprisingly, the model plasmid persisted in all strains, but was quickly eliminated from the 7th 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 7th pandemic V. cholerae strains. Furthermore, our discovery suggests that the ability of the 7th 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?
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).
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 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.
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:
Either their preferred 'intelligent [sic] designer' is intentionally modifying its original design to overcome human efforts to contain and control the pandemic.
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.
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).
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:
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.
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.
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.
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.
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.
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.
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.
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.
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
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
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.
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:
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.
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.
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?
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.
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.
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!
