US Religious Affiliation News - Accelerating Decline in Church Membership to Below 50%.

U.S. Church Membership Falls Below Majority for First Time.

According to the latest Gallop survey, religious affiliation and church membership is declining at an accelerating rate in the USA and the religiously unaffiliated are now in the majority, with affiliates to the various religions falling below 50% for the first time since Gallup began polling in 1937!

In the 60 years between 1940 and 2000, this figure declined only 3% from 73 to 70%, a figure that, given the distribution of values over the period from about 66% to 76% probably represents a steady figure of about 70%, subject to random sampling error.

The significant decline began at the turn of the millennium, falling 9%age points from 70 to 61% in the first 10 years, 6%age points in the next 5 years and a full 8%age points in the last 5 years, an annual rate of decline of 0.9, 1.2 and 1.6 percentage points, respectively. In Gallop's survey, religious affiliation means self-identifying as belonging to a church, synagogue or mosque. In Gallop's words:

Gallup asks Americans a battery of questions on their religious attitudes and practices twice each year. The following analysis of declines in church membership relies on three-year aggregates from 1998-2000 (when church membership averaged 69%), 2008-2010 (62%), and 2018-2020 (49%). The aggregates allow for reliable estimates by subgroup, with each three-year period consisting of data from more than 6,000 U.S. adults.

Although not the same thing, there is a close correlation between not having a religious preference and having no religion. The decline in church membership is probably a function of the decline in religious preference. Since the turn of the millennium, the percentage of Americans who do not self-identify with any religion has grown from 8% to 21%; a 162.5% increase in absolute numbers.

Americans are quickly losing faith in faith!

Not only that, but opinions appear to be firming up with the, perhaps surprising, figure for those who, while having no religious preference are nevertheless members of a church, synagogue or mosque, falling from 10% in 1998-2000 to just 4% in 2018-2020.

Given the nearly perfect alignment between not having a religious preference and not belonging to a church, the 13-percentage-point increase in no religious affiliation since 1998-2000 appears to account for more than half of the 20-point decline in church membership over the same time. Most of the rest of the drop can be attributed to a decline in formal church membership among Americans who do have a religious preference. Between 1998 and 2000, an average of 73% of religious Americans belonged to a church, synagogue or mosque. Over the past three years, the average has fallen to 60%.

As has been noted before, there is a marked difference between generations in the degree of affiliation to and membership of, a religion, with the youngest group being the least religious and the most inclined to reject religion, with 'Millennials' (born between 1981 and 1996) only about half as likely to be members of a church, synagogue or mosque as 'Traditionalists' (born before 1946) at 36% and 66% respectively. 'Baby boomers' (born between 1946 and 1964) and 'Generation X' (born between 1965 and 1980) are 58% and 50% respectively.

The two major trends driving the drop in church membership -- more adults with no religious preference and falling rates of church membership among people who do have a religion -- are apparent in each of the generations over time. Since the turn of the century, there has been a near doubling in the percentage of traditionalists (from 4% to 7%), baby boomers (from 7% to 13%) and Gen Xers (11% to 20%) with no religious affiliation.

Religions are suffering the double-whammy of declining religious beliefs per se, and declining church membership amongst those who do admit to holding religious beliefs.

Currently, 31% of millennials have no religious affiliation, which is up from 22% a decade ago. Similarly, 33% of the portion of Generation Z that has reached adulthood have no religious preference. Also, each generation has seen a decline in church membership among those who do affiliate with a specific religion. These declines have ranged between six and eight points over the past two decades for traditionalists, baby boomers and Generation X who identify with a religious faith. In just the past 10 years, the share of religious millennials who are church members has declined from 63% to 50%.

As the final two charts show, the result is always the same, differing only in magnitude and then not by a great deal. No matter how the data is sliced up, every demographic has shown a marked and accelerating decline in church membership, even amongst the conservatives and republicans amongst whom are to be found the Evangelical Christian fundamentalists, who on the US political stage, have tended to be the loudest and most vociferous, so much so that to us from outside the USA, America sometimes seems to be a nation of loopy religious extremists.

Over this period too, the Catholics have had sexual abuse scandal after sexual abuse scandal with even the most senior US Catholic cleric being sacked and defrocked and diocese after diocese declaring bankruptcy to avoid paying the very large compensation and reparation bills. Scandals of sexual and financial impropriety have even engulfed the Vatican with the former pope standing accused of complicity in child abuse scandals and their coverup, in his former German archdiocese of Munich, and making deliberately misleading and inaccurate statements to the enquiry into the abuses.

Nevertheless, the decline in membership of the Catholic church (-18%), while being double that of the Protestant churches (9%), it is within the normal range of decline for other demographics. The highest rates of decline (25%) are to be found in Democrat-leaning voters and residents in the Eastern United States (presumably East Coast, New England). The protestant churches show the smallest decline at 9%. This possibly reflects the fact that evangelical, Republican-voting, Americans tend also to be white Protestant.

Perhaps surprisingly, given that earlier polls tended to show that religiosity was declining faster in American men than women, this polls show a reversal of that trend, with a steeper decline for women (20%) than for men (18%). American women are making up for their earlier tardiness in abandoning religious institutions.

Just as a bit of fun, if the rate of decline over the last 5 years is maintained and projected into the future, let alone continues to accelerate at the rate its's been accelerating since 2000, membership of religious establishments in the USA should be in single percentage points within the next 15-20 years and should be a mere footnote in history by the middle of the 21st century.

What seems to be happening is what Europe and the rest of the industrial world experience since 1945 - the decline in religiosity proceedes exponentially as first a few, then more and finally very many people abandoned religion as Atheism and non-affiliation first became thinkable, then acceptable, and now the norm as we realised that we did not need the church involved in our daily lives and as the church reacted by becoming even more reactionary and condemning of an increasingly Humanist society, freed from the straight-jacket imposed by dubious religious 'morality' with its support for intolerance, division, hate and bigotry.

Hopefully, in the USA, the support given to the odious and deplorable Donald Trump by the Christian churches has opened the eyes of many Americans to the hypocritical, misogynistic, racist, self-serving and socially divisive nature of fundamentalist Christianity in the USA where, more than perhaps anywhere else in the developed world:

Religion provides excuses for people who need excuses.

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Evolution News - The Evolution of the Dingo

Dingo on the Nullarbor Plain, Australia

By Henry Whitehead - Original photograph, CC BY-SA 3.0

An international team, led by scientists from Australia and including scientists from the USA, Denmark and Germany, has generated high quality genomes of the dingo, the German shepherd and basenji domestic dogs, and compared them to the genomes of the Greenland wolf and other domestic dogs, to discover exactly where in the evolutionary tree of dogs, the dingo split off from other dogs.

Dingoes have existed in Australia, in isolation from other dogs, for tens of thousands of years, and appear to have split off early in the domestication of dogs from their wolf ancestors. They still carry some of the characteristic genes of wolves, which have been modified in domestic dogs. For example, domestic dogs have multiple copies of a gene (amylase 2B) for digesting starch, while wolves and dingoes only have a single copy. A recently evolved trait in domestic dogs is the ability to raise their eyebrows as a non-verbal communication with humans. This ability is absent from wolves and domestic dogs.

But the question of whether dingoes are descended from feral domestic dogs taken to Australia by the first human migrants or are descended from an ancestral species to the domestic dog has still not been settled.

The team have published their findings, open access, in the journal Science Advances, and, unusual for a scientific publication, two of the team, have also written an open access article describing their work, in The Conversation

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

Creationism's Demon

The Keeper at the Gate of Creationists' Perception

Creationism's Demon, or Morton's Demon to give it its correct name, was discovered by Glenn Morton, a former YEC, who, when he graduated as a geologist and began to do some serious scientific research, not only realised the data did not support the notion of a young Earth but actually falsified it. If he was going to earn his living as a professional geologist, he needed to abandon creationism and use real science.

Trying to understand how he had been deluding himself, he realised there was an explanation already in the form of a psychological devise, which was analogous to an idea invented by James Clark Maxwell in 1867 (Maxwell's Demon) to explain how the 2nd Law of Thermodynamics could theoretically be violated. This psychological devise he called Morton's Demon.

In Morton's own words (reproduced in full as a copyright condition):

Evolution News - How Our Gut Biota May Be Dictating What We Eat.

Got food cravings? What’s living in your gut may be responsible | University of Pittsburgh

In a fascinating example of the kind of thing that co-evolution can produce, scientist at Pittsburg University believe they have shown how the gut biota of mice could be controlling the mouse's cravings for particular foods.

If this holds true for humans, it could mean that our gut biota could be telling us what they want us to eat, based not on our nutritional needs, but on theirs. We have, of course, been evolving along with our gut organisms since the first multicellular organisms evolved the first alimentary cannal, and possibly even earlier. More recently, it has proved possible to track the dispersion out of Africa and across the globe by subtle differences in the strains of organisms in our gut biota.

In other words, evolution has had plenty of time to evolve suptle relationships between us and our internal biota and, biologically speaking, we have not been evolving as a single species but as a collony, so any species in the colony could be influencing the evolution of the colony as a whole.

That evolutionary relationship was behind the research by the Pittsburgh Scientists, Assistant professor, Kevin Kohl and Doctor Brian Trevelline, as the Pittsburgh University new release explains:

Evolution News - Yet Another of the 'Missing' Transitional Form

Artist’s reconstruction of the feathered pterosaur Tupandactylus, showing the feather types along the bottom of the headcrest: dark monofilaments and lighter-coloured branched feathers.

© Bob Nicholls

Artist’s reconstruction of the feathered pterosaur Tupandactylus, showing the feather types along the bottom of the headcrest: dark monofilaments and lighter-coloured branched feathers.

© Bob Nicholls

News and Views | University College Cork

It's difficult to keep track of all these 'non-existent' transitional fossils. Like London buses, you can wait for ages, then several will turn up together. One can't help but wonder how creationist find the time to ignore all of them.

Here for instance is one recently discovered fossil showing the transition from dinosaur to bird feathers, complete with evidence of pigmentation, showing that colour was important for display, even in these pterosaurs.

The discovery was made by an international team of palaeontologists led by Dr Aude Cincotta and Prof. Maria McNamara from University College Cork (UCC), Ireland and Dr Pascal Godefroit from the Royal Belgian Institute of Natural Sciences, together with colleagues from Belgium and Brazil.

The discovery was made when the team examined the 115 million year old fossilized headcrest of the pterosaur, Tupandactylus imperator, from north-eastern Brazil.

The news item from University College, Cork, give the detils:

Covidiot Antivaxxer News - Study Shows That Covid-19 Can Cause Dementia

COVID-19 Pneumonia Increases Dementia Risk - MU School of Medicine

There are two ways of looking at the latest findings concerning the long-term effects of severe COVID-19.

• If you are a creationist, you could marvel at the inventive genius of any intelligent designer who could design such a thing as the SARS-CoV-2 virus that causes COVID-19 just to increase the suffering in the world
• If you are a caring and compassionate person, you can appreciate how this findings makes it imperative that as many people as possible are vaccinated and boosted in order to reduce the likelihood of someone else catching the disease and to help make the pandemic a thing of the past.

The finding, by researchers from the University of Missouri School of Medicine and MU Health Care shows that there is a significantly increased risk of developing dementia following a case of COVID-29-induced pneumonia, severe enough to requiring hospitalization.

The risk of new onset dementia was more common in COVID-19 pneumonia patients over the age of 70 in our study.

The type of dementia seen in survivors of COVID-19 infection mainly affects memory, ability to perform everyday tasks and self-regulation. Language and awareness of time and location remained relatively preserved.

The findings suggest a role for screening for cognitive deficits among COVID-19 survivors. If there is evidence of impairment during screening and if the patient continues to report cognitive symptoms, a referral for comprehensive assessment may be necessary.

Professor Adnan I. Qureshi, MD. Professor of clinical neurology
MU School of Medicine.

For the study, the researchers analysed the records of 1.4 billion medical encounters prior to July 31, 2021. They selected patients hospitalized with pneumonia for more than 24 hours. Among 10,403 patients with COVID-19 pneumonia, 312 (3%) developed new onset dementia after recovering, compared to 263 (2.5%) of the 10,403 patients with other types of pneumonia diagnosed with dementia. This represents a 20% increase in the risk of dementia following COVID-19 pneumonia.

The study was only of new onset dementia. The median time interval between infection and dementia diagnosis was 182 days for COVID-19 patients. The study only included new onset dementia associated with hospital admission during a short follow-up period. Dr Qureshi said a more detailed study, conducted over a longer time may help to determine the reasons why COVID-19 is linked to dementia.
The authors give more details in the abstract to their open access paper published in the journal Open Forum Infectious Diseases:

Abstract

Background
Case series without control groups suggest that severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) infection may result in cognitive deficits and dementia in the postinfectious period.

Methods
Adult pneumonia patients with SARS-CoV-2 infection (index hospitalization) and age-, gender-, and race/ethnicity-matched contemporary control pneumonia patients without SARS-CoV-2 infection were identified from 110 healthcare facilities in United States. The risk of new diagnosis of dementia following >30 days after the index hospitalization event without any previous history of dementia was identified using logistic regression analysis to adjust for potential confounders.

Results
Among 10 403 patients with pneumonia associated with SARS-CoV-2 infection, 312 patients (3% [95% confidence interval {CI}, 2.7%–3.4%]) developed new-onset dementia over a median period of 182 days (quartile 1 = 113 days, quartile 3 = 277 days). After adjustment for age, gender, race/ethnicity, hypertension, diabetes mellitus, hyperlipidemia, nicotine dependence/tobacco use, alcohol use/abuse, atrial fibrillation, previous stroke, and congestive heart failure, the risk of new-onset dementia was significantly higher with pneumonia associated with SARS-CoV-2 infection compared with pneumonia unrelated to SARS-CoV-2 infection (odds ratio [OR], 1.3 [95% CI, 1.1–1.5]). The association remained significant after further adjustment for occurrence of stroke, septic shock, and intubation/mechanical ventilation during index hospitalization (OR, 1.3 [95% CI, 1.1–1.5]).

Conclusions
Approximately 3% of patients with pneumonia associated with SARS-CoV-2 infection developed new-onset dementia, which was significantly higher than the rate seen with other pneumonias.

Qureshi, Adnan I; Baskett, William I; Huang, Wei; Naqvi, S Hasan; Shyu, Chi-Ren
New-Onset Dementia Among Survivors of Pneumonia Associated With Severe Acute Respiratory Syndrome Coronavirus 2 Infection
Open Forum Infectious Diseases, Volume 9, Issue 4, April 2022, ofac115, doi: 10.1093/ofid/ofac115

Copyright: © 2022 The authors. Published by Oxford University Press on behalf of Infectious Diseases Society of America.
Open access
Reprinted under a Creative Commons Attribution-NonCommercial-NoDerivs licence (CC BY-NC-ND 4.0)

The findings from this study, with the findings in the study which was the subject of my last blog post which showed the efficacy of the vaccines in children, give a very clear message to anyone with a sense of social responsibility, which I appreciate tends not to include evangelical creationists and members of extremist right-wing antivaxxer cults, is that vaccinations work and should be encouraged, if we are ever to put an end to this pandemic and to reduce the suffering it has wrecked worldwide.

Probably what evangelical creationists hate most about the vaccines is that they represent a considerable triumph of science over what they believe to be the creation of their god, visited on mankind for disagreeing with evangelical creationists.

Don't be a Covidiot!
Get vaccinated or get boosted, Now!

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Antivaxx Covidiots Wrong Again. Vaccinations Protect Children

COVID-19 Vaccine Protects Kids and Teens from Severe Illness | Lurie Children's

A new study has shown that the Pfizer-BioNTech mRNA COVID-19 vaccine significantly reduces the proportion of sever COVID-19 infections, reducing the risk of hospitalisation in 5–11-year-olds by two-thirds. Although it was lower for the Omicron variant than for Delta, protection against hospitalisation remained high for 12–18-year-olds. It also gave high protection against critical COVID-19 requiring life-supporting interventions for adults during both Delta and Omicron waves.

The study was carried out by researchers at the Ann & Robert H. Lurie Children’s Hospital, Chicago, IL, USA and is published in the New England Journal of Medicine.

As explained in the news release from the Ann & Robert H. Lurie Children’s Hospital:

Unintelligent Design - Scientists are Improving on the Designer's Blunder

Structure and function of Rubisco. (A) Schematic depiction of photosynthesis in chloroplasts and the role of Rubisco. The light reaction and Calvin-Benson-Bassham (CBB) cycle of CO 2 fixation, as well as the side-reaction of photorespiration are shown. RuBP, ribulose-1,5-bisphosphate; 3PG, 3-phosphoglycerate; G3P, glyceraldehyde-3-phosphate; 2P-glycolate, 2-phosphoglycolate. (B) Structure of hexadecameric form I Rubisco. Side and top views of Rubisco are shown in surface representation (PDB: 1RCX, Taylor and Andersson, 1997). One antiparallel RbcL dimer with RuBP bound in the active sites is shown in ribbon representation. (C) Superposition of open and closed conformations (PDB: 1RXO and 1RCX, respectively; Taylor and Andersson, 1997) of Rubisco. In the closed state (dark green), loop 6 (cyan) covers the active site, trapping the bound RuBP (red), and is pinned down by the flexible C-terminal peptide (pink) that stretches across the RbcL subunit. In the open conformation (pale green), loop 6 (dark blue) is retracted and the C-terminal peptide (pink) is disordered.

Scientists resurrect ancient enzymes to improve photosynthesis | Cornell Chronicle

As I have said before in these blogs and in my popular book, Unintelligent Design: Refuting the Intelligent Design Hoax, if only they understood the subject, creationists should be acutely embarrassed by a ubiquitous enzyme known by the common name, RuBisCo, which stands for ribulose-1,5-bisphosphate carboxylase/oxygenase.

RuBisCo is probably the least efficient of all enzymes - which is why it is so abundant in nature, accounting for the green we see where photosynthesising plants are growing. It's what gives the planet its characteristic green colour everywhere, apart from the deserts, oceans, polar ice caps and mountain peaks.

It is the enzyme responsible for 'fixing' the carbon in carbon dioxide in the atmosphere, so it can be built up into glucose in photosynthesis. Glucose is the basic sugar from which most other carbohydrates are built and the source of energy on which almost all living organisms ultimately depend. It is also the building block of structural material such as cellulose and lignin for plants and chitin for the exoskeletons of arthropods.

In fact, RuBisCo is so inefficient that it would be a major breakthrough in agriculture if scientists could make it more efficient so more food could be produced with the same resources. An added bonus would be that more CO₂ would be extracted from the atmosphere, so reducing global warming.

Imagine that! Something creationists believe was intelligently designed by an omniscient, omnipotent designer that is so badly designed that mere humans are having to redesign it to make it more efficient!

Talibangelical Christian Theocracy News - Pastor Tony Spell Spills the Beans

Pastor Tony Spell, Life Tabernacle Church, Baton Rouge, Louisiana
"Government of USA should be by prophets (himself) at the top, then priests, then princes, then the people, God sez!"

Christian Nationalist Tony Spell Says Prophets Should Reign Over Government and the People | Right Wing Watch

It is unusual for a Talibangelical Christian pastor to be so honest (and lacking in nouse) as to admit their political ambitions in public, knowing full well that they need to pretend to be good democrats and supportive of US democracy if they are to keep fleecing their dupes, but extreme right-winger, Pastor Tony Spell, of the Life Tabernacle Church in Baton Rouge, Louisiana, has no such qualms. He wants to run the government, or at least have the right to veto government policies he doesn't like and command others instead.

Not to put too fine a point on it, he has ambitions to be the American equivalent of the Iranian Supreme Leader or the equivalent of a Taliban Caliph. Unelected, accountable to no-one but himself and having the power to meddle in every aspect of public and private life in the USA.

How Science Works - Questioning the Existence of Time Itself

In contrast to religion, which depends on a closed mind and fixed, unchangeable dogmas and axioms which cannot be questioned without effectively leaving the 'faith', science is an open-minded process of constant reassessment and revision.

In science, dogma is anathema and the only certainty is that there are no certainties. There is always the possibility that what we think we know is merely an illusion or the product of our limited perception, and not reality itself.

This is perhaps perfectly illustrated by the curent debate in theoretical physics about the nature of space-time, and time in paticular.

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

What Is The SARS-Cov-2 Omicron XE Variant and Should You Be Worried?

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

What’s the new Omicron XE variant and should I be worried?

Shutterstock

Paul Griffin, The University of Queensland

It seems every few weeks we hear about a new COVID variant, and it’s hard to know how concerned we ought to be.

A “recombinant” variant has emerged, dubbed “Omicron XE”, which is the result of two omicron strains merging together in a single host and then going on to infect others.

So what do we know about this new hybrid, and do we need to worry?

Covidiot News - Why Boosters are Important.

Ebony Hilton, MD, receives the first COVID-19 vaccine administered at UVA Health.

Study Tracks COVID-19 Antibodies Over Time

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:

Anti-Vaxxer, Covidiot News - Why Vaccination Is a Good Thing

COVID-19: Vaccination greatly reduces infectious viral load - Press Release - UNIGE

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:

Abiogenesis News - Earliest Signs of Life Found in Canada

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.

Credit: D. Papineau.

Diverse life forms may have evolved earlier than previously thought | UCL News - UCL – University College London

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:

Unintelligent Designer News - How the Genetics of Egg Mimicry in a Brood Parasite Could Cause Their Extinction

Cuckoo finch egg in zitting cisticola nest.

Scientists crack egg forging evolutionary puzzle

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.

I wrote about this very phenomenon in my popular, illustrated book, The Malevolent Designer: Why Nature's God is not Good, in which I said:

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.

Cuckoo finch, Anomalospinza imberbis

Illustration: Catherine Hounslow-Webber

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).

Rosa Rubicondior, The Malevolent Designer: Why Nature's God is not Good, pp. 99-100.

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:

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.