F Rosa Rubicondior: Health
Showing posts with label Health. Show all posts
Showing posts with label Health. Show all posts

Tuesday 12 March 2024

Malevolent Design - How The Malaria Parasite is 'Designed' To Evolve And Outwit Medical Science


The malaria parasite generates genetic diversity using an evolutionary ‘copy-paste’ tactic | EMBL

Devotees of creationism’s divine malevolence would be conflicted by this news if they understood it, because it shows the creative genius of any intelligent designer who could come up with this system, but, it looks like it did so (if you believe it couldn't happen naturally) by setting up an evolutionary process that creationists are obliged by dogma to believe doesn't work.

The news is that the organisms that causes malaria, Plasmodium falciparum, is 'designed' to quickly find a way to overcome the anti-malarial drugs medical science has developed to cure people suffering from it and to prevent others from getting malaria, by evolving very quickly.

The discovery was by researchers at European Molecular Biology Laboratory's (EMBL’s) European Bioinformatics Institute who have identified a mechanism of ‘copy-paste’ genetics that increases the genetic diversity of the parasite at accelerated time scales. This helps solve a long-standing mystery regarding why the parasite displays hotspots of genetic diversity in an otherwise unremarkable genetic landscape. Copy-paste' is a way of doing something creationists insist is impossible without the aid of god-magic of increasing the genetic information in a genome and making it available for evolution by mutation and selection without any loss of function in the original copied genes.

The team have recently published their finding in the open access journal PLOS Biology and describe it in an EMBL news item:

Sunday 10 March 2024

Covidiot News - Just Because You Haven't Had COVID-19 Yet, Doesn't Mean You Won't!


Haven't had COVID yet? It could be more than just luck

There are some scary questions for creationists at the end of this article. They follow on naturally from what's being discussed, so creationists should probably avoid reading too far, unless they have a responsible adult with them.

This article from The Conversation is from May 2022, when we were into the second year of the COVID-19 pandemic and most vulnerable people had had the two-step vaccinations and many would have had the spring booster. At that point neither me nor my partner had had COVID-19, which we put down to rigorously following the recommendations regarding mask-wearing, social distancing, hand washing, etc. and had tried to reduce our vulnerability to the sever forms of it by losing about 3 stone in weight and, in my case, getting my blood pressure under control with medication. We also tried to ensure our immune systems were healthy by taking vitamin D3, vitamin C, zinc and iron supplements.

In the early days of the pandemic, even before the official restrictions on social contact, we had observed the basic rules of hygiene and everyone who came into the house used hand-cleanser at the front door. I had even managed to obtain a supply of face-masks and plastic gloves online, which we wore at all times outside the house. Every package that was delivered to the house was left for several hours before we touched it, and all our weekly shopping was delivered or bought with click and collect. Delivered bags were left for four hours before unpacking. And we took weekly tests just in case we had it asymptomatically. All that might seem a little over the top now, but we were vindicated as events were to prove.

We put the fact that we hadn't caught it by mid-2022 down to our preventative measures, not to luck or genetics - a view that was vindicated last year when we both came back from a two-week vacation in France with a mild form of COVID-19, despite having had all the boosters on offer. We probably picked it up in a crowded airport or on the plane, where all the social distancing measures had been forgotten and even face masks were no longer worn. We both felt like we had a mild case of flu for a couple of days and after a week we were testing negative. Had we contracted it in Spring 2020, the outcome would probably have been very different as we had no immunity, and both had three of the risk-factors - overweight, high BP and over 70. In addition, my partner had had a mastectomy and was receiving treatment for breast cancer.

One reason you can't ever be sure that you won't catch COVID-19 is because the virus keeps mutating to produce new variants so, even if you were fortunate enough to have natural or acquired immunity to the variants so far, it is quite possible that the next or subsequent variants will have evolved a way round it. The following chart from the UK NHS, shows the rise and fall of the main variants over the course of the pandemic:
But still, a few people managed to stay free from the virus. In the following article, reprinted from The Conversation under a Creative Commons license, Lindsay Broadbent, Research Fellow, School of Medicine, Dentistry and Biomedical Sciences, Queen's University Belfast, explains why. Her article has been reformatted for stylistic consistency:

Monday 4 March 2024

Anti-Vaxxer Conspiracists News - How Trumpanzee Cult Conspiracists Are Risking People's Lives For Money While Feeding Populist Extremism


Anti-vaccine conspiracies fuel divisive political discourse | The University of Tokyo
According to a news item carried today by Agence France-Presse (AFP), US antivaxx conspiracists are deliberately spreading fear and disinformation to sell quack medical kits to gullible fools and in doing so are risking the lives of anyone foolish enough to believe them. And a recent paper published by a Japanese research group has shown how extremist parties are trading on growing antivaxx paranoia, originating in Trump-supporting conspiracists in the USA, by incorporating it into the political platforms.

This team of researchers recall how Donald Trump first of all tried to take credit for developing the mRNA vaccines against Covid-19, as though he had personally directed the research and invented the science behind mRNA vaccines, then switched to curry favour with the antivaxxers by casting doubt on the need for boosters. And of course, antivaxxer conspiracy theories became a central theme of the rabidly pro-Trump QAnon conspiracy theorists.

Firstly, the AFP report:

Saturday 2 March 2024

Unintelligent Design - The Heath-Robinson Workaround For A Design Fault In The Immune System


The “switch” that keeps the immune system from attacking the body - EPFL

A Machine for Testing Golf Drivers - William Heath-Robinson
A characteristic of designs by creationism's putative intelligent designer, is the needless complexity which often arises because earlier solutions were suboptimal and either didn't work very well or tended to cause problems that needed to be mitigated with another layer of (often suboptimal) complexity.

This is also a characteristic of systems 'designed' by a mindless natural process with no power or mechanism for scrapping a suboptimal design and starting again and no ability to predict the future and design for problems which will arise later.

In fact, what creationists think is evidence of a supreme intelligence, more often seems to resemble the designs of the British cartoonist and eccentric designer, William Heath-Robinson, who was famous for his machines designed to solve every-day problem, which were invariably far more complex than they need have been, and which incorporated everyday objects such as umbrellas, full coal-scuttles for counter-weights, lengths of knotted string and stepladders balanced on upright pianos to give them enough height. Take away any of these unlikely components and the whole machine would fail, in an almost perfect metaphor for how evolution can exapt pre-exiting structures from other processes and structures for novel functions, to give the appearance of irreducible complexity.

And yet they work, or at least look as though they would if anyone ever made one.

An example of a Heath-Robinson machine in mammalian 'design' was revealed by a scientists working at the Swiss École polytechnique fédérale de Lausanne (EPFL), who have discovered how the body prevents the immune system from attacking itself.

But, as the very many auto-immune diseases show, this system is far from perfect and frequently fails, sometime with serious, even fatal, consequences.

But the whole immune system is only needed because something designed pathogens such as bacteria, viruses and other parasites, apparently to attack us and make us sick in the first place. Parasites are a source of conflict for creationists who have to believe both that the putative designer god is the only entity capable of designing living things, and that something else created parasites because their god wouldn't do such a thing, and both that their god is omnipotent, but powerless against that other designer.

So, what is this mechanism the EPFL researchers have discovered?

Their findings are the subject of an open access paper in Nature and is explained in an EPFL news release:

Friday 1 March 2024

Malevolent Designer News - How Creationism's Divine Malevolence Is Adapting The Avian Flu Virus to Kill Marine Mammals


Avian Influenza Virus Is Adapting to Spread to Marine Mammals | UC Davis

Elephant seals lie dead on a beach in Argentina following an outbreak of avian influenza in the region.
Photo: Maxi Jonas.
As an example of creationist double-think and intellectual bankruptcy, their attitude toward parasites like viruses is a classic:
  • "Only God is capable of designing organisms, so "Look at the trees!" and "What about irreducible complexity?"
  • "Something else created parasites like bacteria, worms and viruses, because God wouldn't do something like that!"

Simultaneously committing blasphemy and refuting their own argument from teleology!

I wonder then how that rarest of animals, the intellectually honest creationist copes with the news that the creator of the avian flu virus, H5N1, is in the process of adapting it to kill marine mammals such as elephant seals, just as it adapted the SARS-CoV-2 virus from a bat virus to one that could kill humans and cause economic collapse.

Evidence that it is doing so, if you believe viruses are created and don't evolve naturally, which dogma forbids a creationist from believing, comes in the form of a study by scientists from University of California, Davis, and the National Institute of Agricultural Technology (INTA) in Argentina. The study, the first genomic characterization of H5N1 in marine wildlife on the Atlantic shore of South America, is published in the journal Emerging Infectious Diseases and is described in a UC Davis news release:

Wednesday 28 February 2024

Covidiot News - How the mRNA Vaccines Give Long-Term Protection Against COVID-19


Long-Term Data Reveals SARS-CoV-2 Infection and Vaccine-Induced Antibody Responses Are Long-Lasting | Mount Sinai - New York

If you listen to antivaxxer covidiots you would believe:
  • COVID-19 is no worse than the common cold.
  • The SARS-CoV-2 virus which causes COVID-19, is a deadly organism developed by the Chinese for biological warfare.
  • COVID-19 was a hoax (which even normally hostile nations had signed up to, apparently).
  • God sent the virus to punish America for legalising same-sex marriage (and the rest of the world was collateral damage)
  • The vaccines developed against it don't work (regardless of what the clinic trials showed).
  • The vaccines contain microchips and special genes to make you become gay and/or subject to satellite control.
  • The vaccines contain deadly viruses that can be activated via the 5G phone network.
  • Millions of people have died or will die soon because they've been vaccinated.
  • [Fill in your own crackpot theory because someone will already have claimed it to be true].

The truth is, however, that millions of people died of COVID-19 in the first year of the pandemic, before a vaccine was generally available and this death rate fell to low levels following the roll out of the first vaccines and subsequent boosters to allow for new variants. Although the virus is still very much with us, people have been able to resume normal activities and the economic and health impact of the virus is now no more than that of seasonal flu, but there were concerns that antibody levels produced in response to the mRNA vaccines were short-lived, giving only temporary protection.

Now a large-scale analysis conducted by leading microbiologists at the Icahn School of Medicine at Mount Sinai has shown that antibody responses induced by COVId-19 vaccines are long-lasting. The results of this analysis are published, open access, in the Cell Press journal, Immunity, and are discussed in a Mount Sinai press release:
The emergence of SARS-CoV-2, the virus that causes COVID-19, in late 2019 sparked the global pandemic that is now in its fifth year. Vaccines that were developed at record speed have saved millions of lives. However, the emergence of SARS-CoV-2 variants and waning immunity have decreased the effectiveness of the vaccines against symptomatic disease. The common perception now is that mRNA-based vaccine-induced immunity wanes quickly. However, this assumption is largely based on data from short-term studies that include a very limited number of data points following peak responses.

The Mount Sinai research team’s analysis of more than 8,000 samples collected over a three-year period in New York City examined how antibody responses to the virus’s spike protein changed after infections, during the primary immunization series, during monovalent and bivalent booster vaccination, and during breakthrough infections.

They found that upon primary immunization, participants with pre-existing immunity (those who had previously been infected with the virus) mounted higher antibody responses faster and achieved higher steady-state antibody titers than individuals who had not been previously infected. The waning of antibody response was characterized by two phases: an initial rapid decay from the strong peak after vaccination, followed by a stabilization phase with very slow decay, suggesting that antibody levels were very long-lasting. Booster vaccination equalized the differences in antibody concentration between participants with and without pre-existing immunity. Breakthrough infections increased antibodies to similar levels as an additional vaccine dose in individuals who had not previously been infected.

This investigation represents one of the most extensive and in-depth assessments of the longevity of SARS-CoV-2 immune responses to date. Its major conclusion is that changes in the virus that allow it to evade immunity, rather than waning immunity, are the major reason for breakthrough infections.

Ours is one of the longest-running COVID-19 studies out there. Following the same group of people monthly over time is rare and powerful because you can compare immune responses on an individual level. SARS-CoV-2 continues to evolve, so this research is important to provide an understanding about the impact of new variants and new vaccine doses on a healthy immune system, and to guide all of us to make the best choices to maintain protection against the virus that continues to circulate in our communities.

Professor Viviana Simon, MD, PhD, lead author
Professor of Microbiology, Medicine and Pathology, Molecular and Cell-Based Medicine
Department of Microbiology
Icahn School of Medicine at Mount Sinai, New York, NY, USA.
This in-depth analysis was made possible through the Protection Associated with Rapid Immunity to SARS-CoV-2 (PARIS) study, an observational, longitudinal cohort of health care workers of the Mount Sinai Health System that was initiated in April 2020. At that time, the densely populated New York metropolitan area was hit with an exponential increase in severe SARS-CoV-2 infections, and essential workers in the health care system were at high risk for infection. In response to the crisis, a team of leading virologists, physician-scientists, and pathologists at Mount Sinai established a specific and sensitive SARS-CoV-2 binding enzyme-linked immunosorbent assay to accurately measure the SARS-CoV-2 antibody titers. This test was used to measure immune responses in the PARIS cohort in order to determine how quickly the antibody defenses were mounted and much these changed over the months and years of follow up.

In addition to showing the impact on a person’s individual antibody response to vaccines based on the type of vaccine received and whether or not they were infected before receiving the first dose, the PARIS study made possible the development of a mathematical model that can be used to predict and characterize antibody responses of both individual people and populations.

People have pandemic fatigue and vaccine uptake has slowed, especially after the vaccines started to be charged to insurance*. We were pleasantly surprised to see that the booster doses promoted a large antibody response regardless of a person’s personal infection history, so we are hopeful that our study findings will encourage people to get their vaccine boosters when eligible and to stay engaged in research. Our work also showcases the impact of viral evolution over time and why it’s critical to keep studies like this going, despite the pandemic fatigue.

Komal Srivastava, MS, Co-first author
Director of Strategy and Operation
Mount Sinai Center for Vaccine Research and Pandemic Preparedness.

According to the research team, the PARIS model has broad applications for studying the kinetics of antibodies produced to different COVID-19 vaccines in diverse populations. They stress much more work remains to analyze side effects, applications of the antibody model and continued research about new vaccines and viral variants.

This study adds an essential piece of data to understand the intricate immune response elicited by SARS-CoV-2 infection and COVID-19 vaccination. In light of the emerging viral variants, which predominantly induce a cross-reactive antibody response against the spike protein, it will be exciting to characterize in depth the role of these antibodies - in particular the non-neutralizing ones - in protection against the most recent circulating viral variants. Likewise, monitoring the induction of variant-specific antibodies after multiple exposures by breakthrough infections and by administration of updated COVID-19 vaccines, such as the XBB.1.5 monovalent booster, will be key to understand the evolution of the antibody response over time.

Assistant Professor Dr Juan Manuel Carreno Quiroz, PhD, Co-first author.
Department of Microbiology
Icahn School of Medicine at Mount Sinai, New York, NY, USA.


*Note: in the UK, vaccines are provided free by the NHS. Other non-US countries will have their own health-care systems which may or may not include charges for the vaccines.
More technical detail and the background to the research is given in the team's paper in Immunology:
Graphical abstract
Highlights
  • COVID-19-vaccine-induced immunity wanes but stabilizes at an individual setpoint
  • Pre-existing immunity results in rapid antibody responses upon vaccination
  • Boosters equalize antibody titers between individuals with and without hybrid immunity
  • Antibody kinetics show two phases: an initial rapid decay followed by a steady state

Summary

It is thought that mRNA-based vaccine-induced immunity to severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) wanes quickly, based mostly on short-term studies. Here, we analyzed the kinetics and durability of the humoral responses to SARS-CoV-2 infection and vaccination using >8,000 longitudinal samples collected over a 3-year period in New York City. Upon primary immunization, participants with pre-existing immunity mounted higher antibody responses faster and achieved higher steady-state antibody titers than naive individuals. Antibody kinetics were characterized by two phases: an initial rapid decay, followed by a stabilization phase with very slow decay. Booster vaccination equalized the differences in antibody concentration between participants with and without hybrid immunity, but the peak antibody titers decreased with each successive antigen exposure. Breakthrough infections increased antibodies to similar titers as an additional vaccine dose in naive individuals. Our study provides strong evidence that SARS-CoV-2 antibody responses are long lasting, with initial waning followed by stabilization.

Introduction

The emergence of severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) in late 2019 sparked the global coronavirus disease 2019 (COVID-19) pandemic that is now in its 4th year. Vaccines to mitigate the impact of the pandemic were developed at record speed and have saved millions of lives. However, the emergence of SARS-CoV-2 variants1 and waning immunity2 have decreased the effectiveness of the vaccines against symptomatic disease.3 These two issues, the emergence of antigenically distinct SARS-CoV-2 variants and waning immunity, are often conflated and used interchangeably but represent two different phenomena.4 Most vaccines used in North America and Europe are based on lipid nanoparticles (LNPs) containing messenger RNA (mRNA) produced by Pfizer/BioNTech (BNT162b2) or Moderna (mRNA-1273), and the common perception now is that mRNA-based vaccine-induced immunity wanes quickly.5 However, this assumption is mostly based on data from short-term studies that include a very limited number of data points following peak responses.2,5

In March of 2020, the densely populated New York metropolitan area was hit with an exponential increase of severe SARS-CoV-2 infections, resulting in a staggering number of fatalities and a severely overburdened healthcare system.6,7,8 Due to shortages of personal protective equipment, essential workers in the health care system were at high risk for infection. In response to this crisis, we established (1) a specific and sensitive SARS-CoV-2 binding enzyme-linked immunosorbent assay (ELISA) to measure humoral immune responses,9 and (2) an observational longitudinal cohort of health care workers of the Mount Sinai Health System to determine the kinetics of these humoral responses. This study, named Protection Associated with Rapid Immunity to SARS-CoV-2 (PARIS),10 aims to capture the dynamics of SARS-CoV-2 antibody responses to infection as well as vaccinations, to determine re-infection rates, and to assess correlates of protection in the context of individual immune histories.

With over 8,000 longitudinal study visits across a single cohort during the first 3 years of the pandemic, our investigation represents one of the most extensive and in-depth assessments of the longevity of SARS-CoV-2 immune responses to date. Using this longitudinal cohort, we determined the kinetics of antibody responses to spike protein after infections, during the primary immunization series, during monovalent and bivalent booster vaccination, as well as during breakthrough infections. Our findings indicate that, in contrast to common perception, COVID-19 mRNA vaccination induces long-lasting antibody responses in humans. The PARIS Study also provides insights into the effect of booster vaccination and breakthrough infections on the stability of antibody responses.
What is clear from this study is that antibody levels remain at protective levels for very much longer that was previously thought and that they continue to give protection against the severe form of the disease. However, as the virus evolves in an environment in which the vast majority of possible victims have already been vaccinated or have had previous infections so have high antibody levels, the variants that can 'escape' this protection will continue to evolve and become the predominant variant.

This diagram from UK data shows how the different variants have evolved and either replaced earlier variants or have reached an equilibrium with them:
Changes in proportions of SARS-CoV-2 variants in UK over time. This diagram is a good illustration of how the proportions of different alleles of a gene change in a species gene pool over time as the species evolves.

It is essential then that regular boosters, which provide protection against the latest variants, should continue to be given. We are in a long-term struggle with this virus and vaccines keep us ahead of the game.

Wednesday 21 February 2024

Creationism in Crisis - 275 Million New Human Genetic Variants in USA Alone - Why So Many?


275 Million New Genetic Variants Identified in NIH Precision Medicine Data | All of Us Research Program | NIH

Researchers at the American NIH have identified 275 million previously unknown genetic variants in samples from 250,000 representative American adults who participated in their All of Us research program. Half the participants were of non-European ancestry. Nearly 4 million of these newly discovered variants are from areas of the genome tied to known disease risks.

Let's consider that from the point of view of someone who believes in intelligent [sic] design:

Why on Earth would an intelligent designer design so many variations on the same theme? An intelligent designer, especially one endowed with the foresight of omniscience and unlimited powers and who is omnibenevolent and perfect, would design the perfect solution to every problem, and stick with it, not design lots of different solutions to the same problem. And every iteration through the cycle of replication would produce an exact copy of that perfect design, so there is no logical way all those variations could be the result of random mutations which all happened to be equally good at whatever they did, so there was no element of selection involved.

Quite simply, lots of variations on the same theme are evidence not of intelligent design, but of utilitarian, mindless 'design' working without a plan and with no conception of the ideal or perfection. Variation is kept because it works; maybe not exactly as well as other alleles, but well enough for the carrier to survive and reproduce. Even if the differences are too small to play a significant part in evolution by natural selection, unless they are serious deleterious, genetic drift can account for them being a significant part of the species genome.

Thursday 15 February 2024

Creationism in Crisis - The Inner Ear Of A 6 Million-Year-Old Hominoid Fossil Gives A Clue To The Evolution Of Bipedalism In Humans


How Did Humans Learn to Walk? New Evolutionary Study Offers an Earful

To walk upright successfully needs a fully functioning balance organ in the inner ear, as anyone suffering from Ménière's disease will testify, so the study of the origins of bipedalism in the remote ancestors of humans needs to take into account changes in the inner ear that would facilitate it.

Humans and our closest relatives, the great apes and the simians, display a range of locomotion but only humans are normally fully bipedal, although chimpanzees can use bipedal locomotion when carrying a load for example.

The monkeys normally run along branches on all fours, balanced on top of them and jumping from branch to branch; the apes hang beneath the branches in locomotion known as brachiation, but humans are ungainly in trees and prefer bipedal locomotion on the ground. The question is, when did this ability evolve in our ancestry?

We can be sure our hominin ancestors the Australopithecines, were fully bipedal because we have a record of their footprints in volcanic ash at Laetoli, and their lower limbs and feet were almost indistinguishable from those of Homo sapiens. 'Lucy' (Au afarensis) was probably mostly bipedal but may have taken to trees for safety and possibly to sleep on constructed platforms like chimpanzees do. The evidence of injuries to her fossilised skeletal remains suggests she may have died by falling out of a tree.

To investigate this stage in our evolution a group of researchers, led by Professor Xijun Ni, which included Yinan Zhang, a doctoral student, both of the Institute of Vertebrate Paleontology and Paleoanthropology of the Chinese Academy of Sciences (IVPP), and Terry Harrison, a New York University anthropologist, used 3-dimensional CT scanning to examine the inner ear of a 6-million-year-old fossil ape, Lufengpithecus, unearthed in China’s Yunnan Province in the early 1980s, and compared it to the inner ear of other living and fossil apes and humans from Asia, Europe, and Africa.

The formation the fossil was found in has been previously dated magnetobiostratigraphically to about 6 million years. This technique depends on the record of periodic changes in Earth's polarity trapped in magnetic particles in sedimentary rocks and by recording the microfossils such as pollen associated with these changes:

Friday 9 February 2024

Unintelligent Design - How A Design Blunder Causes Inflammatory Diseases, Especially In Later Life


Faulty DNA disposal system causes inflammation - Salk Institute for Biological Studies

In another example of the ramshackle Heath Robinson design process that created humans, scientists today published their findings that show how when a cell process goes wrong, as it frequently does, the result can be a serious health condition, causing suffering and unhappiness.

And of course, it’s another example of how we can tell humans weren't intelligently designed by an omnibenevolent god who wants to minimise the suffering in the world, but by a mindless, amoral natural process that has no option but to settle for the sub-optimal as long as it’s better than nothing.

The discovery, by researchers at the Salk Institute and their colleagues at UC San Diego , is the way when mitochondrial DNA (mtDNA) goes wrong and the cell tried to dispose of it, some of it leaks out into the cell, the cell’s immune system treats it like the DNA of a parasitic organism and sets up an immune response which caused inflammation.

Given the origin of mitochondria in our Heath Robinson contraptions we call cells, this is hardly surprising since mitochondria started out, probably as the free-living bacterial prey of another prokaryote, possibly an archaeon. They then became symbiotic, providing the cell with free ATP in return for protection and nutrients in the form of sugar, water and oxygen. Because they need to provide a handful of enzymes to do this with, and they are self-replicating, they retained a small amount of their original DNA while giving up most of it to the host cell's nucleus.

Wednesday 7 February 2024

Unintelligent Design - How Scientists Are Overcoming The "Designer's" Incompetence


Systemic lupus erythematosus
World-first discovery may enable an effective long-term lupus treatment - Monash University

Readers may recall my recent article on Lupus and why women are nine times more likely to suffer from it than men, because the epigenetic process for switching off genes on their X-chromosome sometimes goes wrong and produces proteins that induce an immune response to their own tissues.

From a creationist perspective, this can only be for one of two reasons: either the designer was incompetent, or this was by design. The choice being either incompetence, or malevolence and misogyny.

Now a team of researchers at Monash University, Clayton, VIC, Australia, have reported success in finding a way to overcome this design defect - which begs the question: if scientists can do it, why couldn't an omnipotent intelligent designer? Could the answer be that the human immune system was not designed by an omnipotent, intelligent designer, but is the result of a mindless, utilitarian process that inevitably produces sub-optimal 'designs' that can't be scrapped and redesigned?

But that is the kind of thought that would cause panic in the mind of most creationists because it would raise the terrible spectre of wondering if they could be wrong.
The Australian team have just published their results, open access, in Nature Communications. They are also explained in a Monash University news release:

Tuesday 6 February 2024

Unintelligent Design News - A Newly-Discovered Virus-Like Particle That Doesn't Appear to Do Anything Other Than Replicate Itself


Figure 2.

Obelisks encode putatively well-folded proteins
a) Obelisk open reading frame 1 (Oblin-1) is predicted (total mean-pLDDT ± SD = 83.8 ± 13.4, see methods) to fold into a stereotyped N-terminal “globule” formed of a three alpha helix (orange) bundle partially wrapping around an orthogonal four helix bundle, capped with a beta sheet “clasp” (blue, globule mean-pLDDT = 90.1 ± 8.7), joined by an intervening region harbouring the conserved domain-A (magenta) with no predicted tertiary structure, to an arbitrarily placed C-terminal alpha helix. “Globule” emphasised on the right. b) a to-scale (secondary structure) topological representation of Oblin-1 with the “globule” shaded in grey, and the domain-A emphasised with this bit-score sequence logo (see methods). c) Obelisk Oblin-2 is confidently predicted (mean-pLDDT = 97.1 ± 4.6 ) to fold into an alpha helix which appears to be a leucine zipper. Sequence logo of an “i+7” leucine spacing emphasised in red, with hydrophobic “d” position residues emphasised in yellow (expanded in Supplementary Figure 4b). d) homo-multimer predictions of Obelisk-alpha Oblin-2. top: dimer (mean-pLDDT = 94.6 ± 0.6), bottom: trimer (mean-pLDDT = 93.6 ± 0.6). Side-on representations of homomultimers shown with numbers of inter-helix salt-bridges (see Supplementary Figure 5).
A new virus-like entity has just been discovered – ‘obelisks’ explained

At least with most of creationism's putative 'intelligent' designer, there is something that they appear to be for, other than simply reproducing themselves - even if it is, in the case of viruses and bacteria, increasing the suffering in the world by making other organisms sick.

But scientists have just discovered a small particle that seems to be in the edge of life, less so even than a virus, which doesn’t appear to do anything other than replicate, although it seems to need bacteria in which to do this. It’s not clear what harm it does to its bacterial host or even if it has some symbiotic function. But it appears to be almost everywhere, especially in our mouths and gut, where it appears to have speciated into several different forms. The team have named it 'obelisk' because it forms a rod-like shape.

It was discovered by a team of Stanford University researchers led by Andrew Z. Fire, a previous recipient of the 2006 Nobel Prize for Physiology or Medicine who have reported to have 'identified 29,959 Obelisks (clustered at 90% nucleotide identity), with examples from all seven continents and in diverse ecological niches'. Their report has been provided with free access ahead of peer-reviewed publication, in the preprint server, bioRxiv.

The question remains, what do these particles do exactly and are they potentially harmful, or are they beneficial in some way? At least one of their hosts in which they replicate is one of the bacteria responsible for the plaque on our teeth that is responsible for dental caries and gum disease that can result in lost teeth, Streptococcus sanguinis.
Like most viruses, obelisks are a single, circular strand of RNA, but unlike viruses, they don't have a protein coat. They have one and maybe two genes which code for proteins named 'oblins' which are unrelated to any other known proteins. In this respect they differ from other recently (1970) discovered free-living strands of RNA called viroids, which don't have any recognisable genes but are known to cause serious diseases in plants.

In the following article, reprinted from The Conversation under a Creative Commons license, Professor Ed Feil, Professor of Microbial Evolution at The Milner Centre for Evolution, University of Bath, explains the significance of this discovery. His article is reformatted for stylistic consistency:

Unintelligent Design - How Scientists Are Learning to Do What Creationism's 'Intelligent' Designer Found Too Difficult - Or Didn't Want To Do!


The proteins needed to create limb progenitor cells are marked with different colors under a microscope.
Images: Yuji Atsuta/Tabin lab
The Surprisingly Simple Recipe for Starting to Grow a Limb | Harvard Medical School

Visit any site of a supposed Marian miracle, such as Lourdes, now selling 'miracle cures' that almost never work and those that do can be attributed to the medication the pilgrim was receiving prior to the visit, or to spontaneous regression, the placebo effect or a psychosomatic condition, and you may find lots of crutches supposedly left there as testament to the cure of mobility disorders, but what you will never find is the artificial limb discarded by someone who had a spontaneous regeneration of an amputated limb.

Or visit any of the lucrative travelling, carefully stage-managed 'faith healing circuses' where people appear to be 'cured' of all manner of ailments at the touch of a 'healer', who, for perhaps obvious reasons, never works in a hospital, and you will never witness the regeneration of a limb, or even part of a limb. Not even a finger or toe.

And before some-one cites, the 'Miracle of Calanda', this is such an obvious hoax that it's a miracle anyone believes it.

Despite having allegedly created a universe from nothing and all living things from dirt, creationism's god appears to be incapable, even with the help of his miracle-working mother, to be able to regrow a human limb.

The problem is one of the designer's own making (if you believe creationists) because it would involve the epigenetic resetting of the cells at the end of the stump, so they become stem cells again, capable of making all the different specialist cells in a limb, like bone, muscle, skin, nerves and blood vessels and growing to the right shape in the right place. That was a once-only ability in the developing embryo.

Epigenetics, as I have written about many times, is necessary because the cells of a multicellular organism replicate the same way our single-celled ancestors did - by replicating the entire genome every time in every daughter cell. But the benefit of multicellularity is that cells are specialised so only need a few genes, not the entire genome and having the wrong genes active in a specialist cell would be detrimental, so most of them need to be switched off by the epigenetic system. A problem which could have been avoided by any omniscient, omnipotent designer by just replicating those genes that were going to be needed by the specialist cells, but not something a mindless, natural process with no foresight, no reverse gear and no means of scrapping a bad design and starting again, could have avoided.

And yet medical scientists investigating the problem believe they have discovered the basic principles involved, which turn out to be "surprisingly simple", so well within the capabilities of even creationism's rather limited god.

The scientists, led by Harvard Medical School geneticists, have published their findings in an open access paper in a Cell Press journal, Developmental Cell and explain it in a Harvard Medical School news release by Stephanie Dutchen:

Saturday 3 February 2024

Unintelligent Design News - Why Women Are More Prone To Lupus Than Men - Evolution, Or Does Creationism's God Just Hate Women More?


The classic 'butterfly rash' of systemic lupus erythematosus (SLE)
Lupus and other autoimmune diseases strike far more women than men. Now there's a clue why

In my days as an operational paramedic, I once had to move a 26 your old women to hospital because lupus had made her so ill her blood pressure was below the safe level to maintain her renal function.

It was so low I couldn't even sit her up to carry her down stairs without her losing consciousness, so I had to run a couple of units of IV fluid into her to bring it up enough to make it safe to move her. She really was profoundly ill and at death's door. But such was the nature of the profession that, having delivered her safely to hospital and handed her over to the care of doctors and nurses, that was the end of my role in her care, so I never heard the outcome.

The autoimmune condition, lupus erythematosus, is caused by a malfunction of the immune system in which something triggers it to turn against the sufferer's own body instead of the invasive pathogens from which it has evolved to protect us. Although, of course, a creationist would hotly dispute the idea that a system like our immune system evolved at all, and would insist that it was intelligently [sic] designed by their favourite, evidence-free, supernatural deity without whom nothing can be created, presumably because they believe chemistry and physics don't know how to behave without a magic god telling them.

But an intelligently-designed immune system would only malfunction and turn against the person it is supposedly designed to protect if it were either incompetently designed or malevolently designed and is doing what it was designed to do - randomly increasing the suffering in the world. The evidence is that lupus is far more common in women than in men by a ratio of 9:1, which begs the question, does the designer just hate women more than men or was he more diligent when designing men's immune system then when designing women's?

The answer, as anyone who understands anatomy and physiology and particularly, evolution, will tell you, is that as an evolved system, we can expect compromises and a lack of perfection because evolution is a utilitarian process with no foresight and no reverse gear, so we are stuck with a sub-optimal immune system that evolved in an ancient ancestor, maybe even a pre-vertebrate ancestor. Certainly, all known vertebrates have one, and some, like that of bats, is far superior to ours.

Now a team of researchers at Stanford University School of Medicine, Stanford, CA, USA have worked out why lupus is far more common in women than men. Ther results are published, open access, in Cell and explained in a Stanford Medical news release. But first, a little AI background:

Malevolent Designer News - Creationism's Divine Malevolence Has Just Released An E. Coli Upgrade With Added Malice


New and highly infectiousE. coli strain resistant to powerful antibiotics - University of Birmingham

Escherichia coli is a pathogenic bacterium that is loved by creationists because they have been taken in by Michael J. Behe's book, Darwin's Black Box, that made him a millionaire because so many creationists bought it (though few appear to have read it) and which they love to wave around as 'proof' that the locally popular god exists.

Behe, a leading light in the Deception Institute, which was set up to try to win converts for fundamentalist, Bible literalist Christianity, by spreading disinformation about science, had argued, falsely, that the flagellum of E. coli must have been intelligently designed, since all the components need to be present for it to work (the 'irreducibly complex' fallacy) and it is too complex to have evolved in a single step because, so he claimed none of the components on their own could have given an advantage for natural selection to select for (which of course ignores genetic drift as a cause of evolution).

What Behe neglected to do was tell his readers that almost all the components of the flagellum and the proton pump that drives it, were present in a structure called the Type III Secretory system with which bacteria bind themselves to their host and kill them, and this could easily have evolved from simpler beginning over the billions of years that bacteria were evolving into their present forms.

Since its publication, Behe has been repeatedly told of the errors in it, and as a professional microbiologist, he should be aware of the growing body of research explaining how the E.coli flagellum evolved1,2, 3, 4, 5, yet he refused to correct his errors in later editions and continues to promote and defend the misinformation in it, whilst pocketing the royalties from sales, in a classic case of bearing false witness.

Friday 2 February 2024

Creationism in Crisis - How Our Need For Vitamin D Was A Bad Design That Went From Bad To Worse


Fig 3. Permanent central maxillary incisors of CL 66.
Plane form hypoplasia is exhibited on the occlusal and labial surfaces.
Archaeological evidence of seasonal vitamin D deficiency discovered | University of Otago

The human need for vitamin D to ensure proper bone growth and development and various other health-related needs, is an example of how we were not intelligently designed but are the result utilitarian evolutionary compromises that balance benefit against detriment and that balance depends on the environment in which we evolved. It shows that we evolved in sunny climates where the sun comes directly through the atmosphere as it does in the tropics, rather than obliquely, as it does in the northern and southern parts of the globe.

We do not generally get enough vitamin D from our diet, so we need to manufacture it in our skin by the action of sunlight, in particular the ultraviolet B (UVB) spectrum. However, UVB sunlight is also harmful, so our skin needs to be protected from it with the pigment, melanin, which gives our skin its varying shades of brown or black. Generally, the darker the skin, the better protection it has from UVB but the less it can produce vitamin D.

This AI explanation outlines the problem:

Wednesday 31 January 2024

Creationism in Crisis - Evolution Of The Human Imune System - By Repurposing An Existing Protein


The Joining chain (J chain) that helps bind and regulate the subunits that make up antibodies was evolutionarily co-opted by the human immune system from another biological process, according to a study by researchers from Penn State, the University of Maryland and the University of Chicago. The J chain, shown here in purple, assembles and stabilizes, from left, immunoglobin A (IgA) and immunoglobin M (IgM) antibodies. It is also required to move IgA and IgM across the mucus-producing tissue lining body structures with external exposure, like the intestine, nasal cavity and lungs.

Credit: Ttsz/Getty Images.
Evolutionary origin of mysterious immune system molecule in humans revealed | Penn State University

The human immune system is a problem for creationists who insist that their putative creator god designed humans perfectly but didn't create pathogenic parasites, which were created later by another creator called 'Sin' because of 'The Fall' after which this 'Sin' thing was free to create everything that increases the suffering in the world, so the question that throws creationists into confusion is when was the human immune system created?

If it was created before 'The Fall' then their designer god was planning for 'The Fall' all along and Adam & Eve had no choice but to comply with this god's plan for them, so there was no disobedience; just compliance with the plan.,

If, on the other hand, the creator had to upgrade its design later to protect its creation from pathogens, then it had failed to anticipate 'The Fall' so can't be omniscient.

And, since pathogens can and do get passed our immune defences, then a perfect, omnipotent creator did not design the immune system because it fails to work as designed, or 'Sin' can outwit it.

And now creationists have another problem, especially those who have been fooled into believing there is evidence of intelligent design to be found in 'irreducibly complex' structures and processes, because the simple biological explanation for such structures and processes is that they are composed of elements that originally evolved for other purposes and were later exapted for a novel function as part of the 'irreducibly complex' structure. For example, almost all the elements of the bacterial flagellum are to be found in the Type III secretion system (T3SS) which bacteria used to bind themselves to their potential host, but motility was such an advantage that the T3SS was repurposed for a flagellum with a few additional proteins and a slight modification of others to improve its efficiency.

Two of the components of the immune system are protein complexes which are the antibodies produced in response to infection by pathogens. These are the immunoglobin M (IgM) and immunoglobin A (IgA). Both these are stabilised by a Joining chain (a short length of protein) called the J chain. And this is the component that was co-opted from an entirely unrelated biological process, as a team of researchers at Penn State University, which included Kazuhiko Kawasaki, associate research professor of anthropology, discovered.

Their research was published a few days ago in Proceeding of the National Academy of Science (PNAS) and is explained in a Penn State University news release:

Friday 26 January 2024

Malevolent Designer News - How The SARS-CoV-2 Virus Has Been Redesigned to Have Another Go


The emergence of JN.1 is an evolutionary ‘step change’ in the COVID pandemic. Why is this significant?

To anyone but a reality-denying creationist, the SARS-CoV-2 virus that causes COVID-19, is a classic example of evolution by natural selection, as it continually mutates and those mutations that make it more successful are retained, so it continually improves in its ability to infect and be passed on to another victim, so producing more offspring in the virus gene pool than rival versions.

The latest version to gain predominance, JN.1, currently spreading across the world, is yet another variation on the omicron version, which itself ousted delta as the predominant variety. This new improved version may prove to be so different to omicron that is should be given a new Greek letter designation.

One point that shouldn't go unnoticed is that because, unlike the original, the virus now exists in an environment in which most of its potential victims have a degree of immunity to it, either by vaccination or by previous infection. Because that immunity usually means the ability to produce antibodies to the 'spike' proteins on the surface of the virus, most of the mutations of progressively more successful variants are in the genes that code for those proteins - making it more difficult for antibodies to bind to them.

To a creationist, the SARS-CoV-2 virus, like all the other pathological viruses, presents the paradox of trying to believe their putative designer god is the supreme ruler of and creator of everything in, the universe and is the only entity capable of creating biological organisms, but, because it is omnibenevolent, it would not have designed SARS-CoV-2 and would not be responsible for continually redesigning it to continue making us sick, by evading the immune system it supposedly also designed to protect us from viruses and other pathogens.

Curiously, creationists who continually present what they think is evidence of design as evidence for their magic creator on the grounds that it is the only entity capable of biological design, never use evidence of malevolent design as evidence for the same magic creator. That has to be ascribed to another entity with even greater powers than their supposedly supreme-in-all-things god and with the ability to outwit it, even though that claim is blasphemous within their own religious beliefs. They need to hold those two diametrically opposite views of 'creation' simultaneously to continue to deny the evidence for evolution by natural selection of which the SARS-CoV-2 virus is a perfect example.

And those creationists who do actually believe the religion they purport to believe and who won't contemplate blasphemy, have no recourse but to believe that the SARS-CoV-2 virus was not only designed by their putative designer god but that it also regularly updates it to continue making us sick despite the efforts of biomedical scientists, because the alternative it to accept the unthinkable and ascribe it all the a god-free natural process of evolution by natural selection, just as science claims.

The following article by Suman Majumdar, Associate Professor and Chief Health Officer - COVID and Health Emergencies, Burnet Institute; Brendan Crabb, Director and CEO, Burnet Institute; Emma Pakula, Senior Research and Policy Officer, Burnet Institute; and Stuart Turville, Associate Professor, Immunovirology and Pathogenesis Program, Kirby Institute, University of New South Wales, Australia, explains why the emergence of the JN.1 variant of SARS-CoV-2 is a significant evolutionary step change. It is reprinted from The Conversation under a Creative Commons licence, reformatted for stylistic consistency:

Thursday 25 January 2024

Unintelligent Design - How Ovulation Goes Wrong Because It Wasn't Intelligently Designed


Gene expression atlas captures where ovulation can go awry | Cornell Chronicle

Back in the late 1960s and early 1970, in what seems like a different lifetime now, I was a senior research assistant in the Oxford University/MRC Neuroendocrinology Research Unit, researching the hormonal control of ovulation in guinea pigs. Two of our tools were radioimmunoassays I had adapted for measuring extremely low levels of a hormone in guinea pig anterior pituitary glands known as luteinizing hormone (LH), and another similar assay for measuring the level of the steroid progesterone in guinea pig blood.

Sadly, having worked for close on two years towards producing a research paper with hundreds of assay results, thousands of microscope slides, hundreds of electron micrographs and a freezer full of samples waiting to be assayed, the government pulled the rug from under our feet by withdrawing our research funding, and I was made redundant, so my work was never published. Disillusioned and with a young family to support, I left research and perused a career in the NHS Ambulance Service instead - but that's a different story, and not relevant to the subject of this blogpost, which illustrates how much science has progressed in the last 50-60 years.

Researchers are no longer researching the hormonal control of ovulation but the fine details of the genetic control of the process of ovulation at the cell level, and what they've found is that the process is far from intelligently designed by anything resembling a perfect, omniscient, omnipotent designer. It is a process that is so complex that it can, and does, go wrong. An intelligent designer who didn't want random women to be unable to shed viable eggs, could have designed a less complicated process, but you can depend on creationism's putative intelligent[sic] designer to never do something simple when there is a far more complicated and wasteful way to achieve the same result.

The research, published a few days ago in Proceedings of the National Academy of Sciences, was led by Iwijn De Vlaminck, associate professor of biomedical engineering in Cornell Engineering, and Yi Athena Ren, assistant professor of animal science in the College of Agriculture and Life Sciences. The paper’s lead author is Madhav Mantri, Ph.D., now a postdoctoral researcher at Stanford University.

The team used a form of RNA tagging to map the gene expressions that occur during ovarian follicle maturation and ovulation in mice.

This spatial transcriptomics map depicts the cell types of a mouse ovary undergoing hormone-induced ovulation
The research is explained in a Cornell University Press release:

Wednesday 24 January 2024

Malevolent Designer News - How To Keep Ahead In The COVID Game Against Creationism's Divine Malevolence - Keep Being Boosted


How long does immunity last after a COVID infection?

Creationists stuck with the evidence of parasites and viruses that appear to be designed for two purposes only - making more copies of themselves and increasing the suffering in the world by making us sick and die - traditionally try to ride two horses. They blame something else, like 'The Fall' or 'Sin' for them, whilst still arguing that their putative designer god is supreme in all things and the only entity capable of creating complex organisms.

They also get in a terrible muddle when asked whether their 'designer' god included an immune system to protect us from these parasites when it designed us before 'The Fall', in which case it was planning for it all along, or whether there was a subsequent upgrade to V.1.2, in which case it couldn't have been omniscient and had to redo its design to account for the unforeseen.

But whatever rationalisation creationists can think up for these mutually contradictory beliefs, we are left with the fact that viruses like the SARS-CoV-2 virus and our immune system are locked in an arms race, in which human medical science has had to get involved because the immune system isn't fit for purpose, and the protection it gives us is only temporary.

Meanwhile, medical scientists, aware of the fact that evolution by natural selection is going to continually produce new variants of the virus and that these viruses may become better at evading our defences, continue to apply that knowledge and develop new vaccines against the latest variants.

The following article by Lara Herrero, Research Leader in Virology and Infectious Disease, and Wesley Freppel, Research Fellow, Institute for Glycomics, both of Griffith University, Australia explains why regular vaccination with boosters to keep out immune system primed for the latest iteration of the arms race with a latest version of the virus. The article is reproduced from The Conversation under a Creative Commons licence, reformatted for stylistic consistency:

Malevolent Designer News - How Bacterial Pathogens Are Cleverly Designed to Invade Their Victim's Body


Functional model for Yen-Tc toxicity. Following ingestion of the Tc, it is likely that the surface-bound chitinases bind to and/or degrade the chitin-rich peritrophic membrane of the insect midgut. Cell surface recognition is likely facilitated by motifs within the A subunits prior to internalization. Similarities to the well characterized bacterial binary toxin systems (e.g., anthrax, cholera, diphtheria) suggest a mechanism involving receptor-mediated endocytosis followed by pore formation and translocation of the B and/or C components into the cytosol (I), although alternative mechanisms (e.g., II, III) cannot be ruled out.

Landsberg, MJ., Jones, SA., Rothnagel R., et al (2011)
24-01-18 | Max Planck Institute of Molecular Physiology

Imagine you're in charge of an invading army laying siege to your enemy's outer defences. How do you neutralise them?

One way would be to send a small group of soldiers, packed with high explosives and deadly toxins on a kamikaze mission into the defences, with instructions to detonate their explosives and so spread the toxins when inside to destroy the defences and kill the defenders. You could improve on that by removing any temptation the suicide bombers might have to not detonate their defences by automating the trigger to fire as soon as they encountered the defender.

That's exactly what a team at the Max Planck Institute for Molecular Physiology (MPI MOPH), Dortmund, Germany, have found bacteria use to gain access to their victim’s body and make their hosts sick and die. The team, led by Stefan Raunser, Director of MPI MOPH, have published their findings, open access, in Nature Microbiology. Their work is described in a MPI MOPH press release:
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