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

Friday 8 March 2024

Creationism in Crisis - Like Humans, Bumblebees Learn Through Social Interaction And May Have Cumulative Culture


Buff-tailed Bumblebee, Bombus terrestris
Source: Wikipedia.
Bees master complex tasks through social interaction - Queen Mary University of London

A sacred Tenet of creationism is that we humans are a special creation by the creator of the universe who made everything just for us. They point to the many 'unique' traits and abilities of humans as evidence of this - the ability to teach and learn, to form cultures, even walking upright are frequently cited as examples. It's also a sacred Tenet of creationism that anything which might refute the sacred tenets of creationism must be ignore, hand-waved aside or misrepresented but never, ever acknowledged for what it is - a refutation of creationism.

So, we can expect one or more of those tactics for handling the cognitive dissonance that news that bumble bees can teach and learn and so have at least the basis for forming cumulative cultures. The news itself comes in the form of an open access research paper in Nature by a team Led by Dr Alice Bridges and Lars Chittka, Professor of Sensory and Behavioural Ecology at Queen Mary University of London.

The team showed that a complex, two-step task, which needed to be performed to receive a reward in the form of a sweet liquid could be learned by bees who were allowed to watch a trained 'demonstrator' perform the task. The bees not only learned how to perform the steps involved but that there was a reward to be had for doing so.

The 'demonstrators' had previously been trained by giving intermediate rewards as each stage was completed successfully, which were eventually withdrawn, leaving only the final reward. The experiment and its significance are explained in a Queen Mary University news release:

Monday 4 December 2023

Wonderful World - Ten Reasons to Like Spiders


Female house spider, Tegenaria domestica
Don't like spiders? Here are 10 reasons to change your mind

Back in the past, in what now seems like a lifetime ago, I managed the Emergency Operations Centre for my local Ambulance Service which was housed in a single-storey building in the grounds of the Church Hospital, Oxford. One of my nicknames was 'Spiderman' because of my fondness for spiders.

The roof space of this building was home to a population of 'house spider' or Tegenaria domestica, a good-sized one of which can be 4 inches or more across its outstretched legs. They frequently paid us a visit by coming through the light fittings or round the edges of the aircon unit.

The house spider is well-named, being one of those commensal species that, like barn swallows, can't exist without human habitation and so must have evolved after we became settled and built permanent dwellings.

Despite its large fangs, it is entirely harmless to humans, even if it does manage to pierce the skin - something I tried to impress on my staff, whose first response to one running across the floor was to stamp on it.

Despite this reassurance, one of my assistants was so arachnophobic she refused to enter the room until the spider was gone - although what she thought it would do to her was a mystery, so one of my tasks was to gently catch the spider in my hands and put it outside, whereupon I would deliver my famous (or maybe infamous) spider talk, in which I explained why spiders are such fascinating creatures - their very long evolutionary history from a common ancestor with scorpions; their multiple eyes (some for binocular vision and some for detecting movement) and above all their amazingly engineered webs.

Orb web spiders like the common garden spider, Araneus diadematus, make two sorts of silk - one to act as scaffolding and the radial threads of the web and sticky one to form the circular strands. Each thread of silk consists of multiple fine filaments that stretch very quickly to catch a flying insect without it bouncing off, then recoil slowly to avoid throwing the insect free. All this is controlled by the fine molecular structure and electrostatic bonds between the filaments. The result is a thread that, weight for weight, is stronger than steel.

One small spider that is common on walls and buildings in Oxford is the zebra spider, Salticus scenicus, a tiny black and white-striped spider, only a few millimeters long, that has amazing eyes. It is a hunting spider that preys on small insects, even some three times its size, by jumping on them. Its modus operandum is to crawl over the surface of walls and roofs and, when it sees its prey, it approaches slowly and when close enough, judges the distance perfectly and pounces. It will also jump across gaps, again with a perfectly judged jump, many times its own body length, rather like a human jumping the Grand Canyon from a standing start, but before it does so, it dabs the tip of its abdomen down to fix a 'safety line' of silk, just in case. To perform these feats, the zebra spider needs a high degree of visual acuity and binocular vison. The amazing thing about this spider is the way it overcomes the problem for visual acuity of such a small retina; it rapidly moves the retina up and down, effectively increasing its size.

The jump is accomplished, not by muscles in the legs, but by a sudden increase in haemocoelic blood pressure which straightens the front and back legs, so the spider always jumps with its legs extended.
I always hoped my spider talk would impress my staff enough to take an interest in spiders rather than seeing them as creepy-crawly things to be half-feared and killed simply for sharing the building with us. Alas, only one or two ever followed my example and picked them up to put them out of a window.

All that was by way of introduction to an article in The Conversation in which Leanda Denise Mason, an Associate Lecturer, Curtin University, Australia give her ten reasons to like spiders, or at least change your mind it you don't. Her article is reprinted here under a Creative Commons licence, reformatted for stylistic consistency. The original can be read here.

Sunday 1 October 2023

Creationism in Crisis - Killer Whales Exibit 'Uniquely Human' Behaviour


Why Are Killer Whales Harassing and Killing Porpoises Without Eating Them? | UC Davis
A pod of Southern Resident orcas
Photo: NOAA Fisheries.

The problem creationists have with trying to cling to a counter-factual superstition like theirs is that so many facts run counter to it. To normal people, that might be considered a good reason to reassess their opinions and drop those shown to be at odds with the facts and form some based on reality instead.

Not so creationists. To a creationist, the thought of being wrong is an existential threat which, if allowed to develop, would destroy their entire world view which has them at the centre of a specially created universe, the creator of which holds them in high regard. Dropping this childish belief would mean they don't feel as important as they think they are and would maybe have to think the unthinkable - a universe which doesn't have them at the centre of it and eventual oblivion in which the world continues to exist and function without them in it or able to observe it from a privileged position.

The Salish Sea. Location for the study.
All my recent blog posts, especially the 'Creationism in Crisis' series, have shown instances where scientific research has revealed facts which refute basic creationist articles of faith and cult dogmas, and this one is no exception. It deals with a core dogma - that humans were a special creation, created in some material way differently to all other life forms, to which they bear no relationship.

Traditionally, creationists cite examples of how humans are unique, having characteristics shared by no other species - ignoring the fact that that pretty much defines a species and the same case can be made for every other species. One of these is of course another creationist sacred cow - humans have social ethics and a conscience, which creationist dogma asserts could only have come from their particular creator god - the same god whom they believe inflicted a mass genocide on Earth and creates parasites, apparently.

Explaining social ethics, or pr-social behaviour, and a conscience which motivates pro-social behaviour, rewarded by endorphins, is not difficult for science to explain as the result of gene-meme co-evolution in a cooperative species that could not survive as individuals without the support of a social group.

And, to reinforce that, we now have evidence of pro-social behaviour and human-like activities in another species - the orca or killer whale.

At least, that's the explanation for an observed change in behaviour of a pod of orca in the Salish Sea, described in a paper published, open access, in Marine Mammal Science. The investigating team was co-led by Deborah Giles of Wild Orca and Sarah Teman of the SeaDoc Society, a program of University of California Davis (UCDavis) School of Veterinary Medicine.

First a little background on the Southern Resident killer whales, the subject of the study:

Saturday 30 September 2023

Extinction News - How Britain is Exterminating its Wildlife - And What is to be Done


Norfolk damsel fly, Now extinct in UK.

One in six UK species threatened with extinction – here's what we could lose (plus how to save them)

One of the great crimes of the Abrahamic religions is the allegedly 'God-given' dominion over the entire planet Earth, its wildlife, its mineral wealth and its land and sea to humankind, to be treated as free and there for the sole benefit of humankind with no other purpose.

In the British Isles this has resulted in a landscape dominated by towns and cities, agriculture and monoclonal forestry, and coastal waters where anything edible is hoovered up and consumed, leaving, in many cases, stocks too small and immature, or too scarce to maintain a stable population, let alone recover.

And our waste in the form of single-use plastics, sewerage, industrial waste such as CO2 and heavy metals, agricultural run-off containing artificial fertilisers, have polluted and destroyed many waterways. Agricultural monocultures have produced virtual deserts, so far as many species are concerned and destroyed soil structure with over-use of pesticides and artificial fertilisers has led, in a few years, to loss of precious topsoil that took hundreds of thousands of years to create and ploughed-up water-meadows have gone, taking their biodiversity with them.

Consequently, our wild bird, wild mammal, insect and wild plant populations have been in steep and accelerating decline for most of the last two centuries.

According to the following report, we are now faced with the extinction of 1,500 of our 10,000 species. The report, "State of Nature" is the result of a collaboration between a large number of British and Irish conservation and wildlife charities. It can be read here:
The State of Nature report referred to in the article may be read here:

Tuesday 5 September 2023

Creationism in Crisis - The James Webb Space Telescope Reveals an Ancient Universe


Webb Reveals New Structures Within Iconic Supernova | NASA

The age of the universe is guaranteed to get creationists tying themselves in knots while performing the most contorted mental gymnastics ad foaming at the mouth. Their problem is that they have been conditioned to dismiss scientific dating by chanting mindlessly about all radiometric dating methods being wrong because radioactive decay rates changed over time and dating the same sample by different methods gives different results.

The latter point, to a creationist, is the clincher because, to a simplistic, black vs white, thinker any discrepancy means the entire process is wrong and therefore its rational to argue that they can make 8,000 years look like several billion years.

But their problem is, dating the age of celestial objects such as the Ring Nebula does not rely on radiometric dating. Astronomers use a variety of methods to calculate the distance of the object from Earth, or in this case the JWST:

Saturday 20 May 2023

Evolution in Action - Giant Spiders Spreading Across Southern USA

Slideshow code developed in collaboration with ChatGPT3 at https://chat.openai.com/

The Jorō spider, Trichonephila clavata
Joro spiders aren’t scary. They’re shy.

A rather beautiful large spider is rapidly spreading across the southern USA, aided by a couple of attributes that enable it to adapt to human habitation, in a stunning example of how the environment can select for species fitted to live and thrive in it. A related species, T. clavipes, has already established itself in southern USA.

The spider, Trichonephila clavata, is a very large, but harmless (to humans), Jorō spider, the subject of a recent research paper in the journal Arthropoda. The research, carried out by researchers, by Andrew K. Davis and Amitesh V. Anerao of Odum School of Ecology, University of Georgia, Athens, GA, USA.

The study shows that, in a classic example of how particular traits can enable a species to extend its range, T. clavata is good at living alongside humans. Rather than being aggressive, which most people would assume is the reason it is out-competing native American spiders, T. clavate is particularly shy and non-aggressive. Despite their size and warning colouration, they are harmless to humans and pets. They will only attempt to bite if picked up and trapped and even then, their fangs aren't large enough to pierce human skin.

Interestingly, their avoidance strategy is to remain completely motionless for about an hour when disturbed, unlike most spiders which normally resume activity after few minutes, leading the researchers to classify them as 'shy' rather than aggressive.

The research is explained in a University of Georgia press release:
New study suggests the massive spiders are gentle giants, mean people no harm

One of the ways that people think this spider could be affecting other species is that it’s aggressive and out-competing all the other native spiders, so we wanted to get to know the personality of these spiders and see if they’re capable of being that aggressive. It turns out they’re not.

They basically shut down and wait for the disturbance to go away. Our paper shows that these spiders are really more afraid of you than the reverse.

One thing this paper tells me is that the Joros’ rapid spread must be because of their incredible reproductive potential,” Davis said. “They’re simply outbreeding everybody else. It’s not because they’re displacing native spiders or kicking them out of their own webs.

Dr. Andrew Davis, lead author Odum School of Ecology, University of Georgia, Athens, GA, USA.
Despite their intimidating appearance, the giant yellow and blue-black spiders spreading across the Southeastern U.S. owe their survival to a surprising trait: They’re rather timid.

According to a new study from the University of Georgia, the Jorō (Joro) spider may be the shyest spider ever documented.

The researchers compared more than 450 spiders’ responses to a brief and harmless disturbance across 10 different species.

While most spiders froze for less than a minute before resuming their normal activities, the Joro spiders remained motionless for more than an hour.

In fact, Joros are relatively harmless to people and pets. Joros won’t bite unless cornered. And even if you did manage to somehow annoy a Joro into biting you, its fangs likely wouldn’t be large enough to pierce your skin.
A female Joro spider spins its web. The 30mm scale bar is included for size reference.

Credit: Jeremy Howell

Most spiders begin moving quickly after stress, Joros remain immobile for 60-plus minutes

To examine the spiders’ reaction to stress, the researchers used a turkey baster to gently blow two rapid puffs of air onto individual spiders. This minor disturbance causes the spiders to “freeze” for a period of time, going absolutely still.

The researchers tested more than 30 garden spiders, banded garden spiders and marbled orb weavers. They also analyzed similar data from previously published, peer-reviewed papers that assessed the response of 389 more spiders, comprising five additional species.

All of those spiders began moving again after an average of about a minute and half of stillness.

The Joros, however, stayed frozen with no body or leg movement for over an hour in most cases.

The only other spider species that exhibited a similarly extended response was the Joro spider’s cousin, the golden silk spider. Known as Trichonephila clavipes, the golden silk spider and the Joro spider are from the same genus.
A Joro spider feasts on a caterpillar.

Joros may be invasive, but they’re not aggressive

Most people think ‘invasive’ and ‘aggressive’ are synonymous. People were freaking out about the Joro spiders at first, but maybe this paper can help calm people down.

They’re so good at living with humans that they’re probably not going away anytime soon.

Amitesh Anerao, co-author of the study,
Undergraduate researcher, Georgia University, Athens, GA, USA
Officially known as Trichonephila clavata, the East Asian Joro spider first arrived in Georgia around 2013. The species is native to Japan, Korea, Taiwan and China, and likely hitched a ride stateside on a shipping container.

The species has since rapidly spread across the state and much of the Southeast. Joro spiders easily number in the millions now. And there’s not much we can do to stop them from increasing their range.

Davis’ previous research even suggested the invasive arachnids could spread beyond their current habitats and through most of the Eastern Seaboard.

Sunlight streams through the elaborate webs made by Joro spiders
Joro spiders built to withstand human activity

Joros are regularly spotted in areas native Georgia spiders don’t typically inhabit.

They build their golden webs between powerlines, on top of stoplights and even above the pumps at local gas stations—none of which are particularly peaceful spots.

The researchers believe the Joro spiders’ shyness may help them better endure the barrage of noise, vibrations and visual stimuli they consistently encounter in urban settings. Their prolonged freeze response to being startled could help conserve the Joro spiders’ energy.

If you’re wondering how something so mild-mannered could spread the way Joro spiders have, you aren’t the only one.

Arachnophobes can take solace in the Joro spiders’ meek and gentle temperament. But the spiders are likely here to stay.
Bar chart of results
Figure 2. Behavioral responses of spiders to a mild disturbance stimulus (air puff), from our tests, plus from data presented in published studies (see Table 1). Shown are the mean durations of time spent in a “thanatosis” state after receiving the stimulus.

Copyright: © 2023 The authors.
Published by MDPI (Basel, Switzerland). Open access. (CC BY 4.0)
The researcher’s paper is available, open access, in the journal,Arthropoda:
Abstract

The jorō spider (Trichonephila clavata, originally from east Asia) has been introduced in the southeastern United States, and is rapidly expanding this range, leading to questions about what facilitates this spread. Meanwhile, its cousin, the golden silk spider (T. clavipes), already has a range that covers most of the southeast. In an ongoing effort to understand the behavior of jorō spiders in their introduced range, we undertook the current project to evaluate how they react to perceived threats, which can inform us on how a species interacts with conspecifics, or how well it can tolerate anthropogenic disturbances. We collected mature females of both Trichonephila species, plus three locally common orb-weaving species in Georgia, and we evaluated the time spent immobile after experiencing a mild disturbance (a brief puff of air). We also collected similar “air puff response” data for five other North American species from the published literature. Collectively, the dataset totaled 453 observations of freezing behavior across 10 spider species. Comparing these data across species revealed that most spiders remained immobile for under a minute after the stimulus. Meanwhile, both Trichonephila spiders remained immobile for over an hour, which appears to be unprecedented, and suggests that spiders in this genus are the “shyest” ever documented. This reaction could also allow Trichonephila spiders to tolerate urban environments by remaining motionless throughout each disturbance instead of fleeing.

A classic study showing how traits can facilitate the spread of a species into new territories provided the local environment provides the right selectors, if not, of course, introduction won't succeed. And once again confirming the relationship between a species and its environment and how the latter selects for traits which produce more copies than other alleles.

All perfectly understandable in terms of natural processes, with not a hint that supernatural magic had to be involved at some point.

And yet creationism is still managing to recruit new scientifically illiterate fools into the cult, despite all its counter-factual claims and readily available evidence refuting them.

Thank you for sharing!









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Wednesday 15 March 2023

Climate Emergency News - Large-Scale Failure of Entire Bird Population to Breed

Climate Emergency News
Large-Scale Failure of Entire Bird Population to Breed
Dronning Maud Land (Queen Maud Land), Antarctica

Extreme snowstorms lead to large-scale seabird breeding failures in Antarctica: Current Biology
Map of Antarctica showing Dronning Maud Land
Map of Antarctica showing Dronning Maud Land
South Polar skua , <i>Stercorarius maccormicki</i>, with nest containing two eggs
South Polar skua, Stercorarius maccormicki, with nest
According to a survey published, open access, yesterday in the Cell Press journal, Current Biology almost the entire breeding population of three seabirds failed to breed on important breeding grounds in Antarctica, due to unseasonably high snowfall in the Antarctic 'Summer' (December 2020-January 2022) when breeding normally takes place. The unusual weather is almost certainly due to man-made climate change.

The researchers found not a single nest of the South Polar skua, and only a handful of the nests of the Antarctic petrel, Thalassoica antarctica, and Snow petrel, Pagodroma nivea, on the main breeding ground of Dronning Maud Land (Queen Maud Land) in the Norwegian-administered sector of Antarctica.

According to information from Cell Press:

Sunday 26 February 2023

Malevolent Designer News - How The Intelligent [sic] Designer Could Have Been Kinder, But Chose Not To Be

Malevolent Designer News

How The Intelligent [sic] Designer Could Have Been Kinder, But Chose Not To Be
White-tailed deer, Odocoileus virginianus
Photo: Shutterstock

White-teiled deer, <i>Odocoileus virginianus</i>
White-tailed deer, Odocoileus virginianus

Image: Pixabay
Deer protected from deadly disease by newly discovered genetic differences | College of Agricultural, Consumer and Environmental Sciences | UIUC.

An open access paper published a couple of weeks ago in the journal Genes should have set alarm bells ringing in Creationists circles, assuming anyone in Creationist circles reads peer-reviewed science and risks having their cherished superstitions spoilt with facts.

The paper was a report on the findings of a team of researchers from the University of Illinois at Urbana-Champaign, Illinois, USA into why, during a summer 2022 outbreak of the highly infectious viral disease of white-tailed deer, Odocoileus virginianus, some deer remained unaffected while scores of others died within days of infection.

The disease, epizootic haemorrhagic disease (EHD), is caused by a double-stranded RNA virus, spread by a midge. There are outbreaks of this disease every 3-5 years.

The team sequenced the entire genome of the white-tailed deer for the first time and found variations in one particular gene associated with apparent immunity to EHD.

So, why should this concern Creationists?

Bearing in mind that Creationists insist their supposed intelligent [sic] designer is omniscient and so knows exactly what its designs will do when it designs them, if we buy into this evidence-free superstition, we have to believe:
  1. Creationist's intelligent [sic] designer designed the virus that causes EHD to kill white-tailed deer, and designed the midge to act as the vector for the disease to ensure the virus gets spread to kill new victims.
  2. It then gave some deer a modified gene which protects it from the virus it designed to kill them.
  3. It could have given all white-tailed deer this protective gene, but chose not to.
  4. Therefore the only conclusion is that it wanted most deer to be susceptible to the fatal disease it had designed to make them suffer and die.
As though that evidence of malevolence wasn't enough, what we have here is a simple example of how a mutant alle can give carriers of that mutation a significant advantage over carriers of the non-advantageous alle. It would take an exceptional degree of denialism to conclude that killing carriers of the non-protective allele while allowing carriers of the protective mutation to survive is not going to lead to an increase in the copies of that protective allele in the population gene pool over time.

In other words, what we have here is a perfect example of evolution by mutation and natural selection - the very same process that created the viral parasite in the first place. Evolution being defined by biological science as change in allele frequency in a population over time, not the childish Creationist parody of one species magically turning into another, unrelated species, in a single event.

Creationists need to explain why the patently obvious isn't true and why malevolent intent is a better explanation for these deer being killed by a virus, and Creationism's putative designer's apparent malevolent intent in creating the disease in the first place.

The research team's work was explained in a University of Illinois news release. As you read this, bear in mind that what the article is describing is what Creationists believe was created deliberately by their allegedly omniscient, omni-benevolent deity:
URBANA, Ill. – It was the height of summer 2022 when the calls started coming in. Scores of dead deer suddenly littered rural properties and park preserves, alarming the public and inconveniencing landowners. According to officials at the Urbana Park District, it was Epizootic Hemorrhagic Disease (EHD), a midge-borne viral illness that pops up in white-tailed deer populations around the state every few years. And when susceptible deer are infected, they die within days.

Now, University of Illinois scientists have found gene variants in deer associated with the animals’ susceptibility to EHD.

This is the first time this gene has been sequenced completely in white-tailed deer. This is important because without the sequences, there's no starting point to do any kind of research.

The team sequenced the gene for Toll-Like Receptor 3 (TLR3), a protein that spans membranes of intracellular organelles in immune cells and helps recognize double-stranded RNA (dsRNA) viruses. When a dsRNA virus, such as the one that causes EHD, enters the cell, TLR3 activates the host’s first immune defenses, triggering inflammation and priming the rest of the immune system.

When the team sequenced TLR3 from EHD-infected and uninfected deer, they found dozens of variable sites in the DNA known as single-nucleotide polymorphisms (SNPs). Two of the SNPs were significantly more common in uninfected deer.

Because we found mutations in TLR3 more frequently in EHD-negative animals, we think deer with these mutations are less susceptible to EHD.

Yasuko Ishida, co-author
Department of Animal Sciences
University of Illinois, Urbana-Champaign, USA.
That conclusion is rooted in the probability that many white-tailed deer in Illinois are exposed to EHD in their lifetimes, but only some will die from the disease.

In many areas, outbreaks occur every 3-5 years, when environmental conditions favor the life cycle of midges that carry the virus. The midges spend their larval stages in mud under ponds and puddles where deer drink during drought conditions. As those water sources dry up, usually during late summer, the midges’ muddy habitat is exposed and the adult flies emerge to bite and infect deer. The cycle can be interrupted locally by a soaking rain or a cold snap, which is why outbreaks don’t happen every year.

The researchers emphasize that EHD is not transmissible to humans or pets through midge bites or consumption of infected deer meat.

Although there’s not much wildlife managers can do to disrupt the cycle and prevent outbreaks in natural habitats, the team says it’s still helpful to understand the genetic underpinnings of the disease. Theoretically, deer in captive herds could be sampled to characterize the level of vulnerability to EHD, and wild herds could be sampled during the hunting and EHD-outbreak seasons, informing managers and the public of future risk.

The value of this research is that it helps inform the public about EHD. It helps them to understand not only what the disease will look like, but potentially the severity of an outbreak in a particular area. Sometimes there's value in knowing what to expect.

Nohra Mateus-Pinilla, co-author
Wildlife veterinary epidemiologist
Illinois Natural History Survey
And the Department of Animal Sciences
The Department of Natural Resources and Environmental Sciences in ACES
And the Department of Pathobiology
University of Illinois, Urbana-Champaign, USA.

It’s very complicated to respond to an outbreak of EHD because there are often large numbers of deer found dead near water. People don’t know what to do when that happens, but we encourage the public to report potential EHD outbreaks to their local IDNR wildlife biologist for the surveillance and future study of the disease.

Jacob Wessels, first author
Now a conservation police officer with the Illinois Department of Natural Resources
Considering the disease’s episodic nature, it’s not likely to present as a severe outbreak again in Urbana parks anytime soon. But it is an increasing threat to the state’s northern regions, including Chicagoland. Another recent study by Mateus-Pinilla, Roca, and others shows the disease has been slowly but steadily moving northward in Illinois. The researchers don’t know whether that’s due to climate change or greater reporting, but it’s clear EHD isn’t restricted to rural parts of Illinois.

The article, “The Impact of Variation in the Toll-like Receptor 3 Gene on Epizootic Hemorrhagic Disease in Illinois Wild White-tailed Deer (Odocoileus virginianus),” is published in Genes [DOI: 10.3390/genes14020426].
Copyright: © 2023 The authors.
Published by MDPI, Basel, Switzerland. Open access. (CC BY 4.0)
More detail is provided in the team's open access paper in Genes:
Abstract

Epizootic hemorrhagic disease (EHD) leads to high mortality in white-tailed deer (Odocoileus virginianus) and is caused by a double-stranded RNA (dsRNA) virus. Toll-like receptor 3 (TLR3) plays a role in host immune detection and response to dsRNA viruses. We, therefore, examined the role of genetic variation within the TLR3 gene in EHD among 84 Illinois wild white-tailed deer (26 EHD-positive deer and 58 EHD-negative controls). The entire coding region of the TLR3 gene was sequenced: 2715 base pairs encoding 904 amino acids. We identified 85 haplotypes with 77 single nucleotide polymorphisms (SNPs), of which 45 were synonymous mutations and 32 were non-synonymous. Two non-synonymous SNPs differed significantly in frequency between EHD-positive and EHD-negative deer. In the EHD-positive deer, phenylalanine was relatively less likely to be encoded at codon positions 59 and 116, whereas leucine and serine (respectively) were detected less frequently in EHD-negative deer. Both amino acid substitutions were predicted to impact protein structure or function. Understanding associations between TLR3 polymorphisms and EHD provides insights into the role of host genetics in outbreaks of EHD in deer, which may allow wildlife agencies to better understand the severity of outbreaks.

Wessels JE, Ishida Y, Rivera NA, Stirewalt SL, Brown WM, Novakofski JE, Roca AL, Mateus-Pinilla NE.
The Impact of Variation in the Toll-like Receptor 3 Gene on Epizootic Hemorrhagic Disease in Illinois Wild White-Tailed Deer (Odocoileus virginianus).
Genes. 2023; 14(2):426. https://doi.org/10.3390/genes14020426

Copyright: © 2023 The authors.
Published by MDPI, Basel, Switzerland. Open access
Reprinted under a Creative Commons Attribution 4.0 International license (CC BY 4.0)
These examples of how the childish Creationist notion of intelligent [sic] design simply makes no sense at all, are almost daily occurrences in biological science, as are the examples of evolution in progress that we see in this example of natural selection favouring immunity to a viral parasite. The basic problem with Creationism and Creationists is that facts and deductive logic are irrelevant, otherwise there wouldn’t be Creationism and Creationists.

The psychology needed to maintain a superstition despite the overwhelming evidence against it must amount to a mental disorder that can only be accounted for by intensive mental abuse in childhood that gives rise to a mind-numbing acute anxiety disorder, or psychotic theophobia. Creationism and the wilful ignorance and science denial that it requires are not normal psychological states.

To inflict this mental disorder on the vulnerable minds of children, reinforced by threats of eternal torture, is a form of coercive child abuse. As someone once said, there are good people who do good things and bad people who do bad thing, but with religion, good people can do bad things believing them to be good. Inflicting Creationism on children is a case in point.

Tuesday 6 December 2022

Biodiversity News - How Man-Made Climate Change is Damaging German Beech Forests.

Press release: Climate change in the forests of northern Germany - Georg-August-Universität Göttingen
Typical north German beech forest
Typical beech forest in northern Germany: the scientists took samples of wood from dominant trees at 30 locations.

Photo: Banzragch Bat-Enerel
Scientists from Germany have shown the negative effects of man-made climate change on the health of beech trees in German forests. These forests are important wild-life refuges with a rich and complex ecosystem, so any damage to the health of the trees will have a major impact of the biodiversity of Central Europe.

The scientists took samples of wood from major trees in 30 different locations so that comparisons could be made between areas with different average rainfall levels. They then analysed the tree rings to obtain a retrospective measure of tree growth.

The news release from Georg-August-Universität, Göttingen, describes the study and its significant findings:

Wednesday 23 November 2022

Creationism in Crisis - Modern Humans Are Not The First To Appreciate Art

How we discovered that Neanderthals could make art
Neanderthal woman
Reconstruction of a Neanderthal woman

Morten Jacobsen (CC BY 2.5)
Creationist superstition says that human beings were made somehow differently to all the other animals, although they can never say how, exactly. Some believe only humans have an unproven and undefined magic entity living inside their body, called a 'soul', but other animals don't have this magic ingredient; others argue that animals also have this magic ingredient. They disagree endlessly on this point simply because they have no facts by which to determine the truth. If the 'soul' was detectable, the issue could be resolved easily and quickly. As it is, all they have is dogma.

But whatever their view of who has a magic soul and who doesn't, high on their list of abilities that humans have that other animals allegedly don't have will be aesthetic appreciation of art, music, love, etc. Some attribute this to the magic soul thing, others are happy to regard it as part of some unique aspect of human psychology, neuro-physiology, and/or genetics, so, of course, any evidence that another species has aesthetic appreciation is a major embarrassment for them.

However, with regard to artistic appreciation, there is now strong evidence that our cousin species, Neanderthals, could make artistic or symbolic designs, so, since we are related through a common ancestor - probably Homo heidelbergensis or Homo erectus, if indeed they were different species, it is highly likely that at least the potential for making symbolic drawings was present in that ancestor.

How do we know Neanderthals could make art?

In this article reprinted from The Conversation under a Creative Commons license, Dr Chris Standish, Postdoctoral Fellow of Archaeology, and Professor Alistair Pike, Professor of Archaeological Sciences, both of Southampton University, Hampshire, UK, present the evidence.

The article is reformatted for stylistic consistence. The original can be read here:

How we discovered that Neanderthals could make art

Neanderthal art.
Credit: P. Saura

Chris Standish, University of Southampton and Alistair Pike, University of Southampton

What makes us human? A lot of people would argue it is the ability of our species to engage in complex behaviour such as using language, creating art and being moral. But when and how did we first become “human” in this sense? While skeletal remains can reveal when our ancestors first became “anatomically modern”, it is much harder for scientists to decipher when the human lineage became “behaviourally modern”.

One of the key traits of behavioural modernity is the capacity to use, interpret and respond to symbols. We know that Homo sapiens have been doing this for at least 80,000 years. But its predecessor in parts of Eurasia, the Neanderthal, a human ancestor that became extinct around 40,000 years ago, has traditionally been regarded as uncultured and behaviourally inferior. Now our new study, published in Science, has challenged this view by showing that Neanderthals were able to create cave art.

The earliest examples of symbolic behaviour in African Homo sapiens populations include the use of mineral pigments and shell beads – presumably for body adornment and expressions of identity.

However, evidence for such behaviour by other human species is far more contentious. There are some tantalising clues that Neanderthals in Europe also used body ornamentation around 40,000 to 45,000 years ago. But scientists have so far argued that this must have been inspired by the modern humans who had just arrived there – we know that humans and Neanderthals interacted and even interbred.

Wall in Maltravieso Cave showing three hand stencils (centre right, centre top and top left).

Credit: H. Collado
Cave art is seen as a more sophisticated example of symbolic behaviour than body ornamentation, and has traditionally been thought of as a defining characteristic of Homo sapiens. In fact, most researchers believe that the cave art found in Europe and dating back over 40,000 years must have been painted by modern humans, even though Neanderthals were around at this time.

Dating cave art

Unfortunately, we have a poor understanding of the origins of cave art, primarily due to difficulties in accurately dating it. Archaeologists typically rely on radiocarbon dating when trying to date events from our past, but this requires the sample to contain organic material.

Calcium carbonate crust overlying pigment in La Pasiega.

Credit: J. Zilhão
Cave art, however, is often produced from mineral-based pigments which contain no organics, meaning radiocarbon dating isn’t possible. Even when when it is – such as when a charcoal-based pigment has been used – it suffers from issues of contamination which can lead to inaccurate dates. It is also a destructive technique, as the sample of pigment has to be taken from the art itself.

Uranium-thorium dating of carbonate minerals is often a better option. This well-established geochronological technique measures the natural decay of trace amounts of uranium to date the mineralisation of recent geological formations such as stalagmites and stalactites – collectively known as “speleothems”. Tiny speleothem formations are often found on top of cave paintings, making it possible to use this technique to constrain the age of cave art without impacting on the art itself.

A new era

We used uranium-thorium dating to investigate cave art from three previously discovered sites in Spain. In La Pasiega, northern Spain, we showed that a red linear motif is older than 64,800 years. In Ardales, southern Spain, various red painted stalagmite formations date to different episodes of painting, including one between 45,300 and 48,700 years ago, and another before 65,500 years ago. In Maltravieso in western central Spain, we showed a red hand stencil is older than 66,700 years.

Ladder shape in red painted in the La Pasiega cave.

Credit: C.D Standish, A.W.G. Pike and D.L. Hoffmann
These results demonstrate that cave art was being created in all three sites at least 20,000 years prior to the arrival of Homo sapiens in western Europe. They show for the first time that Neanderthals did produce cave art, and that is was not a one off event. It was created in caves across the full breadth of Spain, and at Ardales it occurred at multiple times over at least an 18,000-year period. Excitingly, the types of paintings produced (red lines, dots and hand stencils) are also found in caves elsewhere in Europe so it would not be surprising if some of these were made by Neanderthals, too.

Drawing of the ladder symbol painted on the walls.

Credit: Breuil et al. (1913)
We don’t know the exact meaning of the paintings, such as the ladder shape, but we do know they must have been important to Neanderthals. Some of them were painted in pitch black areas deep in the caves – requiring the preparation of a light source as well as the pigment. The locations appear deliberately selected, the ceilings of low overhangs or impressive stalagmite formations. These must have been meaningful symbols in meaningful places.

Our results are tremendously significant, both for our understanding of Neanderthals and for the emergence of behavioural complexity in the human lineage. Neanderthals undoubtedly had the capacity for symbolic behaviour, much like contemporaneous modern human populations residing in Africa.

To understand how behavioural modernity arose, we now need to shift our focus back to periods when Homo sapiens and Neanderthals interacted and to the period of their last common ancestor. The most likely candidate for this ancestor is Homo heidelbergensis, which lived over half a million years ago.

It is perhaps also now time that we move beyond a focus on what makes Homo sapiens and Neanderthals different. Modern humans may have “replaced” Neanderthals, but it is becoming increasingly clear that Neanderthals had similar cognitive and behavioural abilities – they were, in fact, equally “human”. The Conversation
Chris Standish, Postdoctoral Fellow of Archaeology, University of Southampton and Alistair Pike, Professor of Archaeological Sciences, University of Southampton

Published by The Conversation.
Open access. (CC BY 4.0)

Tuesday 15 November 2022

Walking in Bagley Wood in November - Slide Show

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Bagley Wood, near Abingdon, Oxfordshire, UK is a lightly managed ancient mixed broadleaf and conifer wood belonging to St Johns College, Oxford, who acquired it in 1557. Prior to that it had been owned by Abingdon Abbey between 955 and 1538. It is now used for field research by members of the University Zoology Department and is probably one of the most closely studied areas of woodland in Europe.

These photographs were taken on a sunny sunday afternoon in November on one of the warmest November days on record. Of particular note are the profusion of holly berries and the variety of fungi to be seen.

Walkers are welcome to use the wood but are politely requested to stay on the footpaths, to keep dogs on a lead and not to disturb the wildlife, so the woodland remains almost completely undisturbed.

A feature in Late Spring are the carpets of bluebells as well as the many nesting birds, especially finches, warblers, blackcaps, chiff chaffs and tits. In recent years, red kites and buzzards have both increased in numbers, and muntjac deer have become common.

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