Evolution News - Chimpanzees Diversifying Into Subspecies

Chimpanzee dung samples were collected across Africa to determine if populations were recently connected despite historical barriers to gene flow.

© PanAf

Chimpanzees without borders | Max-Planck-Gesellschaft

Unlike humans who also occupy diverse habitats and have marked cultural differences but whose genetics form a gradient between groups, chimpanzees form much more sharply delineated difference to the extent that they form four subspecies. However, there are signs of a recent remixing of these groups, accelerated by human interference with their habitats. This is the conclusion of an international research team led by scientists from the Max Planck Institute for Evolutionary Anthropology.

Pan spp. range map showing modern bonobo and chimpanzee geographic distribution.

User:Cody.pope, Public domain, via Wikimedia Commons

There is evidence that through our evolutionary history, humans probably also began to diversify into distinct subspecies or regional varieties, only to merge and remix later, in much the same way that we interbred with the much more diversified species of humans when we emerged from Africa and met the descendants of a first wave of migration by archaic hominins.

With chimpanzees, the divergence was less pronounced amongst the Pan troglodytes species than by the early extra-African humans, although the Pan genus did diverge into P. troglodytes (common chimpanzee) and P. paniscus (bonobo) in geographical isolation. The belief is that as the climate changed and the West African forests split up, chimpanzees became isolated in fragmented refugia and began to speciate.

Malevolent Designer News - The Pestilential Sadist is Hitting Back?

Physician assistant Philana Liang prepares a vial of COVID-19 vaccine on the Washington University Medical Campus. New research from Washington University School of Medicine in St. Louis has found that new variants of the virus that causes COVID-19 can evade antibodies that work against the original form of the virus that sparked the pandemic, potentially undermining the effectiveness of vaccines and antibody-based drugs now being used to prevent or treat COVID-19.

New evidence COVID-19 antibodies, vaccines less effective against variants – Washington University School of Medicine in St. Louis

Let's pretend there really is an intelligent [sic] designer designing things like the SARS-CoV-2 virus currently killing people throughout the world, like Creationists claim.

In that fantasy, what we are seeing right now is this designer hitting back against the fantastic response of medical science in developing a vaccine against its invention in record time, by redesigning its pet virus to be able to survive attack from the anti-bodies these vaccines produce. The same modification also allows the virus to re-infect those it didn't kill first time round and whose immune systems did what they were intelligently designed by the same designer to do - and make antibodies to protect us from its other creations- viruses and bacteria that were designed to parasitise us. (Seriously! Creationists regard this sort of pointless arms race as evidence of high intelligence and perfection in design!)

The thing is, these antibodies all work by attacking the 'spike' proteins that are part of the virus' protein coat and which are an important part of its ability to break into a cell to infect it and produce more copies of itself. So, our putative intelligent [sic] designer has modified the gene that makes this spike protein so it is no longer recognised by the antibodies.

At least this is the preferred interpretation by the Creationist industry promulgated by the Discovery Institute, apparently oblivious of, or indifferent to, the fact that this makes their putative designer god look like a malevolent sadist and its religion look like the worship of a monstrous evil. Clearly, there is a political agenda at work here in which even the reputation of their god is being sacrificed, just as the evangelical Christians abandoned any pretence of moral superiority by supporting the odious Donald J. Trump.

Today we have news that a team of researchers at Washington University School of Medicine, St. Louis, MO, USA and Department of Biochemistry and Molecular Biology, University of Texas Medical Branch, Galveston, TX, USA have shown that three new, fast-spreading variants of the virus that cause COVID-19 can evade antibodies that work against the original form of the virus that sparked the pandemic.

Why Biodiversity Matters - Anti-Cancer Chemical from Blue-Green Algae

The cyanobacteria species that produces gatorbulin-1, tentatively identified as Lyngbya confervoides, forms these reddish-green, hair-like structures which are a collection of connected single cells rather than a true multicellular organism.

Photo: Raphael Ritson-Williams

Scientists Find Blue-Green Algae Chemical with Cancer Fighting Potential | Smithsonian Voices | National Museum of Natural History | Smithsonian Magazine

I've written several articles recently showing why biodiversity is important because, if for no other reason, it represents a potential untapped resource of useful chemicals such as antibiotics, fungicides, etc.

Now here's another one, this time yielding a potential anti-cancer drug.

It was found by a team of scientists from the Smithsonian’s National Museum of Natural History and University of Florida in blue-green algae, or cyanobacteria, tentatively identified as Lyngbya confervoides, in the sea off south Florida. These cyanobacteria are simple organisms that form hair-like filaments which look superficially like plants but which are just simple chains of single cells with no specialisation or division of labour.

Evolution News - Unraveling the History of Limb Bones

How tetrapods acquired new bone characteristics as they transitioned from water to land.

(A) About 380 million years ago, lobe-finned tetrapods were still water-bound (top). Yet, lengthwise cross sections of their forelimb bones (bottom) show that they had already evolved limbs that elongate through calcified cartilage columns (dark blue) within the metaphysis – the area near the extremities of the bones that features a ‘growth plate’ formed of cartilage (light blue). Marrow processes — the blood vessels (red) between the mineralized columns in the growth plate — were also present at this stage. However they did not communicate freely with the open cavity inside the shaft.

(B) Tetrapods that first ventured onto land 360 million years ago (top) also elongated their limbs at the growth plate. Their bones do show evidence of marrow processes occurring within the metaphysis (bottom), but they still produce red blood cells via their liver and kidney. Indeed, a trait necessary for red blood cell production in the bone is missing: the blood vessels of the marrow processes open into small connected cavities in the bone rather than communicating with the open marrow cavity.

(C) Fully terrestrial tetrapods appeared 300 million years ago (top), and they retained the fan-like growth plate of their ancestors (bottom). However, the cavities within their bones indicate that the marrow processes were interconnected via blood vessels, and that they communicated with the bone marrow. This suggests that red blood cells were now produced within bone.

New light shed on the early evolution of limb-bone growth plate and bone marrow | eLife

An open access paper published in eLife a couple of days ago, sheds light on a mystery surrounding the evolution of the limb bones of terrestrial tetrapods; in particular the evolution of bone marrow and the transfer of red blood cell production into the bone marrow and away from the liver and kidneys, where they are normally produced in most aquatic vertebrates such as fish.

Using the powerful x-ray beam produced by the European Synchrotron Radiation Facility, an internationa team of scientists led by Jordi Estefa of Department of Organismal Biology, Evolution and Development, Uppsala University, Uppsala, Sweden, examined the limb bones of fossil lobe-finned fish and early terrestrial tetrapods.

The eLife Digest explains:

For many aquatic creatures, the red blood cells that rush through their bodies are created in organs such as the liver or the kidney. In most land vertebrates however, blood-cell production occurs in the bone marrow. There, the process is shielded from the ultraviolet light or starker temperature changes experienced out of the water.

It is possible that this difference evolved long before the first animal with a backbone crawled out of the aquatic environment and faced new, harsher conditions: yet very little fossil evidence exists to support this idea. A definitive answer demands a close examination of fossils from the water-to-land transition including lobe-finned fish and early limbed vertebrates. To support the production of red blood cells, their fin and limb bones would have needed an internal cavity that can house a specific niche that opens onto a complex network of blood vessels.

Evolution News - Our Ancestors Walked (or Probably Crawled) With Dinosaurs

Artists impression of the newly discovered early primate species, Purgatorius mckeeveri.

Illustration by Andrey Atuchin

New Fossil Discovery Illuminates the Lives of the Earliest Primates

No matter what forgeries and inventions Creation frauds resort to to fool their dupes into believing humans lived amongst dinosaurs, we know they died out some 63, million years before even archaic pro-hominins were around. They were killed in the sudden Cretaceous-Paleogene mass extinction event 66 million years ago.

However, dinosaurs did live alongside the earliest ancestors of the primates, according to the discovery by a team from the City University of New York (CUNY) Graduate Centre. This claim is based on an examination of fossil teeth found in the Hell Creek area of north-eastern Montana which have been dated to 65.9 million years old, in other words, to between 105,000 and 139,000 years after the dinosaurs vanished.

The extinction of the dinosaurs freed up lots of ecological niches that the early ancestors of the mammals were able to radiate into, giving rise to most of the stem species of modern mammalian families, including the primates.

The CUNY New release explains:

Evolution News - A 3.67 Million-Year-Old Hominin Skull CT Scan Shows Amazing Detail.

Fossil skull ("Little Foot")

New technology allows scientists first glimpse of intricate details of Little Foot’s life - - Diamond Light Source

It must be difficult for a dedicated creationist to have to live with these regular accounts of things happening many millions of years before their dogma requires them to believe the Universe existed, but then I suppose as would be Christian martyrs, they like a cross to bear.

So here for them then is yet another one. This is a scientific account of the amazingly detailed examination of a 3.67 million-year-old hominid skull from South Africa, using a new technology that allows fragile speciments to be non-destructively examined.

The skull is that of a female Australopithecine - a genus of hominin that were the immediate ancestors of the Homo genus, were widely distributed in eastern and southern Africa.
This examination was made possible by using a technology developed just a stone's throw from where I live, by Diamond Light Source - the UK's national synchrotron science facility at Harwell Science and Innovation Campus in Southeast Oxfordshire.

The Diamond Light news release explains:

Abiogenesis News - That God-Shaped Gap is Getting Smaller!

A replicator made of tRNA-like sequences

© Kudella / LMU

Origin of life: The chicken-and-the-egg problem | News - LMU München

Another shovel-full of science just got thrown into Creationism's favourite God-shaped gap, abiogenesis.

A Team of German scientists led by Professor Dieter Braun of the Ludwig Maximilians Universität (LMU), München, have shown how to resolve the classic 'chicken and egg' conundrum when explaining the origins of living systems, that proteins are required for transcription of the genetic information, but their synthesis itself depends on transcription.

It involved Darwinian evolution at a molecular level! As always when science solves a problem, magic was found not to be required!

The LMU press release explains the problem:

Evolution News - Neanderthals Could Speak and Process Spoken Communication

3D model and virtual reconstruction of the ear in a modern human (left) and the Amud 1 Neandertal (right)

Image: Mercedes Conde-Valverde.

Neanderthals had the capacity to perceive and produce human speech | Binghamton News

When the ancestors of anatomically-modern non-Africans came out of Africa and met their Neanderthal sister species, they would probably have been able to communicate with them with speech. The fact that two related species of hominin could very probably use speech in exactly the same way, is strongly suggestive that our common ancestor could too, even if not to such a developed standard.

This is the conclusion of an international team of researchers including Binghamton University anthropology professor Rolf Quam and graduate student Alex Velez, and scientists from several Spanish universities and research institutions. The team was led by Professor Mercedes Conde-Valverde of Universidad de Alcalá, Spain.

Talibangelical Sore Losers - Three False Prophets for Trump

Three False Prophets

Robin Bullock "Joe Biden doesn't exist"
Shane Vaughn "Trump will serve 12 years as leader of the nation"	Jeff Jansen "Trump is still President. Military will return him to the White House this summer"

Robin Bullock declares President Biden isn't really there!

It's fast becoming a characteristic of Talibangelical Trumpanzee Christians that they find reality too difficult to cope with, so need to make up an alternative one.

Here, by way of illustration are three fundamentalist preachers struggling to come to terms with the fact that their idol, Donald J. Trump, lost the presidential election and that Joe Biden is the duly elected President of the United States of America.

First up we have Robin Bullock, a well-known fruitcake, who last November told his followers that God brought about the Covid-19 pandemic to punish people who voted for Hilary Clinton in 2016. Apparently, neither Robin Bullock nor God realised that most of those who caught the virus and died weren't even Americans because it's a pandemic, but Bullock managed to find this prophesied in the Book of Revelations (where anyone can find anything they want prophesied).

Imagine that! The book of Revelations contains prophesies about the outcome of an election in a country that didn't exist at the time it was written and about a democratic process that no-one then had even heard of! And it just happened to be exactly what Robin Bullock needed to justify his earlier false prophesies!

Malevolent Designer News - God Hates Koalas

Wild koala, Phascolarctos cinereus

© A. Gillet

Retroviruses are re-writing the koala genome and causing cancer - Leibniz Institute for Zoo and Wildlife Research

Intelligent [sic] Design Creationists are stuck with a dogma that denies the role of amoral, purposeless natural forces in nature and must ascribe everything to the deliberate intent of a magic deity, whom they equate to the supposedly all-loving god of the Bible.

This means of course that the devastation the koalas are suffering right now is the result of this putative magic designer's intention. As the press release from the Leibniz Institute for Zoo and Wildlife Research, Berlin, Germany, reports:

Koalas are facing multiple environmental and health issues which threaten their survival. Along with habitat loss - accelerated by last year’s devastating bush fires – domestic dog attacks and road accidents, they suffer from deadly chlamydial infections and extremely high frequency of cancer. An international team of scientists led by the Leibniz Institute for Zoo and Wildlife Research (Leibniz-IZW) now demonstrate that a retrovirus invading the koala germline explains the high frequency of koala cancer. The results are reported in the journal Nature Communications.

Evolution News - Million-Year-Old Mammoth DNA Shows a New Species Arose From Hybrids

Ancient DNA retrieved from different mammoth species is illuminating a complex evolutionary picture.

Picture: Beth Zaiken/Centre for Palaeogenetics

Million-year-old mammoth genomes shatter record for oldest ancient DNA

In a paper published in Nature a few days ago, a team of palaeontologists led by Tom van der Valk of the Centre for Palaeogenetics, Stockholm, Sweden, report recovering useable DNA from the million-year-old remains of mammoths. This sets a new record, the previous one being established in 2013 when a team from the University of Copenhagen led by Ludovic Orlando reported extracting DNA from the leg-bone of a horse dated to 560-780 thousand years old.

This mammoth DNA was extracted from three teeth, two of which have been dated to over a million years old, which had been preserved in Siberian permafrost. According to this report in Nature:

Covidiot News - SCOTUS Gives the Go-Ahead for California's Religious Super-Spreaders

US Supreme Court, Washington DC

Supreme Court Again Allows Indoor Church Services, Lifts Ban - Bloomberg

Showing their partisan divide, with Trump's conservative appointees siding with them, the US Supreme Court has granted California's churches the right to obstruct efforts to control the coronavirus pandemic and hold Covid super-spreader events.

This ruling follows a string of similar rulings limiting the powers of government to regulate gatherings in places of worship in the same way that it regulates gatherings in shops, shopping malls, sports arenas and other public spaces.

Malevolent Designer News - Nasty Little Thai and Die Parasites

Figure 1. Distribution of collected snails from 13 localities, along the coast of Andaman Sea, south Thailand.
Figure 2. Shells of Stenomelania sp. (Fisher 1885) from south of Thailand. a. Morph 1: S. cf. aspirans, Krabi Province; b. Morph 2: S. cf. crenulata, Krabi Province; c. Morph 3: Neoradina aff. prasongi, Krabi and Trang Provinces; d. Morph 4: S. cf. punctata, Krabi and Trang Provinces; e. Morph 5: S. cf. torulosa, Krabi, Trang and Satun Provinces. Scale bar: 10 mm.	Figure 3. Images of Loxogenoides bicolor (Krull, 1933) Kaw 1945. a. Specimen stained with 0.5% neutral red; b. Drawing image; c. Sporocyst stained with 0.5% neutral red. Abbreviations – eb: excretory bladder; p: pharynx; pg: penetration gland; os: oral sucker; s: stylet; sp: sporocyst; ta: tail; vi: virgulate organ; vs: ventral sucker. Scale bars: 100 μm.
Figure 4. Haplorchis taichui (Nishigori, 1924) Chen 1936. a. Specimen stained with 0.5% neutral red; b. Drawing image; c. Redia stained with 0.5% neutral red. Abbreviations – dvf: dorso-ventral finfold; eb: excretory bladder; exp: excretory pore; es: eyespot; lf: lateral finfold; os: oral sucker; p: pharynx; pg: penetration gland; re: redia; ta: tail. Scale bar: 100 μm.	Figure 5. Images of Procerovum cheni Hsȕ, 1951. a. Specimen stained with 0.5% neutral red; b. Drawing of image; c. Sporocyst stained with 0.5% neutral red. Abbreviations – dvf: dorso-ventral finfold eb: excretory bladder; es: eyespot; lf: lateral finfold; os: oral sucker; p: pharynx; pg: penetration gland; re: redia; ta: tail. Scale bar: 100 μm.
Source

Agents of food-borne zoonoses confirmed to parasitise newly-recorded in Thailand snails | EurekAlert! Science News

You have to hand it to the intelligent [sic] designer. He or she leaves very little to chance in his/her determination to make humans sick or suffer. Here, for instance, we have an example of the lengths he/she has gone to to turm people in southeast Asia blind with liver and intestinal flukes, using three different species of trematode and four different species of snail.

Trematode flatworm parasites that cause severe ocular infections in humans have been found to use these common snails as their secondary host.

Like a lot of flat-worm parasites, this one has the problem of getting back into its host when its eggs are expelled into the environment. This one does it by infecting a secondary host that is eaten by a tertiary host that itself is eaten by a human. The tertiary host is a fish that is commonly consumed by humans, sometimes only partially cooked.

Now researchers at Silpakorn University, Thailand, led by Kitja Apiraksena, working in South Thailand have discovered that snails commonly found in fresh and brackish water in southeast Asia can carry the parasite as the secondary host. The Eureka Alert news item explains:

"Trematode infections are major public health problems affecting humans in southeast Asia," explain the scientists. "Trematode infections depend not only on the habit of people, but also on the presence of first and second intermediate host species, resulting in the endemic spread of parasites, such as intestinal and liver flukes in Thailand".

The snails of concern belong to the genus Stenomelania, have elongated and pointed shells and can be found near and in the brackish water environment of estuaries in the Oriental Region, from India to the Western Pacific islands. Worryingly enough, science does not know much else about these snails to date. Further, these species are hard to distinguish from related trumpet snails, because of the similarities in their shell morphology.

In order to provide some basic knowledge about the parasitic worms in Thailand and neighbouring countries, the research team collected a total of 1,551 Stenomelania snails, identified as four species, from streams and rivers near the coastline of the south of Thailand in Krabi, Trang and Satun Provinces. Of them, ten were infected with trematodes. The parasites were found at seven of the studied localities and belonged to three different species. In Krabi Province, the researchers observed all three species.

Speculating on their presence, the scientists suspect that it could be related to the circulation of sea currents, as the flow of water along the Andaman coast is affected by the monsoon season.

Bigotry News - Christians for Hate and Discrimination

Bill Donohue
President, Catholic League

Equality Act: US House passes sweeping LGBTQ+ rights bill | LGBT rights | The Guardian

Religion provides excuses for people who need excuses.

Were you ever under the impression that Christian values include the fundamental equality of all people? How about the idea that all people are born with the unalienable right to life, liberty and the pursuit of happiness?

Not so, according to a gaggle of right-wing extremist Christian bigots who are furious at the passing of the Equality Act by the US House yesterday. They see the LGBTQ community enjoying the same rights as them as a frontal attack on them and their faith by the Biden administration.

Malevolent Designer News - Designing a Pointless Arms Race

Credit: CC0 Public Domain

Disease tolerance: Skeletons reveal humans evolved to fight pathogens | EurekAlert! Science News

Using evidence from the skeletons of about 70,000 ancient individuals, scientists at Flinders University have shown a pattern of co-evolution of humans and three major pathogens.

Biologist would interpret this as a typical evolutionary arms race, ending in a level of accommodation, as is predicted from the Theory of Evolution by Natural Selection.

Creationists, however, are obliged by dogma to interpret this as the work of a single designer, whom they have designated as 'intelligent' although there are precious few signs of any intelligence, or basic principles of good design for that matter. It is difficult to think of a suitable description of a designer who appears to be in competition with him/herself, constantly seeing the solution to the problem it created last as a problem to find a solution to next, but the terms 'intelligent' or 'designer' don't seem very appropriate or accurate.

Abiogenesis News - Creationism's Favourite God-Shaped Gap Just Got Smaller Again

“Protocells” containing bubble-like compartments formed spontaneously on a mineral-like and encapsulated fluorescent dye. This could have been what happened 3.8 billion years ago when cells first began to form.

Image: Karolina Spustova.

Evidence That Earth’s First Cells Could Have Made Specialized Compartments

No wonder Creationists often come across as paranoid. At times it must feel as though their favourite dogmas and god-shaped gaps are under siege by science and constantly in danger of being overthrown or closed altogether, like so many former gaps in which they sat their favourite god(s); all found to be empty when science shone a light in them.

One of their favourites, and often their only fall-back position, is that abiogenesis hasn't been explained by science, and that easily becomes a claim that it can't be explained without resort to magic by a magic man because living things contain special god-magic called 'life' that can't be identified or even explained.

Then along comes another paper, like this one from scientists at the University of Oslo, published by the Biophysics Society, that chips away a little more at this dogma, by showing not only how simple cells got started but by showing how 'life' is simply chemical and physical processes, all understandable as properties of matter, with no magic involved.

This paper is yet another in a long line of papers all reducing the size of creationism's god-shaped abiogenesis gap, and deals with how proto-cells became internally organised, in this case, with the formation of 'bubbles' or vacuoles that are a fundamental part of living cells today.

The Biophysical Society press release explains:

Evolution News - European Blackcaps Diverging in Plain View

Male blackcap, Sylvia atricapilla

Scientists attach geolocators to the backs of blackcaps to record the light intensity at any time of day. In this way, hiking trails can be precisely determined.

© Ben Porter

Variety in the migratory behavior of blackcaps | Max-Planck-Gesellschaft

Like the paper on the origins of East Asian peoples, in my last blog post, this one on the migration of the European warbler, the blackcap (Sylvia atricapilla), also shows how little makes sense in biology unless seen with an understanding of evolution and how it works. Supernatural ''explanations' actually explain nothing and have no predictive power because, when you add magic to any explanation, literally anything becomes possible and nothing is falsifiable.

This little bird is a favourite of mine if for no other reason that we had one spend two of the last three winters in our garden, feeding regularly at our bird feeders and fat balls (and that is a clue to their recent change of habit, which this paper records). Readers may recall I wrote about this just over 2 years ago, explaining the evolutionary significance of it.

Now this piece of work, led by Miriam Liedvogel of the Max Planck Institute for Evolutionary Biology in Plön, Germany, sets out to uncover some of the remaining mysteries surrounding blackcap migration.

Evolution News - How the East Asian People Evolved

Mountainous area in the Shaoguan district, Guangdong province, China.

© wklzzz | 123RF.com

Genomic insights into the origin of pre-historic populations in East Asia | Max-Planck-Gesellschaft

Creationist frauds will try to tell you that the Theory of Evolution by Natural Selection is a theory in crisis and about to be overthrown by their superstition, Intelligent [sic] Design, in which magic plays the major part. If so, this would be the first scientific theory to be replaced by a supernatural, evidence-free notion with no predictive powers, based on nothing more substantial then superstition, wishful thinking and ignorant incredulity. However, it won't be since there is no sign in the scientific world of any serious doubt about the validity of the TOE and its usefulness in making sense of the natural world, including human populations, as this paper shows.

As we can see from work such as this by a very large, international group of geneticists, anthropologists and linguists, led by researchers from the Max Planck Institute, Germany, what we see today only makes sense biologically in the context of evolution over time from common ancestors. In this case, a large team of scientists have shown how the different populations of East Asia, the most densely populated area of Earth, are related.

From the Max Planck Insitute's press release:

Evolution is a PROCESS, Not an Event!

Where does one colour end and the next start?

As species evolve over time, there is no one time or place where one species turns into another and never a point where it is not the same species as its parents.

Evolution is a PROCESS not an event!

All fossils are transitional!

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Malevolent Designer News - How TB Evades Our Defences

3D illustration of the bacterial pathogen Mycobacterium tuberculosis.

Image: 123rf

Study could explain tuberculosis bacteria paradox

A study by computational bioengineers at Rice University and infectious disease experts at Rutgers New Jersey Medical School (NJMS) has revealed how Mycobacterium tuberculosis, the organism that causes TB, is able to resist our immune system and lie dormant for many years, before becoming active and pathological again. It has a genetic mechanism that enables it to resist stress and 'remember' how id did it, so it can do it again more quickly.

Creationists, for whom evolution by entirely natural processes must be dogmatically rejected, must attribute this ability to the intentional design of their putative intelligent [sic] designer, who is one and the same as the Christian god and allegedly omni-benevolent, only wanting a maximally good world for its creation. Why then it came up with this apparently malevolent design remains a mystery that I have yet to get a creationist to explain, other than by dismissing it as a mystery that we can't ever expect to understand, and calling me arrogant for "trying to understand the mind of God", whilst still pretending it is real science and a sound basis for investigating biology.