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

Tuesday 14 May 2024

Unintelligent Design - How a Cell Division Error Sometimes Causes Cancers - Incompetence or Malevolence?


Two microscopy images of chromosomes. The left image shows chromosomes during mitosis (white). In orange, a centromere is visible consisting of two subdomains (arrows), each bound to a discrete bundle of microtubules (magenta). The right image depicts a dividing cancer cell showing a missegregating chromosome in the middle. The two centromere subdomains (arrows) of this chromosome appear split.

Credit: Carlos Sacristan Lopez. Copyright: Hubrecht Institute.
Research on centromere structure yields new insights.

Creationists, who, generally speaking, know little or nothing of biology and don't want to either because the risk of wondering it they could be wrong is far too great, are easily fooled by the frauds with a vested interest in keeping them simultaneously ignorant and imagining they have a deeper understanding than the millions of educated, working biomedical scientists who apply the Theory of Evolution every day of their working lives.

One thing they've been fooled into believing is that there is some sort of perfection in design inside a cell and that same designer is responsible for everything about living organisms.

But, in the last few years, under the onslaught of science, the frauds have needed to fall back from the demonstrably false notion of perfection of design in view if cancers, diseases and parasites, and now blame something for these obvious imperfections, which, by definition, could not be the products of a perfect designer god, do they have invented the biologically nonsensical notion of 'genetic entropy' and devolution caused by 'Sin' over which their omnipotent, omnibenevolent designer god is powerless.

And, again under the onslaught of science, the frauds have also conceded that evolution does indeed happen and happened at a massively accelerated rate to account for all the biodiversity produced by a small number of survivors of a genocidal flood just a few thousand years ago.

Monday 13 May 2024

Evolution in Progress - How Two Isolated Populations in Papua New Guinea Have Diverged


Genetic adaptations have impacted the blood compositions of two populations from Papua New Guinea | Tartu Ülikool

An example of evolution if progress this week comes from a team of researchers from the universities of Tartu (Estonia), Toulouse (France), and Papua New Guinea. They have carried out an extensive analysis on blood samples from two populations in Papua New-Guinea who have remained isolated for the 50,000 years since Homo sapiens arrived on the Island.

One group occupies the highlands and the other group lives in the lowlands, making this a living laboratory to measure the effects of the different environments on the genomes of the two populations.

Different environments provide different drivers of evolutionary adaptation; for instance, the highlanders have adapted to a low oxygen partial pressure and comparatively few pathogens and an absence of mosquitoes; while the lowlands have both mosquitoes and a higher level of endemic pathogens. How each group has adapted to these different environments provides a text-book example of how the environment drives evolution and how isolation results in divergence.

The team's work is published, open access, in Nature Communications and is explained in a press release from Tartu University, Estonia:

Friday 10 May 2024

Unintelligent Designer News - How Creationism's Idiot Designer Continually Designs Different Solutions To The Same Problem


Squinting bush brown, Bicyclus anynana

© Judy Gallagher (CC BY-SA)
New sex-determining mechanism in African butterfly discovered - News - University of Liverpool

Once sexual reproduction had become established in multicellular organisms, there was selection pressure to determine the gender of a developing embryo, so the result was either genetically male or genetically female. In humans and other mammals, for example, this is achieved by the XY Chromosomes, which, unlike all the other chromosomes (autosomes) are not paired. A zygote with 2X (homozygous) becomes a female and a zygote with XY (heterozygous) becomes male. Because the zygote gets either one or the other of these chromosomes from each parent these are the only combinations possible, so we never see a YY zygote.

Tuesday 7 May 2024

Malevolent Design - How Creationism's Divine Malevolence Co-opted Red Squirrels To Spread Leprosy in Medieval England


Mycobacterium leprae
Ancient Mycobacterium leprae genome reveals medieval English red squirrels as animal leprosy host: Current Biology

Few places in Europe or elsewhere were more pious than Medieval England, but still creationism's pestilential malevolence continued to make people suffer with diseases such as bubonic plague, tuberculosis and the related leprosy. Even the extreme measures taken by believers to atone for imaginary transgressions that had brought about the Black Death had failed to assuage the putative designer god who was believed to be visiting this pestilence upon people.

The superstitious Bible-based belief in evil spirits and 'sin' as the cause of disease led to the social stigma that made the disease so feared and led to the isolation of sufferers in lepper colonies, and often reduced to begging to stay alive. Poor nutrition and poor sanitation led to a worsening of the condition and, although these counter-measures were visibly ineffective, such was the belief in the Bible that it was inconceivable that the disease could be caused by anything other than 'sin' and evil demons being permitted to enter the victim.

The modern equivalent of this victim-blaming superstition can be found in the modern creationist tactic of blaming 'Sin' and 'genetic entropy' for parasites, with demons being replaced by 'entropy' to make it sound sciencey. It is of course, Bible-based superstition without supporting evidence.

And now, if you believe that stuff, there is evidence that creationism's putative designer god designed M. leprae to also infect red squirrels so they would act as a repository to spread leprosy. Red squirrels were common in those days and were often captured in the wild for pets or pelts. Their skins, when used for clothing, would have carried M. leprae and infected anyone who wore them - a brilliant strategy, if you hate people and want them to be sick, suffer and die.

Sunday 5 May 2024

Creationism in Crisis - Humans Had Domesticated Dogs At Least 10 Thousands Years Before 'Creation Week'


Siberian wolf, Canis lupus
Ancient Mitogenomes Reveal the Maternal Genetic History of East Asian Dogs | Molecular Biology and Evolution | Oxford Academic

These days, no serious scientist sets out to prove the Bible is wrong; discovering truth does that anyway - for anyone who can join the dots and do the simple logic. For example, humans could not have domesticated dogs some 23,000 years ago in Siberia by domesticating the local variety of grey wolf, if the Universe is just 10,000 years old.

And yet a paper published recently in the journal Molecular Biology & Evolution shows that they did exactly that.

In the context of mitochondrial DNA, what are haplotypes? In the context of mitochondrial DNA (mtDNA), haplotypes refer to specific combinations of genetic variants or polymorphisms within the mitochondrial genome. Unlike nuclear DNA, which is inherited from both parents, mtDNA is passed down exclusively from the mother to all of her offspring. This maternal inheritance pattern makes mtDNA useful for studying ancestry, population genetics, and evolutionary history.

A haplotype represents a unique combination of nucleotide variations or mutations along the mtDNA sequence. By analyzing these haplotypes, researchers can track maternal lineages, study population migrations, and infer evolutionary relationships among different groups of individuals. Haplotypes are often used in studies of human populations, as well as in forensic genetics and medical research related to mitochondrial disorders.
Refuting the Bible was almost certainly not the intention of the authors, jointly led by Songmei Hu, of Joint International Research Laboratory of Environmental and Social Archaeology, Shandong University, Qingdao, China, and Xijun Ni and Qiaomei Fu, both of the Institute of Vertebrate Paleontology and Paleoanthropology, Center for Excellence in Life and Paleoenvironment, Chinese Academy of Sciences, Beijing, China, but the facts they discovered do just that. They had set out to resolve the question of where exactly dogs had been domesticated, based on an analysis of the mitochondrial DNA.

Mitochondrial DNA (mDNA) is inherited through the maternal line, so an analysis of the geographical and temporal distribution of the various haplotypes of mDNA and how they relate to one another should give an indication of where and when the ancestral haplotype lived.

How the team did this is explained in their paper:

Thursday 2 May 2024

Creationism in Crisis - Batty Evolution On Solomon Islands


Diadem leaf-nosed bat, Hipposideros diadema

Researchers parse oddity of distantly related bats in Solomon Islands that appear identical | KU News

There is something strange about the Solomon Islands, lying east of Papua New Guinea and northeast of Australia. The bats that inhabit the islands seem to have evolved in ways that are difficult to understand.

Before creationists get over-excited and think we've found an example of species that didn't evolve but were made by magic, the question is not whether they evolved, but how? The scientists are in no doubt that the process was an evolutionary one and show no signs of concluding that a supernatural entity was involved. The puzzle is that genetically distinct species on different islands, occupying the same niche, have evolved such a high degree of phenotypic convergence that they are almost indistinguishable, so were previously classified as the same species, although genetically they are not even close relatives. The question is what is it about the environment on these islands that has driven this high level of convergence.

Each of the islands in the archipelago has a population of bats, usually 3-5 species on each island, consisting of a small, medium and large species and on islands with four species, an extra-large. One island has five species so gets an extra small bat.

That all seemed fairly straightforward on the assumption that the five distinct species had each found a niche on each island, and they certainly looked identical when comparing the different sized bats on each island. However, that was before we had DNA sequencing techniques.

DNA analysis has shown that the large bats on different islands, although identical in appearance, are not closely related - they have converged on that appearance from different ancestral bats.

This was discovered by a research team of scientists from University of Melbourne, Australia, the University of Kansas, USA, Jame Cook University, Australia and others. Their work is published open access in the journal, Evolution (the National Journal of Organic Evolution). It is explained in a University of Kansas news release:

Tuesday 30 April 2024

Creationism in Crisis - Yeast Evolution - Not Whether But How


Electron micrograph of budding yeast cells
Photo: Ira Herskowitz and E. Schabtach
Bioinformatics professor discovers surprising evolutionary pattern in landmark yeast study | Inside UNC Charlotte | UNC Charlotte

As I've remarked before, trying to debate with creationists is like boxing with a brain-dead opponent who lacks the cognitive ability to know when they're down and out. Their lumbering body keeps flailing around and like a defeated Donald Trump, insists that they’ve won, and are triumphing over all-comers in the ring.

Creationist frauds have been telling their willfully ignorant cult that they are winning the debate against science and science is about to convert to creationist superstition and abandon the materialist explanations. The science that has produced all of modern technology, including the computers and Internet that they use to inform the world that science is all wrong, and magic done by an unproven supernatural being is a better explanation for the observable facts, endearingly oblivious of the irony.

And yet not a single science paper has ever concluded any such thing and the small handful of pseudo-scientists that the creation cult employs to misinform the world never publish in peer-reviewed science journals. It's almost exactly like science just gazes bemusedly at the hopeless flailings of creationism, which has been on the canvas now for 50 years but still hasn't noticed. The trick has been to remain completely oblivious of real science by never reading anything that might make them wonder if being horizontal on the canvas is the best way of winning a boxing match.

Meanwhile real scientists do real science and science moves on.

An example of this was a paper published recently in Science which is the result on an AI assisted detailed analysis of the genomes of 1,154 strains of the ancient, single-cell yeast, Saccaromycotina, to discover how the different yeasts had evolved. Nowhere in the paper is there the slightest hint that the process that produced the different strains might be magic, not natural evolution. Instead, the research provides more understanding of how the evolutionary processes work.

The research by a team co-led by Professor of Bioinformatics Abigail Leavitt LaBella of the University of North Carolina at Charlotte, is explained in a University of North Carolina news release:

Saturday 27 April 2024

Creationism in Crisis - How Human Society Was Changing When Creationists Believe There Was A Genocidal Global Flood


Social change may explain decline in genetic diversity of the Y chromosome at the end of the Neolithic period | CNRS

The problem with having a childish superstition based on the campfire tales of primitive people who knew nothing of the world outside their own narrow horizons and folk memory is that it can cause you to believe the most ludicrous things that require you to maintain a pristine ignorance in order to retain your superstition.

This is especially true if an integral part of your irrational superstition is that there is a mind-reading bogeyman in the sky who will become angry if you have the slightest doubt or learn things that cause you to question your superstition. Your irrational phobia imposes a sort of information filter on your perception that doesn't allow anything to pass through that might cause you to change your mind.

This is why creationists will believe such absurdities as a global genocidal flood that left no geological evidence and reduced the human population to such a low number that the lack of genetic diversity would have guaranteed extinction within a handful of generations, yet this left no mark on human genetic diversity. Instead, what we see in the genetic record of human history in the Y chromosome is a change in the demographic profile just about the time when the Bronze Age story-tellers were setting their genocidal flood tale.

This shows that not only were there far more humans alive than the tales relate, but that there was a significant change in the form of society, probably as a result of technological change, to a more patrilineal society. This created the conditions for powerful male tribal leaders to inherit the powers to dominate other males and so to father many more children, resulting in a functional reduction in the male population, and fall in genetic diversity in the Y chromosome, while the female population continued to grow.

Some time ago I wrote about how gene-meme co-evolution can result in genetic changes which are not directly related to fitness of those genes, as this phenomenon illustrates. One of the examples I gave was that of Western Ireland where there is a cluster of Y chromosomes inherited from the legendary founder of the Uí Néill, Niall Noígíallach (Niall of the 9 hostages). In that part of Ireland an estimated 21% of males carry his Y chromosome and 8% in the rest of Ireland. I also cited another such cluster in China where an estimated 1.5 million males, mostly in Northern China and Mongolia have the same Y chromosome as descendants of Giocangga, a Qing emperor who died in 1582. These men were able to father many children because of the power they had in their societies, and their sons inherited both their Y chromosome and their power and authority. Because of their authority, they were able to command better resources in terms of food and shelter for their offspring, so improving their breeding success.

It was not necessary to use military power to dominate and exterminate neighbouring peoples to achieve the resulting reduction in genetic diversity in the Y chromosome.

Both these examples are cited in this paper.

This is the explanation proposed by a team of researchers from the French Centre national de la recherche scientifique (CNRS), the Muséum national d'Histoire naturelle (MNHN) and the Université Paris Cité, who have published their research findings, open access, in the journal Nature Communications. It is explained in a brief CNRS news item:

Sunday 21 April 2024

Malevolent Designer News - How The Monkeypox Virus (MPVX) Was Redesigned To Make It More Contagious


Monkeypox virus (MPXV)
New Research Defines Specific Genomic Changes Associated with the Transmissibility of the Monkeypox Virus | Mount Sinai - New York


Why did the monkeypox virus (MPXV) suddenly become much more contagious in 2022 to transform it from a relatively harmless, low-level infection of humans and other animals into a potential pandemic virus?

Scientists from Mount Sinai, New York, USA, in collaboration with researchers from the Carlos III Health Institute (ISCIII) in Madrid, Spain believe they have worked out the answer to this puzzle - a substantive change in the DNA virus' genome.

Creationists will reject the idea that this change was an evolutionary change driven by environmental selectors, despite the obvious explanation of the observed facts that this explanation offers because their cult dogma states that changes in genomes only happen if caused by their putative intelligent [sic] designer, although, to be fair to creationists, some of them will betray the religious nature of creationism by blaming viruses and these sorts of changes in their genomes on another creator, called 'Sin' to make it compliant with fundamentalist beliefs in a literal Bible.

But these apologists are continually undermined by those fundamentalists who generally, in their kind, caring and compassionate way, greet every new epidemic as their god's punishment for something they don't like. This will usually be some far-right political hobbyhorse in the USA, the way HIV was greeted with great jubilation by Christians as a 'Gay Plague', sent to punish homosexuals, and COVID-19 was declared to be God's punishment on New Yorkers for voting for Democrats.

However, those few creationists intelligent enough to realise they should be supporting the Discovery Institutes efforts to disguise creationism as science, will avoid these excuse, but they are then left with either evolution by natural selection, or intelligent [sic] design, so let's go with those who claim to see their god's hand in these viruses, so at least have managed to avoid the blasphemy of believing in two or more creators, while presenting their allegedly loving god as a pestilential malevolence.

Friday 19 April 2024

Creationism in Crisis - How A Small Mutation Made Us Human - And Shows Our Common Origin With Other Apes


A regulatory variant impacting TXB1 expression contributes to the morphology at the base of the skull. (SNP = single nucleotide polymorphisms).
Genetic Variant Identified that Shaped the Human Skull Base|Tokyo Medical and Dental University, National University Corporation

Creationists like Michael J Behe try to fool their fellow cultists that all mutations are 'devolutionary' and move the organism away from some notional idea of created perfection, although perfection for what is never stated. It is left to the parochial ignorance of the reader to fill the gap and conclude that the religious superstition of 'The Fall' must be true, so he can claim his absurd notion is not really Christian fundamentalism in a lab coat like his 'intelligent design' notion, but real science.

The same parochial, ignorant religious fundamentalists will also assume that somehow humans represent the supreme created perfection (how could it be otherwise for those who, with the 'humility' of a religious fundamentalist, see themselves as the perfect creations of a perfect creator?).

So how does that square with the many examples of mutations being what makes humans different to other species, as shown by any comparison of our genome with that of apes such as chimpanzees or bonobos?

Of course, it's biological nonsense to talk of perfection without reference to the environment and how a mutation affects fitness in that environment, and fitness is what the process of natural selection produces. There is no perfect pattern against which to compare what evolution produces, so both Homo sapiens and Pan troglodytes (common chimpanzee) are perfect at being human or common chimpanzee respectively, as is are African elephants, a cabbages, or a bacteria, perfect at being what they are.

And this was demonstrated a few days ago with publication of a paper by a team from Tokyo Medical Dental University (TMDU), the University of Helsinki, and the University of Barcelona who have analysed the genetics of the shape of the base of the human skull and found it to be due to a mutation in a single gene called TBX1. The mutation is a single nucleotide polymorphism (SNP), which means a change in a single letter in the DNA 'code' for a single amino acid. The SNP (“rs41298798”) is in the DNA involved in the regulation of TXB1.

This single mutation allowed the base of our skull to change shape as our brain enlarged as we became more intelligent and more dependent on technology and the cognitive abilities that enabled us to become Homo sapiens.

The team have published their findings, open access, in the Cell Press, American Journal of Human Genetics, the journal of the American Society for Human Genetics, and explain it in a TMDU News release:

Wednesday 17 April 2024

Creationism in Crisis - How Copy & Paste Errors Created New Genetic Information - 700 Million Years Before 'Creation Week'


Examples of bilaterans
Centre for Genomic Regulation Website

Contrary to creationists dogma that no new genetic information can arise in a genome without god-magic because of some half-baked notion that the Third Law of Thermodynamics, which applies to energy, somehow applies to genetic information, researchers at the Centre for Genomic Regulation (CRG) in Barcelona, Catalunya, Spain, have shown how errors in replication in DNA some 700 million years ago eventually resulted in a vast supergroup of animals (the bilaterans, i.e. animals with bilateral symmetry) including vertebrates (fish, amphibians, reptiles, birds, and mammals), and invertebrates (insects, arthropods, molluscs, worms, echinoderms and many more).

These errors where whole genomes and genes were duplicated, created the condition where the original genes could continue to function while copies of them were free to mutate and produce new genes with new functions, under the control of natural selection which retains anything which is better than what preceded it and quickly eliminate anything which is worse.

Bilaterians are animals that exhibit bilateral symmetry, meaning they can be divided into two equal halves along a single plane. The vast majority of animals on Earth are bilaterians, including many familiar groups such as:
  1. Mammals: Humans, dogs, cats, elephants, and dolphins are all examples of bilaterians within the mammalian group.
  2. Birds: Birds, like sparrows, eagles, penguins, and ostriches, are also bilaterians.
  3. Reptiles: Snakes, lizards, turtles, and crocodiles exhibit bilateral symmetry.
  4. Amphibians: Frogs, toads, salamanders, and newts are examples of bilaterians within the amphibian class.
  5. Fish: Most fish species, including tuna, salmon, sharks, and goldfish, are bilaterians.
  6. Insects: Butterflies, ants, bees, beetles, and flies are bilaterians within the vast group of insects.
  7. Arachnids: Spiders, scorpions, ticks, and mites are bilaterians within the arachnid class.
  8. Mollusks: Snails, slugs, octopuses, and squids exhibit bilateral symmetry.
  9. Annelids: Earthworms, leeches, and marine worms are examples of bilaterians within the annelid phylum.
  10. Echinoderms: While not as obvious due to their radial symmetry as adults, echinoderms like sea stars and sea urchins exhibit bilateral symmetry during their larval stages.
These are just a few examples, but bilaterians encompass an incredibly diverse range of animal life on Earth.
The researchers have published their findings in Nature Ecology & Evolution and have explained it in a news release from the Centre for Genomic Regulation (CRG):

Saturday 13 April 2024

Creationism in Crisis - How Multicellularity Evolved - With New Genetic Information


Green Alaga, Stigeoclonium sp.

Macroalgal deep genomics illuminate multiple paths to aquatic, photosynthetic multicellularity: Molecular Plant

What are the main types of algae and how do they differ? Algae are classified into several main groups based on their characteristics, including pigmentation, cellular structure, and mode of reproduction. The main types of algae include:
  1. Diatoms (Bacillariophyta):
    • Diatoms are single-celled algae characterized by their unique glass-like silica cell walls called frustules.
    • They are typically found in freshwater and marine environments.
    • Diatoms are important primary producers and play a significant role in the global carbon cycle.
  2. Green Algae (Chlorophyta):
    • Green algae encompass a diverse group of algae that are mostly freshwater but also found in marine and terrestrial environments.
    • They contain chlorophyll a and b, giving them a green color, similar to land plants.
    • Green algae can be unicellular, colonial, filamentous, or multicellular, with a wide range of morphologies.
  3. Red Algae (Rhodophyta):
    • Red algae are predominantly marine algae, although some species can also be found in freshwater.
    • They contain pigments like chlorophyll a and various accessory pigments, including phycobiliproteins, giving them shades of red, pink, or purple.
    • Red algae often have complex multicellular structures and are important contributors to coral reef ecosystems.
  4. Brown Algae (Phaeophyta):
    • Brown algae are primarily marine algae, commonly found in cold-water habitats.
    • They contain chlorophyll a and c, along with fucoxanthin, which gives them their characteristic brown color.
    • Brown algae can range from small filamentous forms to large, complex seaweeds like kelps.
  5. Blue-Green Algae (Cyanobacteria or Cyanophyta):
    • Despite being called algae, cyanobacteria are actually prokaryotic organisms, classified within the domain Bacteria.
    • They are photosynthetic and often form colonies or filaments.
    • Cyanobacteria can be found in diverse habitats, including freshwater, marine environments, soil, and even extreme environments like hot springs.
    • Some cyanobacteria can produce toxins under certain conditions, leading to harmful algal blooms (HABs) and posing risks to aquatic life and human health.
These main types of algae differ in their pigmentation, cellular structure, habitat preferences, and ecological roles. While some are beneficial and essential for ecosystem health, others can become problematic under certain conditions, such as nutrient pollution or climate change. Understanding the characteristics and ecological functions of different types of algae is crucial for managing and conserving aquatic ecosystems.
Today’s refutation of creationists dogma comes in the form of an open access paper just published in the Cell Press journal, Molecular Plant. Research biologists have revealed how multicellularity evolved several times independently in algae, and how many of the new genes were acquired initially by viruses.

This gives the lie to creationist claims that new information can't arise in the genome because of some half-baked confusion of information with energy and a nonsensical assumption that new genetic information would need to come from nothing.

And of course, like about 99.99% of the history of life on Earth, it all happened in that very long period of pre-'Creation Week' history between Earth forming in an accretion disc around the sun and creationism's little god creating a small flat planet with a dome over it in the Middle East out of nothing, according to creationist mythology

In information provided by Cell Press ahead of publication, the scientists at New York Abu Dhabi University and Technology Innovation Institute, United Arab Emirates, said:
A deep dive into macroalgae genetics has uncovered the genetic underpinnings that enabled macroalgae, or "seaweed," to evolve multicellularity. Three lineages of macroalgae developed multicellularity independently and during very different time periods by acquiring genes that enable cell adhesion, extracellular matrix formation, and cell differentiation, researchers report April 12 in the journal Molecular Plant. Surprisingly, many of these multicellular-enabling genes had viral origins. The study, which increased the total number of sequenced macroalgal genomes from 14 to 124, is the first to investigate macroalgal evolution through the lens of genomics.

This is a big genomic resource that will open the door for many more studies. Macroalgae play an important role in global climate regulation and ecosystems, and they have numerous commercial and ecoengineering applications, but until now, there wasn't a lot of information about their genomes.

Alexandra Mystikou, co-first author
Division of Science and Math
New York University Abu Dhabi, Abu Dhabi, UAE.
Macroalgae live in both fresh and seawater and are complex multicellular organisms with distinct organs and tissues, in contrast to microalgae, which are microscopic and unicellular.

There are three main groups of macroalgae -- red (Rhodophyta), green (Chlorophyta), and brown (Ochrophyta) -- that independently evolved multicellularity at very different times and in very different environmental conditions.

Rhodophytes and Chlorophytes both evolved multicellularity over a billion years ago, while Ochrophytes only became multicellular in the past 200,000 years.

To investigate the evolution of macroalgal multicellularity, the researchers sequenced 110 new macroalgal genomes from 105 different species originating from fresh and saltwater habitats in diverse geographies and climates.

The researchers identified several metabolic pathways that distinguish macroalgae from microalgae, some of which may be responsible for the success of invasive macroalgal species.

Many of these metabolic genes appear to have been donated by algae-infecting viruses, and genes with a viral origin were especially prevalent in the more recently evolved brown algae.

They found that macroalgae acquired many new genes that are not present in microalgae on their road to multicellularity.

For all three lineages, key acquisitions included genes involved in cell adhesion (which enables cells to stick together), cell differentiation (which allows different cells to develop specialized functions), cell communication, and inter-cellular transport.

Many brown algal genes associated with multicellular functions had signature motifs that were only otherwise present in the viruses that infect them. It's kind of a wild theory that's only been hinted at in the past, but from our data it looks like these horizontally transferred genes were critical factors for evolving multicellularity in the brown algae.

David Nelson, co-first author
Division of Science and Math
New York University Abu Dhabi, Abu Dhabi, UAE.

Sunday 7 April 2024

Malevolent Designer News - How Creationism's Divine Malevolence Creates Genetic Defects


UC Irvine-led research team builds first tandem repeat expansions genetic reference maps – UCI News

Creationists assure us that creating new genetic information is impossible without magic performed by the magic creator because they have been sold some half-baked notion that genetic information follows the same laws of physics as energy, so can't be created according to the Third Law of Thermodynamics.

The fact that this is demonstrably wrong since gene duplication is readily observable doesn't stop them trotting out the same refuted claims time after time, but then to a creationist, having a claim refuted is not seen as a reason not to try to get away with it again later. You'll see this repeatedly as an apologist fraud such as William Lane Craig, Ken Ham or Michael J Behe will be comprehensively refuted in a public debate one day, only to try the self-same argument a day or two later on a different opponent in front of a different audience.

Sadly for creationists, however, this tactic leads them down a cul-de-sac where they are left arguing that DNA duplication must have been intelligently designed and, so they will also claim, evidence of intelligent design is evidence that their favourite god (and no other!) exists.

Creationism in Crisis - How Rusty Patched Bumblebee Genes Show Evidence of Evolution Under Intense Selection Pressure


The rusty-patched bumblebee, once common in the United States, has declined from about 90% of its former range.
Photo by Jay Watson
Rusty-patched bumblebee’s struggle for survival found in its genes - Warner College of Natural Resources

Evolution, or more precisely change in allele frequency over time, inevitably records selection pressures on a species resulting in a genome which, when correctly read and compared to predecessors, should tell the story of changes in the species environment.

This principle is illustrated by the threatened species of bumblebee, the rusty patch bumblebee, Bombus affinis, which has recently declined by about 90% in the USA and is now considered an endangered species. If this rate of decline continues the species will probably be extinct within 20 years. This level of intense selection pressure has inevitably left its mark on the genome of the species.

On of the problems facing the species is the result of the way bees breed. The queen can normally produce two sorts of egg - a fertilised, diploid egg which will develop into a female and a haploid, unfertilised egg which will develop into a male or drone. The problem arises when there is a high level of inbreeding, due, for example, to a small population - which the bee is now facing. In that situation, the female can produce diploid males because both sets of chromosomes can be identical. Diploid males are normally sterile so reducing the breeding success of the local species.

Thursday 4 April 2024

Creationism in Crisis - A New Look at Bird Evolution - Not Whether, But How!


A greater flamingo, Mallorca, Spain.
Credit: Daniel J. Field
We’ve had bird evolution all wrong - News - University of Florida

To a child-like black vs white creationist, science changing its mind is science admitting it was wrong - which means it's probably wrong this time too, so all of science can be dismissed as wrong. Unless of course, it's some pseudo-science purporting to support creationism, then it's absolutely incontrovertible proof of creationism, because there is nothing a creationist craves more than proof of creationism provided by the same science they despise so much when it refutes creationism yet again.

So, news that a team of researchers at Florida University have re-examined the genetic evidence for the evolution of birds and revised the family tree will be music to the ears of any creationist fraud looking for some science to misrepresent. However, this research does nothing of the sort, and merely confirms what we already know - that birds diversified from a common ancestor by an evolutionary process. The debate is never about whether that happened, but how and exactly when.

What misled taxonomists was a chunk of DNA that has remained more or less unchanged for some 60 million years. By a process which is poorly understood, this large chunk of DNA avoids recombination during the process of egg and sperm production. Using this section alone gave one family tree, which put doves and flamingoes as close cousins, but using the whole genome gave a different family tree which makes doves and flamingoes much more distantly related (though of course, still related by common ancestry).

The research team have published their findings, open access, in Proceedings of the National Academy of Science (PNAS) and explain them in a University of Florida news release:

Tuesday 2 April 2024

Creationism in Crisis - An Evolutionary 'Family Tree' For All Living Birds


Male wood duck, Aix sponsa
After 10 years of work, landmark study reveals new ‘tree of life’ for all birds living today

The results of a ten-year study, published today in Nature will come as a huge disappointment for any creationists who find the courage to read it (and who have the ability to understand what they're reading - which for creationists is probably asking too much.

Those still under the delusion that mainstream biologists are abandoning the TOE in favour of creationism with its magic and a suppositional supernatural entity, will be especially disappointed. Not only does it show birds have been around for very much longer than creationists believe the universe has been it also shows that the team of scientists are firmly committed to the Theory of Evolution as the only scientific explanation for biodiversity.

Two of the biologists who co-authored the paper along with a large international team of biologists, Jacqueline Nguyen, Scientific Officer in Ornithology, Australian Museum, and ARC DECRA Fellow, Flinders University and Simon Ho, Professor of Molecular Evolution, School of Life and Environmental Sciences, University of Sydney, have described their findings in an article in The Conversation. Their article is reprinted here under a Creative Commons license, reformatted for stylistic consistency:

Friday 22 March 2024

Creationism in Crisis - How Batesian Mimicry In The Female Diadem Butterfly Evolved - Convergently


The female Diadem (bottom left) mimics the African Queen (top left). The male Diadem (right) keeps a distinct pattern to attract mates
Scientists discover how Diadem butterfly mimics African Queen - News

This is the second in a sudden spate of research papers that casually and unintentionally refute creationism without even trying, simply by revealing the facts. It deals with the evolution of Batesian mimicry in a species of butterfly.

Scientists working at the universities of Exeter, Edinburgh and Cambridge, and Mpala Research Centre in Kenya have discovered the genetic basis for the clear example of Batesian mimicry to be found in the female of the pantropical species of butterfly, the Diadem butterfly, Hypolimnas misippus, which closely resembles the toxic African queen butterfly, Danaus chrysippus.

Batesian mimicry is the natural phenomenon where an otherwise harmless species evolves to resemble a harmful or distasteful species as a defence mechanism. The prerequisite for Batesian mimicry to evolve is that a prey species is predated upon by the predator of a harmful species which coexists in the same locality. The predator learns to avoid the dangerous or distasteful species so any other species that comes to resemble the harmful or distasteful species might be mistaken for it and avoided. The more closely it comes to resemble the avoided species, the more likely it is to survive and reproduce.

Thursday 21 March 2024

Creationism in Crisis - How Hair Evolved From A Keratin Gene In A Frog-Human Common Ancestor


Genetic basis for the evolution of hair discovered in the clawed frog
Western Clawed Frog, Xenopus tropicalis
Carries the precursor gene for mammalian hair.


"When sorrows come, they come not single spies but in battalions" - Claudius in Hamlet.

That was never more true of creationism than it is today with the publication of not just the usual casual refutation of creationism we've come to expect most days, but of four disparate papers each of which casually and unintentionally refutes creationism to anyone who understands biology and is familiar with the basic dogmas of the creation cult, simply by revealing real-world facts.

The papers range from this one, which shows how mammalian hair has its genetic origins in a common human-amphibian ancestor, through how a female butterfly evolved Batesian mimicry, through the discovery of a giant Amazonian dolphin from 16 million years before creationists think Earth existed, to how early modern humans survived a super-volcano eruption in South-West Ethiopia a mere 64,000 years before 'Creation Week'.

With so many papers I'll do my best to cover all of them in the next few days, so keep checking back!

Firstly, the evolutionary origin of mammalian hair.

The gene for this originated in a common ancestor of humans (and the other mammals) and a modern clawed frog. The gene controls the growth of keratin, of which the claws of a clawed frog are composed, as is mammalian hair. The evidence for this common origin was found by researchers from the Medical University of Vienna, Austria, led by led by Leopold Eckhart. The team have published their findings open access in Nature Communications and described their work in a Medical University of Vienna new release:

Sunday 10 March 2024

Unintelligent Design - How Epigenetic Settings Are Passed To Daughter Cells - Even William Heath Robinson Would Be Impressed


Cracking Epigenetic Inheritance: HKU Biologists Discovered the Secrets of How Gene Traits are Passed on - Press Releases - Media - HKU

It all started when single-celled organisms started to form colonies of like-minded individuals. The easiest way to do it was for the two daughter cells of a dividing cell to stick together instead of going their own way. They in turn would have had more daughter cells until they formed large clump of cells, but, unless the cells began to perform distinct functions, there was no advantage to forming clumps like that instead of each cell going its own way and fending for itself. Fortunately, there were no large predators around, otherwise a clump of cells would have made a tasty snack and the whole idea would have been abandoned as too risky by half, and we would be stuck now with a world of single-celled organisms and nothing else.

However, with the trial and error which characterises biological development, some of the cells in the clump began to perform specialist functions. For example, as the clump got larger, specialist cells would have been needed to exchange gasses with the environment or the cells at the centre would have been deprived of oxygen and their waste in the form of carbon dioxide would have accumulated because diffusing across a large mass of cells would be too slow to keep up with production and the supply of oxygen would be too slow to keep up with the demand. The same thing applied to getting nutrients into the center of the clump.

So, the clumps which had specialist cells fared better in the competition for resources than those which were just undifferentiated clumps. In fact, the clumps with specialised cells would probably have eaten the undifferentiated clumps and become predators. And with predators there was pressure for increased specialisation for movement, ingestion and excretion, for more efficient respiration and for reproduction. And predation also produced pressure for more motility, for senses like sight and smell and maybe hearing and as the organisms became more complex so they needed nervous systems to coordinate their activities and process and respond to the stimuli their senses were receiving from their environment and some would have evolved defensive armour such as scales and spikes and hard shells and internal structures like cartilage and bone to give their bodies shape and form and to make their swimming apparatus stiffer and more powerful.

But what they never managed to do was find a different way to produce all the different specialist cells by a different method to that used by their single-celled ancestors, so every cell in their body had the full genome whether they needed it or not, and more often than not, they didn't need most of it. A bone cell doesn't need to do what a nerve cell does, and a nerve cell doesn't need to do what a muscle cell does, and neither muscle nor nerve cells need to make bone, and what else needs to make elbow skin other than an elbow skin cell, except perhaps a scrotum skin cell? Yet they all have the genes for doing everything any one cell needs to do.

So, cue creationism's intelligent [sic] designer who has been designing and modifying all these different clumps of specialised cells but who, for some reason, seems incapable of recognising that its designs are heading for disaster unless it can think up a way to make sure each specialised cell has only the genes it needs. For reasons which no creationist apologist has ever managed to explain, their putative designer always behaves as though it can't undo a bad design and start again but is compelled to try to make the best of what it has muddled through with so far. In every way, creationism’s 'intelligent [sic] designer' behaves just like a mindless process operating without a plan, handicapped by acute amnesia, and constantly surprising itself with a new problem it designed just yesterday.

Just like the eccentric British designer and cartoonist, William Heath Robinson, no solution to a problem can be too complex even if it creates a new problem for which another overly complex solution has to be found. Unlikely objects, designed for a completely different purpose, will be pressed into service; a stepladder will be balanced precariously on top of a piano and an umbrella will be used to push a button when prodded by a sink plunger swinging on a length of knotted string. A labour-saving device for peeling potatoes will take half a dozen, intense and serious-looking men to operate it and peeling the potatoes will take considerably longer than had each man been given a potato peeler and left to get on with it. Eggs will be fried in a frying pan held over a candle lit by a match rubbed against a matchbox which swings into action when released by a lever when the scuttle-full of coal, or the boulder suspended on knotted string, lands on it.

Saturday 9 March 2024

Creationism in Crisis - How Genomic Imprinting Evolved - Unintelligently


Revealing the evolutionary origin of genomic imprinting 
Caenorhabditis elegans

Genomic imprinting is the process by which genes are suppressed by epigenetic settings that differ depending on whether the genes come from the father or the mother in a sexually-reproducing species.

This is an example of the sort of Heath Robinson machine which a natural, mindless evolutionary process can and does produce and which distinguishes evolved systems from intelligently designed processes. It comes from the fact that multicellular organism uses the same method to replicate their cells as their single-celled ancestors used, yet only need a small selection of the genes depending on how specialised the particular cells are.

But the reason for genomic imprinting involves something even more embarrassing to any creationists who understand it - it probably evolved out of an arms race not between the organism and a foreign parasite but between the organism and one of its genes that had gone rogue and turned into a 'jumping' gene or 'selfish genetic element':
What exactly are 'selfish genetic elements' and what do they do? Selfish genetic elements are DNA sequences that have evolved to enhance their own transmission to the next generation, often at the expense of the organism's overall fitness. These elements can manipulate various cellular and reproductive processes to increase their own propagation within a population, sometimes even if it is detrimental to the host organism.

One well-known example of selfish genetic elements is transposable elements, also known as jumping genes. These DNA sequences have the ability to move or copy themselves within the genome, potentially disrupting genes or regulatory sequences in the process. While transposable elements can sometimes contribute to genetic variation and evolution, they can also cause harmful mutations or genomic instability.

Another example of selfish genetic elements is meiotic drive elements. These elements bias their own transmission during meiosis, the process by which gametes (sperm and eggs) are formed. Meiotic drive can result in the preferential transmission of one allele (variant of a gene) over another, leading to distortions in genetic inheritance patterns within a population.

Selfish genetic elements can have significant implications for evolutionary processes, population genetics, and genome stability. They can influence patterns of genetic diversity, contribute to speciation, and even drive the evolution of complex biological systems. However, they can also pose challenges for organisms by causing genetic disorders or reducing overall reproductive success.
In the case of the nematode, Caenorhabditis elegans, this arms race has produced a truly bizarre result, and something only an unintelligent, mindless designer, or a malevolent designer, could come up with, known as toxic ascaris, or TAs:
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