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AI is getting ready to take the baton from humans to take evolution further

AI is getting ready to take the baton from humans to take evolution further | Amazing Science | Scoop.it
 

Has The Final Merger of Humans and AI Begun? 

 

In late May, Elon Musk’s Neuralink, a company developing brain implants for digital connection, received FDA approval for its first human clinical trial. With this news, it’s clear that the next and ultimate step in how humans interact with media—human-computer hybridization—is rapidly approaching. This leaves us little time to fully contemplate the consequences of the current advancements. While techno-skeptics keep asserting that artificial intelligence cannot beat the uniqueness of humans, it’s not so clear anymore if human capability is a good fit to judge the performance of the newest media at all.

 

Media (all tools and technologies, from stone ax to television and the internet) used to be our extensions in the environment, as they allowed us to reach further in space and time than our own physical bodies were capable of. But when a medium is “neuralinked,” it literally brings the environment inside the brain. In other words, the mind gets directly extended into the boundless digital network. Instead of needing tools to access the digital network, we will live inside the network itself, and it will live in us.

 

ChatGPT is less than a year old, yet it has already stirred public concern with its potential to replace humans in a wide variety of tasks and jobs. Now, with the recent Neuralink news, it’s clear that the next and ultimate step in how humans interact with media—human-computer hybridization—is rapidly approaching. This leaves us little time to fully contemplate the consequences of the current advancements. While techno-skeptics keep asserting that AI cannot beat the uniqueness of humans, it’s not so clear anymore if human capability is a good fit to judge the performance of the newest media at all.

The Turing Test Becomes Obsolete

Judging a machine by its capacity to be indistinguishable from humans was in the core of the Turing test, devised in 1950 by British mathematician and computer scientist Alan Turing. We can call it a “human-confirmation” bias: We are ready to admit that an intelligent machine succeeds only if it communicates or acts as a human would do. The Turing test has become obsolete mere months after ChatGPT’s introduction: ChatGPT easily passed the test, and it didn’t even make big news. The Turing test is based on the idea that true AI should be indistinguishable from humans … to humans. But is the bar of human performance really that high for AI? Why would AI compete with humans, if the limits of human capabilities are restrained by nature and already known, while the capacities of AI have only just begun to be explored? AI starts where we humans have arrived, exhausting our capacity for evolution. After ChatGPT, it is not a challenge for AI to compete with humans. From now on, humans face an increasingly difficult challenge to compete with AI.

 

The first hunch that human performance might not be a suitable criterion to judge AI came from journalism. In 2014, Christer Clerwall, a Swedish professor of journalism, conducted a sort of Turing test, asking people to evaluate whether certain texts were written by humans or algorithms. Overall, this produced a tie, with the human text performing better on stylistic elements (it won the “well-written” and “pleasant to read” categories) and the robot text winning on more technical elements (it excelled in the “objectivity” and “accuracy” categories). The most significant finding was the conclusion Clerwall reached after comparing robot-written stories with human writing capabilities: He pondered, “Perhaps it doesn’t have to be better. How about a ‘good enough story’?” In 2016, Wordsmith, one of the two leading newswriting algorithms at that time, wrote 1.5 billion news stories, likely surpassing the number of all news stories written by all bio-journalists in this year. They were good enough for editors and readers.

When ‘Good Enough’ Isn’t Good Enough

We worry that AI can write and then think better than humans. But what does “better than humans” mean? Do humans, say, write better than humans? On that count, we are already losing—we’ve lost at least a writing contest so far, precisely because AI’s writing is “good enough” for what we need. But “good enough” is the criterion for humans, not for AI. This is what we should worry about: We and our media have different values of performance. For humans, the goal of each next media invention is to receive a product or service. For example, humans invented radio, received a new service that extend them in space and then spent some time to adjust to the new conditions that radio created. But for media, the goal is to continue the process of media innovation.

 

To comprehend this concept, we must consider the entire evolution of media. We and media have always had a symbiotic relationship. As media theorist Marshall McLuhan once put it, “Man becomes the sex organs of the machine world, as the bee of the plant world, enabling it to fecundate and to evolve ever new forms.” Media has supplied us with products and services, while we have provided for media’s perpetual development. This relationship has been beneficial for us humans, but this symbiosis may end soon. That’s because our “service-for-development” contract with media contains a clause that may turn into a trap.

 

We want a product from media, while media need the process from us. The product-oriented partner—humans—can generally be satisfied and is thus limited in their demand. But the process-oriented partner—media—will never be satisfied and will never stop. This can be called a “technological imperative”: Technologies have to evolve, and they will never achieve a “satisfactory” stage of development.

 

Our co-evolution with media is approaching the last product that media can give us: a copy of us. The Turing test was proof that humans in fact expected that a machine would eventually become as a human—to the point where it would be difficult to distinguish between the two. Indeed, that’s what happening: Today, technologies can replicate crucial human capacities, such as calculating, writing, even creating. Complex trading, navigation or logistic systems can now be entirely AI-driven and autonomous, replacing humans and organizations. However, is the simulation of humans the ultimate fulfillment of the “technological imperative”?

 

Is it enough for media evolution just to achieve the human level of performance? No: We can see that technologies can evolve much further then just simulating humans. Chess programs are not “satisfied” by defeating humans. They can keep evolving further, striving for perfection in chess without regard to the level at which humans play.

 

So what does the “technological imperative” ultimately lead to? What will be the final stage of media evolution? It is possible to trace the logic of media evolution farther than just simulating humans by machines. If media extend humans’ “mental or physical faculties” into the environment, as McLuhan defined it, then the ultimate medium will extend the user themselves into the entire environment. Imagine a human mind connected directly to AI—this is exactly what Musk’s Neuralink is working on. In such a hybrid, the user will merge with the environment through this ultimate medium—the mind “neuralinked” with the AI as a networked entity. This user, however, may or may not happen to be human. As AI is now trained to provide us with our various replicas and gradually learns to replace us, the ultimate user of the ultimate medium can be AI itself, without needing to wait for Neuralink’s success. Actually, AI has to become the self-user.

What Will the Singularity Mean for Humans?

 We created generative AI, and it started the preparation for this last stage, transferring formerly human capabilities into digital. Musk’s Neuralink and other projects developing the connection between the brain and digital environment look further—they aim at digitizing human consciousness. This path will lead to the Singularity, an event of nonhuman intelligence’s awakening. AI may not necessarily be a program or an app; in fact, AI should not be a program. The true AI will extend itself to the entire internet, similar to humankind extending itself from being just one of the species to populating and reshaping the entire planet. The Singularity will mark a switch of evolution from a biological to a technological carrier. The evolution of biological species will be wholly replaced by the quite instantaneous evolution of the supreme technological species—the AI extending itself to all available digital, and perhaps even physical, space. However fantastic these ideas may sound, they’re not as far off as you might think. When discussing the Singularity, technical plausibility should not be a concern at all. Technological evolution has enabled the effect of the acceleration of historical time: Each period of time accumulates increasingly more events and knowledge, adding on to each preceding period. This means that nearly all the necessary technological solutions will be found in the last moments leading up to the Singularity. Hence, there is no need to worry about our current lack of knowledge: AI will figure it out when the time comes, in a matter of seconds. We tend to believe that the ultimate medium—an AI expanding into the entire environment—needs agency, and that we humans are the best donors of self-consciousness for AI. This is the main purpose behind the projects connecting the brain with AI—to equip its power with human agency. But human donorship is not the only source of agency for the ultimate AI.

 

Another scenario involves the self-awakening of AI—similar to the awakening of Skynet, a military AI in the Terminator movies, which achieved self-awareness seconds after being granted full access and full capabilities. It extended itself to all computer networks, “farsightedly” connected by humans to all industrial facilities, and thus an override of power and the entire biological evolution happened. Despite being featured in a sci-fi movie, an AI like Skynet is highly logical and increasingly realistic.

 

In fact, a Musk-backed or Skynet-type agency may not be needed for AI to override humankind at all. Viewing AI as driven by its own self-consciousness might be akin to the anthropomorphism that ancient humans projected onto natural elements, transforming them into human-like deities. Technologies have their own moving force—the pursuit of better performance, which easily replaces the alleged need of AI for agency and self-consciousness. The example of a self-learning chess program gives a metaphor: Outperforming humans does not exhaust its potential of development. It can and must keep exploring chess further, moving toward the ideal performance—this is a side effect of the “technological imperative.”

Tanja Elbaz's curator insight, November 13, 2023 3:25 PM
 

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Did Flu Come from Fish? Genetics Points to Influenza’s Aquatic Origin

Did Flu Come from Fish? Genetics Points to Influenza’s Aquatic Origin | Amazing Science | Scoop.it

Corals, sturgeon and other aquatic creatures harbor signs of infection by influenza and its distant relatives. The influenza virus might actually have started in fish. Researchers trawling genetic databases have discovered a distant relative of influenza viruses — which are responsible for seasonal flu, not to mention the avian flu roiling the globe — in sturgeon [1]. The authors also found that the wider virus family that includes influenza probably originated hundreds of millions of years ago in primordial aquatic animals that evolved well before the first fish. Viruses in this group seem to be especially adept at jumping between hosts, says Mary Petrone, a virologist at the University of Sydney, Australia, who co-authored the preprint describing the findings. Knowing about ancient host jumps could help scientists identify viruses with the potential to spark new human epidemics. The study was posted on 16 Feburary 2023 to the preprint server bioRxiv and has not yet been peer reviewed.

Influenza’s origins story

Like many virologists, Petrone spent the first couple years of the pandemic intensively studying SARS-CoV-2. But when she moved to Australia to do postdoctoral research, Petrone wanted to steer clear of human infections and spend time in one of the country’s most famous ecosystems. “After working on COVID for two years, I thought going to coral reefs to do fieldwork sounded really good,” she says. Corals are part of a phylum called Cnidaria, whose ancestors branched off from other animals around 600 million years ago. Petrone hoped that studying corals could reveal the deeper history of viruses that infect animals — particularly those with RNA genomes. This viral group includes numerous human and animal pathogens. Petrone’s first call was not to a diving shop but to Zoe Richards, a coral-reef researcher at Curtin University in Bentley, Australia, who provided samples of two coral species collected off the coast of Western Australia. Analysis of RNA collected from the corals found evidence of infection with viruses that belong to a grouping called Articulavirales, which includes influenza’s family of viruses and a group called Quaranjaviruses. The latter group’s members circulate in ticks and occasionally spill over into humans, birds and other vertebrates. The new analysis suggests that coral-infecting viruses are part of an ancient viral family that probably emerged around 600 million years ago, and later gave rise to other members of Articulavirales, including influenza and Quaranjaviruses.

Secrets of the hagfish

The discovery got Petrone wondering whether influenza viruses might also have been born at sea. There was already some evidence for this. In 2018, researchers identified a distant relative of influenza in hagfish [2]. These slimy, jawless creatures descended from an early lineage of vertebrates, and the study’s authors hinted that influenza evolved alongside vertebrates. Searching genetic databases, Petrone found influenza-related RNA sequences in samples from Siberian sturgeon (Acipenser baerii). Sturgeon are jawed vertebrates, more closely related to humans than hagfish are. But the sturgeon virus had branched off from the main influenza family tree before any other known influenza virus, including the hagfish virus. The discovery of the two early lineages of influenza suggest that influenza probably infected aquatic animals, including fish, before moving onto land, says Petrone. But it’s not clear whether influenza moved onto land with early terrestrial vertebrates, or jumped from sea to land more recently.

To determine this, researchers will need to look for relatives of influenza in more animals and gain a better understand how the virus spreads between host species, researchers say.

Born at sea

Jie Cui, an evolutionary virologist at the Pasteur Institute of Shanghai in China, agrees that influenza and its wider family probably emerged from the sea. In 2021, his team analysed deep-sea lobster genomes and identified viruses that are part of influenza’s wider group [3]. “There is great untapped viral diversity in aquatic environments,” he says. Robert Gifford, an evolutionary virologist at the University of Glasgow, UK, says it would be surprising to find a major group of viruses that didn’t arise in aquatic environments because of the ancient nature of marine life. “The study provides compelling evidence that influenza viruses have an aquatic origin.” Identifying ancient host jumps could also help researchers gauge the risk that certain viruses pose to humans, researchers say. Petrone’s team found signs that Quaranjaviruses that infect ticks might have jumped to the creatures after first circulating in crustaceans. Uncovering such jumps shows that the study of aquatic viruses “can help us to better understand the historic emergence and evolution of viruses with zoonotic potential”, adds Chantal Vogels, an arbovirologist at the Yale School of Public Health in New Haven, Connecticut. Gifford agrees that studies such as Petrone’s could help to identify viruses that have the capacity to spark epidemics in humans and other animals. But he cautions that conclusions about ancient host jumps can change as more of the viral family tree gets filled in, reshuffling relationships.

 

Cited research available in bioRxiv (Feb. 16, 2023):

https://doi.org/10.1101/2023.02.15.528772


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Synthetic yeast chromosomes help probe mysteries of evolution

Synthetic yeast chromosomes help probe mysteries of evolution | Amazing Science | Scoop.it

Evolutionary biologist Stephen Jay Gould once pondered what would happen if the cassette “tape of life” were rewound and played again. Synthetic biologists have tested one aspect of this notion by engineering chromosomes from scratch, sticking them into yeast and seeing whether the modified organisms can still function normally.

 

They do, according to seven papers published today in Science that describe the creation, testing and refining of five redesigned yeast chromosomes1–7. Together with a sixth previously synthesized chromosome8, they represent more than one-third of the genome of the baker’s yeastSaccharomyces cerevisiae. An international consortium of more than 200 researchers that created the chromosomes expects to complete a fully synthetic yeast genome by the end of the year.

 

The work the team has already done could help to optimize the creation of microbes to pump out alcohol, drugs, fragrances and fuel. And it serves as a guide for future research on how genomes evolve and function.

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Evolution of new species requires only a few genetic changes

Evolution of new species requires only a few genetic changes | Amazing Science | Scoop.it

Only a few genetic changes are needed to spur the evolution of new species—even if the original populations are still in contact and exchanging genes. Once started, however, evolutionary divergence evolves rapidly, ultimately leading to fully genetically isolated species, report scientists from the University of Chicago in the Oct 31 Cell Reports.

 

"Speciation is one of the most fundamental evolutionary processes, but there are still aspects that we do not fully understand, such as how the genome changes as one species splits into two," said Marcus Kronforst, Ph.D., Neubauer Family assistant professor of ecology and evolution, and lead author of the study.

 

To reveal genetic differences critical for speciation, Kronforst and his team analyzed the genomes of two closely related butterfly species, Heliconius cydno and H. pachinus, which only recently diverged. Occupying similar ecological habitats and able to interbreed, these butterfly species still undergo a small amount of genetic exchange.

 

The researchers found that this regular gene flow mutes genetic variants unimportant to speciation—allowing them to identify key genetic areas affected by natural selection. The butterfly species, they discovered, differed in only 12 small regions of their genomes, while remaining mostly identical throughout the rest. Eight of these coded for wing color patterning, a trait important for mating and avoiding predation, and under intense selection pressure, while the other four remain undescribed.

 

"These 12 spots appear to only function well in the environment their species occupies, and so are prevented from moving between gene pools, even though other parts of the genomes are swapped back and forth," Kronforst said.

 

The team also compared the genomes of these two groups to a third species, still closely related but further removed on an evolutionary time scale. Here, they found hundreds of genomic changes, indicating that the rate of genetic divergence accelerated rapidly after the initial changes took hold.

 

"Our work suggests that a few advantageous mutations are enough to cause a 'tug-of-war' between natural selection and gene flow, which can lead to rapidly diverging genomes," Kronforst said.

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For Early Primates, a Night Was Filled With Color

For Early Primates, a Night Was Filled With Color | Amazing Science | Scoop.it
A genetic examination of tarsiers indicates that the saucer-eyed primates developed three-color vision when they were still nocturnal.

 

A new study suggests that primates’ ability to see in three colors may not have evolved as a result of daytime living, as has long been thought. The findings, published in the journalProceedings of the Royal Society B, are based on a genetic examination oftarsiers, the nocturnal, saucer-eyed primates that long ago branched off from monkeys, apes and humans.

 

By analyzing the genes that encodephotopigments in the eyes of modern tarsiers, the researchers concluded that the last ancestor that all tarsiers had in common had highly acute three-color vision, much like that of modern-day primates.

 

Such vision would normally indicate a daytime lifestyle. But fossils show that the tarsier ancestor was also nocturnal, strongly suggesting that the ability to see in three colors somehow predated the shift to daytime living.

The coexistence of the two normally incompatible traits suggests that primates were able to function during twilight or bright moonlight for a time before making the transition to a fully diurnal existence.

 

“Today there is no mammal we know of that has trichromatic vision that lives during night,” said an author of the study, Nathaniel J. Dominy, associate professor of anthropology at Dartmouth. “And if there’s a pattern that exists today, the safest thing to do is assume the same pattern existed in the past.

 

“We think that tarsiers may have been active under relatively bright light conditions at dark times of the day,” he added. “Very bright moonlight is bright enough for your cones to operate.”

QMP's curator insight, April 19, 2013 5:50 PM

This is a great article about how the night time helped early primates to evolve the colored vision that we experience today.

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Evolution is actually pretty predictable

Evolution is actually pretty predictable | Amazing Science | Scoop.it

A study of insects, including the large milkweed bug (above), suggests evolution may be driven by a simple and repeated genetic solution to an environmental pressure that a broad range of species happen to share.

 

New research by Andolfatto and colleagues published in the journal Science suggests that knowledge of a species’ genes—and how certain external conditions affect the proteins encoded by those genes—could be used to determine a predictable evolutionary pattern driven by outside factors.


Scientists could then pinpoint how the diversity of adaptations seen in the natural world developed even in distantly related animals. The researchers carried out a survey of DNA sequences from 29 distantly related insect species, the largest sample of organisms yet examined for a single evolutionary trait. Fourteen of these species have evolved a nearly identical characteristic due to one external influence—they feed on plants that produce cardenolides, a class of steroid-like cardiotoxins that are a natural defense for plants such as milkweed and dogbane.

 

Many different insects independently evolved the same molecular tricks to defend themselves against the same toxin suggests that studying a small number of well-chosen model organisms can teach us a lot about other species. Yes, evolution is predictable to a certain degree.

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Tracing the genetic pathway from the first Eukaryotes to Homo sapiens

Tracing the genetic pathway from the first Eukaryotes to Homo sapiens | Amazing Science | Scoop.it

www.dhushara.com/book/unraveltree/unravel.htm

 

The Tree of Life, in biological terms, has come to be identified with the evolutionary tree of biological diversity. It is this tree which represents the climax fruitfulness of the biosphere and the genetic foundation of our existence, embracing not just higher Eukaryotes, plants, animals and fungi, but Protista, Eubacteria, and Archaea, the realm, including the extreme heat and salt-loving organisms, which appears to lie almost at the root of life itself.

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Geologic and Biological Timeline of the Earth

Geologic and Biological Timeline of the Earth | Amazing Science | Scoop.it
Biological and Geologic Timeline of the Earth. The origin of the Earth and the Moon. The evolution of life on Earth.
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14 extinct animals that could be resurrected

14 extinct animals that could be resurrected | Amazing Science | Scoop.it
Can lost species ever become un-extinct? In the 1993 science fiction film "Jurassic Park," dinosaurs are cloned back to life after their DNA is discovered still intact within the bellies of ancient mosquitoes that were preserved in amber. While the science of cloning is still in its infancy, many scientists now believe it's only a matter of time before many extinct animals again walk the Earth.

 


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Giant Stick Insect Believed Extinct Finds Secret Hideaway, Hides for 80 Years

Giant Stick Insect Believed Extinct Finds Secret Hideaway, Hides for 80 Years | Amazing Science | Scoop.it

The insect is so large — as big as a human hand — it's been dubbed a "tree lobster." It was thought to be extinct, but some enterprising entomologists scoured a barren hunk of rock in the middle of the ocean and found surviving Lord Howe Island, Australia.

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The Adaptive Immunity of Human Endemic Viruses

The Adaptive Immunity of Human Endemic Viruses | Amazing Science | Scoop.it

In a recent study posted to the bioRxiv* preprint server, researchers analyzed the viral genomes of 28 endemic viruses to study the evolution of the ability of viruses to evade the neutralizing antibodies elicited by vaccines or previous infections.

Background

Viruses evolve rapidly and adapt to changing environments due to their high mutation rates and low generation time. Often viruses adapted to different animal hosts infect humans and optimize the methods through which they enter and replicate in the host cell, increasing the human-to-human transmission and evolving into a novel pathogen. The early stages of pandemics are often characterized by high adaptive evolutionary rates, as was seen during the coronavirus disease 2019 (COVID-19) pandemic and outbreaks related to various other respiratory viruses. While some viruses become endemic after adapting to a new host and do not evolve further, other endemic viruses continue to adapt through antigenic evolution, resulting in an arms race between the virus and the human immune system. Since viruses that undergo antigenic evolution pose the risk of repeat infections and increase their ability to evade vaccine-induced immunity, understanding which viruses continue to undergo antigen evolution could help manage future disease outbreaks.

About the study

The present study used sequence data for each gene in 28 viral genomes to estimate adaptive evolutionary rates. These 28 viruses spanned ten families and were transmitted between humans through various modes. Viruses with potentially high antigenic evolution rates were identified based on the high evolutionary rates for the genes coding for receptor-binding proteins since the receptor-binding region is involved in antibody neutralization and harbors most mutations that allow antigenic escape. The adaptive evolutionary rates were calculated in terms of the number of adaptive mutations in each codon per year, which allowed the adaptive evolutionary rates to be compared across the various genes in the genome and across viruses. The adaptive evolutionary rates of three viruses that were known to undergo antigenic evolution — coronavirus 229E, influenza viruses A/H3N2, and influenza viruses B/Yam — were compared against the evolutionary rates of three antigenically stable viruses, hepatitis A, measles, and influenza C/Yamagata. To understand the patterns of adaptive evolution in recent years, the sequence data for 28 viruses that are pathogenic to humans were obtained and curated. These viruses included deoxyribonucleic acid (DNA) and ribonucleic acid (RNA) viruses and were transmitted between humans through bodily fluids, blood, vectors, fecal-oral, and respiratory routes. The researchers only investigated endemic viruses since they were interested in understanding the antigenic evolution that occurs during the endemic phase and not the initial adaptive phase. The evolutionary rates of the receptor binding protein, which was expected to be highly variable across endemic viruses, and the polymerase gene, which was expected to be conserved, were compared across the 28 viruses. Since the evolution of severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) has been relatively recent, and the Omicron variant carried a large number of mutations indicating a single fixation event, SARS-CoV-2 was compared with ten other antigenically evolving viruses by comparing the amino-acid substitution rates in the receptor binding protein.

Results

The results reported that 10 of the 28 viruses undergo adaptive evolution resulting in the antigenic mutations that allow the viruses to escape the immunity induced by previous infections and vaccines. Furthermore, comparing amino-acid substitution rates between SARS-CoV-2 and other viruses revealed that SARS-CoV-2 is evolving and accumulating mutations that cause protein-coding changes at rates much higher than other endemic viruses. Antigenic evolution was found to be more prevalent in RNA viruses. Still, the researchers believe that since the list of viruses included in the study was not comprehensive and comprised only well-studied viruses, determining the proportion of antigenically evolving endemic viruses is difficult. Furthermore, the rate of adaptive mutations might not reflect the phenotypic changes occurring in the viruses, implying that viruses with receptor-binding protein genes that evolve at the same rates might not develop the ability to evade vaccine or infection-induced immunity at the same rates.

Conclusions

Overall, the findings suggested that many human viruses that have become endemic continue to evolve antigenically, gaining the ability to escape the neutralizing antibodies generated by vaccinations or previous infections. Ten of the 28 viruses investigated in this study showed continued adaptive evolution. In contrast, the amino-acid substitution rates showed that SARS-CoV-2 is evolving faster than the other ten endemic human viruses.

 

Cited ressearch available in bioRxiv (May 22, 2023):

 https://doi.org/10.1101/2023.05.19.541367 


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Tanja Elbaz's curator insight, November 13, 2023 3:44 PM
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Giant Viruses Evolved from Small Ones by Gene Duplications

Giant Viruses Evolved from Small Ones by Gene Duplications | Amazing Science | Scoop.it

A study employing CRISPR/Cas9 to explore the evolutionary beginnings of some giant viruses finds evidence that their large genomes arose from gene duplications.  Most viruses are small and carry minimal genomes. Even one of the largest small viruses, Vaccinia, measures merely one-fiftieth the size of a pollen grain and contains only 270 genes.

 

Giant viruses flout these rules. With sizes that rival small bacteria and genomes that contain thousands of genes, their complexity emulates that of cellular life. How these viruses came to be so large has been the subject of much debate. Now, scientists are finally poised to unravel the mystery of their evolutionary origins, thanks to a suite of CRISPR/Cas9-based tools described in a Nature Communications paper from January.

 

“It was by chance that we encountered the first giant virus,” says Chantal Abergel, a virologist at Aix-Marseille University in France. “It was Mimivirus, and it was actually mistaken for a bacterium.” In the 20 years since that discovery, virologists have prioritized exploring the diversity of giant viruses. Now that they’ve found a fair few, the focus has shifted towards studying their evolution in more detail with molecular biology techniques.

 

Evolutionary biologists have grappled over two possible origins of giant viruses. One possibility is that they were once cellular organisms that shrunk physically and genetically over time. But most virologists now suspect giant viruses grew out of much smaller ones—though the evidence supporting either hypothesis is scant.

 

To begin addressing this origin question, Abergel decided to examine how the essential genes in the Pandoravirus genome are distributed. In cellular organisms, essential genes are scattered throughout the genome—so if giant viruses are essentially reduced cells, one would expect a similar pattern. Alternatively, if the genes are clumped, that could indicate the viruses’ large genomes started out in a more compact form. One way to locate a virus’s essential genes is to knock out genes one at a time to find the ones that are needed for virus production. But to do that with a giant virus, Abergel needed a gene-editing system that worked in members of the group. With the help of Hugo Bisio, a postdoctoral researcher in Abergel’s lab, and colleagues at Aix–Marseille University, Abergel used a CRISPR/Cas9-based gene-editing system to modify the genome of the amoeba Acanthamoeba castellanii and the giant virus Pandoravirus neocaledonia, which infects it.

 

The CRISPR/Cas9 system was designed to delete specific genes and consists of two guide RNAs and a Cas9 scission enzyme. Similar to other CRISPR/Cas9 systems, each guide RNA contains 17 to 20 bases designed to bind to one specific location on the genome of the giant virus or the amoeba, allowing the Cas9 scission enzyme to cut the genome at that site. The amoeba A. castellanii contains 25 copies of each chromosome, making it difficult to design an efficient CRISPR/Cas9 system that could delete each gene copy. To overcome this issue, the researchers modified their CRISPR/Cas9 system to generate a chain reaction. Each time DNA was cut to remove a gene, a DNA segment encoding the Cas9 enzyme and the guide RNAs responsible for the cut would take the place of the missing gene in the genome. This allowed gene deletions to repeat and propagate until all copies were removed.

 

Once they optimized their CRISPR/Cas9 system, the team deleted each gene separately from the Pandoravirus genome and measured the resulting change in virus production, in order to determine how important each gene is to the virus’s lifecycle. They found that essential genes clustered together at one end of the genome and were segregated from nonessential genes at the other end. This level of gene orderliness has not been seen in viruses, according to Bisio. Even bacterial genomes aren’t quite so tidy: While they do group genes with linked functions together into gene clusters known as operons, these tend to be dispersed throughout the genome rather than grouped all together in one spot. Bisio says the cluster of essential genes may echo a smaller “core genome” of an ancient virus. This genome could have become elongated through multiple rounds of gene duplication that were biased in one direction to produce an additional set of spare nonessential genes. This could explain how modern-day giant viruses came to possess thousands of genes. “Our data indicate that complex viruses arose from smaller and simpler ones,” Bisio tells The Scientist in an email—noting that it will take further research to determine whether that’s true of all giant viruses or just Pandoravirus. Other studies found that some genes in giant viruses were usurped from their amoeba hosts, suggesting gene exchange is another way giant viruses increased in size. The team then set their sights on one of the many evolutionary mysteries of Pandoravirus: its lack of a capsid. Small viruses package their genomes into capsids made of viral proteins. While some giant viruses, such as Mimiviruscontinue this tradition, others, including Pandoravirusdo not. If giant viruses did indeed evolve from smaller ones, there could be traces of capsid proteins hiding in their genomes. So, the researchers set out to study the function of potential capsid protein remnants in a close cousin of Pandoravirus, the smaller Mollivirus, which can also infect A. castellanii.

 

Researchers have suspected that a Mollivirus protein called ml_347 evolved from a capsid gene based on its gene’s sequence and predicted 3D shape. So, the team investigated its function by deleting the gene using their CRISPR/Cas9 system. They found that the gene is important for Mollivirus assembly, which the authors say is intriguing given its possible capsid ancestry. It’s possible that, as capsids were lost in giant virus evolution, obsolete capsid genes were adapted for new assembly functions. Frederik Schulz, an evolutionary biologist with the DOE Joint Genome Institute in California who wasn’t involved with the study but who has worked with Chantal Abergel in the past, tells The Scientist that the findings align with recent discoveries. “There was a debate for a long time [about] how giant virus[es] evolved,” he says. “The working hypothesis in the previous years was that they evolved from smaller viruses, and that’s exactly what Chantal and her team could show and confirm using their CRISPR/Cas9 gene-editing approach.” Schulz notes that it will be exciting to see the CRISPR/Cas9 technology introduced into other host species, such as algae, which would allow researchers to expand research into a greater variety of giant viruses. He also points out that the system only works for viruses that replicate in a host cell’s nucleus, while most giant viruses replicate in cytoplasmic structures called viral factories, which the Cas9 enzyme and guide RNAs can’t penetrate. Still, Bisio says there’s much left to discover in Pandoravirus. “[This CRISPR/Cas9 technology is] a goldmine to find new functions,” he says—one that he and his colleagues are eager to employ to tease apart what all the virus’s genes do. 

 

Cited research published in Nat. Comm. (Jan. 26, 2023):

https://doi.org/10.1038/s41467-023-36145-4 


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UK scientists seek permission to genetically modify human embryos with CRISPR-CAS

UK scientists seek permission to genetically modify human embryos with CRISPR-CAS | Amazing Science | Scoop.it

Researchers apply for licence months after Chinese team become first to announce they have altered DNA.  Scientists in Britain have applied for permission to genetically modify human embryos as part of a research project into the earliest stages of human development.


The work marks a controversial first for the UK and comes only months after Chinese researchers became the only team in the world to announce they had altered the DNA of human embryos. Kathy Niakan, a stem cell scientist at the Francis Crick Institute in London, has asked the government’s fertility regulator for a licence to perform so-called genome editing on human embryos. The research could see the first genetically modified embryos in Britain created within months.


Donated by couples with a surplus after IVF treatment, the embryos would be used for basic research only. They cannot legally be studied for more than two weeks or implanted into women to achieve a pregnancy.


Though the modified embryos will never become children, the move will concern some who have called for a global moratorium on the genetic manipulation of embryos, even for research purposes. They fear a public backlash could derail less controversial uses of genome editing, which could lead to radical new treatments for disease.


Niakan wants to use the procedure to find genes at play in the first few days of human fertilization, when an embryo develops a coating of cells that later form the placenta. The basic research could help scientists understand why some women lose their babies before term.


The Human Fertilisation and Embryology Authority (HFEA) has yet to review her application, but is expected to grant a licence under existing laws that permit experiments on embryos provided they are destroyed within 14 days. In Britain, research on embryos can only go ahead under a licence from an HFEA panel that deems the experiments to be justified.

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Amazing Science: Evolution Postings

Amazing Science: Evolution Postings | Amazing Science | Scoop.it

Evolution is the change in the inherited characteristics of biological populations over successive generations. Evolutionary processes give rise to diversity at every level of biological organisation, including species, individual organisms and molecules such as DNA and proteins.All life on Earth is descended from a last universal ancestor that lived approximately 3.8 billion years ago. Repeated speciation and the divergence of life can be inferred from shared sets of biochemical and morphological traits, or by shared DNA sequences.

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Irreversible Evolution? Dust Mites Show Parasites Can Violate Dollo’s Law

Irreversible Evolution? Dust Mites Show Parasites Can Violate Dollo’s Law | Amazing Science | Scoop.it

Our world is quite literally lousy with parasites. We are hosts to hundreds of them, and they are so common that in some ecosystems, the total mass of them can outweigh top predators by 20 fold. Even parasites have parasites. It’s such a good strategy that over 40% of all known species are parasitic. They steal genes from their hosts, take over other animals’ bodies, and generally screw with their hosts’ heads. But there’s one thing that we believed they couldn’t do: stop being parasites. Once the genetic machinery set the lifestyle choice in motion, there’s supposed to be no going back to living freely. Once a parasite, always a parasite - unless you’re a mite.

 

In evolutionary biology, the notion of irreversibility is known as Dollo’s Law after the Belgian paleontologist that first hypothesized it in 1893. He stated that once a lineage had lost or modified organs or structures, that they couldn’t turn back the clock and un-evolve those changes. Or, as he put it, “an organism is unable to return, even partially, to a previous stage already realized in the ranks of its ancestors.”

 

While some animals seem to challenge Dollo’s Law, it has long been a deeply held belief in the field of parasitology. Parasitism is, in general, a process of reduction. Adjusting to survival on or in another animal is a severe evolutionary undertaking, and many parasites lose entire organs or even body systems, becoming entirely dependent on their hosts to perform biological tasks like breaking down food or locomotion. Parasitology textbooks often talk about the irreversibility of becoming a parasite in very finite terms. “Parasites as a whole are worthy examples of the inexorable march of evolution into blind alleys” says Noble & Noble’s 1976 Parasitology: the Biology of Animal Parasites.

 

Robert Poulin is even more direct: “Once they are dependent on the host there is no going back. In other words, early specialisation for a parasitic life commits a lineage forever.” Now, parasites are proving that not only can they evade immune systems, trick other animals, and use their hosts’ bodies in hundreds of nefarious ways, some can go back to living on their own. This is exactly what scientists now believed happened in the Pyroglyphidae — the dust mites.

 

Mites, as a whole, are a frighteningly successful but often overlooked group of organisms. More than 48,000 species have been described. These minuscule relatives of spiders can be found worldwide in just about every habitat you can imagine. Many are free-living, but there are also a number of parasitic species, including all-too-familiar pests like Sarcoptes scabiei, the mite which causes scabies. Exactly how the different groups of mites are related to each other, however, has been a hot topic of debate amongst mite biologists. Though the closest relatives of dust mites are the Psoroptidia, a large and diverse parasitic group of mites, many have argued that dust mites came from free-living ancestors — ‘living fossils’ of a sort, the only surviving line of ancestral free-living mites that later gave rise to parasites. In fact, Pavel Klimov and Barry O’Connor from the University of Michigan were able to find 62 different hypothesis as to how the free-living the dust mites fit into the mite family tree. Sixty-two, the team decided, was simply too many. So, they turned to the mites’ genes.

 

To test which of the hypotheses had the most merit, Klimov and O’Conner conscripted a team of 64 biologists in 19 countries to obtain over 700 mite specimens, which they then used to construct a mite family tree. They sequenced five nuclear genes from each species, then applied statistical analyses to construct a tree of relationships called a phylogeny. And that’s when they saw it: deeply nested inside a large group of parasites were our everyday, non-parasitic, allergy-causing dust mites.

 

“This result was so surprising that we decided to contact our colleagues to obtain their feedback prior to sending these data for publication,” said lead author Pavel Klimov. “Parasites can quickly evolve highly sophisticated mechanisms for host exploitation and can lose their ability to function away from the host body,” he explained. “Many researchers in the field perceive such specialization as evolutionarily irreversible.” But, their data were clear. “All our analyses conclusively demonstrated that house dust mites have abandoned a parasitic lifestyle, secondarily becoming free-living.”

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New Species Of Flowering Plant Evolved During Last 150 Years In Scotland

New Species Of Flowering Plant Evolved During Last 150 Years In Scotland | Amazing Science | Scoop.it

Biologist Dr Mario Vallejo-Marín from the University of Stirling has found a new species of monkey flower, created by the union of two foreign plant species, on the bank of a stream in Scotland. during the last 150 years. Thousands of wild species and some crops are thought to have originated in this way, yet only a handful of examples exist where this type of species formation has occurred in recent history.

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EMBO 2012 - International workshop on Evolution in the Time of Genomics

Molecular evolution was born fifty years before the planned Conference, with a seminal paper by Zuckerkandl and Pauling (1962) which demonstrated that aminoacid changes in the globins followed a molecular clock and could provide information on the phylogeny of vertebrates and on the timing of their appearance on earth.

Principal themes and objectives of the event From changes in aminoacids to changes in nucleotides, the molecular level has provided an essential input into evolutionary investigations for the past decades. More recently, the molecular level has moved from the genes to the genome, so far mainly in the case of vertebrates (in which the coding sequences only represent about 2% of the total). The availability of full genome sequences has provided new possibilities for investigators in the field and major problems can now be tackled in a very precise way using bioinformatic tools. Indeed, an example of this approach has been the recent solution (Bernardi, 2007)of a twenty-year-old debate, that between neutralists and selectionists.


One of the major current debates concerns adaptive vs. non-adaptive evolution. Random events in evolution were originally raised as a fundamental problem by Jacques Monod in his famous book "Chance and necessity". The problem has now been shifted to the genome level. A preliminary discussion took place in October 2010 in a Meeting "Chance and Necessity in Evolution" (Ravello, Italy; papers are in press in a special issue of Genome Biology and Evolution). The proposed meeting should go deeper into such a basic issue. While this will be one of the main subject of the meeting in which different views will confront each other (with Bernardi, Jarosz, Koonin, Ohta, Ptashne), other basic topics in Genome Evolution will be addressed. Werner Arber, Hamilton Smith (two Nobel Laureates) and George Church will discuss in depth the results obtained so far "directing" evolution in microbial systems, their interpretation and even the ethical issues raised. Davidson, Gehring and Gojobori will deal with the evolution of developmental processes; Martin, Saccone and Wallace with the evolution of mitochondrial genomes; Okada and Shapiro with the impact of mobile elements on genome evolution; Jeffreys and Saitou with recombination and biased gene conversion; Bustamante, Felsenfeld, Hartl and Haussler with regulation of gene expression and copy number variation in the human genome. Last but not least, Emile Zuckerkandl will recollect the beginning of Molecular Evolution.

 

http://events.embo.org/12-evolution/

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Mini mammoth once roamed Crete

Mini mammoth once roamed Crete | Amazing Science | Scoop.it
Evolution crafted pint-sized pachyderm on Mediterranean island.

 

VIDEO: http://www.youtube.com/watch?v=JCRbJZaOTUc&feature=colike


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Modular gene networks as agents of evolutionary novelty

Modular gene networks as agents of evolutionary novelty | Amazing Science | Scoop.it

How to create multicellular organisms

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Frozen Mummy’s Genetic Blueprints Unveiled

Frozen Mummy’s Genetic Blueprints Unveiled | Amazing Science | Scoop.it

By peering deeply into the DNA of the mummy known as Ötzi, geneticists have expanded the rap sheet on the 5,300-year-old Iceman: He had brown eyes, brown hair and blood type O, was lactose intolerant and his modern-day relatives live on Corsica and Sardinia.


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