https://phys.org/news/2023-09-scientists-uncover-ways-bacteria-antibiotic-resistant.html

"Plasmids, found in bacteria and some other microorganisms, are physically separate from chromosomal DNA and can replicate on their own. Bacteria can acquire plasmids from other bacterial cells or from viruses, and as plasmids build up, they give bacteria antibiotic resistance.

"But some plasmids are easier for bacteria to acquire than others. What makes these plasmids spread more easily?

"While common sense might suggest that plasmids that spread the easiest are the ones that allow bacteria to grow the fastest, a new study in Nature Communications, led by Allison Lopatkin, an assistant professor of chemical engineering at the University of Rochester, outlines the surprising evolutionary tradeoff between lag time and growth rate.

***

"Lopatkin and her team studied the growth rates of single colonies of bacteria immediately following plasmid acquisition. Across nearly 60 conditions covering diverse plasmids, selection environments, and clinical strains, they found that intermediate-cost plasmids outcompete both their low and high-cost counterparts.

"The research shows plasmid costs are more complex than previously believed and is a step toward better understanding why certain types of pathogens are better at acquiring plasmids than others. If scientists can understand what controls the costs of acquiring a plasmid, they can potentially use that information to limit the spread of antibiotic-resistant genes.

"'We see horizontal gene transfer as an engineering tool to control how genes can spread and help bacterial communities interact," says Lopatkin. "By understanding the individual parts, we hope not only to be able to fight things like antibiotic resistance, but also to use plasmids to deliver genes that can help natural bacteria degrade oil from oil spills. There are many applications microbiomes can be useful for.'"

Comment: more evidence that at the single-cell-level, a bacterium is the most complicated form of a cell. The original animal at the start of life and through all of evolution an integral part of all developments. Now performing as useful microbiomes. They can extensively edit their own DNA. Other single cells as part of multicellular organisms have specific consigned duties to perform, actively manufacturing proteins and other molecules or monitoring levels of oxygen in the hypothalamus or sodium in the kidney. They do not edit their own DNA.

https://www.sciencemagazinedigital.org/sciencemagazine/library/item/30_june_2023/411231...

"While studying the evolutionary origin of a selfish element in the nematode Caenorhabditis briggsae, we discovered that Mavericks, ancient virus-like transposons related to giant viruses and virophages, are one of the long-sought vectors of horizontal gene transfer. We found that Mavericks gained a novel herpesvirus-like fusogen in nematodes, leading to the widespread exchange of cargo genes between extremely divergent species, bypassing sexual and genetic barriers spanning hundreds of millions of years. Our results show how the union between viruses and transposons causes horizontal gene transfer and ultimately genetic incompatibilities in natural populations.

***

"...transfer of genes between eukaryotes is thought to be rare, especially in metazoans, because it requires a chain of unlikely events: DNA must find its way out of the donor species, come in close contact with the germline of a second species, and finally integrate itself in the genome of the new host. Nonetheless, from antiparasitic toxins in butterflies to antifreeze proteins in fish, a growing body of evidence indicates that HGT between eukaryotes is far more common than was previously thought and could be an important evolutionary force.

***

"Here, by studying the evolutionary origin of a selfish toxin-antidote (TA) element in the nematode Caenorhabditis briggsae, we found that Mavericks, ancient eukaryotic viruslike transposons, are widespread vectors of HGT between nematodes. Further, we showhowHGT fueled the evolution of genetic incompatibilities in natural populations.

***

"Overall, our results indicate that two novel nematode protein families, WOSP proteases and KRMA kinases, are preferentially associated with Mavericks. These genes likely correspond to cargo sequences that were originally “captured” by Mavericks from nematode genomes during transposition and, as a result, broadly exchanged between species that have been reproductively isolated for tens or even hundreds of millions of years. In support of this view, we found that the GC content of wosp and krma genes largely matched that of host genes but differed significantly from that of Maverick core genes.

***

"In this study, we provide evidence for widespread Maverick-mediated horizontal gene transfer across extremely divergent nematode species that drove the evolution of a novelMULE-associated selfish TA element. The TA found in C. briggsae is capable of both spreading in nature by poisoning individuals homozygous for the susceptible allele and changing its position in the genome through transposition.

***

"We show in unprecedented detail how cooperation between parasitic genetic elements can lead to the evolution of new biological function and ultimately affect gene flow between populations. However, several intriguing aspects of the TA evolution are still unknown. For instance, it is not clear whether msft-1 became a toxin before or after its capture by the MULE transposon and if msft-1 has nonselfish roles that could also have contributed to the evolution of the TA.

"Our work reveals Mavericks as one of the long sought-after vectors of HGT. Because of their unique biology, which shares features of both transposons and viruses, Mavericks are responsible for the widespread transfer of genes across extremely divergent species...We hypothesize that Mavericks, like E. coli λ phage and human herpesvirus, integrate into the genome of their host and passively replicate until an environmental factor triggers the formation of infective particles (Fig. 6B). In support of this model, maviruses, virophages evolutionary related to Mavericks, are not constitutively expressed when integrated in protozoan genomes, but they are specifically transcribed after superinfection by the giant virus CrV."

Comment: wow!!! viruses and transposon-like viruses acting like bandits in the night, attacking genomes indiscriminately. A hidden mechanism for evolution?

https://phys.org/news/2023-06-complexity-barrier-horizontal-gene.html

"This process is a major contributor to microbial evolution, accounting for 10–20% of the protein-coding genes in most bacterial genomes, while HGT is less prevalent among eukaryotes. Through HGT, bacteria and archaea can acquire new traits, ranging from antibiotic resistance to metabolic capabilities, which enhances their ability to adapt to changing environments.

"In a new study from Genome Biology and Evolution titled "Empirical evidence that complexity limits horizontal gene transfer," researchers from the University of North Carolina, led by Christina Burch and Corbin Jones, investigated the factors that influence the ability of individual genes to be transferred into a new recipient bacterial strain via HGT.

"Their study reveals that a gene's transferability is affected by several factors, including its sequence divergence from the recipient and how many interaction partners the resulting protein has (i.e., its connectivity). Moreover, a gene's divergence and connectivity interact to further influence its transferability.

"While previous studies have observed a relationship between gene transferability and protein connectivity, scientists have puzzled over the mechanism underlying this link. Two potential hypotheses have been suggested: the Balance Hypothesis and the Complexity Hypothesis.

"The Balance Hypothesis suggests that newly transferred genes may result in gene dysregulation by upsetting the balance between expressed proteins, while the Complexity Hypothesis proposes that newly transferred genes may fail to engage in normal protein-protein interactions. Importantly, while the divergence between the donor and recipient strains should not affect the former process, it is expected to impact the latter, as more divergent proteins are more likely to experience protein-protein interaction failure.

***

"After correcting for biases related to bacterial physiology (i.e., frequent initiation of replication in actively growing cells), the authors investigated the relationship between gene transferability (as estimated by sequencing coverage) and several factors that may affect HGT, including gene function, protein connectivity, the divergence between the donor species and E. coli, and the expression level of the native gene in E. coli.

"Importantly, they found a significant interaction between divergence and connectivity, supporting the Complexity Hypothesis and suggesting that the ability of a transferred gene to engage in normal protein-protein interactions plays a key role in the success or failure of HGT.

"In addition to these findings, an important contribution of this study was the development of a statistical test capable of evaluating the Complexity Hypothesis. Burch notes, "Prior to this work, the Complexity Hypothesis had been described only using verbal arguments. I think it was an important step forward to translate the hypothesis into a specific statistical test. The fact that we could then conduct the statistical test on existing genomic data was icing on the cake. We are grateful to the Sorek team for leading the way."

"One caveat of this analysis is that all the genes studied were on the plasmids (i.e., extrachromosomal DNA) used to transfer them into the recipient cell. Different dynamics may be observed when genes are transferred directly onto bacterial or archaeal chromosomes.

"Ultimately, we would like to understand better the consequences of incorporating transferred genes into recipient genomes," says Burch. "Modern genome sequencing technology makes it possible to investigate that question using microbial evolution experiments, and a few have been done, but a lot more data are needed."

"Moreover, the current analysis was necessarily limited to genes that were already present in the E. coli genome. "We would also like to understand better the horizontal transfer of new or accessory genes that are not already present in recipient cells," continues Burch. "Those genes are not relevant to the Complexity Hypothesis, so that investigation remains for future work.."

Comment: it is not surprising that complexity limits horizontal gene transfer. As organisms become very complex through evolution the process disappears. In humans viral infections have added to our DNA without making us something different. It is not a significant event.

https://www.the-scientist.com/news-opinion/archaea-sport-structures-that-shuttle-genes-...

“'We’ve known for a while that there are a lot of genes that bacteria and archaea exchange,” says Olga Zhaxybayeva, an evolutionary biologist at Dartmouth College who was not involved in the study. If integrons turn out to be widespread in archaea, “it could be another mechanism for microbes to exchange the traits they need.”

"Gene exchange can help bacteria survive in new, harsh environments, or strengthen their symbiotic relationships with plants. Study coauthor Timothy Ghaly, a microbiologist at Macquarie University in Sydney, says that he and his team had always been interested in how integrons allow bacteria to take on novel, sometimes incredibly useful traits such as antibiotic resistance.

"It was unknown if archaea have integrons, partly because they’re hard to study, says Ghaly, as they live in a variety of difficult-to-access environments, from our guts to muddy, sulfuric hot springs. But recent advances in genomic sequencing, in particular a technique used to generate what are known as metagenome-assembled genomes (MAG), have allowed researchers to piece together archaea genomes from environmental samples.

***

"Bacteria swap genes in the form of a gene cassette that consists of a single gene and a gene recombination site called AttC. When they encounter stressful circumstances, bacteria exchange these cassettes like mixtapes, plugging them into and taking them out of their genomes.

***

"In the nearly 6,700 archeal genomes they scanned, the researchers found 75, spanning nine phyla, that had evidence of integrons. All of the archaeal integrons had the same structure and components as bacterial integrons.

"Based on the sequences they found, the researchers then synthesized archaeal AttC-containing cassettes and found that, when exposed, E. coli bacteria incorporated these cassettes into their genomes.

“"It’s always interesting to find [horizontal gene transfer] in new organisms,” says Zhaxybayeva. She adds that, in the future, it would be useful to have a complete genome of a cultured archaea, as opposed to a constructed MAG as the team used in this study, and begin to piece together the mechanism behind the gene transfer. She’s particularly interested in whether archaea in the human gut have integrons, “and whether they participate in the exchange around antibiotic resistance.'”

Comment: not surprising that all bacteria use the same mechanisms of gene transfer.

https://www.the-scientist.com/news-opinion/archaea-sport-structures-that-shuttle-genes-...

"Studies show that members of different domains can traffic genes back and forth, potentially fast-tracking evolution. How they do so remains unknown, but a study published today (November 16) in Science Advances provides a possible clue with the first report that archaea have integrons—gene exchange machinery previously thought only to exist in bacteria. This may allow microbes from the two domains to swap information and instantly acquire new functions. (my bold)

***

"It was unknown if archaea have integrons, partly because they’re hard to study, says Ghaly, as they live in a variety of difficult-to-access environments, from our guts to muddy, sulfuric hot springs. But recent advances in genomic sequencing, in particular a technique called metagenome-assembled genomes (MAG), have allowed researchers to piece together archaea genomes from environmental samples.

***

"Bacteria swap genes in the form of a gene cassette that consists of a single gene and a gene recombination site called AttC. When they encounter stressful circumstances, bacteria exchange these cassettes like mixtapes, plugging them into and taking them out of their genomes.

"To begin the DNA transfer process, bacteria use integron integrase (IntI), a protein in the tyrosine kinase family. Intl induces recombination between the gene cassette’s AttC site and a region on the bacterium’s genome called an integron attachment site, or AttI. Bacteria end up with a long string of gene cassettes, strung together by AttC sites, in their genomes.

"On the bacterial genome, integrons consist of a gene for an IntI protein, Int, followed by a series of integrated gene cassettes. In the new study, the researchers screened all publicly available genomes of archaea, 95 percent of which were MAGs. They searched for AttC-like sequences and for sequences coding for IntI-like proteins. The researchers say they haven’t found a way to predict AttI sequences, and thus didn’t look for them.

"In the nearly 6,700 archeal genomes they scanned, the researchers found 75, spanning nine phyla, that had evidence of integrons. All of the archaeal integrons had the same structure and components as bacterial integrons. (my bold)

Comment: it is widely accepted Archaea were the first life, so it is no surprise transferring integrons were there. Note my bolds. They are a way to fast-track evolution. It is a tool for a designing God to use.

https://www.quantamagazine.org/how-genes-can-leap-from-snakes-to-frogs-20221027/

"Perched on a leaf in the rainforest, the tiny golden mantella frog harbors a secret. It shares that secret with the fork-tongued frog, the reed frog and myriad other frogs in the hills and forests of the island nation of Madagascar, as well as with the boas and other snakes that prey on them. On this island, many of whose animal species occur nowhere else, geneticists recently made a surprising discovery: Sprinkled through the genomes of the frogs is a gene, BovB, that seemingly came from snakes.

"After poring over genomes from frog and snake species around the world, the scientists reported in April in a paper in Molecular Biology and Evolution that this gene has somehow traveled from snakes to frogs at least 50 times all over the planet. But in Madagascar it has inserted itself into frogs with startling promiscuity: 91% of the frog species sampled there have it. Something seems to make Madagascar an exceptionally conducive place for the gene to get mobile.

***

"...this new paper, which shows that the horizontal transfer of genes may be more likely in some places than others, complicates the story even more. It suggests that when seeking explanations for horizontal transfers, researchers may need to look beyond simple genetic mechanisms to the ecological contexts in which species live. Genomicists are still struggling to understand how common or rare horizontal transfers are in complex organisms, but some places, like Madagascar, may be hot spots for them.

***

"The cells of eukaryotic organisms like humans, frogs and snakes, however, are different [than bacteria] Their cell nucleus usually seems like a fortress for protecting the genome. The DNA is carefully coiled up and stored in that citadel’s library, with enzymes calling forth only the genes they need to examine at any given time. The cell is loaded with fail-safes to prevent damage to its DNA and to repair wear and tear. If the genome is like a priceless illuminated manuscript, its librarians carry swords.

***

"As strange as it might seem for eukaryotes to pick up genes from bacteria, stranger still is the fact that examples of horizontal gene transfer in the other direction are vastly rarer. For some reason, bacteria don’t want our genes. Eukaryotic genes have structural features that make them less than perfect material for bacteria, but there may be other contributing factors as well.

***

"Findings like these have persuaded some biologists that at least some horizontal gene transfers may be facilitated by viruses. If viruses can pick up genes from their hosts, and if they can leave behind pieces of their genomes, it seems possible that they could also sometimes ferry over genes from the last host they infected, or even one from generations ago, and give them to a new host.

***

"The involvement of viruses could also help to solve another puzzle about horizontal transfers in eukaryotes. For the transfers to occur, the traveling genes need to clear an entire series of hurdles. First they must get from the donor species to the new host species. Then they must get into the nucleus and ensconce themselves in the host genome. But getting into the genome of just any cell won’t do: In multicellular creatures like frogs and herrings, a gene won’t be passed down to the animal’s offspring unless it can sneak into a germline cell — a sperm or an egg.

***

"Is there something about the environment of Madagascar that makes it a hot spot for gene transfers?

***

"But the abundance of parasites on the island might also be a contributing factor. For example, “in Madagascar, there are lots of leeches,”

***

"Unfortunately, it isn’t easy to prove or disprove scenarios describing how such horizontal transfers might have occurred. Without selection to preserve DNA sequences, they tend to mutate and get scrambled over long stretches of time, erasing the molecular evidence of a transfer. And if a virus is involved in the transfer, it may leave very little evidence in the first place, Graham said. Researchers might therefore almost need to catch a genetic jump in the act to know how it is happening."

Comment: lots of evidence but still no answers as to how horizontal transfer occurs in eukaryotes.

https://www.the-scientist.com/features/horizontal-gene-transfer-happens-more-often-than...

"Horizontal Gene Transfer Happens More Often Than Anyone Thought
DNA passed to and from all kinds of organisms, even across kingdoms, has helped shape the tree of life, to a large and undisputed degree in microbes and also unexpectedly in multicellular fungi, plants, and animals.

"...whatever the delivery vehicle, one thing is clear: in contrast to the simplicity of evolution from a common ancestor as commonly depicted, the branches of the tree of life appear to be inextricably tangled, and scientists are only just beginning to understand the extent of this complexity.

“'As our sampling increases, so does our power to detect horizontal gene transfers,” says Rokas. “So as we sequence more and more and more diverse lineages, I think we’re going to find more and more cases.”

***

"Still, when the first studies hinting at the possibility of HGT in eukaryotic organisms came out in the 2000s, researchers were hesitant to trust the results, citing numerous barriers that seemed insurmountable. For example, while foreign DNA can easily access bacterial genomes free-floating in the cytoplasm, in eukaryotes it would have to cross through highly regulated nuclear pores to enter the genome’s nuclear home. Also, because eukaryotic genomes are organized into pairs of homologous chromosomes that need to line up properly during meiosis, some researchers argued that large insertions would simply be too physically disruptive and would impede gamete production.

"To this day, the evidence for eukaryotic HGT is far sparser than that for bacterial HGT, and some scientists remain skeptical of its prevalence or importance in the evolution of diverse taxa. But Andrew Roger, a comparative genomicist at Dalhousie University in Nova Scotia, says that those who work with single-celled eukaryotes have readily embraced the idea. Genomic data—particularly long-read sequencing data, which establishes the genomic context for putatively foreign genes—has been unequivocal, he says. “The more genomes you get, the more you realize: here’s this chunk of chromosome from this organism in this one over here. And it’s just clearly a transfer.” In his mind, he adds, there’s little doubt that horizontal gene transfer has played a large role in the evolution of protists.

***

"Now, Rokas says, he thinks that DNA is not only moving around the tree of life, but it’s moving a lot more frequently than anyone had imagined, and the cases of HGT that have been identified are just a small sample of the total transfers that have taken place over evolutionary time. “My sense is there is orders of magnitude more integration than retention,” Rokas says. “So there is a lot more DNA coming into fungal genomes, and only a tiny fraction of that DNA is adaptive or selected enough to be maintained.”

***

“'We have the tools and the data now that allow us to quantify these transfers and quantify the impact they’ve had on evolution of eukaryotic genomes,” he adds. “I think the [whitefly] study that we did prompts us and prompts many others to start conducting such systematic analyses now. And we may come to realize that these transfers are not that not as rare as we thought they were.”

"Even if transfers in multicellular organisms are indeed less common than in microbes, Gilbert notes that evolutionary importance is not just a numbers game. “We want to think not [just] in terms of number, but also in terms of impacts. Perhaps just one transfer may have had a huge impact on the viability of some species.”

"Moran agrees. “In many cases, [horizontally transferred DNA] seems really central to the ecology or lifestyle of that particular group. Even if it’s only a tiny part of the genome, it can still be a major influence.'”

Comment: an enormous review article filled with research examples. I've pulled out the researcher's conclusions. HGT is a major evolutionary mechanism and as I view God's controls, a way He can step in for a 'dabble'.

QUOTES: "By forming a 'temporary union' with another bacterium in our gut, a microbe can therefore transfer its genes to another – it doesn't even have to be the same species.

"All the microbe has to do is stick out a tube, called a pilus, and attach itself to another cell, shooting off a transferable package of DNA called a mobile genetic element when it's ready."

"The discovery of bacterial sex was made over 70 years ago, when scientists realized this horizontal gene transfer was how microbes were sharing resistance genes for certain antibiotics, thereby spreading antibiotic resistance.”

dhw: Wow! This is a real eye-opener for me, though obviously not for people in the field. I’ve always thought that sexual reproduction was an astonishing leap forward in evolution, but the basic principle was already established by bacteria through horizontal gene transfer! For me, this provides a crucial link in the chain of common descent. Many thanks to David for this “revelation”!

QUOTE: “The horizontal gene exchange among microbes is likely used for anything that increases their ability to survive.”

dhw: Yes indeed, all these steps in life’s history are likely to be motivated by the quest to improve chances of survival.

Yes, organisms must survive long enough for the next stage of evolution to develop.

"All the microbe has to do is stick out a tube, called a pilus, and attach itself to another cell, shooting off a transferable package of DNA called a mobile genetic element when it's ready."

"The discovery of bacterial sex was made over 70 years ago, when scientists realized this horizontal gene transfer was how microbes were sharing resistance genes for certain antibiotics, thereby spreading antibiotic resistance.”

Wow! This is a real eye-opener for me, though obviously not for people in the field. I’ve always thought that sexual reproduction was an astonishing leap forward in evolution, but the basic principle was already established by bacteria through horizontal gene transfer! For me, this provides a crucial link in the chain of common descent. Many thanks to David for this “revelation”!

QUOTE: “The horizontal gene exchange among microbes is likely used for anything that increases their ability to survive.”

Yes indeed, all these steps in life’s history are likely to be motivated by the quest to improve chances of survival.

https://www.sciencealert.com/there-are-a-bunch-of-bacteria-having-sex-in-your-gut-right...

"By forming a 'temporary union' with another bacterium in our gut, a microbe can therefore transfer its genes to another – it doesn't even have to be the same species.

"All the microbe has to do is stick out a tube, called a pilus, and attach itself to another cell, shooting off a transferable package of DNA called a mobile genetic element when it's ready.

"The discovery of bacterial sex was made over 70 years ago, when scientists realized this horizontal gene transfer was how microbes were sharing resistance genes for certain antibiotics, thereby spreading antibiotic resistance.

"More recently, it's become clear that bacterial sex doesn't just occur when microbes are under attack. It happens all the time, and it's probably part of what keeps our microbiome fit and healthy.

***

"'The big, long molecules from sweet potatoes, beans, whole grains, and vegetables would pass through our bodies entirely without these bacteria," explains microbiologist Patrick Degnan from the University of California Riverside.

"'They break those down so we can get energy from them."

"To colonize the human gut and help us break down carbohydrates, however, these microbes must compete for limited resources in the large intestine. Such resources include vitamin B12 and other related compounds, which help fuel the bacteria's metabolism and synthesis of proteins.

"Most microbes in the gut don't have the ability to synthesize these crucial compounds on their own, which means they have to soak up what they can from their environment.

"For this to be effective, it pays to have genes for an efficient vitamin B12 transport system at the ready.

"In both petri dishes and in living mouse models, researchers have now identified B12 transporters that are shared via bacterial sex.

***

"'The horizontal gene exchange among microbes is likely used for anything that increases their ability to survive, including sharing [genes for the transport of] vitamin B12."

"When two gut microbes were placed on a dish in the lab, researchers noticed the bacterium that couldn't synthesize B12 transport systems connected up with the bacterium that could. Once the sex pilus bridged the gap between the two, the 'receiving' bacterium could unpack its precious cargo.

"After the experiment, researchers examined the genome of the receiving bacterium, which was still alive, and found it had incorporated an extra band of DNA from the donor.

"Among living mice, something similar appears to happen. When researchers administered two forms of Bacteroidetes to a mouse – one that possessed the genes for transferring B12, and another that didn't – they found the genes of the former had 'jumped' to the latter after five to nine days."

Comment: a well-recognized process now shown to happen in very short times. Luckily for us the gut bacteria like to work for us and process veggies we cannot on our own.

https://www.quantamagazine.org/dna-jumps-between-animal-species-no-one-knows-how-often-...

"To survive in the frigid ocean waters around the Arctic and Antarctica, marine life evolved many defenses against the lethal cold. One common adaptation is the ability to make antifreezing proteins (AFPs) that prevent ice crystals from growing in blood, tissues and cells. It’s a solution that has evolved repeatedly and independently, not just in fish but in plants, fungi and bacteria.

"It isn’t surprising, then, that herrings and smelts, two groups of fish that commonly roam the northernmost reaches of the Atlantic and Pacific Oceans, both make AFPs. But it is very surprising, even weird, that both fish do so with the same AFP gene — particularly since their ancestors diverged more than 250 million years ago and the gene is absent from all the other fish species related to them.

"A March paper in Trends in Genetics holds the unorthodox explanation: The gene became part of the smelt genome through a direct horizontal transfer from a herring. It wasn’t through hybridization, because herring and smelt can’t crossbreed, as many failed attempts have shown. The herring gene made its way into the smelt genome outside the normal sexual channels.

***

"Nor are the smelt unique. Recent studies of a range of animals — other fish, reptiles, birds and mammals — point to a similar conclusion: The lateral inheritance of DNA, once thought to be exclusive to microbes, occurs on branches throughout the tree of life.

***

"...the smelt discovery and other recent examples all point to horizontal transfers playing an influential role in evolution."

Comment: The paper then covers many pages of research review om possible mechanism including parasite transfer. Nothing is conclusive but it certainly fits my notion of God dabbling.

https://www.nature.com/articles/d41586-021-00782-w

"The finding, reported today in Cell1, is the first known example of a natural gene transfer from a plant to an insect. It also explains one reason why the whitefly Bemisia tabaci is so adept at munching on crops: the gene that it swiped from plants enables it to neutralize a toxin that some plants produce to defend against insects.

***

"That some species of whitefly could owe part of their predatory prowess to genes from other organisms is not entirely surprising, because genetic thievery is common in the arms race between plants and their pests. Over millions of years, plants and insects alike have borrowed heavily from microbial genomes, sometimes using their newly acquired genes to develop defensive or offensive strategies.

"Some insects, such as the coffee berry borer (Hypothenemus hampei), have plundered microbial genes to extract more nutrition from hard-to-digest plant cell walls2, and a wild relative of wheat has pilfered a fungal gene to fight off a fungal disease called head blight3. But plants and insects were not known to steal from each other before now.

***

"study showed that the gene can transfer a chemical group on to defensive compounds called phenolic glucosides. Such compounds are made by many plants, including tomatoes, to ward off pests. But the modification caused by the whitefly gene rendered the compounds harmless.

***

"The results were surprising, but convincing, says Yannick Pauchet, a molecular entomologist also at the Max Planck Institute for Chemical Ecology. “According to the data they provide, horizontal gene transfer is the most parsimonious explanation,” he says.

"But how the whitefly managed to swipe a plant gene is unclear. One possibility, says Turlings, is that a virus served as an intermediate, shuttling genetic material from a plant into the whitefly genome.

"As researchers sequence more genomes, it’s possible that they’ll uncover more examples of gene transfer between plants and animals, says Gloss.

“'Insects taking the genes from the plants themselves is just that last bit of the arsenal that we hadn’t found yet,” he says. “In the battle between plants and their insect pests or pathogens, there are genes being drawn from all over the tree of life.'”

Comment: Undoubtedly more of this type of transfer will be found, and virus is the best guess as the agent. Horizontal gene transfer is shown again to be a driver of evolutionary change. This may be another answer/reason to why viruses are present at all?

https://www.newscientist.com/article/2231210-antibiotic-resistance-genes-can-be-passed-...

"Genes that make bacteria resistant to antibiotics have been found in dust in buildings in a form that could be passed to disease-causing microbes.

"The finding suggests that people in households where people frequently take antibiotics could be at higher risk of getting infected with antibiotic resistant “superbugs” – although it isn’t known if this is actually happening.

"Antibiotic resistance is seen as one of the biggest global threats to public health, as growing numbers of dangerous bacteria have evolved the ability to withstand antibiotic treatment.

"To try to slow the spread of resistance, we are supposed to limit our use of antibiotics, for example by not taking them for coughs or colds, which are usually caused by viruses.
However, it is unclear how useful it is for individuals to take such steps when resistant bacteria are common in the environment, such as in hospitals and perhaps our homes and workplaces too.

"Previously, resistant bacteria have been found in dust – but it is unclear how dangerous this is, as most bacteria that can survive the dry conditions of dust are harmless to people.

"Erica Hartmann at Northwestern University in Illinois and her colleagues wondered whether the antibiotic resistance genes in the bacteria in dust could get passed to more dangerous microbes. Bacteria often share genes with each other by swapping small sections of DNA called plasmids.

"The researchers looked at dust samples from 43 public buildings. Over a quarter of the resistance genes they found were on plasmids or other transferrable forms of DNA.

"It raises the possibility that if a home were contaminated with a bacterium such as the food poisoning microbe Salmonella, the microorganism could become more dangerous, says Hartmann. “It’s possible that something that would make you sick could pick up an antibiotic resistance gene.'”

Comment: Should we now wear masks in public. Considering the Chinese corona pneumonia virus running around the world, perhaps we should.

dhw: It certainly is amazing. You assume your God had to specially preprogramme this midge (= provide adaptive instructions for this particular situation) in order to keep life going so that he could eventually design H. sapiens. If he exists, I would be more inclined to believe that he equipped cells with the intelligence to find ways of adapting to all kinds of conditions. Not much point in inventing life if he didn’t give organisms the means of surviving! Even you have suggested that your God may have given cells the ability to make minor epigenetic changes to themselves, so I wonder where you draw the borderline between major and minor.

DAVID: As before: minor is simple alterations, while major involves body design changes and/or complex physiological changes.

I’m just checking the extent to which you think your God did it, as opposed to the organism did it. Here we have him specially preprogramming the Antarctic midge (he provided “adaptive instructions”) to survive in extreme conditions so that it would provide food to keep life going until he could design the only thing he wanted to design, H. sapiens.

Dhw (under “Hybridisation”): This is a cop-out. All the varieties of cichlid are still cichlid. The real mystery is how different species in the broader sense of the word can have evolved from common ancestors: how come there are insects, fish, animals, birds, all descended from the first single cells with which life began? “Combinatorial speciation” is no different from Margulis’s emphasis on cooperation. Even you agree that cell communities combine or cooperate autonomously to create minor changes, and the question is whether they can also do the same to create major changes. But you refuse to accept this possibility.

DAVID: Because it involves the major use of mentally planned complex designs.

dhw: Yes, you refuse to accept the possibility that microorganisms are capable of mental activity. It’s not just major designs you discount. Your God has to preprogramme or dabble every bacterial response to every situation in the history of life past, present and future, and he even has to engineer midge adaptation. Billions of programmes and dabbles, all for the sole purpose of covering the time before he specially designed H. sapiens.

You are describing the wrong God. My God understood the time He would need to evolve humans He did not have the sole purpose of filling time. Have you forgotten evolution is a stepwise process? He proceeded step by step in a logical fashion. Pre-programming made his work easier.

DAVID: As before: minor is simple alterations, while major involves body design changes and/or complex physiological changes.

I’m just checking the extent to which you think your God did it, as opposed to the organism did it. Here we have him specially preprogramming the Antarctic midge (he provided “adaptive instructions”) to survive in extreme conditions so that it would provide food to keep life going until he could design the only thing he wanted to design, H. sapiens.

Dhw (under “Hybridisation”): This is a cop-out. All the varieties of cichlid are still cichlid. The real mystery is how different species in the broader sense of the word can have evolved from common ancestors: how come there are insects, fish, animals, birds, all descended from the first single cells with which life began? “Combinatorial speciation” is no different from Margulis’s emphasis on cooperation. Even you agree that cell communities combine or cooperate autonomously to create minor changes, and the question is whether they can also do the same to create major changes. But you refuse to accept this possibility.

DAVID: Because it involves the major use of mentally planned complex designs.

Yes, you refuse to accept the possibility that microorganisms are capable of mental activity. It’s not just major designs you discount. Your God has to preprogramme or dabble every bacterial response to every situation in the history of life past, present and future, and he even has to engineer midge adaptation. Billions of programmes and dabbles, all for the sole purpose of covering the time before he specially designed H. sapiens.

DAVID: My thought is I don't think God would permit your autonomous mechanism.

dhw: “Permit”? I am suggesting that if he exists, he would have invented it! I know you don’t think he would have invented it. You have a fixed belief that he preprogrammed or dabbled the Antarctic midge’s adaptation, not to mention every bacterial response to every situation throughout the history of life. But I’m glad you have now discarded your thought that preprogramming, dabbling and autonomous cellular design “may all be the same”.

Autonomous under guidelines

DAVID: (Under "Antarctic midges") It is always amazing to see how tenacious life can be. […] dhw will want to know about God's role. I assume adaptive instructions were provided.

dhw: It certainly is amazing. You assume your God had to specially preprogramme this midge (= provide adaptive instructions for this particular situation) in order to keep life going so that he could eventually design H. sapiens. If he exists, I would be more inclined to believe that he equipped cells with the intelligence to find ways of adapting to all kinds of conditions. Not much point in inventing life if he didn’t give organisms the means of surviving! Even you have suggested that your God may have given cells the ability to make minor epigenetic changes to themselves, so I wonder where you draw the borderline between major and minor.

As before: minor is simple alterations, while major involves body design changes and/or complex physiological changes.

Hybridisation
DAVID: New findings suggest this may be a more rapid mechanism than chance mutations and natural selection:
https://www.quantamagazine.org/new-hybrid-species-remix-old-genes-creatively-20190910/

QUOTES: "The three authors’ views are shaped by their work on one of nature’s most explosive species radiations — that of African cichlid fish. In just 150,000 years, well over 700 species have radiated into a technicolor panoply of shapes, sizes and ecologies.”

"But Marques and his colleagues suggest that the accumulated genomic evidence warrants the introduction of “combinatorial speciation” as a new term to frame future research.

dhw: This is a cop-out. All the varieties of cichlid are still cichlid. The real mystery is how different species in the broader sense of the word can have evolved from common ancestors: how come there are insects, fish, animals, birds, all descended from the first single cells with which life began? “Combinatorial speciation” is no different from Margulis’s emphasis on cooperation. Even you agree that cell communities combine or cooperate autonomously to create minor changes, and the question is whether they can also do the same to create major changes. But you refuse to accept this possibility.

Because it involves the major use of mentally planned complex designs.

dhw: You are simply saying that if cellular intelligence (3) was in fact information provided by God (1) or (2), it would be the same as (1) or (2). You are juggling with the term “information” to blur the distinction between an autonomous mechanism that uses information and a mechanism which is preprogrammed with the information that enables it to use information according to an existing programme of information. This is a silly game. There is no way an autonomous mechanism can be the same as a preprogrammed mechanism or a mechanism that is directly dabbled with by the hand of your God.

DAVID: My thought is I don't think God would permit your autonomous mechanism.

“Permit”? I am suggesting that if he exists, he would have invented it! I know you don’t think he would have invented it. You have a fixed belief that he preprogrammed or dabbled the Antarctic midge’s adaptation, not to mention every bacterial response to every situation throughout the history of life. But I’m glad you have now discarded your thought that preprogramming, dabbling and autonomous cellular design “may all be the same”.

DAVID: (Under "Antarctic midges") It is always amazing to see how tenacious life can be. […] dhw will want to know about God's role. I assume adaptive instructions were provided.

It certainly is amazing. You assume your God had to specially preprogramme this midge (= provide adaptive instructions for this particular situation) in order to keep life going so that he could eventually design H. sapiens. If he exists, I would be more inclined to believe that he equipped cells with the intelligence to find ways of adapting to all kinds of conditions. Not much point in inventing life if he didn’t give organisms the means of surviving! Even you have suggested that your God may have given cells the ability to make minor epigenetic changes to themselves, so I wonder where you draw the borderline between major and minor.

Hybridisation
DAVID: New findings suggest this may be a more rapid mechanism than chance mutations and natural selection:
https://www.quantamagazine.org/new-hybrid-species-remix-old-genes-creatively-20190910/

QUOTES: "The three authors’ views are shaped by their work on one of nature’s most explosive species radiations — that of African cichlid fish. In just 150,000 years, well over 700 species have radiated into a technicolor panoply of shapes, sizes and ecologies.”

"But Marques and his colleagues suggest that the accumulated genomic evidence warrants the introduction of “combinatorial speciation” as a new term to frame future research.

This is a cop-out. All the varieties of cichlid are still cichlid. The real mystery is how different species in the broader sense of the word can have evolved from common ancestors: how come there are insects, fish, animals, birds, all descended from the first single cells with which life began? “Combinatorial speciation” is no different from Margulis’s emphasis on cooperation. Even you agree that cell communities combine or cooperate autonomously to create minor changes, and the question is whether they can also do the same to create major changes. But you refuse to accept this possibility.

DAVID: No question horizontal gene transfer is a major contributor to the course of evolution.

dhw: And so we begin the process with cells cooperating in order to enhance their chances of survival. Between us we have come up with three separate theories as to how this cooperation has led to evolution: 1) David’s God preprogrammed every single new combination of cells; 2) David’s God personally manipulated each new combination as and when he felt like it (dabbling); 3) (theistic version) David’s God designed the cells with the intelligence to work out their own ways of cooperating. This particular article uses interesting language: “unbridled zeal”, “excellent strategy”, “are concerned with”, “a chance to advance itself…it will not hesitate”. Sounds like (3) to me!

DAVID: Or the 'intelligence of cells' is the programmed information from God. 1,2, and 3 may all be the same.

dhw: I don’t know why you have to bring in the term “information”, when the alternatives are already perfectly clear. There is no way divine preprogramming (fixed beforehand), divine dabbling (fixed on the spot) and autonomous cooperation (fixed by the cells themselves) could possibly be the same.

DAVID: You have always resented the concept of information contained in DNA. Of course it is information. That is what codes contain, and 1,2 and 3 are an exchange or development of new information, instructions.

dhw: You are simply saying that if cellular intelligence (3) was in fact information provided by God (1) or (2), it would be the same as (1) or (2). You are juggling with the term “information” to blur the distinction between an autonomous mechanism that uses information and a mechanism which is preprogrammed with the information that enables it to use information according to an existing programme of information. This is a silly game. There is no way an autonomous mechanism can be the same as a preprogrammed mechanism or a mechanism that is directly dabbled with by the hand of your God.

My thought is I don't think God would permit your autonomous mechanism

dhw: And so we begin the process with cells cooperating in order to enhance their chances of survival. Between us we have come up with three separate theories as to how this cooperation has led to evolution: 1) David’s God preprogrammed every single new combination of cells; 2) David’s God personally manipulated each new combination as and when he felt like it (dabbling); 3) (theistic version) David’s God designed the cells with the intelligence to work out their own ways of cooperating. This particular article uses interesting language: “unbridled zeal”, “excellent strategy”, “are concerned with”, “a chance to advance itself…it will not hesitate”. Sounds like (3) to me!

DAVID: Or the 'intelligence of cells' is the programmed information from God. 1,2, and 3 may all be the same.

dhw: I don’t know why you have to bring in the term “information”, when the alternatives are already perfectly clear. There is no way divine preprogramming (fixed beforehand), divine dabbling (fixed on the spot) and autonomous cooperation (fixed by the cells themselves) could possibly be the same.

DAVID: You have always resented the concept of information contained in DNA. Of course it is information. That is what codes contain, and 1,2 and 3 are an exchange or development of new information, instructions.

You are simply saying that if cellular intelligence (3) was in fact information provided by God (1) or (2), it would be the same as (1) or (2). You are juggling with the term “information” to blur the distinction between an autonomous mechanism that uses information and a mechanism which is preprogrammed with the information that enables it to use information according to an existing programme of information. This is a silly game. There is no way an autonomous mechanism can be the same as a preprogrammed mechanism or a mechanism that is directly dabbled with by the hand of your God.

DAVID: No question horizontal gene transfer is a major contributor to the course of evolution.

dhw: And so we begin the process with cells cooperating in order to enhance their chances of survival. Between us we have come up with three separate theories as to how this cooperation has led to evolution: 1) David’s God preprogrammed every single new combination of cells; 2) David’s God personally manipulated each new combination as and when he felt like it (dabbling); 3) (theistic version) David’s God designed the cells with the intelligence to work out their own ways of cooperating. This particular article uses interesting language: “unbridled zeal”, “excellent strategy”, “are concerned with”, “a chance to advance itself…it will not hesitate”. Sounds like (3) to me!

DAVID: Or the 'intelligence of cells' is the programmed information from God. 1,2, and 3 may all be the same.

dhw: I don’t know why you have to bring in the term “information”, when the alternatives are already perfectly clear. There is no way divine preprogramming (fixed beforehand), divine dabbling (fixed on the spot) and autonomous cooperation (fixed by the cells themselves) could possibly be the same.

You have always resented the concept of information contained in DNA. Of course it is information. That is what codes contain, and 1,2 and 3 are an exchange or development of new information, instructions.