Genetics

From science writer Suzan Mazur, author of Paradigm Shifters, continuing her interview at Huffington Post with Swedish deep evolution investigators Charles Kurland and Ajith Harish regarding … their central position on deep evolution, which is that the most recent universal common ancestor (MRUCA) is complex not a simple bacteria and “is the root of eukaryote and akaryote lineages” containing “more than a thousand Superfamilies.” Kurland and Harish think MRUCA represents complex survivors from a now extinct biosphere. On horizontal gene transfer as routine: Charles Kurland: We have to remember there’s only a little background of horizontal gene transfer in bacterial populations. The simple reason is that bacteria eat DNA. So sequences are going in all the time. Most of them get Read More ›

From science writer Suzan Mazur, author of Paradigm Shifters, at Huffington Post: I recently had a three-way phone conversation with Swedish deep evolution investigators Charles Kurland and Ajith Harish about their phylogenomic Tree of Life (ToL) based on protein structure, which shows that we are descended from a “complex” ancestor — MRUCA (most recent universal common ancestor) — not a simple bacteria. Kurland and Harish think a ToL paradigm shift may be in order. What’s more, Kurland and Harish figure that MRUCA was not the first ancestor, but represents complex survivors of a now-extinct biosphere. The findings of Kurland and Harish challenge not only mainstream ToL perspectives, but also those of endosymbiosis hypothesis fans, as well as the “HGT industry” Read More ›

From Kelly Rae Chi at Nature: n 2004, oncologist Gideon Rechavi at Tel Aviv University in Israel and his colleagues compared all the human genomic DNA sequences then available with their corresponding messenger RNAs — the molecules that carry the information needed to make a protein from a gene. They were looking for signs that one of the nucleotide building blocks in the RNA sequence, called adenosine (A), had changed to another building block called inosine (I). This ‘A-to-I editing’ can alter a protein’s coding sequence, and, in humans, is crucial for keeping the innate immune response in check. “It sounds simple, but in real life it was really complicated,” Rechavi recalls. “Several groups had tried it before and failed” Read More ›

From Cassandra Willyard at Nature: At the time, biologists were getting excited about the epigenome — the broad array of chemical marks that decorate DNA and its protein scaffold. These marks act like a chemical notation, telling the cell which genes to express and which to keep silent. As such, the epigenome helps to explain how cells with identical DNA can develop into the multitude of specialized types that make up different tissues. The marks help cells in the heart, for example, maintain their identity and not turn into neurons or fat cells. Misplaced epigenetic marks are often found in cancerous cells. Why didn’t it happen sooner?: The governing rule of molecular biology – the central dogma – holds that Read More ›

From ScienceDaily: Evolution is often thought of as a gradual remodeling of the genome, the genetic blueprints for building an organism. But in some instances it might be more appropriate to call it an overhaul. Over the past 100 million years, the human lineage has lost one-fifth of its DNA, while an even greater amount was added, report scientists at the University of Utah School of Medicine. Until now, the extent to which our genome has expanded and contracted had been underappreciated, masked by its relatively constant size over evolutionary time. Humans aren’t the only ones with elastic genomes. A new look at a virtual zoo-full of animals, from hummingbirds to bats to elephants, suggests that many vertebrate genomes have Read More ›

In Biological Theory (2015): There are currently three major theories on the origin and evolution of the genetic code: the stereochemical theory, the coevolution theory, and the error-minimization theory. The first two assume that the genetic code originated respectively from chemical affinities and from metabolic relationships between codons and amino acids. The error-minimization theory maintains that in primitive systems the apparatus of protein synthesis was extremely prone to errors, and postulates that the genetic code evolved in order to minimize the deleterious effects of the translation errors. This article describes a fourth theory which starts from the hypothesis that the ancestral genetic code was ambiguous and proposes that its evolution took place with a mechanism that systematically reduced its ambiguity Read More ›

From Joshua A. Krisch at The Scientist: Ninety-six hours after 43 zebrafish were frozen to death and 48 hours after 20 mice had their necks snapped, specific cells within their bodies were still hard at work. Gene transcription continued apace, and occasionally increased, according to a study published today (January 25) in Royal Society Open Biology. Genes linked to embryonic development, stress, and cancer were among those increasingly transcribed into RNA, researchers at the University of Washington and their colleagues reported. The results suggest that organismal death is an orderly, predictable process, and could help forensic scientists pinpoint time of death, plus help explain why organs from recently deceased donors seem to be more prone to cancer. “Death is a Read More ›

From Ann Gauger at at Evolution News & Views: Yesterday started out as an ordinary Tuesday. Then I set out to read a recent paper published in the journal Cell, “Nuclear Localization of Mitochondrial TCA Cycle Enzymes as a Critical Step in Mammalian Zygotic Genome Activation,” by R Nagaraj et al. It reported something rather odd that caught my eye. Very early embryos (at the two- or four-cell stage in mouse or human respectively) undergo a critical transition: they have to go from relying on RNAs and proteins loaded into the egg before fertilization by the mother, to making their own RNA and protein. The phenomenon is called embryonic genome activation. In order to activate their genomes, embryos have to Read More ›

From Jernej Ule at RealClearScience, where he explains his team’s findings, then reflects, We’ve known for decades that evolution needs to tinker with genetic elements so they can accumulate mutations while minimising disruption to the fitness of a species. Our most recent research, published in the journal eLife, looked at over 6,000 Alu elements to show that our code does exactly this. The two forces are tightly coupled in evolution, so that as soon as any mutations make the ying stronger, the yang catches up and stops them. This allows the Alu elements to remain in a harmless state in our DNA over long evolutionary periods, during which they accumulate a lot of change via mutations. As a result, they Read More ›

From Ross Pomeroy at RealClearScience: We know this thanks to a lengthy chain reaction of scientific discoveries. And according to Cobb, if there was a single man who catalyzed this reaction, it was Oswald Avery. In 1944, Avery, a medical researcher at Rockefeller University, published a paper with his colleagues Colin MacLeod and Maclyn McCarty. The experiment they described showed that DNA carries genetic information. While that seems obvious today, back then it was a controversial conclusion, countering decades of entrenched thought. DNA had originally been discovered back in 1869, but the majority of scientists considered it to be too simple to carry meaningful biological information. That duty, they assumed, belonged to proteins. But a decade before Avery dented that Read More ›

From Nathaniel Comfort at Aeon: While inflated medical promises are hardly peculiar to molecular medicine, that field does seem particularly prone to breathless rhetoric. You can almost hear K Eric Drexler panting when he writes, in his manifesto Engines of Creation (1986), that protein-based nanomachines ‘promise to bring changes as profound as the Industrial Revolution, antibiotics, and nuclear weapons all rolled up in one massive breakthrough’. Bluster, overstatement and aspirations masquerading as hard targets have no single cause. One reason, surely, is the heady sense of impending omnipotence that accompanies major technological and scientific advances. Charles Darwin’s theory of evolution by natural selection, the rediscovery of Gregor Mendel’s laws of heredity, the cracking of the genetic code, genetic engineering, the Read More ›

From Kevin Loria at Business Insider: A Harvard scientist just won $3 million for discovering the hidden ‘intelligence’ that defends our cells … It’s only thanks to a mechanism in our cells that can recognize when something has gone wrong that we aren’t all riddled with cancer. That mechanism, known as the DNA damage response, functions like an individual intelligent agent, able to monitor when things are going wrong and then try to come up with a way to deal with them. … Discoveries explaining how that mechanism works are so significant that on December 4, geneticist Stephen Elledge was awarded one of five $3 million Breakthrough Prizes in life sciences. … “One of the remarkable properties of nature’s most Read More ›

From Carrie Arnold at Nature: “This bird acts like it has four sexes,” says Christopher Balakrishnan, an evolutionary biologist at East Carolina University in Greenville, North Carolina, who worked with Tuttle and Gonser. “One individual can only mate with one-quarter of the population. There are very few sexual systems with more than two sexes.” The work helps to explain a long-standing puzzle for biologists. It shows how two identical chromosomes can evolve into distinct subtypes that can define the sexes of a species and their different behaviours. “These birds are an amazing system,” says Catherine Peichel, an evolutionary ecologist at the University of Berne. “The process of sex-chromosome evolution tends to erase much of the evidence of how it happened, Read More ›

From ScienceDaily: A gene that regulates bone growth and muscle metabolism in mammals may take on an additional role as a promoter of brain maturation, cognition and learning in human and nonhuman primates, according to a new study led by neurobiologists at Harvard Medical School. Describing their findings in the Nov. 10 issue of Nature, researchers say their work provides a dramatic illustration of evolutionary economizing and creative gene retooling — mechanisms that contribute to the vast variability across species that share nearly identical set of genes yet differ profoundly in their physiology. … For their experiments, the team analyzed RNA levels — the molecular footprints of gene activity — in the brain cells of mice, rats and humans. Although Read More ›

From ScienceDaily: A groundbreaking study of the virosphere of the most populous animals — those without backbones such as insects, spiders and worms and that live around our houses — has uncovered 1445 viruses, revealing people have only scratched the surface of the world of viruses — but it is likely that only a few cause disease. … “This groundbreaking study re-writes the virology text book by showing that invertebrates carry an extraordinary number of viruses — far more than we ever thought,” Professor Holmes said. “We have discovered that most groups of viruses that infect vertebrates — including humans, such as those that cause well-known diseases like influenza — are in fact derived from those present in invertebrates,” said Read More ›