Genomics

From ScienceDaily: To make the iconic, twisted double helix that accounts for the diversity of life, DNA rules specify that G always pairs with C, and A with T. But, when it’s all added up, the amount of G+C vs A+T content among species is not a simple fixed percentage or, standard one-to-one ratio. For example, within single-celled organisms, the amount of G+C content can vary from 72 percent in a bacteria like Streptomyces coelicolor while the protozoan parasite that causes malaria, Plasmondium falciparum, has as little as 20 percent. In single-celled eukaryotes, yeast contain 38 percent G+C content, plants like corn have 47 percent, and humans contain about 41 percent. The big question is, why? … Now that they’ve Read More ›

Against theistic evolutionists who insist that a single human pair is not biologically possible. Recently, British plant geneticist Richard Buggs posted a letter he had sent in May to BioLogos’ Dennis Venema, taking issue with the claim that a population of 10,000 is required, as stated in Dennis Venema and Scot McKnight, Adam and the Genome. Buggs never got an answer and he has since posted further thoughts at Nature: Ecology and Evolution (community): Does genomic evidence make it scientifically impossible that the human lineage could have ever passed through a population bottleneck of just two individuals? This is a question I am asked semi-frequently by religious friends. With my current understanding of the genetic evidence, I can’t state categorically Read More ›

From ScienceDaily: Researchers from the Institute of Population Genetics at Vetmeduni Vienna, using a new and highly specific analysis method, could now provide fresh momentum to help decode the evolutionary dynamics of the Y chromosome. Their study shows that ten times more new genes are transferred onto the Y chromosome in fruit flies than had been previously thought. Some of these new genes even appear to have taken on important functions. … A special surprise for the research team was that four of the 25 newly transferred genes on the Y chromosome have already assumed an important function there. “As these new genes can be found in all individuals of a species, the question arises as to which functions these Read More ›

From Mikhail Tikhonov at The Scientist: More profoundly, microbial ecosystems are a strange world where many familiar concepts start to break down, including “species,” “fitness,” and maybe even “organism.” In our everyday experience, we are rarely in doubt whether a given creature is a fox or a rabbit. Further, it seems very easy to delineate where an “individual” ends, and its “environment” begins. Our ability to do so is often taken for granted, and underlies how we think about both ecology and evolution. Whether these assumptions remain adequate for microbes is, however, increasingly doubtful. … The issue of microbial species being ill-defined is a hot topic in the biological literature. In a recent paper in Physical Review E, I try Read More ›

In response to Jumpin’ Genes!: A quarter of cow DNA came from reptiles, our physics color commentator writes, This whole business of parasites transmitting retrotransposons from reptiles to cows is just so zoo-centric. What about plants? What about viruses? Don’t they get to originate DNA too? When are they going to admit that this whole business of descent-with-modification really disrespects half the tree of life? Zoo-racist, that’s what they are. Most human beings must confess to a lack of genuine empathy with bugs, worms, and germs. Seriously, although no one talks about it much, these types of finds can’t be good news for the End of Science rent-a-riot (Darwin-in-the-schools lobby). See also: Jumpin’ Genes!: A quarter of cow DNA came from Read More ›

From Ed Yong at The Atlantic: This jumping gene seems to have entered the cow genome from the unlikeliest of sources: snakes and lizards. Retrotransposons typically jump around within a single genome, but sometimes they can travel further afield. Through means that scientists still don’t fully understand, they can leave the DNA of one species and enter that of another. And so it is with BovB. No one knows the animal in which it originated. But from that mystery source, it has jumped into the DNA of snakes and cows, elephants and butterflies, ants and rhinos. … No one knows how BovB travels between species, but Ivancevic and Adelson suspect that it might spread via blood-sucking parasites. They have found Read More ›

Watch the human genome fold itself in four dimensions: By removing and then adding this protein, called cohesin, researchers made specific DNA loops that disappear and then reappear, they report this month in Cell. But cohesin really only affects looping that brings genes on the same chromosome into contact. A second, still-undefined mechanism seems to bring genes from different chromosomes together, the team notes. Notes: Will we ever… reveal all the secrets of life from DNA?: Our metaphors let us down. Science writers like to compare the genome to a textbook or a blueprint. That conveys the fact that it stores information, but glosses over its buzzing, dynamic nature – proteins docking on and off to control the activity of Read More ›

From Michael Le Page at New Scientist: The number of known species of geckos has just jumped upwards, with 15 new species being formally described this week. … The 19 species all live in a small area of Myanmar just 90 by 50 kilometres in size. “That’s the really amazing thing about it,” says Grismer. “They all come from such a small area.” It’s common to find lots of closely-related species of invertebrates like snails or insects in such a small area, but it is unprecedented for a backboned animal, say Grismer. “For lizards, it is remarkable.”More. A friend asks why no criteria are offered in the article as to how the scientists determined that the groups of lizards are Read More ›

Archaea are thought to be about 3.8 billion years old. From ScienceDaily: By studying the 3-D structure of proteins bound to DNA in microbes called archaea, researchers have turned up surprising similarities to DNA packing in more complicated organisms. “If you look at the nitty gritty, it’s identical,” says Howard Hughes Medical Institute Investigator Karolin Luger, a structural biologist and biochemist at the University of Colorado Boulder. “It just blows my mind.” The archaeal DNA folding, reported August 10 in Science, hints at the evolutionary origins of genome folding, a process that involves bending DNA and one that is remarkably conserved across all eukaryotes (organisms that have a defined nucleus surrounded by a membrane). Like Eukarya and Bacteria, Archaea represents Read More ›

From ScienceDaily:“During cell division, a mother cell divides into two daughter cells, and during this process the DNA in the mother cell, wrapped up in the form of chromosomes, is divided into two equal sets. To achieve this, rope-like structures called microtubules capture the chromosomes at a special site called the kinetochore, and pull the DNA apart,” said Dr Viji Draviam, senior lecturer in structural cell and molecular biology from QMUL’s School of Biological and Chemical Sciences. “We have identified two proteins — tiny molecular machines — that enable the correct attachment between the chromosomes and microtubules. When these proteins don’t function properly, the cells can lose or gain a chromosome. This finding gives us a glimpse of an important Read More ›

But leaves phylogeny unclear. From ScienceDaily: Tardigrades are microscopic animals, justly famous for their amazing ability to withstand complete dehydration, resurrecting years later when water is again available. Once desiccated, they have been frozen in ice, exposed to radiation, sent into space vacuum… and still they spring back to life. Tardigrades became more famous recently when it was suggested that their DNA was a mix of animal and bacterial segments, making them “Frankenstein” hybrids. The new research has now laid the Frankenstein idea to rest by arguing that tardigrade DNA looks “normal,” with no evidence that these special animals use extraordinary means to survive. Previous ideas that they might have taken up large numbers of foreign genes from bacteria are Read More ›

Missed this earlier: From Phys.org: Humanity may soon generate more data than hard drives or magnetic tape can handle, a problem that has scientists turning to nature’s age-old solution for information-storage—DNA. In a new study in Science, a pair of researchers at Columbia University and the New York Genome Center (NYGC) show that an algorithm designed for streaming video on a cellphone can unlock DNA’s nearly full storage potential by squeezing more information into its four base nucleotides. They demonstrate that this technology is also extremely reliable. DNA is an ideal storage medium because it’s ultra-compact and can last hundreds of thousands of years if kept in a cool, dry place, as demonstrated by the recent recovery of DNA from Read More ›

We’d heard about Craig Venter’s dissent before but you should read the whole story: From Tom Bethell in Darwin’s House of Cards: A Journalist’s Odyssey Through the Darwin Debates, This was publicized in a science forum held at Arizona State University in February 2011, a little over a year after Dawkins’s Greatest Show was published. The physicist Paul Davies and others, including two Nobel Prize winners, participated in the event, which was videotaped. Richard Dawkins himself was on the panel. The forum addressed the question, “What is life?” Most of the panelists accepted that all organisms on Earth represent a single kind of life because they believed that the genetic code is universal. The NASA scientist and panelist Chris McKay 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 ›