Genetics

From John Timmer at Ars Technica: Why are people excited about Kelly’s DNA? The simple answer would seem to be that he has an identical twin, who must have identical DNA, and so we have a chance to see what space does to DNA. After all, space is a high-radiation environment, and we know that radiation damages DNA. But there’s quite a bit more to it than that. First and foremost, the Kelly twins’ DNA is not identical. Every time a cell divides, it typically picks up a mutation or two. Further mutations happen simply because of the stresses of life, which expose us all to some radiation and DNA-damaging chemicals, no matter how careful we are about diet and Read More ›

From NASA: The Twin Study propelled NASA into the genomics era of space travel. It was a ground-breaking study comparing what happened to astronaut Scott Kelly, in space, to his identical twin brother, Mark, who remained on Earth. The perfect nature versus nurture study was born. The Twins Study brought ten research teams from around the country together to accomplish one goal: discover what happens to the human body after spending one year in space. NASA has a grasp on what happens to the body after the standard-duration six-month missions aboard the International Space Station, but Scott Kelly’s one-year mission is a stepping stone to a three-year mission to Mars. More. So what did they find? Among other things, After Read More ›

Readers may remember Nick Matzke, especially for getting a publisher to abandon the Cornell University papers and for other contributions to Darwinism. A reader now writes to tell us that two Field Museum researchers have just published a critique of Nick Matzke’s (probable) most important contribution to research so far. “Conceptual and statistical problems with the DEC+J model of founder-event speciation and its comparison with DEC via model selection” by Richard H. Ree, Isabel Sanmartín, Journal of Biogeography. 2018 Abstract: Phylogenetic studies of geographic range evolution are increasingly using statistical model selection methods to choose among variants of the dispersal-extinction-cladogenesis (DEC) model, especially between DEC and DEC+J, a variant that emphasizes “jump dispersal,” or founder-event speciation, as a type of Read More ›

From Philip Ball at Chemistry World: Richard Dawkins’ 1976 book The selfish gene, which topped a poll last year for the most inspiring science books of all time, has set the agenda for how we think about genes and DNA. ‘We are,’ he famously said, ‘all survival machines for the same kind of replicator – molecules called DNA.’ Battles have been fought over whether this is a good use of metaphor (and as with the ‘selfish gene’ itself, metaphor was all it was ever meant to be). But the fundamental premise on which it is built – DNA as replicator – seemed always to be sound. Not from what we know today. However, once you accept that genes are not Read More ›

They withered under study. There’s been a lively discussion between geneticists Dennis Venema and Richard Buggs and about whether the human race must have had more than one pair of ancestors (Venema yes, Buggs no). From Evolution News and Science Today: Earlier, we saw that evolutionary genomicist Richard Buggs has been engaged in a dialogue with Venema about the latter’s arguments against a short bottleneck of two individuals in human history. Buggs is skeptical that methods of measuring human genetic diversity cited by Venema can adequately test such an “Adam and Eve” hypothesis. Buggs’s initial email to Venema thus concluded, “I would encourage you to step back a bit from the strong claims you are making that a two person bottleneck Read More ›

From Guenther Witzany, Telos-Philosophische Praxis, Salzburg-Austria, Corrado Spadafora, CNR National Research Council of Italy, and Luis Villarreal, University of California here: Evolution – Genetic Novelty/Genomic Variations by RNA Networks and Viruses, 4 – 8 July 2018 Salzburg – Austria For more than half a century it has been accepted that new genetic information is mostly derived from random‚ error-based’ events. Now it is recognized that errors cannot explain genetic novelty and complexity. Empirical evidence establishes the crucial role of non-random genetic content editors such as viruses and RNA-networks to create genetic novelty, complex regulatory control, inheritance vectors, genetic identity, immunity, new sequence space, evolution of complex organisms and evolutionary transitions. Genetic identities of RNA stem loop groups (RNA-networks) such as e.g., group Read More ›

From ScienceDaily: Every time our cells divide, the DNA within them must replicate so that each new cell receives the same set of instructions. Molecular machines known as polymerases make these copies of DNA by recognizing the shape of the right base pair combinations — G with C and A with T — and adding them into each new double helix, while discarding those that don’t fit together correctly. Though they are good at their job, polymerases are known to slip up from time to time, generating a mistake roughly one out of every 10,000 bases. If not fixed these become immortalized in the genome as a mutation. … The study, published in a 2015 issue of Nature, showed the Read More ›

From ScienceDaily: In a new PLOS ONE study, scientists from Kyoto University’s Graduate School of Biostudies have shown that certain ‘mechanosensitive’ genes are suppressed when subjected to audible sound. Moreover, these effects vary depending on cell type, where some don’t show any sensitivity. … “One such gene we examined helps in bone formation, and is known to be upregulated with low-intensity ultrasound pulses,” continues Kumeta. “The other genes were associated with wound healing and the extracellular matrix.” Series of cells were placed in an incubator outfitted with a full-range loudspeaker. After several hours of exposure to sounds with specific frequencies, expression levels of the target genes were analysed. The team found that these mechanosensitive genes were suppressed by up to Read More ›

From ScienceDaily: The team studied the transparent roundworm (C. elegans), which shares about 60-80% of the same genes as humans, to shed light on the importance of mechanisms regulating the frequency of gene mutations in different cells and organs. “C. elegans and humans share very similar mitochondria, and it is a useful organism as we can genetically tease apart the mechanisms of what is happening at a cellular level,” he said. The researchers developed an exceptionally pure method of isolating mitochondria from specific cells in the body to study them in detail. “We now suspect that there is a mechanism in all animals that can filter out these mutations before they are passed to future offspring, which could otherwise cause Read More ›

From Alex Barash at Slate: The not-quite life forms have a bad rap. But they’re a reliable sign of life, and it would be exciting to find them in space. For one thing, viruses are an excellent indicator for life itself: Wherever there’s life on Earth, there are viruses, too, and almost invariably in far greater numbers. Some scientists think that’s been true from the very beginning. While we know that RNA, the genetic material that makes up some viruses, came before DNA, the genetic material required by everything else, the fact that all modern viruses depend on cells to reproduce has led to something of a chicken-or-the-egg scenario. The NIH’s Eugene V. Koonin has spent decades investigating the evolution Read More ›

From ScienceDaily: Dodder, a parasitic plant that causes major damage to crops in the US and worldwide every year, can silence the expression of genes in the host plants from which it obtains water and nutrients. This cross-species gene regulation, which includes genes that contribute to the host plant’s defense against parasites, has never before been seen from a parasitic plant. … “Dodder is an obligate parasite, meaning that it can’t live on its own,” said Michael J. Axtell, professor of biology at Penn State and an author of the paper. “Unlike most plants that get energy through photosynthesis, dodder siphons off water and nutrients from other plants by connecting itself to the host vascular system using structures called haustoria. Read More ›

From ScienceDaily: Scientists have found an explanation for how flowering plants became dominant so rapidly in ecosystems across the world — a problem that Charles Darwin called an ‘abominable mystery’. In a study publishing on January 11 in the open access journal PLOS Biology, Kevin Simonin and Adam Roddy, from San Francisco State University and Yale University respectively, found that flowering plants have small cells relative to other major plant groups and that this small cell size is made possible by a greatly reduced genome size. … This new research provides a mechanism. By scouring the literature for data, the authors argue that these anatomical innovations are directly linked to the size of their genome. Because each cell has to Read More ›

From ScienceDaily: An international group of researchers has discovered a new phenomenon that occurs in identical twins: independent of their identical genes, they share an additional level of molecular similarity that influences their biological characteristics. The researchers propose a mechanism to explain the extra level of similarity and show that it is associated with risk of cancer in adulthood. The results appear in the journal Genome Biology. “The characteristics of an individual depend not only on genes inherited from the parents but also on epigenetics, which refers to molecular mechanisms that determine which genes will be turned on or off in different cell types. If we view one’s DNA as the computer hardware, epigenetics is the software that determines what Read More ›

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 ›

From Coner Friedersdorf at the Atlantic: ‘I Am a Man With Down Syndrome and My Life Is Worth Living’ Last week, the actor, Special Olympian, and advocate Frank Stephens gave this testimony to Congress: “I am a man with Down syndrome and my life is worth living.” In fact, he went farther: “I have a great life!” For those conceived with his developmental disability, it is the best and worst of times. “The life expectancy for someone born with Down syndrome has increased from twenty-five in the early 1980s to more than fifty today,” Caitrin Keiper writes in The New Atlantis. “In many other ways as well, a child born with Down syndrome today has brighter prospects than at any Read More ›