Genetics

From ScienceDaily: A core assumption in the study of disease-causing genes has been that they are clustered in molecular pathways directly connected to the disease. But work by a group of researchers at the Stanford University School of Medicine suggests otherwise. The gene activity of cells is so broadly networked that virtually any gene can influence disease, the researchers found. As a result, most of the heritability of diseases is due not to a handful of core genes, but to tiny contributions from vast numbers of peripheral genes that function outside disease pathways. Any given trait, it seems, is not controlled by a small set of genes. Instead, nearly every gene in the genome influences everything about us. The effects Read More ›

From BEC Crew at ScienceAlert: Here’s proof of how far we’ve come in science – in a world-first, researchers have recorded up-close footage of a single DNA molecule replicating itself, and it’s raising questions about how we assumed the process played out. The real-time footage has revealed that this fundamental part of life incorporates an unexpected amount of ‘randomness’, and it could force a major rethink into how genetic replication occurs without mutations. “It’s a real paradigm shift, and undermines a great deal of what’s in the textbooks,” says one of the team, Stephen Kowalczykowski from the University of California, Davis. More. It may not be as random as they think. A subway crowd’s movements may appear random at times, but Read More ›

From Sydney Perkowitz at JStor: We can find guidance in two classic works about the dangers of modifying people and labeling them as “superior” or “inferior”—the novel Brave New World (1932) and the film Gattaca (1997). Their publication anniversaries in 2017 are sharp reminders of the costs of embracing any kind of twenty-first-century eugenics. … In the final analysis, Brave New World portrays a “hard eugenics” created by a government to suppress human rights, diversity, and opportunities for its citizens. But like the world in Gattaca, our own society could instead display a eugenic element not imposed from above, but arising from our society’s dynamics. Unless our society balances the undoubted benefits of gene editing against its equally undoubted risks, Read More ›

From Ed Yong at the Atlantic: What If (Almost) Every Gene Affects (Almost) Everything? Three Stanford scientists have proposed a provocative new way of thinking about genetic variants, and how they affect people’s bodies and health. In 1999, a group of scientists scoured the genomes of around 150 pairs of siblings in an attempt to find genes that are involved in autism. They came up empty. They reasoned that this was because the risk of autism is not governed by a small number of powerful genes, which their study would have uncovered. Instead, it’s likely affected by a large number of genes that each have a small effect. Perhaps, they wrote, there might be 15 such genes or more. Two Read More ›

From Carl Zimmer at New York Times: In ‘Enormous Success,’ Scientists Tie 52 Genes to Human Intelligence In a significant advance in the study of mental ability, a team of European and American scientists announced on Monday that they had identified 52 genes linked to intelligence in nearly 80,000 people. These genes do not determine intelligence, however. Their combined influence is minuscule, the researchers said, suggesting that thousands more are likely to be involved and still await discovery. Just as important, intelligence is profoundly shaped by the environment. More. So? Is this ambivalence an “enormous success” in science today? If you still subscribe to the New York Times, please quit and save trees. See also: Science fictions series 4: Naturalism Read More ›

A thought from Raya Bidshahri at Singularity Hub: Today, what survives on Earth can be determined entirely by human beings. We can alter the genetics of almost any life form and potentially design entirely new ones. According to renowned physicist Freeman Dyson, “In the future, a new generation of artists will be writing genomes as fluently as Blake and Byron wrote verses.” In their book Evolving Ourselves, Juan Enriquez and Steve Gullans describe a world where evolution is no longer driven by natural processes. Instead, it is driven by human choices, through what they call unnatural selection and non-random mutation. As a result, we will see the emergence of an entirely new species of human beings. More. The sheer volume Read More ›

From Jef Akst at the Scientist: Researchers uncover thousands of genes whose activity varies between men and women. Drawing on data on organ-, tissue-, and individual-specific gene expression from the Genotype-Tissue Expression (GTex) Portal, Shmuel Pietrokovski and Moran Gershoni of the Weizmann Institute of Science in Israel developed a comprehensive map of genes that are differentially expressed in men and women. … To explore whether other genes expressed differentially between the sexes might be similarly subject to mutation accumulation, Pietrokovski and Gershoni examined some 20,000 protein-coding genes, of which around 6,500 were expressed more in one sex than the other somewhere in the body. And sure enough, selection was effectively weaker in these genes, leading to the pile up of Read More ›

From ScienceDaily: From sediment samples collected at seven archaeological sites, the researchers “fished out” tiny DNA fragments that had once belonged to a variety of mammals, including our extinct human relatives. They retrieved DNA from Neandertals in cave sediments of four archaeological sites, also in layers where no hominin skeletal remains have been discovered. In addition, they found Denisovan DNA in sediments from Denisova Cave in Russia. These new developments now enable researchers to uncover the genetic affiliations of the former inhabitants of many archaeological sites which do not yield human remains. … “By retrieving hominin DNA from sediments, we can detect the presence of hominin groups at sites and in areas where this cannot be achieved with other methods,” Read More ›

From Kacey Deamer at LiveScience: The wild-born, pure Australian desert dingo recently took first place in the World’s Most Interesting Genome competition, and will have her DNA decoded thanks to the Pacific Biosciences SMRT Grant Program. The grant provides genome sequencing for “a particularly fascinating plant or animal.” … “Sandy is truly a gift to science. As a rare, wild-born pure dingo, she provides a unique case study,” Ballard, who submitted the bid to sequence Sandy’s DNA, said in a statement. “Pure dingoes are intermediate between wild wolves and domestic dogs, with a range of non-domesticated traits. So sequencing Sandy’s genome will help pinpoint some of the genes for temperament and behavior that underlie the transition from wild animals to Read More ›

Here is the next video from the AM-Nat conference. In this video, Paul Nelson talks about genes that are both taxonomically-restricted (ORFan genes) and essential to the function of organisms. Then he describes the impact of these findings on common descent.
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From ScienceDaily: Paper. (paywall)Our genome is made up of 6,000 million pieces of DNA that combine four “flavors”: A, C, G and T (Adenine, Cytosine, Guanine and Thymine). It is our Alphabet. But to this base we must add some regulation, just like the spelling and grammar of that alphabet: this is what we call Epigenetics. “In epigenetics, there there are “accents,” called DNA methylation, which means having a C or a methyl-C. The first one usually means that a gene is expressed and active, while the second one implies that a gene is silent and inactive. Our DNA “speaks” when it produces another molecule called RNA (Ribonucleic Acid). Until very recently, it was believed that this molecule was only Read More ›

From ScienceDaily: Most people are familiar with the well-known ‘X’ shape of chromosomes, but in fact chromosomes only take on this shape when the cell divides. Using their new approach, the researchers have now been able to determine the structures of active chromosomes inside the cell, and how they interact with each other to form an intact genome. This is important because knowledge of the way DNA folds inside the cell allows scientists to study how specific genes, and the DNA regions that control them, interact with each other. The genome’s structure controls when and how strongly genes — particular regions of the DNA — are switched ‘on’ or ‘off’. This plays a critical role in the development of organisms Read More ›

From Brian Switek at Nature: A study1 published 2 March in PLOS Genetics gives a rare insight into how genomes change as a species dies out. Towards the end of the last Ice Age, around 11,700 years ago, woolly mammoths ranged through Siberia and into the colder stretches of North America. But by about 4,000 years ago, mainland mammoths had died out and only 300 remained on Wrangel Island off the Siberian coast. In order to examine this disappearance at the genetic level, biologists Rebekah Rogers and Montgomery Slatkin at the University of California, Berkeley, compared the complete genome of a mainland mammoth (Mammuthus primigenius) that lived about 45,000 years ago with that of a Wrangel Island mammoth from about Read More ›

From ScienceDaily: Researchers at the University of Oslo (UiO) keep discovering surprises in the Atlantic cod genome. The most recent study has revealed an unusual amount of short and identical DNA sequences, which might give cod an evolutionary advantage. Or else it is something the cod could live with or else it makes no difference at present. If we don’t have any very definite information, why talk about “evolutionary advantage” at all? Interesting: “We have already found a fish species that has even more tandem repeats than cod, namely the related haddock. Both cod (Latin name: Gadus morhua) and haddock (Melanogrammus aeglefinus) are members of the cod family (Gadidae). This may indicate that the whole group has an increased proportion Read More ›

Well, there are some limitations: From John Timmer at Ars Technica: Nothing about DNA is 100 percent accurate or even as close to the accuracy we’ve come to expect from our electronic bit storage media. Simply synthesizing DNA of a desired sequence will sometimes result in an error, as will amplifying it or decoding it again. And some specific sequences are especially error prone, like long runs of a single base (like TTTTTTTTTT) or stretches that are a mix of Gs and Cs. So any encoding method has to be robust to these issues. Fortunately, we’ve already developed encoding algorithms that stand up to data loss. The authors went with Fountain codes, which allow packet-based data to be transmitted over Read More ›