Genomics

From ecosystem scientist Sean Nee at The Conversation: [Contention 1:] We humans like to think of ourselves as on the top of the heap compared to all the other living things on our planet. Life has evolved over three billion years from simple one-celled creatures through to multicellular plants and animals coming in all shapes and sizes and abilities. In addition to growing ecological complexity, over the history of life we’ve also seen the evolution of intelligence, complex societies and technological invention, until we arrive today at people flying around the world at 35,000 feet discussing the in-flight movie. Yes. It’s almost like we are in charge of the planet, at least morally and intellectually. Researchers assumed that that meant Read More ›

From Karen Zusi at The Scientist: The genetic code—the digital set of instructions often laid out in tidy textbook tables that tells the ribosome how to build a peptide—is identical in most eukaryotes. But as with most rules, there are exceptions. During a recent project on genome rearrangement in ciliates, Mariusz Nowacki, a cell biologist at the University of Bern in Switzerland, and his team stumbled across two striking deviants. Ciliates, complex protozoans with two nuclei, are known to translate RNA transcripts in unorthodox ways. Nowacki’s team, however, discovered that Condylostoma magnum and an unclassified Parduczia species had gone even further, reassigning all of the traditional “stop” codons (UGA, UAA, and UAG) to amino acids. “It didn’t make sense in Read More ›

From Anna Azvolinsky at The Scientist: Multiple stressful events during childhood may have a greater impact on telomere length in adulthood compared to stressful events faced during adulthood. While the accumulation of stressful events throughout life increases the chance of having shorter telomeres later in life, adversities experienced during childhood appeared to have the greatest effect on these chromosome caps, according to a study published today (October 3) in PNAS. Each additional adverse event during childhood was associated with an 11 percent-increased odd of shorter telomeres—a marker of cellular aging—past age 50, the authors reported. The findings “offer new insights into what types of stressors may potentially be most harmful in impacting biological aging markers,” Judith Carroll, who studies the Read More ›

From ScienceDaily: A person’s DNA sequence can provide a lot of information about how genes are turned on and off, but new research out of Case Western Reserve University School of Medicine suggests the 3-D structure DNA forms as it crams into cells may provide an additional layer of gene control. As long strands of DNA twist and fold, regions far away from each other suddenly find themselves in close proximity. The revolutionary study suggests interactions between distant regions may affect how genes are expressed in certain diseases. … According to Scacheri, “The big surprise was when we crunched the numbers and compared the risk associated with the amount of heritability that could be explained by the outside variants. By Read More ›

No, we know… This is not our high school genetics. From the Salk Institute: LA JOLLA—Our brains contain a surprising diversity of DNA. Even though we are taught that every cell in our body has the same DNA, in fact most cells in the brain have changes to their DNA that make each neuron a little different. Now researchers at the Salk Institute and their collaborators have shown that one source of this variation—called long interspersed nuclear elements or L1s—are present in 44 to 63 percent of healthy neurons and can not only insert DNA but also remove it. Previously, these L1s were known to be small bits of DNA called “jumping genes” that copy and paste themselves throughout the Read More ›

In this next installment from the Alternatives to Methodological Naturalism (AM-Nat) conference, Salvador Cordova gives us his perspective on epistemology, which he calls “Gambler’s Epistemology,” which intends to be a metaphysically neutral way of analyzing claims based on their costs and payoff possibilities. Cordova shows that naturalism does not have a history of high payoffs, and that the ENCODE and similar projects by the NIH are good gambling bets but have caused consternation for those metaphysically committed to naturalism, which has historically been shown to be impractical.

From ScienceDaily: Now, a study has found that, contrary to a previous controversial proposal, tardigrades have not acquired a significant proportion of their DNA from other organisms. Instead, new analysis from the University of Edinburgh shows that nearly all of what was proposed to be foreign DNA was simply bacterial contamination. Controversy had been prompted by a November 2015 study suggesting that one-sixth — some 17 per cent — of the DNA of freshwater tardigrades could be traced to transfers from bacteria. The scientific world was abuzz with speculation following this suggestion that tardigrades had the ability to pick up and reuse DNA from other species. More. Everything else that’s weird about them is still weird though: “Tardigrades, also known Read More ›

  My previous post about information jumps, based on the example of the Prickle 1 protein, has generated a very interesting discussion, still ongoing. I add here some more thoughts about an aspect which has not been really analyzed in the first post, and which can probably contribute to the discussion. I will give here only a very quick summary of the basic issue, inviting all those interested to check my first post: Homologies, differences and information jumps and the following discussion, amounting at present at more than 500 posts. So: Prickle 1 is an interesting protein, with rich functional properties, in general still not well understood. With reference to the human form, I have identified two different parts in the protein. Read More ›

From ScienceDaily: A research project has tested the hypothesis that Asian common toad populations across Southeast Asia are genetically similar owing to their commensal nature and high dispersive ability. To the researchers’ surprise, three genetically divergent groups of toads were found, each in a different geographic area (mainland Southeast Asia, coastal Myanmar and the islands of Java and Sumatra). The ranges of these three groups of toads were also found to have statistically different climates. This suggests that the toads may be adapting to local climatic conditions and evolving into separate species. Thus, toads of one group may not be able to disperse and persist within the range of another group because of climatic differences. More. Of course, we would Read More ›

Ann Gauger on “de novo” genes at Evolution News & Views: De novo genes are genes that are present in a particular species or taxonomic group, and not present in any others. Why are they there and where did they come from? To answer these questions we have to first deal with some important assumptions of evolutionary biology. Sometimes called “orphan genes” because they have no parents we can identify. Because the field of research is still developing, different research groups use different criteria for deciding what counts as a TRG. For example, one recent estimate says that there are 634 genes that appear to have arisen de novo in the human genome, as compared with the chimpanzee and macaque Read More ›

From Sharon Begley at Stat News (“reporting from the frontiers of health and medicine”): ore than a decade after leading geneticists argued that race is not a true biological category, many studies continue to use it, harming scientific understanding and possibly patients, researchers argued in a provocative essay in Science on Thursday. “We thought that after the Human Genome Project, with [its leaders] saying it’s time to move beyond race as a biological marker, we would have done that,” said Michael Yudell, a professor in the Dornsife School of Public Health at Drexel University and coauthor of the Science paper calling on journals and researchers to stop using race as a category in genetics studies. “Yet here we are, and Read More ›

From Nature: Opaekaa Falls, like much of Kauai, is teeming with feral chickens — free-ranging fowl related both to the domestic breeds that lay eggs or produce meat for supermarket shelves and to a more ancestral lineage imported to Hawaii hundreds of years ago. … The process of domestication has moulded animals and their genomes to thrive in human environments. Traits that ensure survival in the wild often give way to qualities that benefit humans, such as docility and fast growth. Feralization looks, on its surface, like domestication in reverse. But closer inspection suggests that the chickens of Kauai are evolving into something quite different from their wild predecessors, gaining some traits that reflect that past, but maintaining others that Read More ›

Commenting on a recent PLOS paper, Ann Gauger writes at Evolution News & Views, A recent paper in PLOS Genetics considers the origins of new “genes” in humans and chimps. By comparing RNA sequences, researchers identified over 600 transcriptionally active “genes” that appear to be present only in humans and not in chimps or the other mammal species tested. They claimed that these “genes” were the product of evolution from previously non-coding, untranscribed DNA. They argued that some of the “genes” are made into proteins and perhaps may be subject to selection, meaning that they are evolving. I put genes in quote because this is not what the term gene typically means. It used to be that a gene was Read More ›

The remarkable “powers” of evolution are now shown to degrade (aka “mutate”) the human genes essential to intelligence.

Remarkably, they found that some of the same genes that influence human intelligence in healthy people were also the same genes that cause impaired cognitive ability and epilepsy when mutated, networks which they called M1 and M3.

Read More ›

… is like trusting five-year-olds to edit the Constitution From International Conference on Human Gene Editing (A Global Summit): It would be irresponsible to proceed with any clinical use of germline editing unless and until (i) the relevant safety and efficacy issues have been resolved, based on appropriate understanding and balancing of risks, potential benefits, and alternatives, and (ii) there is broad societal consensus about the appropriateness of the proposed application. Moreover, any clinical use should proceed only under appropriate regulatory oversight. At present, these criteria have not been met for any proposed clinical use: the safety issues have not yet been adequately explored; the cases of most compelling benefit are limited; and many nations have legislative or regulatory bans Read More ›