What we're talking about DNA: The Web Inside the Strands Tuesday, July 29, 2014

DNA: The Web Inside the Strands

Science and its interpretation is wonderful. Today I saw a post on Twitter from @LAbizar, referencing an @GEN, post that stated 8.2% of Human DNA is Functional with a link to a GEN article: “Surprise: Only 8.2% of Human DNA Is Functional.” The GEN writeup cited a PLoS Genetics article, “8.2% of the Human Genome Is Constrained: Variation in Rates of…

But we have to be clear that it is only a hypothesis at this point. I was reading about domestication syndrome (DS) — selecting animals for domestication has a whole collection of secondary traits that come along for the ride, in addition to tameness. We are selecting for animals that tolerate the presence of humans,…

Researchers have successfully created a draft sequence of the complete genome of a 700,000 year old horse from a bone fragment extracted from permafrost in the Yukon Territory (Canada). This is the oldest specimen ever sequenced by almost 10-fold. Prior sequencing of the whole genome from a hominid from Siberia who lived 80,000 years ago…

Only 1% of the human genome codes for proteins, which might make you wonder what the rest of the nucleotide sequence is good for. In 2012 the Encyclopedia of DNA Elements (or ENCODE) announced that a full 80% of the genome played a biochemical role, interacting with proteins in some way. But a new study says it takes only about 8% of our non-protein-coding genes to make us human. This is the percentage of genes that are 'conserved' by the human species: change one of these genes, and you'll alter the fitness of the individual. These genes evolve slowly (although not as slowly as protein-coding genes). The rest of the genome is free to drift about and see what happens.

On Pharyngula, PZ Myers wonders why, when you tame a canine species (thus reducing the size of its adrenal gland), you automatically get floppy ears, spotted coats, and neoteny. PZ Myers says of genes, "everything is tangled together in interacting patterns of connectivity, so you often get unexpected results from single inputs." A new paper argues that an embryonic population of cells known as the neural crest explains why domestication causes changes throughout a mammal's body.

Channel Surfing

Life Science

“HIV mutates a lot”. People ‘get’ that. Why is HIV hard to stop? Why is HIV hard to treat? “HIV mutates a lot”. But HIV does not mutate willy-nilly. It mutates at an evolutionarily defined rate. The reverse transcriptase enzyme makes mistakes during replication that are beneficial to HIV– creating a diverse population, a quasispecies,…

“Ignorance is hardly unusual, Miss Davar. The longer I live, the more I come to realize that it is the natural state of the human mind. There are many who will strive to defend its sanctity and then expect you to be impressed with their efforts.” -Brandon Sanderson At the risk of inflaming everyone who…

Physical Science

“From a little spark may burst a flame.” -Dante Alighieri It’s hard to believe that less than two years ago, we hadn’t even begun Messier Monday, and now there are fewer than 20 objects left! Today represents a great milestone, as we finally take on the last of fifteen galaxies that Messier catalogued as part of the…

“General Kenobi. Years ago you served my father in the Clone Wars. Now he begs you to help him in his struggle against the Empire. I regret that I am unable to convey my father’s request to you in person, but my ship has fallen under attack, and I’m afraid my mission to bring you…

“As far as the laws of mathematics refer to reality, they are not certain; and as far as they are certain, they do not refer to reality.” -Albert Einstein It’s been a fabulous, fun-filled week over at the main Starts With A Bang blog, and we’ve taken on a variety of topics that range from the small…

Environment

On Significant Figures, Peter Gleick examines the rather relaxed attitudes of some Californians to an extreme drought fostered by three years of dry weather. Gleick writes “reservoirs are at record low levels. Deliveries of surface water to some farmers are lower than at any time in recent history. Streams are drying up and fisheries are being…

No happy ending for us tonight alas. We had a good start, and not one but two whistles on Tabs into Grassy, and all of that was the plan, but we lacked the oomph to close down the last half length plus the overlap. Which was the bit that wasn’t under our control. We also…

The original hoser, I’m told by an unimpeachable source from way up in Canada, was the guy who went out to his front yard in the middle of the winter and hosed down the lawn in order to make some flat ice, so he and his friends could play hockey. A better way to get…

Humanities

Many hourly workers struggle to get by with too few hours and schedules that are erratic and subject to last-minute changes. The Schedules that Work Act, just introduced by Representative George Miller and Congressional colleagues, aims to help hourly workers achieve flexible and predictable schedules that let them balance work with other obligations.

Lance Mannion has a really nice contrast between childhood now and back in the 1970′s that doesn’t go in the usual decline-of-society direction. He grew up not too far from where I now live, and after describing his free-ranging youth, points out some of the key factors distinguishing it from today, that need to be…

Nearly two years ago, American schoolchildren began sitting down to healthier school lunches, thanks to new federal nutrition guidelines. Media reports of the nutrition upgrade weren’t terribly encouraging, with stories of unhappy kids, unhappy parents and politicians who think addressing childhood obesity is an example of the “nanny state.” However, recent research has found what most parents probably already know: Kids are pretty adaptable — they just need some time.

Education

I should really know better than to click any tweeted link with a huff.to shortened URL, but for some reason, I actually followed one to an article with the limited-reach clickbait title Curious About Quantum Physics? Read These 10 Articles!. Which is only part one, because Huffington Post, so it’s actually five articles. Three of…

From the current issue of The New York Times Magazine: One of the most vivid arithmetic failings displayed by Americans occurred in the early 1980s, when the A&W restaurant chain released a new hamburger to rival the McDonald’s Quarter Pounder. With a third-pound of beef, the A&W burger had more meat than the Quarter Pounder;…

Like Aesop’s fable, rats have another reason to be envious of elephants. Elephants also have significantly more genes that can detect different smells (i.e. olfactory receptor genes) than other super-sniffers like rats and dogs. In fact, compared to 13 other species, African elephants have 1,948 genes related to smell putting them ahead of the previous…

Politics

Consider this profile of NPR reporter Diane Rehm, in which she relates the harrowing story of her husband’s final days: His Parkinson’s disease had become unbearable. “He just kept getting weaker,” the NPR host told NBC News. “We called in the doctor and John said to him: `I am ready today.’ He said `I can…

But they did not call it that then. This isn’t actually the anniversary of the war, but it is the wedding anniversary plus one month of Archduke Ferdinand and his wife, Sophie, and the day the two of them were assassinated by Mlada Bosna. Today, one month later one hundred years ago, the first of…

Lance Mannion has a really nice contrast between childhood now and back in the 1970′s that doesn’t go in the usual decline-of-society direction. He grew up not too far from where I now live, and after describing his free-ranging youth, points out some of the key factors distinguishing it from today, that need to be…

Medicine

Consider this profile of NPR reporter Diane Rehm, in which she relates the harrowing story of her husband’s final days: His Parkinson’s disease had become unbearable. “He just kept getting weaker,” the NPR host told NBC News. “We called in the doctor and John said to him: `I am ready today.’ He said `I can…

Regular readers will know that über-quack Mike Adams got himself into a bit of a pickle last week. Basically, he wrote a now-infamous post in which he likened scientists working on GMOs to Nazi scientists and pro-science bloggers refuting the sort of nonsensical fear mongering (from a scientific perspective) Adams and other anti-GMO activists like…

There is an Ebola Outbreak currently underway in several West African countries, mainly Sierra Leone, Liberia, and Guinea. This is the most extreme known Ebola outbreak to date. The first known outbreak of this virus was in 1976, and there have been several instances since then ranging from single cases (which by definition are not…

Brain & Behavior

Like Aesop’s fable, rats have another reason to be envious of elephants. Elephants also have significantly more genes that can detect different smells (i.e. olfactory receptor genes) than other super-sniffers like rats and dogs. In fact, compared to 13 other species, African elephants have 1,948 genes related to smell putting them ahead of the previous…

The discovery of  this non-avian dinosaur, Changyuraptor yangi, that lived 125 million years ago suggests that flight came before birds. The fossil was discovered in the Liaoning Province of northeastern China by Luis Chiappe from the Natural History Museum in Los Angeles, CA. At nearly 4 feet long, it is the largest so-called 4-winged dinosaur discovered. The term “4-winged”…

Brandy Velten (doctoral student) and Dr. Kenneth Welch (Comparative Physiologist) from the University of Toronto wanted to know whether birds with very different speeds at which they flaps their wings (i.e. wingbeat frequencies) had correspondingly varying types of myosin proteins in their muscles. Their findings were published in the American Journal of Physiology last month.…

Technology

Like Aesop’s fable, rats have another reason to be envious of elephants. Elephants also have significantly more genes that can detect different smells (i.e. olfactory receptor genes) than other super-sniffers like rats and dogs. In fact, compared to 13 other species, African elephants have 1,948 genes related to smell putting them ahead of the previous…

If the IT resources exist to simulate 90 billion neurons and 100 trillion connections between them, mediated by dozens of different neurotransmitters and organized into highly specialized networks, there’s still no reason to expect intelligence to emerge or a ghost to glom on to the machine.

It looks like a simple piece of paper and it’s nearly as cheap, ideally costing just pennies. But despite its small size, it’s poised to make an enormous impact and potentially save thousands of lives.

Information Science

I have some theories about both children’s books and about science-themed graphic works. There are basically two kinds of children’s books: those that are designed to please children versus those that are designed to attract the adults that buy most children’s books. There are also basically two kinds of science-themed graphic works: those that are…

When Bethany Boggess first debuted her online mapping project, she didn’t expect it to attract so much attention. But within just six months of its launch, people from all over the world are sending in reports and helping her build a dynamic picture of the lives and deaths of workers.

Phew!! I just submitted my abstract for the Comparative Physiology meeting that will be held this October. Judging from the preliminary program, it is going to be an exciting meeting! Here is a description of the meeting from the American Physiological Society’s website: “Comparative physiology takes advantage of the diverse evolutionary histories and ecological settings…

Jobs

This week’s snapshot of just one work-related fatality. This one occurred on July 21 at a construction site in Fort Lauderdale, Florida.

When Bethany Boggess first debuted her online mapping project, she didn’t expect it to attract so much attention. But within just six months of its launch, people from all over the world are sending in reports and helping her build a dynamic picture of the lives and deaths of workers.

An OSHA news release about a cell tower inspection gave me reason to visit the White House’s Recovery.gov website.