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What we're talking about DNA: The Web Inside the Strands Thursday, July 31, 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

Next week, I think I will!

Mark Your Cosmic Calendar: 774/775 One wonders if anyone felt it. Did Charlemagne feel it as he led his forces across Pagan Saxon Westphalia, knocking down Irminsuls and making everyone pretend to be Christian or else? Did the people of Bagdad, just becoming the world’s largest city, notice anything aside from their own metro-bigness? Did…

Living in Seattle fosters a certain pessimism when it comes to large companies.  Boeing has always been a poster child for employment uncertainty, regularly hiring large numbers of people and just as regularly, laying them off.  Now, we have Microsoft and Amgen joining the club, with Microsoft layoffs impacting an estimate 1350 people in the area, and…

Physical Science

“By allowing the positive ions to pass through an electric field and thus giving them a certain velocity, it is possible to distinguish them from the neutral, stationary atoms.” -Johannes Stark One of the simplest tenets of electromagnetism — the second of the fundamental forces ever discovered — is that charged particles are accelerated parallel to electric…

Mark Your Cosmic Calendar: 774/775 One wonders if anyone felt it. Did Charlemagne feel it as he led his forces across Pagan Saxon Westphalia, knocking down Irminsuls and making everyone pretend to be Christian or else? Did the people of Bagdad, just becoming the world’s largest city, notice anything aside from their own metro-bigness? Did…

In which Rhett and I talk about awful academic computing systems, Worldcon, our Wikipedia pages, and AAPT meeting envy. Some links: – Rhett’s Wikipedia entry – My Wikipedia entry – The 2014 AAPT Summer Meeting – LonCon 3, this year’s Worldcon – My puzzling Worldcon schedule We have some ideas for what to do next…

Environment

The US Drought Monitor produces an assessment of drought conditions every week. The drought in California has taken a large jump over the last few days, with the highest category, “Exceptional,” jumping from 36.49% to 58.41%. At the start of the calendar year, that category was represented in California by 0%, so this is a…

The cause of “angel wing”, a deformity found in waterfowl such as ducks, geese and swans has been uncovered. Sadly, it is often caused by well-intended people feeding birds foods that are too high in proteins or carbohydrates (bread, crackers and popcorn anyone?). Not surprisingly, this condition mainly impacts birds that live in public areas.…

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…

Humanities

Guest Blog by Diane Bock The Age of Enlightenment is associated with intellectual exchange, reason and sharing of the new ideas. We think of names like Isaac newton, Thomas Jefferson and John Locke. Could this new way of thinking also be connected with coffee? During this period the coffee house emerged as a social center.  People from…

McDonald’s ruling could be a major turning point for the fast food worker movement; federal commission clarifies rules for pregnant workers; miners with black lung may have been wrongly denied benefits; and a new OSHA whistleblower partnership is launched to support commercial carrier workers.

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.

Education

Guest Blog by Diane Bock The Age of Enlightenment is associated with intellectual exchange, reason and sharing of the new ideas. We think of names like Isaac newton, Thomas Jefferson and John Locke. Could this new way of thinking also be connected with coffee? During this period the coffee house emerged as a social center.  People from…

Living in Seattle fosters a certain pessimism when it comes to large companies.  Boeing has always been a poster child for employment uncertainty, regularly hiring large numbers of people and just as regularly, laying them off.  Now, we have Microsoft and Amgen joining the club, with Microsoft layoffs impacting an estimate 1350 people in the area, and…

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…

Politics

McDonald’s ruling could be a major turning point for the fast food worker movement; federal commission clarifies rules for pregnant workers; miners with black lung may have been wrongly denied benefits; and a new OSHA whistleblower partnership is launched to support commercial carrier workers.

Wesley Smith and David Klinghoffer have now replied to yesterday’s post, here and here respectively. Smith’s reply simply ignores all of the main points that I made. He’s mostly sore that I did not discuss two specific cases from his original essay, of people who faced great physical suffering but overcame it to live long…

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…

Medicine

We all seek immortality in some way. Death has been a terror of nearly all since humans first started realizing that everybody dies. After all, no one wants to face the end of everything that one has been, is, and will be, so much so that a key feature of many religions is a belief…

Leave it to my good buddy Mark Crislip over at the Society for Science-Based Medicine to have my back when I don’t have a lot of time for a detailed post. (Basically, I was being a good university and cancer center citizen last night, going out to dinner with a visiting professor, and I ended…

Wesley Smith and David Klinghoffer have now replied to yesterday’s post, here and here respectively. Smith’s reply simply ignores all of the main points that I made. He’s mostly sore that I did not discuss two specific cases from his original essay, of people who faced great physical suffering but overcame it to live long…

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

Mine safety penalties are pretty meaningless if they aren’t paid, and more so if they aren’t assessed.

McDonald’s ruling could be a major turning point for the fast food worker movement; federal commission clarifies rules for pregnant workers; miners with black lung may have been wrongly denied benefits; and a new OSHA whistleblower partnership is launched to support commercial carrier workers.

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