Occupational Health News Roundup [The Pump Handle]

With the new year just around the corner, it’s the perfect time to celebrate worker victories of 2014. At In These Times, reporter Amien Essif gathered a list of the nine most important victories of 2014, writing:



Much has been made of the incredibly hostile climate for labor over the past few decades. Yet this past year, workers still organized on shop floors, went out on strike, marched in the street and shuffled into courthouses to hold their employers accountable, and campaigned hard for those who earned (or, often enough, didn’t earn) their vote. Legislators, meanwhile, tarried on with their anti-worker “right-to-work” laws, and union busters busted up unions. But if state legislatures and the U.S. Supreme Court were harsh on workers, the National Labor Relations Board (NLRB) was refreshingly helpful, passing down several rulings that made organizing easier and wage-theft harder.



Among Essif’s top nine were the nationwide protests organized by fast food workers, which “have brought international attention to the plight of low-wage workers in this country and around the world.” Other victories highlighted include the more than 18,000 workers with American, Virgin and JetBlue airlines who voted to join unions; the passage of San Francisco’s Retail Workers Bill of Rights; court rulings that found that FedEx misclassified employees as independent contractors; and the historic union drive among college athletes at Northwestern University in Illinois.


To read the full list and get inspired to kick off a new year of worker victories, visit In These Times.


In other news:


Charleston Gazette : The nation’s coal mines are on track to report record lows in work-related deaths, writes reporter Dylan Lovan. According to Lovan, federal mine safety officials attribute the good news to changes made in the wake of the 2010 Upper Big Branch disaster in West Virginia, in which 29 miners were killed in an explosion. (Don Blankenship, former CEO of Massey Energy, which owned the mine, was recently indicted on charges that he conspired to violate safety and health standards.) As of about a week ago, 15 coal mining-related deaths happened in 2014; the previous low mark was 18 deaths in 2009. However, Lovan writes that the “improved record has coincided with a plummet in coal production in Appalachia, leaving far fewer mines operating in a region where many of the worst violators have historically been found. Eight of the coal deaths this year have been in Appalachian mines.”


Los Angeles Times : Reporter Amy Hubbard writes that police deaths surged in 2014, with 126 officers killed nationwide while on duty. The number represents a 24 percent increase over 2013. California leads the country in law enforcement deaths, with Texas coming in second, Hubbard writes. However, the article notes that the 2014 toll is less than the average for the last decade, which comes to about 151 deaths per year.


Huffington Post: Fast food company Shake Shack released financial numbers showing that the industry can make money even while paying employees livable wages. Reporter Jillian Berman writes that the company is going public and recently filed the necessary paperwork with the Securities and Exchange Commission showing that Shake Shack is experiencing “blockbuster growth in recent years, even as it pledged to keep paying its workers better than the industry standard.” Shake Shack employees start off at $10 an hour, which is nearly $3 more than the federal minimum wage of $7.25. However, the company is still reporting a mighty profit, Berman reports, with sales growing from $21 million in 2010 to $140 million in 2013. In related Huffington Post news, minimum wage workers in 20 states will get raises in the new year.


Miami Herald : Publix, a major grocery store chain throughout the South, has announced that same-sex couples who are legally married will be eligible for spousal insurance benefits regardless of whether they work in a state where gay marriage has yet to be legalized. Reporter Steve Rothaus writes that the “grocer said that there will be a special 30-day enrollment period for same-sex married employees beginning Jan. 1. Thirty days later, same-sex spouses will receive the same insurance benefits as opposite-sex spouses.” The Florida-based grocery chain owns nearly 2,000 stores in Alabama, Florida, Georgia, North Carolina and Tennessee.


The Atlantic : The publication’s business editors break down the 17 top lessons Americans learned about income inequality in 2014. Among the list: High income inequality is associated with stunted overall economic growth; the middle class is shrinking, with American households becoming more concentrated at the top and bottom of the earnings spectrum; and while service sector jobs are leading the recession recovery, low pay and erratic scheduling practices mean workers are still struggling to meet their most basic needs.


Kim Krisberg is a freelance public health writer living in Austin, Texas, and has been writing about public health for more than a decade.






from ScienceBlogs http://scienceblogs.com/thepumphandle/2014/12/30/occupational-health-news-roundup-187/

With the new year just around the corner, it’s the perfect time to celebrate worker victories of 2014. At In These Times, reporter Amien Essif gathered a list of the nine most important victories of 2014, writing:



Much has been made of the incredibly hostile climate for labor over the past few decades. Yet this past year, workers still organized on shop floors, went out on strike, marched in the street and shuffled into courthouses to hold their employers accountable, and campaigned hard for those who earned (or, often enough, didn’t earn) their vote. Legislators, meanwhile, tarried on with their anti-worker “right-to-work” laws, and union busters busted up unions. But if state legislatures and the U.S. Supreme Court were harsh on workers, the National Labor Relations Board (NLRB) was refreshingly helpful, passing down several rulings that made organizing easier and wage-theft harder.



Among Essif’s top nine were the nationwide protests organized by fast food workers, which “have brought international attention to the plight of low-wage workers in this country and around the world.” Other victories highlighted include the more than 18,000 workers with American, Virgin and JetBlue airlines who voted to join unions; the passage of San Francisco’s Retail Workers Bill of Rights; court rulings that found that FedEx misclassified employees as independent contractors; and the historic union drive among college athletes at Northwestern University in Illinois.


To read the full list and get inspired to kick off a new year of worker victories, visit In These Times.


In other news:


Charleston Gazette : The nation’s coal mines are on track to report record lows in work-related deaths, writes reporter Dylan Lovan. According to Lovan, federal mine safety officials attribute the good news to changes made in the wake of the 2010 Upper Big Branch disaster in West Virginia, in which 29 miners were killed in an explosion. (Don Blankenship, former CEO of Massey Energy, which owned the mine, was recently indicted on charges that he conspired to violate safety and health standards.) As of about a week ago, 15 coal mining-related deaths happened in 2014; the previous low mark was 18 deaths in 2009. However, Lovan writes that the “improved record has coincided with a plummet in coal production in Appalachia, leaving far fewer mines operating in a region where many of the worst violators have historically been found. Eight of the coal deaths this year have been in Appalachian mines.”


Los Angeles Times : Reporter Amy Hubbard writes that police deaths surged in 2014, with 126 officers killed nationwide while on duty. The number represents a 24 percent increase over 2013. California leads the country in law enforcement deaths, with Texas coming in second, Hubbard writes. However, the article notes that the 2014 toll is less than the average for the last decade, which comes to about 151 deaths per year.


Huffington Post: Fast food company Shake Shack released financial numbers showing that the industry can make money even while paying employees livable wages. Reporter Jillian Berman writes that the company is going public and recently filed the necessary paperwork with the Securities and Exchange Commission showing that Shake Shack is experiencing “blockbuster growth in recent years, even as it pledged to keep paying its workers better than the industry standard.” Shake Shack employees start off at $10 an hour, which is nearly $3 more than the federal minimum wage of $7.25. However, the company is still reporting a mighty profit, Berman reports, with sales growing from $21 million in 2010 to $140 million in 2013. In related Huffington Post news, minimum wage workers in 20 states will get raises in the new year.


Miami Herald : Publix, a major grocery store chain throughout the South, has announced that same-sex couples who are legally married will be eligible for spousal insurance benefits regardless of whether they work in a state where gay marriage has yet to be legalized. Reporter Steve Rothaus writes that the “grocer said that there will be a special 30-day enrollment period for same-sex married employees beginning Jan. 1. Thirty days later, same-sex spouses will receive the same insurance benefits as opposite-sex spouses.” The Florida-based grocery chain owns nearly 2,000 stores in Alabama, Florida, Georgia, North Carolina and Tennessee.


The Atlantic : The publication’s business editors break down the 17 top lessons Americans learned about income inequality in 2014. Among the list: High income inequality is associated with stunted overall economic growth; the middle class is shrinking, with American households becoming more concentrated at the top and bottom of the earnings spectrum; and while service sector jobs are leading the recession recovery, low pay and erratic scheduling practices mean workers are still struggling to meet their most basic needs.


Kim Krisberg is a freelance public health writer living in Austin, Texas, and has been writing about public health for more than a decade.






from ScienceBlogs http://scienceblogs.com/thepumphandle/2014/12/30/occupational-health-news-roundup-187/

Ruderhofspitze: fail [Stoat]

Prev: September 9th: Dresdener to Neue Regensburger


Another in the line of mountain climbing posts; I need to get them all out before next year. This one contains few decent photos because I failed due at least in part due to cloud; but its still quite instructive I think. Here’s a portion of the GPS trace for orientation:


ruder-fail


The green dot on the left is the summit, 3474 m. We’ll be going back there in a future post. My high point this day was 3230 ish, say 250 m short, but more than just distance I had very little clue where to go. The green dot on the right is the col, with the Neue Regensburger hut much further right. I got up, pre-packed, for breakfast at 6:30; and gave myself 7 hours, because we wanted to go off to the Franz Senn in the afternoon. That’s a bit tight, but not much, as the most likely fail was what happened, viz, not being able to find the route.


Summitpost waxes quite lyrical about the Ruderhofspitze: Of the 7 summits of the Stubai range over 3400m, Ruderhofspitze is the most central, the 3rd highest, and probably the most remote. This combined makes it a really great mountain and a noble aim. Which is quite Germanic, but also true.


The day started well, with a beautiful cloud sea below the hut:


DSC_4650


However, the clouds somewhat unsportingly chased me up the valley. By the time I’d got to the col (see end of prev for views up to the col) and looked up, I saw this:


DSC_4663


The central spire is the beginning of the Grawawand, clear enough as the long spine just north of my route. At that point – though I didn’t really notice it at the time, and have only just realised it – the cloud is thin enough that the snow couloir leading up into the ?first? snow bowl is visible in the distance. Its more clearly visible in this Summitpost pic and looks somewhat intimidating in that picture. Quite what I’d have done if I’d managed to get that far in decent viz I don’t know.


However, the cloud got worse. Here’s me, a bit further up, sitting on the rocks for 15 mins or so thinking “I wonder if there’ll be a bit enough tear in the cloud to give me some hint of where to go”:


DSC_4670


And here, roughly, is my high point, with me thinking: I really don’t know where I am:


DSC_4675


But judging from the GPS trace, I needed to be off left beyond the rockfall, probably going up the only-vaguely-visible snowpath leading upwards.


And, here’s the hut:


DSC_4694






from ScienceBlogs http://scienceblogs.com/stoat/2014/12/30/ruderhofspitze-fail/

Prev: September 9th: Dresdener to Neue Regensburger


Another in the line of mountain climbing posts; I need to get them all out before next year. This one contains few decent photos because I failed due at least in part due to cloud; but its still quite instructive I think. Here’s a portion of the GPS trace for orientation:


ruder-fail


The green dot on the left is the summit, 3474 m. We’ll be going back there in a future post. My high point this day was 3230 ish, say 250 m short, but more than just distance I had very little clue where to go. The green dot on the right is the col, with the Neue Regensburger hut much further right. I got up, pre-packed, for breakfast at 6:30; and gave myself 7 hours, because we wanted to go off to the Franz Senn in the afternoon. That’s a bit tight, but not much, as the most likely fail was what happened, viz, not being able to find the route.


Summitpost waxes quite lyrical about the Ruderhofspitze: Of the 7 summits of the Stubai range over 3400m, Ruderhofspitze is the most central, the 3rd highest, and probably the most remote. This combined makes it a really great mountain and a noble aim. Which is quite Germanic, but also true.


The day started well, with a beautiful cloud sea below the hut:


DSC_4650


However, the clouds somewhat unsportingly chased me up the valley. By the time I’d got to the col (see end of prev for views up to the col) and looked up, I saw this:


DSC_4663


The central spire is the beginning of the Grawawand, clear enough as the long spine just north of my route. At that point – though I didn’t really notice it at the time, and have only just realised it – the cloud is thin enough that the snow couloir leading up into the ?first? snow bowl is visible in the distance. Its more clearly visible in this Summitpost pic and looks somewhat intimidating in that picture. Quite what I’d have done if I’d managed to get that far in decent viz I don’t know.


However, the cloud got worse. Here’s me, a bit further up, sitting on the rocks for 15 mins or so thinking “I wonder if there’ll be a bit enough tear in the cloud to give me some hint of where to go”:


DSC_4670


And here, roughly, is my high point, with me thinking: I really don’t know where I am:


DSC_4675


But judging from the GPS trace, I needed to be off left beyond the rockfall, probably going up the only-vaguely-visible snowpath leading upwards.


And, here’s the hut:


DSC_4694






from ScienceBlogs http://scienceblogs.com/stoat/2014/12/30/ruderhofspitze-fail/

Dawn spacecraft starts approach toward Ceres


This artist's concept shows NASA's Dawn spacecraft heading toward the dwarf planet Ceres. Image credit: NASA/JPL-Caltech

This artist’s concept shows NASA’s Dawn spacecraft heading toward the dwarf planet Ceres. Image credit: NASA/JPL-Caltech



NASA’s Dawn spacecraft has entered an approach phase in which it will continue to close in on Ceres, the largest object in the asteroid belt between planets Mars and Jupiter. Dawn launched in 2007 and is scheduled to enter Ceres orbit in March 2015.


Dawn recently emerged from solar conjunction, in which the spacecraft is on the opposite side of the sun, limiting communication with antennas on Earth. Now that Dawn can reliably communicate with Earth again, mission controllers have programmed the maneuvers necessary for the next stage of the rendezvous. Dawn is currently 400,000 miles (640,000 kilometers) from Ceres, approaching it at around 450 miles per hour (725 kilometers per hour).


The spacecraft’s arrival at Ceres will mark the first time that a spacecraft has ever orbited two solar system targets. Dawn previously explored the protoplanet Vesta for 14 months, from 2011 to 2012, capturing detailed images and data about that body.


Christopher Russell is principal investigator for the Dawn mission. He said:



Ceres is almost a complete mystery to us. Ceres, unlike Vesta, has no meteorites linked to it to help reveal its secrets. All we can predict with confidence is that we will be surprised.



The two planetary bodies are thought to be different in a few important ways. Ceres may have formed later than Vesta, and with a cooler interior. Current evidence suggests that Vesta only retained a small amount of water because it formed earlier, when radioactive material was more abundant, which would have produced more heat. Ceres, in contrast, has a thick ice mantle and may even have an ocean beneath its icy crust.


Ceres, with an average diameter of 590 miles (950 kilometers), is also the largest body in the asteroid belt, the strip of solar system real estate between Mars and Jupiter. By comparison, Vesta has an average diameter of 326 miles (525 kilometers), and is the second most massive body in the belt.


The next couple of months promise continually improving views of Ceres, prior to Dawn’s arrival. By the end of January, the spacecraft’s images and other data will be the best ever taken of the dwarf planet.


Read more from NASA/JPL






from EarthSky http://earthsky.org/space/dawn-spacecraft-starts-approach-toward-ceres

This artist's concept shows NASA's Dawn spacecraft heading toward the dwarf planet Ceres. Image credit: NASA/JPL-Caltech

This artist’s concept shows NASA’s Dawn spacecraft heading toward the dwarf planet Ceres. Image credit: NASA/JPL-Caltech



NASA’s Dawn spacecraft has entered an approach phase in which it will continue to close in on Ceres, the largest object in the asteroid belt between planets Mars and Jupiter. Dawn launched in 2007 and is scheduled to enter Ceres orbit in March 2015.


Dawn recently emerged from solar conjunction, in which the spacecraft is on the opposite side of the sun, limiting communication with antennas on Earth. Now that Dawn can reliably communicate with Earth again, mission controllers have programmed the maneuvers necessary for the next stage of the rendezvous. Dawn is currently 400,000 miles (640,000 kilometers) from Ceres, approaching it at around 450 miles per hour (725 kilometers per hour).


The spacecraft’s arrival at Ceres will mark the first time that a spacecraft has ever orbited two solar system targets. Dawn previously explored the protoplanet Vesta for 14 months, from 2011 to 2012, capturing detailed images and data about that body.


Christopher Russell is principal investigator for the Dawn mission. He said:



Ceres is almost a complete mystery to us. Ceres, unlike Vesta, has no meteorites linked to it to help reveal its secrets. All we can predict with confidence is that we will be surprised.



The two planetary bodies are thought to be different in a few important ways. Ceres may have formed later than Vesta, and with a cooler interior. Current evidence suggests that Vesta only retained a small amount of water because it formed earlier, when radioactive material was more abundant, which would have produced more heat. Ceres, in contrast, has a thick ice mantle and may even have an ocean beneath its icy crust.


Ceres, with an average diameter of 590 miles (950 kilometers), is also the largest body in the asteroid belt, the strip of solar system real estate between Mars and Jupiter. By comparison, Vesta has an average diameter of 326 miles (525 kilometers), and is the second most massive body in the belt.


The next couple of months promise continually improving views of Ceres, prior to Dawn’s arrival. By the end of January, the spacecraft’s images and other data will be the best ever taken of the dwarf planet.


Read more from NASA/JPL






from EarthSky http://earthsky.org/space/dawn-spacecraft-starts-approach-toward-ceres

2014 Was the Year We Finally Started to Do Something About Climate Change

A year of extreme weather, climate denial, and some hope.



2014 was a big year for climate news, good and bad. In June, the Obama administration took its biggest step yet in the fight against global warming by introducing regulations to limit greenhouse gases from existing power plants. And while there was plenty of anti-science rhetoric and opposition to climate action (no, the polar vortex does not disprove climate change), the year came to a dramatic end with at least three landmark climate-related stories: In September, hundreds of thousands of protesters around the world marched to demand climate action. November’s historic deal between the US and China to curb greenhouse emissions breathed new life into international climate negotiations. And finally, after a series of last-minute compromises, leaders from nearly 200 countries produced the Lima Accord, which, for the first time, calls on all nations to develop plans to limit their emissions. All eyes are now on Paris, where next year world leaders will meet in an attempt to work out a major global warming deal.






from Climate Desk http://climatedesk.org/2014/12/2014-was-the-year-we-finally-started-to-do-something-about-climate-change/

A year of extreme weather, climate denial, and some hope.



2014 was a big year for climate news, good and bad. In June, the Obama administration took its biggest step yet in the fight against global warming by introducing regulations to limit greenhouse gases from existing power plants. And while there was plenty of anti-science rhetoric and opposition to climate action (no, the polar vortex does not disprove climate change), the year came to a dramatic end with at least three landmark climate-related stories: In September, hundreds of thousands of protesters around the world marched to demand climate action. November’s historic deal between the US and China to curb greenhouse emissions breathed new life into international climate negotiations. And finally, after a series of last-minute compromises, leaders from nearly 200 countries produced the Lima Accord, which, for the first time, calls on all nations to develop plans to limit their emissions. All eyes are now on Paris, where next year world leaders will meet in an attempt to work out a major global warming deal.






from Climate Desk http://climatedesk.org/2014/12/2014-was-the-year-we-finally-started-to-do-something-about-climate-change/

Let’s slap ENCODE around some more [Pharyngula]

Since we still have someone arguing poorly for the virtues of the ENCODE project, I thought it might be worthwhile to go straight to the source and and cite an ENCODE project paper, Defining functional DNA elements in the human genome. It is a bizarre thing that actually makes the case for rejecting the idea of high degrees of functionality, which is a good approach, since it demonstrates that they’ve at least seen the arguments against them. But then it sails blithely past those objections to basically declare that we should just ignore the evolutionary evidence.


Here’s the paragraph where they discuss the idea that most of the genome is non-functional.



Case for Abundant Junk DNA. The possibility that much of a complex genome could be nonfunctional was raised decades ago. The C-value paradox refers to the observation that genome size does not correlate with perceived organismal complexity and that even closely related species can have vastly different genome sizes. The estimated mutation rate in protein-coding genes suggested that only up to ∼20% of the nucleotides in the human genome can be selectively maintained, as the mutational burden would be otherwise too large. The term “junk DNA” was coined to refer to the majority of the rest of the genome, which represent segments of neutrally evolving DNA. More recent work in population genetics has further developed this idea by emphasizing how the low effective population size of large-bodied eukaryotes leads to less efficient natural selection, permitting proliferation of transposable elements and other neutrally evolving DNA. If repetitive DNA elements could be equated with nonfunctional DNA, then one would surmise that the human genome contains vast nonfunctional regions because nearly 50% of nucleotides in the human genome are readily recognizable as repeat elements, often of high degeneracy. Moreover, comparative genomics studies have found that only 5% of mammalian genomes are under strong evolutionary constraint across multiple species (e.g., human, mouse, and dog).



Yes, that’s part of it: it is theoretically extremely difficult to justify high levels of function in the genome — the genetic load would be simply too high. We also see that much of the genome is not conserved, suggesting that it isn’t maintained by selection. Not mentioned, though, are other observations, such as the extreme variability in genome size between closely related species that does not seem to be correlated with complexity or function at all, or that much “junk” DNA can be deleted without any apparent phenotypic effect. It’s very clear to anyone with any appreciation of evolutionary constraints at all that the genome is largely non-functional, both on theoretical and empirical grounds.


Their next paragraph summarizes their argument for nearly universal function. It’s strange because it is so orthogonal to the previous paragraph: I’d expect at least some token effort would be made to address the constraints imposed by the evolutionary perspective, but no…the authors make no effort at all to reconcile what evolutionary biologists have said with what they claim to have discovered.


That’s just weird.


Here’s their argument: most of the genome gets biochemically modified to some degree and for some of the time.



Case for Abundant Functional Genomic Elements. Genome-wide biochemical studies, including recent reports from ENCODE, have revealed pervasive activity over an unexpectedly large fraction of the genome, including noncoding and nonconserved regions and repeat elements. Such results greatly increase upper bound estimates of candidate functional sequences. Many human genomic regions previously assumed to be nonfunctional have recently been found to be teeming with biochemical activity, including portions of repeat elements, which can be bound by transcription factors and transcribed, and are thought to sometimes be exapted into novel regulatory regions. Outside the 1.5% of the genome covered by protein-coding sequence, 11% of the genome is associated with motifs in transcription factor-bound regions or high-resolution DNase footprints in one or more cell types, indicative of direct contact by regulatory proteins. Transcription factor occupancy and nucleosome-resolution DNase hypersensitivity maps overlap greatly and each cover approximately 15% of the genome. In aggregate, histone modifications associated with promoters or enhancers mark ∼20% of the genome, whereas a third of the genome is marked by modifications associated with transcriptional elongation. Over half of the genome has at least one repressive histone mark. In agreement with prior findings of pervasive transcription, ENCODE maps of polyadenylated and total RNA cover in total more than 75% of the genome. These already large fractions may be underestimates, as only a subset of cell states have been assayed. However, for multiple reasons discussed below, it remains unclear what proportion of these biochemically annotated regions serve specific functions.



That’s fine. Chunks of DNA get shut down to transcription by enzymatic modification; we’ve known that for a long time, but it’s generally regarded as evidence that that bit of DNA does not have a useful function. But to ENCODE, DNA that is silenced counts as a function. Footprint studies find that lots of bits of DNA get weakly or transiently bound by transcription factors; no surprise, it’s what you’d expect of the stochastic processes of biochemistry. Basically they’re describing behavior as functional that which is more reasonably described as noise in the system, and declaring that it trumps all the evolutionary and genetic and developmental and phylogenetic observations of the genome.


No, I’m being too charitable. They aren’t even trying to explain how that counters all the other evidence — they’re just plopping out their observations and hoping we don’t notice that they are failing to account for everything else.


I rather like Dan Graur’s dismissal of their logic.



Actually, ENCODE should have included “DNA replication” in its list of “functions,” and turn the human genome into a perfect 100% functional machine. Then, any functional element would have had a 100% of being in the ENCODE list.







from ScienceBlogs http://scienceblogs.com/pharyngula/2014/12/30/lets-slap-encode-around-some-more/

Since we still have someone arguing poorly for the virtues of the ENCODE project, I thought it might be worthwhile to go straight to the source and and cite an ENCODE project paper, Defining functional DNA elements in the human genome. It is a bizarre thing that actually makes the case for rejecting the idea of high degrees of functionality, which is a good approach, since it demonstrates that they’ve at least seen the arguments against them. But then it sails blithely past those objections to basically declare that we should just ignore the evolutionary evidence.


Here’s the paragraph where they discuss the idea that most of the genome is non-functional.



Case for Abundant Junk DNA. The possibility that much of a complex genome could be nonfunctional was raised decades ago. The C-value paradox refers to the observation that genome size does not correlate with perceived organismal complexity and that even closely related species can have vastly different genome sizes. The estimated mutation rate in protein-coding genes suggested that only up to ∼20% of the nucleotides in the human genome can be selectively maintained, as the mutational burden would be otherwise too large. The term “junk DNA” was coined to refer to the majority of the rest of the genome, which represent segments of neutrally evolving DNA. More recent work in population genetics has further developed this idea by emphasizing how the low effective population size of large-bodied eukaryotes leads to less efficient natural selection, permitting proliferation of transposable elements and other neutrally evolving DNA. If repetitive DNA elements could be equated with nonfunctional DNA, then one would surmise that the human genome contains vast nonfunctional regions because nearly 50% of nucleotides in the human genome are readily recognizable as repeat elements, often of high degeneracy. Moreover, comparative genomics studies have found that only 5% of mammalian genomes are under strong evolutionary constraint across multiple species (e.g., human, mouse, and dog).



Yes, that’s part of it: it is theoretically extremely difficult to justify high levels of function in the genome — the genetic load would be simply too high. We also see that much of the genome is not conserved, suggesting that it isn’t maintained by selection. Not mentioned, though, are other observations, such as the extreme variability in genome size between closely related species that does not seem to be correlated with complexity or function at all, or that much “junk” DNA can be deleted without any apparent phenotypic effect. It’s very clear to anyone with any appreciation of evolutionary constraints at all that the genome is largely non-functional, both on theoretical and empirical grounds.


Their next paragraph summarizes their argument for nearly universal function. It’s strange because it is so orthogonal to the previous paragraph: I’d expect at least some token effort would be made to address the constraints imposed by the evolutionary perspective, but no…the authors make no effort at all to reconcile what evolutionary biologists have said with what they claim to have discovered.


That’s just weird.


Here’s their argument: most of the genome gets biochemically modified to some degree and for some of the time.



Case for Abundant Functional Genomic Elements. Genome-wide biochemical studies, including recent reports from ENCODE, have revealed pervasive activity over an unexpectedly large fraction of the genome, including noncoding and nonconserved regions and repeat elements. Such results greatly increase upper bound estimates of candidate functional sequences. Many human genomic regions previously assumed to be nonfunctional have recently been found to be teeming with biochemical activity, including portions of repeat elements, which can be bound by transcription factors and transcribed, and are thought to sometimes be exapted into novel regulatory regions. Outside the 1.5% of the genome covered by protein-coding sequence, 11% of the genome is associated with motifs in transcription factor-bound regions or high-resolution DNase footprints in one or more cell types, indicative of direct contact by regulatory proteins. Transcription factor occupancy and nucleosome-resolution DNase hypersensitivity maps overlap greatly and each cover approximately 15% of the genome. In aggregate, histone modifications associated with promoters or enhancers mark ∼20% of the genome, whereas a third of the genome is marked by modifications associated with transcriptional elongation. Over half of the genome has at least one repressive histone mark. In agreement with prior findings of pervasive transcription, ENCODE maps of polyadenylated and total RNA cover in total more than 75% of the genome. These already large fractions may be underestimates, as only a subset of cell states have been assayed. However, for multiple reasons discussed below, it remains unclear what proportion of these biochemically annotated regions serve specific functions.



That’s fine. Chunks of DNA get shut down to transcription by enzymatic modification; we’ve known that for a long time, but it’s generally regarded as evidence that that bit of DNA does not have a useful function. But to ENCODE, DNA that is silenced counts as a function. Footprint studies find that lots of bits of DNA get weakly or transiently bound by transcription factors; no surprise, it’s what you’d expect of the stochastic processes of biochemistry. Basically they’re describing behavior as functional that which is more reasonably described as noise in the system, and declaring that it trumps all the evolutionary and genetic and developmental and phylogenetic observations of the genome.


No, I’m being too charitable. They aren’t even trying to explain how that counters all the other evidence — they’re just plopping out their observations and hoping we don’t notice that they are failing to account for everything else.


I rather like Dan Graur’s dismissal of their logic.



Actually, ENCODE should have included “DNA replication” in its list of “functions,” and turn the human genome into a perfect 100% functional machine. Then, any functional element would have had a 100% of being in the ENCODE list.







from ScienceBlogs http://scienceblogs.com/pharyngula/2014/12/30/lets-slap-encode-around-some-more/

Where are they now? [Stoat]





I wander thro’ each charter’d street,

Near where the charter’d Thames does flow.

And mark in every face I meet

Marks of weakness, marks of woe.

In every cry of every Man,

In every Infants cry of fear,

In every voice: in every ban,

The mind-forg’d manacles I hear



Over the year a number of things have seemed dead exciting, or at least a bit important as viewed from this tiny corner of the blogosphere, but have then faded as duds. Let’s pull them back from obscurity and poke them a bit, pull their strings, and make it look as though they’re alive and laugh at them, before tossing them back on the heap of tossed things.


First off the block, and a worthy example of the genre, is Pattern Recognition in Physics. Killed by Copernicus for being wank, it was re-started by Morner so he could fill it with wank. It seems to be having a thin time: there’s a paper from July, which actually references a WUWT blog post presumably so that even the most dim-witted can tell that its nonsense; and one from November featuring a pentagram.


Rather duller, in April AW proposed some kind of “septic.org” but I think even he realised is was a dumb idea; AFAIK it was still-born; similarly the NIPCC. The long-awaited AW et al. “paper” remains at the concept stage and so forgotten that only I seem to bother mock it.


Perhaps the best WATN was l’affaire Lennart Bengtsson in May (for those who forget easily: LB had a paper rejected for being unoriginal; got miffed, and joined the GWPF in a fit of madness; left when all his friends told him the GWPF were nutters; and then blamed everyone but himself for his poor judgement). Its all gone quiet now; spies report that LB has gone back to writing right-wing non-climate politics on climate blogs. But since he has had the decency to do this in Swedish, no one has been reading what he has written; I’ll assume that’s deliberate on his part, and respect his privacy. You can read an analysis of it here (well, actually you probably can’t cos its in foreign, but you can try google translate; or Eli has some earlier stuff, it all looks very similar).


Does the battle of the graphs qualify? In it, Monkers threatened to sue the pants off almost everyone, and then quietly didn’t. But that’s hardly news.


Not-Prof Salby was so 2013 (some took a while to catch up; post to the antipodes can take a while), but questioning the idea that the CO2 rise is anthro seems to be flypaper that every wacko gets stuck to eventually as they buzz around aimlessly. AW hit it, several times but the slightly-surprise victim was “Dr” Roy Spencer who you’d have thought would know better.


Sea ice in 2014 was dull, like 2013. There are still a few – Wadhams springs to mind – who predict collapse-within-a-few-years but I don’t think anyone is listening. The denialists wouldn’t bet on the future though others will. Its still all to play for in the coming years.


Oh, and not-really-fitting but close enough for government work is Spirit of Mawson which returns in the Graun.


Did I miss any?


Refs


* London, by Blake






from ScienceBlogs http://scienceblogs.com/stoat/2014/12/30/where-are-they-now/




I wander thro’ each charter’d street,

Near where the charter’d Thames does flow.

And mark in every face I meet

Marks of weakness, marks of woe.

In every cry of every Man,

In every Infants cry of fear,

In every voice: in every ban,

The mind-forg’d manacles I hear



Over the year a number of things have seemed dead exciting, or at least a bit important as viewed from this tiny corner of the blogosphere, but have then faded as duds. Let’s pull them back from obscurity and poke them a bit, pull their strings, and make it look as though they’re alive and laugh at them, before tossing them back on the heap of tossed things.


First off the block, and a worthy example of the genre, is Pattern Recognition in Physics. Killed by Copernicus for being wank, it was re-started by Morner so he could fill it with wank. It seems to be having a thin time: there’s a paper from July, which actually references a WUWT blog post presumably so that even the most dim-witted can tell that its nonsense; and one from November featuring a pentagram.


Rather duller, in April AW proposed some kind of “septic.org” but I think even he realised is was a dumb idea; AFAIK it was still-born; similarly the NIPCC. The long-awaited AW et al. “paper” remains at the concept stage and so forgotten that only I seem to bother mock it.


Perhaps the best WATN was l’affaire Lennart Bengtsson in May (for those who forget easily: LB had a paper rejected for being unoriginal; got miffed, and joined the GWPF in a fit of madness; left when all his friends told him the GWPF were nutters; and then blamed everyone but himself for his poor judgement). Its all gone quiet now; spies report that LB has gone back to writing right-wing non-climate politics on climate blogs. But since he has had the decency to do this in Swedish, no one has been reading what he has written; I’ll assume that’s deliberate on his part, and respect his privacy. You can read an analysis of it here (well, actually you probably can’t cos its in foreign, but you can try google translate; or Eli has some earlier stuff, it all looks very similar).


Does the battle of the graphs qualify? In it, Monkers threatened to sue the pants off almost everyone, and then quietly didn’t. But that’s hardly news.


Not-Prof Salby was so 2013 (some took a while to catch up; post to the antipodes can take a while), but questioning the idea that the CO2 rise is anthro seems to be flypaper that every wacko gets stuck to eventually as they buzz around aimlessly. AW hit it, several times but the slightly-surprise victim was “Dr” Roy Spencer who you’d have thought would know better.


Sea ice in 2014 was dull, like 2013. There are still a few – Wadhams springs to mind – who predict collapse-within-a-few-years but I don’t think anyone is listening. The denialists wouldn’t bet on the future though others will. Its still all to play for in the coming years.


Oh, and not-really-fitting but close enough for government work is Spirit of Mawson which returns in the Graun.


Did I miss any?


Refs


* London, by Blake






from ScienceBlogs http://scienceblogs.com/stoat/2014/12/30/where-are-they-now/

Why I Do Science: Kandis Elliot



Plant Modifications poster by Kandis Elliot. Click on the image for a larger size.



Kandis Elliot didn’t think she’d make art her profession. “When I was in high school and thinking of a career, we were told back then that you can't make a living as an artist and if you're smart enough you go into the sciences,” said Elliot. She was smart enough- and interested enough- in the sciences to graduate from the University of Wisconsin with a BA in biology and Masters in zoology. “In all these courses I drew like crazy without letting too many people see these drawings,” she recalls.


But art drew her back and after her advanced degree Elliot returned to school, this time in a technical college program in commercial art. Shortly after that, the perfect opportunity came knocking. “I was out about a month when four people, four or five people called me up the same day and said, ‘The botany artist is leaving, go apply for a position,’" Elliot says. The position was as staff artist for the University of Wisconsin’s Botany department, one of the best in the country.


Elliot was strong on science and gifted in art, but she also had another card up her sleeve, “I knew back in 1988 there was this new thing called Apple Computer where you could draw a perfect square. You didn't need a right angle. You could draw a perfect circle, you didn't need a compass. And I said, ‘Surely you want to do this kind of work on a computer.’ And they said, ‘Alright, let's try it.’"


fungi poster

Kandis Elliot's poster "Introduction to Fungi". Click on the image for a larger size.



The idea of using computers appealed to the scientists, but Elliot had never actually used one. So she went to the campus computer center, held up a hundred dollar bill, offering it to anyone who could teach her how to use an Apple. That investment paid off in a position she held for over two decades. As the botany artist, she created charts and graphs for countless scientific publications and perfected the art of digital painting. Starting with less-than-perfect images taken by scientists in the field, or dried, pressed plant samples, Elliot’s job was to transform them into striking, painterly objects that could hold a student’s attention.


“It makes your eye dwell on the picture a little bit longer,” says Elliot, “I guess the only way I can describe it is that the paintings say, ‘Look at me.’”


After years spent shining the spotlight on nature’s botanical beauty, Kandis Elliot retired from the University of Wisconsin in 2011. But not before receiving one of the highest honors in her profession. A poster titled “Introduction to Fungi” won the 2010 prize for information graphics in the National Science Foundation’s International Science & Engineering Visualization Challenge. Mushrooms capped a brilliant career.


This video was updated from the original by producer Eleanor Nelson.




Tags: , , , , , , , , , , , , ,





from QUEST http://science.kqed.org/quest/video/why-i-do-science-kandis-elliot/?utm_source=rss&utm_medium=rss&utm_campaign=why-i-do-science-kandis-elliot


Plant Modifications poster by Kandis Elliot. Click on the image for a larger size.



Kandis Elliot didn’t think she’d make art her profession. “When I was in high school and thinking of a career, we were told back then that you can't make a living as an artist and if you're smart enough you go into the sciences,” said Elliot. She was smart enough- and interested enough- in the sciences to graduate from the University of Wisconsin with a BA in biology and Masters in zoology. “In all these courses I drew like crazy without letting too many people see these drawings,” she recalls.


But art drew her back and after her advanced degree Elliot returned to school, this time in a technical college program in commercial art. Shortly after that, the perfect opportunity came knocking. “I was out about a month when four people, four or five people called me up the same day and said, ‘The botany artist is leaving, go apply for a position,’" Elliot says. The position was as staff artist for the University of Wisconsin’s Botany department, one of the best in the country.


Elliot was strong on science and gifted in art, but she also had another card up her sleeve, “I knew back in 1988 there was this new thing called Apple Computer where you could draw a perfect square. You didn't need a right angle. You could draw a perfect circle, you didn't need a compass. And I said, ‘Surely you want to do this kind of work on a computer.’ And they said, ‘Alright, let's try it.’"


fungi poster

Kandis Elliot's poster "Introduction to Fungi". Click on the image for a larger size.



The idea of using computers appealed to the scientists, but Elliot had never actually used one. So she went to the campus computer center, held up a hundred dollar bill, offering it to anyone who could teach her how to use an Apple. That investment paid off in a position she held for over two decades. As the botany artist, she created charts and graphs for countless scientific publications and perfected the art of digital painting. Starting with less-than-perfect images taken by scientists in the field, or dried, pressed plant samples, Elliot’s job was to transform them into striking, painterly objects that could hold a student’s attention.


“It makes your eye dwell on the picture a little bit longer,” says Elliot, “I guess the only way I can describe it is that the paintings say, ‘Look at me.’”


After years spent shining the spotlight on nature’s botanical beauty, Kandis Elliot retired from the University of Wisconsin in 2011. But not before receiving one of the highest honors in her profession. A poster titled “Introduction to Fungi” won the 2010 prize for information graphics in the National Science Foundation’s International Science & Engineering Visualization Challenge. Mushrooms capped a brilliant career.


This video was updated from the original by producer Eleanor Nelson.




Tags: , , , , , , , , , , , , ,





from QUEST http://science.kqed.org/quest/video/why-i-do-science-kandis-elliot/?utm_source=rss&utm_medium=rss&utm_campaign=why-i-do-science-kandis-elliot