Saturday, May 30, 2015

The Class of 2015

Alyssa Davis, Will Kimball and Elise Gould
Economic Policy Institute
May 27, 2015

Some Key Findings:
  • Wages of young college and high school graduates are performing poorly—and are substantially lower today than in 2000. The real (inflation-adjusted) wages of young high school graduates are 5.5 percent lower today than in 2000, and the wages of young college graduates are 2.5 percent lower.
  • Women in particular have seen large declines in hourly wages, among both high school and college graduates.
  • Young high school and college graduates’ wages follow the same trends as those of older graduates, signaling that the slowdown in young graduates’ wages stems from a wider wage growth problem.
  • The overall unemployment rates, idling rates, and wages of young graduates mask substantial racial and ethnic disparities in these measures.
  • The unemployment rates of blacks and Hispanics are substantially higher than the unemployment rates of white non-Hispanics, for both young high school graduates and young college graduates.
  • The share of young black and Hispanic graduates who remain unemployed and not enrolled in further schooling is substantially higher than that of white graduates.
  • The cost of higher education has grown far more rapidly than median family income, leaving students with little choice but to take out loans which, upon graduating into a labor market with limited job opportunities, they may not have the funds to repay. From the 1983–1984 enrollment year to the 2013–2014 enrollment year, the inflation-adjusted cost of a four-year education, including tuition, fees, and room and board, increased 125.7 percent for private school and 129.0 percent for public school (according to the College Board).
  • Between 2004 and 2014, there was a 92 percent increase in the number of student loan borrowers and a 74 percent increase in average student loan balances (according to the Federal Reserve Bank of New York).
  • Due to young college graduates’ limited job opportunities, stagnating wages, and the rising cost of higher education, college is becoming an increasingly difficult investment.
  • Graduating in a weak economy has long-lasting economic consequences. Economic research suggests that for the next 10 to 15 years, those in the Class of 2015 will likely earn less than if they had graduated when job opportunities were plentiful.


Wednesday, May 27, 2015

Chromosomal rearrangements as barriers to genetic homogenization between archaic and modern humans

Rebekah L. Rogers


Chromosomal rearrangements, which shuffle DNA across the genome, are an important source of divergence across taxa that can modify gene expression and function. Using a paired-end read approach with Illumina sequence data for archaic humans, I identify changes in genome structure that occurred recently in human evolution. Hundreds of rearrangements indicate genomic trafficking between the sex chromosomes and autosomes, raising the possibility of sex-specific changes. Additionally, genes adjacent to genome structure changes in Neanderthals are associated with testis-specific expression, consistent with evolutionary theory that new genes commonly form with expression in the testes. I identify one case of new-gene creation through transposition from the Y chromosome to chromosome 10 that combines the 5' end of the testis-specific gene Fank1 with previously untranscribed sequence. This new transcript experienced copy number expansion in archaic genomes, indicating rapid genomic change. Finally, loci containing genome structure changes show diminished rates of introgression from Neanderthals into modern humans, consistent with the hypothesis that rearrangements serve as barriers to gene flow during hybridization. Together, these results suggest that this previously unidentified source of genomic variation has important biological consequences in human evolution.

Monday, May 25, 2015

Collapse of the world’s largest herbivores

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Related posts on this blog:

Echo, an Unforgettable Elephant

Business, government, education need to go back to school on STEM skills: report

Canadian employers have been complaining about a skills shortage of science, technology, engineering and math grads but as Simona Chiose reports, many STEM grads have just as much trouble finding jobs in their field as those in other disciplines.
The Globe and Mail

Sunday, May 24, 2015

Weighing the Promises of Big Genomics

Buzzfeed Ideas
David Dobbs
May. 21, 2015, at 6:01 a.m

“Success in sight: The eyes have it!” Thus the scientific journal Gene Therapy greeted the news, in 2008, that an experimental treatment was restoring vision to 12 people born with a congenital disorder that slowly left them blind. Healthy genes were injected to replace the faulty mutations in the patients’ retinas, allowing an 8-year-old to ride a bike for the first time. A mother finally saw her child play softball. Every patient, the researchers reported, showed “sustained improvement.” Five years in, a book declared this “breakthrough” — a good-gene-for-bad-gene swap long pursued as a silver bullet for genetic conditions — as The Forever Fix.

Earlier this month, two of the three research teams running these trials quietly reported that the therapy’s benefit had peaked after three years and then begun to fade. The third trial says its patients continue to improve. But in the other two, all the patients tracked for five years or more were again losing their sight.

Not all gene therapy ends in Greek-caliber tragedy. But these trials serve as a sadly apt parable for the current state of human genetics. This goes especially for the big-data branch of human genetics called Big Genomics. In five years of talking to geneticists, biologists, and historians, I’ve found that the field is too often distinguished by the arc shown here: alluring hope, celebratory hype, dark disappointment.

We live in an age of hype. But the overselling of the Age of Genomics — the hype about the hope, the silence about the disappointments — gobbles up funding that we might spend better elsewhere, warps the expectations of patients and the incentives of scientists, and has implications even for people who pay genetics scant attention. Many hospitals, for instance, are now collecting genetic information from patients that they may market to “research partners” such as drug companies. Some take more care than others do to secure informed consent. (Had blood drawn lately? Read everything you signed that day?) It’s not just that they’re selling you this stuff. They may well be selling you. And the sale depends on an exaggerated picture of genetic power and destiny.

(read more)

Saturday, May 23, 2015

Elizabeth Warren is winning: How the progressive icon is remaking politics — without running for president

Salon Magazine

"With most of the political press having finally accepted that Sen. Elizabeth Warren is indeed not running for president, it’s only fitting that the Economist, a neoliberal and generally clueless British magazine that American elites like to pretend they’ve read, has an essay in its new issue all about how she’s too liberal and could never win."
"But more than the essay itself — which is by turns hackneyed (She’s a left-wing Ted Cruz!), objectively wrong (the Trans-Pacific Partnership is not primarily about trade), and misleading (President Obama’s “absolutely wrong” comment wasn’t about the entire TPP) — the Economist’s belated attack is interesting for what it suggests about Warren’s broader goal of leveraging her fame, credibility and fundraising prowess to move the Democratic Party to the left. Which is, simply put, that it seems to be working."

(read more)

Friday, May 22, 2015

Sanders Plan to Break Up Biggest Banks

TPP Twitter Feed

Obscure Government Document Shows Elizabeth Warren Is Right About TPP

Zaid Jilani
May 22, 2015

"As opponents and advocates of the Trans-Pacific Partnership (TPP) continue to battle it out, the debate over the agreement has largely focused on the issue of trade – whether jobs will be lost or gained, what the agreement will do to our trade deficit, and other related matters."
"It's worth pointing out that the United States already trades heavily with the other 11 nations included in the TPP talks. As Paul Krugman says, “this is not a trade agreement. It's about intellectual property and dispute settlement; the big beneficiaries are likely to be pharma companies and firms that want to sue governments.” Senator Elizabeth Warren (D-MA) has been particularly critical of the so-called Investor State Dispute Settlement provisions, which would empower corporations to use international courts to sue the U.S. government and others who are enacting regulations and protections that harm their profits."
"The Obama administration is arguing that the deal is instead about trade and increasing American exports abroad. They have set up a web page on the U.S. Trade Representative's (USTR) site listing the benefits of exports from each of the fifty states in order to argue for the Trans-Pacific agreement."
"Yet an obscure government document put out by that very same office makes Warren's case for her. The office puts out an annual report on “foreign trade barriers” around the world, going country by country to list complaints the U.S. government has about their laws with respect to commerce. If you read the 2015 report, you'll quickly see that many of the complaints are about laws designed to promote environment, labor, and anti-monopolistic practices – and relate only vaguely to the larger issue of trade and tariffs. The complaints seem more focused around opposing regulations that restrict the rights of multi-national corporations and their investors."

Tuesday, May 19, 2015

Retracing Shackleton's Epic Journey of Survival

Antarctica’s Larsen B Ice Shelf: The Final Act

The evolving instability of the remnant Larsen B Ice Shelf and its tributary glaciers
Ala Khazendara, Christopher P. Borstada, Bernd Scheuchl, Eric Rignotb, Helene Seroussia


Following the 2002 disintegration of the northern and central parts of the Larsen B Ice Shelf, the tributary glaciers of the southern surviving part initially appeared relatively unchanged and hence assumed to be buttressed sufficiently by the remnant ice shelf. Here, we modify this perception with observations from IceBridge altimetry and InSAR-inferred ice flow speeds. Our analyses show that the surfaces of Leppard and Flask glaciers directly upstream from their grounding lines lowered by 15 to 20 m in the period 2002–2011. The thinning appears to be dynamic as the flow of both glaciers and the remnant ice shelf accelerated in the same period. Flask Glacier started accelerating even before the 2002 disintegration, increasing its flow speed by ∼55% between 1997 and 2012. Starbuck Glacier meanwhile did not change much. We hypothesize that the different evolutions of the three glaciers are related to their dissimilar bed topographies and degrees of grounding. We apply numerical modeling and data assimilation that show these changes to be accompanied by a reduction in the buttressing afforded by the remnant ice shelf, a weakening of the shear zones between its flow units and an increase in its fracture. The fast flowing northwestern part of the remnant ice shelf exhibits increasing fragmentation, while the stagnant southeastern part seems to be prone to the formation of large rifts, some of which we show have delimited successive calving events. A large rift only 12 km downstream from the grounding line is currently traversing the stagnant part of the ice shelf, defining the likely front of the next large calving event. We propose that the flow acceleration, ice front retreat and enhanced fracture of the remnant Larsen B Ice Shelf presage its approaching demise.

Monday, May 18, 2015

I Refused to Pay and Won: How to Beat Unreasonable Hospital Facility Charges

(Me vs. California Pacific Medical Center over a $1,683.29 hospital "Facility Fee")

I notice today that there is an article in the Washington Post about an unconventional way to beat ever escalating and shockingly high hospital bills.

Most people who have not dealt with hospital bills have no idea how extraordinarily expensive hospital costs in the United States are compared to other countries.  I first got a huge wake up call about this when I gave birth.  It was at a well known public teaching hospital in San Francisco, UCSF, so birthing costs there are probably reasonably representative of the average.  Cost for giving birth to my daughter by natural delivery (plus the required two day minimum in the hospital):  $32,000 in 2004.  It was covered by the insurance of my employer, but ultimately, the high cost of giving birth in the US is borne by employees, because employers cut wages and benefits to cover the cost of paying for employee health insurance.

By comparison, the equivalent cost for giving birth by natural delivery in other countries is at least one third the cost in the US, according to this recent BBC article.

Dial the clock forward a few years.  I go for a routine mammogram, I am told by the hospital mammography specialist that my mammogram should be followed by a biopsy, "just to be sure."  I go to the hospital thinking the procedure is covered under our HMO insurance plan.  I lie on a table for three hours getting my boob poked at, find out that nothing is out of the ordinary, and go home.

But that wasn't the end of the story.  I got a bill from California Pacific Medical Center (CPMC) about a year after the procedure, telling me that, over and above the costs covered by my insurance, they wanted me to pay a non insured $1,683.29 "Facility Fee".  Let's just say I decided it was unreasonable. So I took California Pacific Medical Center to small claims court.

I had no idea what to expect.  On the day of the big event at the San Francisco Court House, an assigned CPMC risk management specialist arrived.  For some reason, she thought she could intimidate me so, right before the hearing, she pulls me aside and tells me, with an air of dire warning, that she has a recording of me yelling at the CPMC billing person.  That's how silly it got.  You can read about it here.  See "Claim of Plaintiff" at the bottom of the page.

I just told her, this silly risk management specialist, that she wasn't going to intimidate me, that it wasn't about the money, but a matter of principle of hospitals and insurance companies not piling on after-the-fact arbitrary charges.  I told her that she could tell the judge that I "yelled" all she wanted, but we were going to court.  She seemed a little breathless.  The judge heard my sorry story, then ruled that "CMPC did not owe me any money."  In other words, I did not owe CPMC the $1,683.29 facility fee, but also wasn't going to win any additional charges or damages beyond what I had refused to pay.  I had won.

I'm sure the baffled risk management specialist didn't get her bonus that year.  I notice that there were a number of other small claims against CPMC after mine, fighting "facility charges".  It must have been a real bummer for CPMC that they couldn't so easily get away with this anymore.

Which brings me back to the Washington Post article:  Hospital bills too high? One benefits firm has a new strategy: Don’t pay.  The article spells it out:  if you receive a hospital bill that you know is grossly inflated above the true cost of the procedure, don't pay . . . Or, as I did, take the hospital to small claims court if you can.   The hospital will almost always negotiate, because they don't want to be caught red handed in their act of grossly over charging their patients.  It's not a good PR move for them to be seen with this.

In retrospect, these two brushes with the American healthcare system left me feeling very skeptical of claims by various entities that there is a magic bullet to improve health outcomes or lower costs for Americans.  We will not be in better health because of Obamacare until something is done about healthcare access and arbitrarily high costs to gain access to care.  Personalized medicine, including that informed by whole genome sequencing, won't help us either, unless it can be shown to hold down costs and improve access.

Wednesday, May 13, 2015

Near-optimal RNA-Seq quantification

Nicolas L. Bray, Harold Pimentel, Páll Melsted, and Lior Pachter
(Link) pdf

[Blog note:  This paper represents a significant advance in RNA sequencing methodology.  The paper is beautifully written and accessible for someone not in the field of bioinformatics.  Lior is covering the paper on his blog.]


We present a novel approach to RNA-Seq quantification that is near optimal in speed and accuracy. Software implementing the approach, called kallisto, can be used to analyze 30 million unaligned RNA-Seq reads in less than 5 minutes on a standard laptop computer while providing results as accurate as those of the best existing tools. This removes a major computational bottleneck in RNA-Seq analysis.

Sunday, May 10, 2015

Mildred Dresselhaus: The Queen of Carbon

IEEE Spectrum
By Mark Anderson

Before silicon got its own valley, this mild-mannered element had to vanquish many other contenders to prove itself the premier semiconductor technology. It did so in the 1950s and 1960s. Today, carbon is poised at a similar crossroads, with carbon-based technologies on the verge of transforming computing and boosting battery-storage capacities. Already, researchers have used these technologies to demonstrate paper-thin batteries, unbreakable touch screens, and terabit-speed wireless communications. And on the farther horizon they envision such carbon-enabled wonders as space elevators, filters that can make seawater drinkable, bionic organs, and transplantable neurons.

Whatever miracles emerge from Carbon Valley, its carbon-tech titans will surely think fondly upon their field’s founding mother, Mildred Dresselhaus. This MIT professor of physics and engineering has, since the early 1960s, been laying the groundwork for networks of nanometer-scale carbon sheets, lattices, wires, and switches. Future engineers will turn these things, fabricated from carbon-based materials such as graphene, into the systems that will carry computing into its next era.

Now, after a half century of quiet work, she is accumulating accolades. This past November, in a ceremony at the White House, President Obama awarded her the Presidential Medal of Freedom, the U.S. government’s highest civilian honor. “Her influence is all around us, in the cars we drive, the energy we generate, the electronic devices that power our lives,” Obama said.

And this June, the IEEE will confer upon Dresselhaus its highest accolade, the IEEE Medal of Honor, for her “leadership and contributions across many fields of science and engineering.” She is the first female Medal of Honor recipient in the award’s nearly century-long history. (Before the IEEE’s formation, the Medal of Honor was presented by the Institute of Radio Engineers, which merged with the American Institute of Electrical Engineers in 1963 to form the IEEE.)

Saturday, May 9, 2015

Archaic admixture in the human genome

Jeffrey D Wall and Michael F Hammer
Current Opinion in Genetics & Development
October 5th, 2006

[Blog note:  This paper was written nine years ago.  It's interesting to read, especially in light of the Oase 1 findings that this 40,000 year old human had a Neandertal ancestor within four to six generations.]


One of the enduring questions in the evolution of our species surrounds the fate of ‘archaic’ forms of Homo. Did Neanderthals go extinct without interbreeding with modern humans 25–40 thousand years ago or are their genes present among modern-day Europeans? Recent work suggests that Neanderthals and an as yet unidentified archaic African population contributed to at least 5% of the modern European and West African gene pools, respectively. Extensive sequencing of Neanderthal and other archaic human nuclear DNA has the potential to answer this question definitively within the next few years.

Friday, May 8, 2015

Team Characterizing DNA from Ancient Human with Recent Neanderthal Ancestry

Genome Web
Andrea Anderson reporting
May 8, 2015
COLD SPRING HARBOR, NY (GenomeWeb) – An international team has discovered recent Neanderthal ancestry in an ancient jaw sample from a modern human who lived in present-day Romania roughly 37,000 to 42,000 years ago, attendees heard at the Biology of Genomes meeting.

The finding clashes with the notion that most mixing between modern humans and Neanderthals occurred in the Middle East shortly after humans migrated out of Africa, explained Qiaomei Fu, a researcher affiliated with the Max Planck Institute for Evolutionary Anthropology, the Chinese Academy of Sciences, and Harvard Medical School. Fu presented the work during a session on evolutionary and non-human genomics here today.

Instead, genetic patterns in the ancient human hint at the potential of admixture between modern humans and Neanderthals in Europe that may have persisted until not long before Neanderthals disappeared from the continent some 40,000 years ago.

Past studies have uncovered gene flow from Neanderthals into all tested modern human populations outside of Africa, with non-African individuals carrying between 1 percent and 4 percent Neanderthal sequences in their genomes, on average. The details of this modern human-Neanderthal mixing remain somewhat murky, though it's believed that the archaic and modern human groups first encountered each other not long after humans migrated out of Africa.

To flesh out the details of these interactions, researchers are tapping into fossils samples found outside of Africa after this time, between about 100,000 years ago and 30,000 years ago, Fu noted.
In this case, she and her colleagues focused on DNA from a mandible found at the Pestera cu Oase site in Romania, which contained relatively low levels of endogenous DNA, pronounced DNA degradation, and a large proportion of microbial contaminants that interfered with attempts to directly shotgun sequence the ancient human.

To get around such complications, the team turned to in-solution capture, isolating ancient DNA from more than 2 million sites in the genome.

Though the individual — known as Oase 1 — was clearly human, Fu explained, the resulting sequences indicated that some 5 to 11 percent of his genome originated from Neanderthals.

To look at this in more detail, the researchers used another capture step to scrutinize more than 78,000 sites in the genome that typically differ between modern humans and Neanderthals.

From those variants, the team detected long stretches of Neanderthal DNA that had not been interrupted by admixture, suggesting the individual's Neanderthal ancestry was more recent than that of any modern human tested previously.

In particular, Fu said, roughly half of the Oase 1 individual's chromosome 12 sequence coincided with Neanderthals rather than modern humans. Based on the SNP patterns detected in the sample, the researchers estimated that the individual had a Neanderthal ancestor within the past four to six generations, pointing to later-than-anticipated admixture between Neanderthals and the modern human population to which Oase 1 belonged.

Meanwhile, comparisons between genetic variants in Oase 1 and those in present-day populations or previously sequenced ancient samples suggested that the ancient individual from Romania belonged to a population that was becoming somewhat European.

But while this group resembled both European and Asian populations, Fu noted, it appears to have been far removed from agricultural populations in Europe and does not appear to have contributed much genetically to present-day human populations.

The team is continuing to tease apart patterns from genetic profiles in the sample, including genotyping analyses of the Oase 1 individual's Y chromosome, she said.

Thursday, May 7, 2015

On Two Feet with Carol Ward

The Leakey Foundation has done a nice write up and audio presentation on the research of Carol Ward, which can be found here (On Two Feet with Carol Ward).

I had the good fortune to hear Carol Ward speak at the California Academy of Sciences last fall.  She's working on the evolution of hominin posture and is a proponent of research that suggests that hominins walked upright earlier than has been traditionally presented. 

Saturday, May 2, 2015

Time depth in Indo-European

James Clackson

In this paper I do not propose to give you a time depth, or even a range of possible time-depths, for the Indo-European language family. Rather, I propose firstly to examine some of the existing assumptions about the time depth of Indo-European in recent scholarship, and then to state why the whole notion of a time depth for a reconstructed language is problematic.

Most authors of handbooks and survey articles on reconstructed Proto-Indo-European (PIE) are reluctant to come clean on their thinking on how old the Indo-European language family is (a notable exception is Mallory, in Mallory& Adams 1997, 583–7). At the same time, it appears that a number of linguists have a gut-feeling or intuition about the likely age of Indo-European — I am unaware of any scholar working in the field who wishes to place PIE later than 2500 BCE, and most scholars, to judge from reactions to Colin Renfrew’s Archaeology and Language (Renfrew 1987), are reluctant to go even as far back as 7000 BCE without qualifying to some extent the PIE with a further ‘Pre-’ or ‘the earliest stages of’. One particular model for PIE which finds quite widespread favour at the moment is not afraid to stratify PIE and date the strata. This is the so-called ‘Space-Time’ or ‘Zeit-Raum’ model put forward by Meid in the 1970s, and since refined by others. (1)  According to Meid’s model, a reconstructed proto-language should be considered not as a monolithic unity, but an entity which exists over time, and through time over ever-increasing space. Hence one can draw a triangular representation of PIE, with the dispersal of the language over space plotted as the horizontal axis, and the time scale plotted on a vertical axis as below:

PIE 1 5000–4000 BCE                          I
PIE 2 4000 BCE                        IIIIIIIIIIIIIIIIIII
                                                   < SPACE>

How do Indo-Europeanists such as Meid come up with such seemingly accurate stratigraphy with so little explanation of what they are doing?  The time scale given in Meid’s model finds widespread acceptance (and not just among those who follow his space–time model) for a number of reasons: age of the attested daughter languages; dating of the culture of the speakers of PIE through the reconstructed lexicon; the Romance model and glottochronology. (2)  I shall consider each of these in turn.

Friday, May 1, 2015

La Parole Humaine, Etudes de philologie nouvelle d'après une langue d'Amérique

A. Berloin
Honoré Champion, Paris & Librairie Beauchemin, Montréal 1908


More thoughts on the "ANE" component

Given the terrific paper on the Kalash, published yesterday, we finally have a clearer picture of the timing of the population processes on the Steppe.

I've discussed the "ANE" component (Lazarides paper in 2014) that is widely distributed from Europe to India back in January in this post.

By the statement I made in this post that "I strongly doubt that the R1* y-DNA haplogroup is widely correlated with "ANE" like components", I specifically mean that there is not a strong correlation of the R1b ydna hgs with this component.   However, there does appear to a stronger correlation of R1a ydna hgs with the "ANE" component. 

The likely reason for this split in the correlation of R1a and R1b ydna hgs is that these groups split prior to or during the last Ice Age, with R1a positioned on the Steppe 25,000 years ago, and R1b positioned somewhere in Europe 25,000 year ago.

I've thought this all along, but it's easier to argue for an Ice Age split for R1a and R1b hgs with the publication of the Kalash paper.