Links 8/30/16

Links for you. Science:

Is Florida About to Be Swamped With Capybara?
At NIH, one woman says gender bias has blocked promotions
Tom Wolfe’s magic combo move
Taking On Chomsky (and Darwin)
23andMe has a problem when it comes to ancestry reports for people of color


I Spent 5 Years With Some of Trump’s Biggest Fans. Here’s What They Won’t Tell You. (must-read)
How racist white people are pissing away what little political power the working class has left
Democrats’ Weak Bench Undermines Hope of Taking Back Senate
Why You Shouldn’t Vote for Gary Johnson
Reports of Metro track defects sat in a database without action for years. One reason: Poor training.
D.C. Mayor Bowser to Don Peebles: Give me my affordable housing (or maybe a campaign contribution?)
In Search of the Lost Empire of the Maya
Jackie Robinson had strong feelings about the National Anthem as well.
Metro badly needs culture change, everyone agrees. Can it pull it off?
Here are 10 good questions for Hillary Clinton (if she ever has another press conference)
Meet the man siphoning money from Donald Trump
Forget Swing States: The Presidential Election Will Be Determined by 20 Swing Counties in Linchpin States
Great Exploitations
What Colleges Can Do Right Now to Help Low-Income Students Succeed
A parallel legal universe, open only to corporations and largely invisible to everyone else, helps executives convicted of crimes escape punishment
‘Toxic environment’ for sons accused of campus sex offenses turns mothers into militants
How San Francisco’s Most Diverse, High-Achieving School Became Mostly White

Posted in Uncategorized | 1 Comment

Stop Calling The Racist Right ‘Alt-Right’

Too many pundits are over-thinking the ‘alt-right.’ They’re just the same mean, bigoted, racists that the right has always appealed to since the Republicans adopted the Southern Strategy decades ago. Since then, Republicans have never been able to win without the bigoted wing of their party.

What’s different isn’t the hatred, though the flavor and language has changed somewhat (few things in life remain completely static), it’s that, for once, Republicans might not be able to win, at least at the presidential level, with the bigoted wing of their party.

So I don’t care about their motivations, or the pecularities of this version of bigotry. They align themselves with the right in the U.S. and they are racists. Everything else is commentary.

Posted in Conservatives, Racism | 3 Comments

Bacterial Whole Genome Sequencing And The Clinic: The Future Is Almost Here

I heard this talk almost a year ago*, so I’m glad this paper is finally out (I’ll translate into English below; boldface mine):

The increasing prevalence of multidrug-resistant (MDR) bacteria is a serious global challenge. Here, we studied prospectively whether bacterial whole genome sequencing (WGS) for real-time MDR surveillance is technical feasible, returns actionable results, and is cost-beneficial. WGS was applied to all MDR isolates of four species (methicillin-resistant Staphylococcus aureus [MRSA], vancomycin-resistant Enterococcus faecium, MDR Escherichia coli, and MDR Pseudomonas aeruginosa) at the University Hospital Muenster, Germany, a tertiary care hospital with 1,450 beds, during two six-month intervals. Turn-around times (TAT) were measured and total costs for sequencing per isolate were calculated. After cancelling prior policies of preemptive isolation of patients harboring certain Gram-negative MDR bacteria in risk areas, the second interval was conducted. During interval I, 645 bacterial isolates were sequenced. From culture, TATs ranged from 4.4 to 5.3 days, and costs were 202.49 € per isolate. During interval II, 550 bacterial isolates were sequenced. Hospital-wide transmission rates of the two most common species (MRSA and MDR E. coli) were low during intervals I (5.8 and 2.3 %, respectively) and II (4.3 % and 5.0 %, respectively). Cancellation of isolation of non-pan-resistant MDR E. coli in risk wards did not increase transmission. When comparing sequencing costs with avoided costs mostly due to less blocked beds during interval II, we saved in excess of at least 200.000 €. Real-time microbial WGS was in our institution feasible, produced precise actionable results, helped to monitor transmission rates that remained low following a modification in isolation procedures, and ultimately saved costs.

Essentially, genome sequencing allowed much more targeted interventions, saving money while not significantly leading to increased infections. Why? Rather than treating every MDR (multi-drug resistant) infection as a possible outbreak, sequencing let the doctors realize that most of these infections were not part of outbreaks. That meant extra–and expensive–precautions, such as patient isolation, could be avoided in most cases. It’s worth noting that the costs of the non-genome sequencing approach are very conservative, so they probably saved even more money.

But you’ll note that I wrote the future is almost here. The next step is to integrate whole genome sequencing data at a scale larger than a single hospital, both to identify inter-facility spread as well as determine new trends and problems. In other words, this genomic information needs to be shared. As Duncan MacCannell noted, this is hard as there are a lot of patient privacy and data ownership issues.

We also need to figure out data standardization. This includes the very basic problem of how do two different hospitals conclude if they have the same bacterial strain: the hospitals might differ in everything from the basic analysis and production of the genomic data to ‘higher level analysis’ used to determine if isolates are closely related (for the genomic cognoscenti, I mean either calling SNPs or whole genome MLST).

So there’s a lot to do–and the study needs to reproduced elsewhere. But this is very promising for infection control and limiting the spread of antibiotic resistance. If nothing else, we might not have to choose between detailed genomic epidemiology and cost.

*I point I’ve made many times is that talks are how biologists communicate with each other (for better and for worse), while papers, to a considerable extent, are currency for grants.

Posted in Antibiotics, E. coli, Genomics, KPC, MRSA, NDM-1, Public Health | 1 Comment

Links 8/29/16

Links for you. Science:

The Secret Life of Science Museums: The federal government is slashing funding for collection museums. Here’s why that’s dangerous
Politics and Personality: Most of What You Read Is Malarkey
Trump wanted to keep Americans critically ill with Ebola out of the U.S.
All Queens Must Die
Benefits of steady growth


Blue Cities, Red States: As cities have moved left and states have moved right, the conflicts between them have escalated.
Fight over fired mechanic shows how union, Metro management deserve each other
Post-Apocalyptic Hellscape
Honey, I’ve been slowly boring hard boards longer than you’ve been alive.
Extinguished Career
On media responsibility in covering immigration and Donald Trump
The Other Side of Cathy Lanier’s Legacy (I never see D.C. police on foot, whereas in Boston, I saw them all of the time)
Thomas Levenson with more on the media’s handling of Clinton Foundation stories
Great Minds Think Alike
Weapons, Pipelines & Wall St: Did Clinton Foundation Donations Impact Clinton State Dept. Decisions?
Ugly McMansion from McLean, Virginia
AP Demonstrates the Perils of Being “Balanced” in the Era of Trump
Sign of the Times
The backlash against open plan offices: segmented space
4 experts make the case that the Clinton Foundation’s fundraising was troubling
More potholed roads turn to gravel. Residents aren’t happy.

Posted in Lotsa Links | 2 Comments

Disturbing, If True

I don’t think this Washington Post obituary headline came out the right way:


Posted in Uncategorized | 1 Comment

Revoke Mylan’s Corporate Charter

By now, you’ve probably heard about Mylan Laboratories’ massive price hikes in the EpiPen, which is used to treat life-threatening allergic reactions. You might have even heard how the EpiPen technology is entirely the result of federally funded research. Perhaps you even read about the possible (who are we kidding, probable) anti-trust violations that Mylan has committed. But this is simply par for the course (boldface mine):

EpiPen price hikes may be causing outrage, but those pale in comparison to the huge increases that Mylan Laboratories took on dozens of other medicines earlier this year.

For instance, the company raised the price of ursodiol, a generic medicine used to treat gallstones, by 542 percent. There was also a 400 percent boost in the price for dicyclomine, which combats irritable bowel syndrome, and a 312 percent increase for metoclopramide, a generic drug that treats gastroesophageal reflux disease.

Those eye-popping increases were actually first disclosed two months ago by Wells Fargo analyst David Maris, amid a national debate over prescription drug prices. The disclosure put Mylan on the defensive because, until then, the company had avoided the harsh spotlight fixed mostly on Valeant Pharmaceuticals and Turing Pharmaceuticals, which was run by Martin Shkreli.

There are grounds to revoke a corporate charter on the grounds of being a complete shithead (boldface mine):

In 1976, California’s conservative Republican attorney general used corporate charter revocation to force a private water company out of business for delivering contaminated water to its customers. The company settled the litigation and its assets were sold before its charter was revoked.

The New York State attorney general used the tool in 1998 in conjunction with other litigation to put two New York corporations, Council for Tobacco Research and Tobacco Institute Inc., out of business and order their assets donated to state education and health institutions. Dennis Vacco argued that the Council was using its tax-exempt status by acting as a propaganda arm of the tobacco industry. The stated mission of the groups was “to provide truthful information about the effects of smoking on public health,” Vacco said. “Instead,” he added, “these entities fed the public a pack of lies in an underhanded effort to promote smoking and to addict America’s kids.”

The tobacco industry eventually agreed to dissolve the two front groups as part of a multistate settlement of a lawsuit over the public health costs of smoking. But first, Vacco convinced the states’ courts to appoint a receiver for the two tobacco groups and dissolve the Council for Tobacco Research because it had violated its nonprofit corporate charter and tax-exempt status.

If there were ever a legitimate reason to disband a company and have the state redeploy the assets, price gouging with life-saving medicines would be it. If nothing else, it would force Mylan to lower its prices.

Update: Mylan announced that it will release a generic version of the EpiPen for ‘only’ $300, which means they jacked up the price roughly three-fold. Crush these fuckers.

Posted in Basic Human Decency, Bidness, Healthcare | 4 Comments

Links 8/28/16

Links for you. Science:

World’s oldest needle found in Siberian cave that stitches together human history
The Micro Monsters Beneath Your Beach Blanket
It Seems the Cigarette Industry Helped Create the Type-A Personality
Humanity’s first photos of Earth from the moon would have been thrown away if not for 3 people and an old McDonald’s
What’s So Significant About Significance?


Will America Finally Stop Privatizing Everything? (depends on how important the Pritzkers are in the next administration)
The EpiPen, a Case Study in Health Care System Dysfunction (if there were ever a case to remove a patent, this is it)
Grifters gonna grift
Ruling Pushes Door to Grad-Student Unions ‘Wide Open’
Read These Tweets To Understand How The Media Are Screwing Up Their Clinton Foundation Coverage
The Trump Campaign Is Now Fully Aligned With White Supremacists
Inside the Very Shady Nonprofit Dealings of the Trump Campaign’s New CEO
Berkeley put a tiny tax on soda. Consumption plummeted by 21 percent.
The District’s HIV clinic was failing. This ‘old, straight white guy’ managed to save it.
On 20th anniversary of welfare reform, D.C. still foots bill for longtime recipients
The EpiPen was her ‘baby.’ Now this pharma CEO is in the hot seat over price hikes
Hillary Clinton’s health care agenda is in danger as Obamacare struggles
From the destruction of Greece to democracy in Europe
Metro fights union lawsuit to reinstate L’Enfant Plaza tunnel inspector (more complex than first reports indicated. Sounds like the worker is being punished when he sort of tried to do the right thing against his managers’ opposition)
The Only Way To Get A Good Resolution
‘I wasn’t crazy’: A homeless woman’s long war to prove the feds owe her $100,000
Trump Normalized Hate Groups. The Media Normalized Trump.
We Don’t Want To Be Like Manhattan
What I Learned from Watching a Week’s Worth of Olympic Ads
Ron Johnson, genius, doesn’t understand why we have college professors

Posted in Uncategorized | 1 Comment