Links 12/9/16

Links for you. Science:

Wild thing: How and why did humans domesticate animals – and what might this tell us about the future of our own species?
Trump’s Plan to Eliminate NASA Climate Research Is Ill-Informed and Dangerous
Psychopaths can regret bad decisions — but don’t learn from them
NFL doctors’ conflicts of interest could endanger players, report says
Altar of Miracle-Making Viking King Discovered in Norway


They Had One Job
Nicholas Kristof’s Burden: First class travel and $30,000 speakers fee makes reporting on poverty easier to endure
Everybody Hates Cornel West
I Was a Teenage Nazi Wannabe: The alt-right is a loser’s poor fantasy of what a radical revolution looks like. I should know
Why Black Voters in Milwaukee Weren’t Enthused by Hillary Clinton
An Autopsy
Help Us Keep the Archive Free, Accessible, and Reader Private
Jeff Sessions: Protections for disabled kids are ruining America’s schools
A Requiem for Obamacare
Advice from Europe for anti-Trump protesters
George Takei: They interned my family. Don’t let them do it to Muslims.
No, this isn’t the 1930s – but yes, this is fascism
These Professors Make More Than a Thousand Bucks an Hour Peddling Mega-Mergers
Trump’s Victory Is Great News for the Defense Industry (Beltway Bandit Keynesianism)
The Letdown
Hillary Clinton lost. Bernie Sanders could have won (dunno, though this maybe suggests so?)

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A Failure Of Data Transmission: The CRE Edition

There’s a very interesting article that came out recently describing the first public report of carbapenem resistance in E. coli from the U.S. food supply. Maryn McKenna provides a good overview:

Bacteria containing a gene that confers resistance to a crucial class of antibiotics have been found in buildings on a pig farm in the midwestern United States, a troubling and mysterious discovery that should ring a warning bell over farm antibiotic use.

The discovery is troubling because the drugs to which the bacteria are resistant are so important. Called carbapenems, they are one of the few drug families that still work against deadly, multi-drug-resistant hospital infections. Carbapenem-resistant bacteria, known as CREs, are considered an “urgent threat” by the Centers for Disease Control and Prevention.

The discovery is mysterious because carbapenems are not used on that farm; in fact, they are not used in agriculture anywhere in the world. So the resistance may have been transported onto the farm in a manner no one can yet explain.

But there’s no question that the discovery is alarming. It’s likely to bring fresh scrutiny to the use of antibiotics on farms in the US, just as a long-delayed set of FDA restrictions on farm use is finally clicking into place.

But that’s not what this post is about. What this post is about is how the authors sequenced the plasmid (a mini-chromosome that can jump from bacterium to bacterium) that contains the carbapenemase gene, and then didn’t deposit the sequence in Genbank (at least as of mid-day Dec. 8th). Mind you, Genbank deposition is standard procedure for most journals (and federally funded work), including the journal in which the study was published. There is no Genbank accession listed–this isn’t a case of a sequence being held by NCBI until the paper is ‘officially published’. The authors were able to put together a map of the plasmid for the paper, so it’s clear there is a sequence:


Other researchers who could use these data for their own work (and verify the validity of the authors’ results as well) are unable to do so, and, as McKenna notes, this is a critical health problem. The worst case scenario–one I think is highly unlikely–is that they could have interpreted the data incorrectly and carbapenemase resistance is not due to the putative carbapenemase gene (e.g., there is a stop codon in the middle of the gene, gene isn’t full length, etc.). Reproducibility requires, at the very least, making the sequence publicly available.

The editors and the reviewers should have caught this. It’s unfortunate because these data could help many researchers, including public health professionals. As genomics becomes more ‘democratized’, it’s all the more vital that the widely accepted standard of post-publication data sharing is enforced by editors and reviewers.

Hopefully, there will be a clarification and correction soon.

Posted in Antibiotics, Data Stuff, Genomics | 1 Comment

Links 12/8/16

Links for you. Science:

Five Lessons From Today’s Pharma Failures
Ravenous Bacteria Eats Poop and Produces Power
This new study may explain why peer review in science often fails
On The Front Lines Of The Overdose Epidemic In Baltimore
Solving a Mystery Behind the Deadly ‘Tsunami of Molasses’ of 1919


What Bernie Sanders Gets Right About Identity Politics
The Election was Stolen – Here’s How…
The No-BS Inside Guide to the Presidential Recount
New congressman Jamie Raskin shows exactly the right attitude Democrats need for taking on Trump
The economic geography of a universal basic income
The Case to Impeach Chris Christie
If You’re 35 Years Into Your Career $70,000 Isn’t A Great Income
The taxi unicorn’s new clothes
The Wreckage of Obama’s Legacy
My Parents, Pat and Fred Cody: An American Story of Resistance and Resilience
Garbage In, Garbage Out
The Story Behind Jared Kushner’s Curious Acceptance into Harvard
The head of National Museum of the American Indian on what we should all know
Data show that a ‘whitelash’ did not elect Trump; It was—like always—about the economy
A Year at the Zoning Board: Have we ever seen anything like this election season’s mixture of anger and cluelessness? Yes, at the local zoning board
An ethical double standard for Trump — and the GOP?
Nationwide, Homelessness Plunged Under Obama

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Democrats Have Always Reached Out To ‘Deplorables’: Lessons From 2008

And “reaching out” isn’t the same as pandering to their ‘deplorableness’. But we seem to forget that quite a few Democratic voters vote Democratic in spite their bigotry (boldface mine):

Democrats dwelled on the most obvious–and politically convenient–part–which indicates that Trump supporters are a lot more racist than anyone else. But this figure also contains an inconvenient truth (to use a phrase). The most optimistic reading of this is that at least one out of five Democrats are racist–and that estimate includes black people (I’m assuming most [black people] don’t believe these things; i.e., the denominator should be smaller). I don’t think it’s unreasonable to assume that one in four Democrats is racist–which admittedly is better than Republicans, especially once the Trumpists are factored in. We, too, have our deplorables.

If white bigots always voted their bigotry, Democrats would be dead in the water–probably everywhere. Yet they don’t. Which brings us to an inconvenient truth from the 2008 elections (boldface mine):

There is no need to pretend the white working class is a monolith of moral excellence. Many working-class people, like many middle- and upper-class people, are bigoted, hostile to all kinds of people and lifestyles. But the job of a presidential candidate is to appeal to our better angels and win votes anyway. In 2008, the Democratic coalition included millions of black churchgoers who opposed same-sex marriage. In 2012, Democrats welcomed millions of Catholic Latino voters who opposed abortion. These people were not scolded for their shortcomings but celebrated for their virtues. This year, Democratic elites decided that the entire white working class was unworthy of sharing their company.

(Most years, according to Pew Research, there is a fifteen to twenty point approval gap for gay marriage between whites and blacks. Hispanic (Pew’s term) voters are more likely (50 to 40 percent) to oppose legal abortion in most or all cases.)

To win certain states nationally and a fair number of down ballot races we need white working class voters (think of that as the ‘Republican firewall‘). The good news is that there are white working class voters who do and would vote Democratic even with all of their flaws, if we try to earn their votes.

Posted in Democrats | 1 Comment

Links 12/7/16

Links for you. Science:

The House Science Committee’s tweets are an embarrassment to science
Will 10 Million People Die a Year due to Antimicrobial Resistance by 2050? (nope)
ECDC: Occurrence of carbapenemase-producing Klebsiella pneumoniae and Escherichia coli in Europe
The Biologists Who Want to Overhaul Evolution
A Forgotten Step in Saving African Wildlife: Protecting the Rangers


The Alternative to Obamacare Is Obamacare
Novo Nordisk pulls ad from Breitbart
Yes Folks, Trade Does Affect Manufacturing Employment
Trump will helm a government of, by and for corporate America
This Is Embarrassing, Donald Trump
Can Uber Ever Deliver? Part Three: Understanding False Claims About Uber’s Innovation and Competitive Advantages
Beaver walks into Md. store, finds only artificial Christmas trees, and proceeds to trash it
The Propaganda About Russian Propaganda
Poverty Doesn’t Need Technology. It Needs Politics.
Diverse US Reps Form “Blue Collar Caucus” as Ta-Nehisi Coates Rejects “NonEconomic Oppression” Frame
Coates: When Clinton said “Not everything is about an economic theory” she was wrong. It is. Even when it’s hard to elucidate. It’s always there.
NTSB: Metro knew of potentially dangerous track conditions more than a year before July derailment
Fired D.C. employee claims Bowser administration tried to steer contracts to donor
Political correctness: how the right invented a phantom enemy
Wilbur Ross and Steve Mnuchin—Profiteers of the Great Foreclosure Machine—Go to Washington
Homeless Advocates Pan Bowser’s Proposed Shelter Reforms

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This Metro Problem Has Nothing To Do With ‘Unions’

And everything to do with managers.

While it’s almost always a bad idea to read the comment sections of local news blog, when I foolishly do read them about Metro, inevitably the idea that Metro employees are paid too much because of TEH UNIONZ! comes up. According to these chuckleheads, every problem Metro faces can be laid at the feet of unionized workers. Well, this episode of mismanagement really can’t be blamed on the workers (boldface mine):

Metro track inspectors copied the same details over and over for months, even years, regarding the condition of the tracks outside the East Falls Church Station, where a train derailed in July, and told investigators that they were pressured not to accurately report the severity of track conditions

Fifteen times this year and 34 times in 2015, Metro track inspection reports show the exact same note: “15 deteriorating ties in the diamond area” of the interlocking outside of East Falls Church Station — the same spot where the derailment occurred.

In interviews with track inspectors, Metro safety officer Robert Davis who worked for years at Amtrak, said the same exact measurements for the width and angle of the track in the area appeared to have been copied over from as far back as 2011. The tracks would typically move a bit month to month due to regular use from the trains running over them. No change was ever recorded.

One track inspector admitted that if it rained or if he was assigned too much to actually accomplish, that some inspections would be skipped. Both inspectors, whose interviews with the Metro safety officer were made public, said that no Metro inspectors had known they were supposed to be regularly checking the center of interlockings on a twice-weekly basis….

Two inspectors interviewed as part of the derailment probe said that they would get pushback, and in some cases face retaliation, when they reported problems along the tracks.

Jovito Azurin, 50, who has worked at Metro for 16 years, blamed supervisors for at least some of the issues when confronted with reports he signed that showed the exact same measurements were detailed in reports twice in 2013, four times in 2014, four times in 2015 and once in 2016.

Azurin said he was told not to enter any changes to the measurements.

In some cases, Azurin said, information on inspection reports were largely preprinted for inspectors. He said he was sometimes assigned far more switches to inspect than he could physically get to in the given time.

Both Azurin and another inspector, Trapp Thomas, said that supervisors would get upset if a problem was identified as one serious enough to slow down trains or take the track out of service if the issue had not been slowly escalated up Metro’s defect reporting system.

“You solved the problem. You prevented something from happening. That’s not how it was looked at. It’s, well, why didn’t you find it before,” Thomas said according to the transcripts…

On the Blue and Yellow lines near Reagan National Airport, Thomas said a supervisor told him to ignore some problems and even took him for drug and alcohol testing as part of an effort to discredit Thomas’s reports of issues.

Staggering incompetence. I really don’t understand how Metro leadership let things reach this point.

Posted in DC, Transportation | Leave a comment

Links 12/6/16

Links for you.Science:

Is the Long Hard Road to Academia Worth It?
A Third of People Given Antibiotics Don’t Need Them
Immigrant and minority scientists shaken by Trump win
Great Barrier Reef Hit by Worst Coral Die-Off on Record, Scientists Say
Incredible discovery of 40,000-year-old tools for art and engineering


The Myth of the Rust Belt Revolt: Donald Trump didn’t flip working-class white voters. Hillary Clinton lost them (important)
Do Better
The James Mattis I Saw Behind Closed Doors
Mike Pence didn’t just privatize Indiana education money, he sent it to religious schools
Dem senator comes out against waiver for Mattis to be Defense head
In Defense of Trump Panic
Dear Donald Trump: You Won’t Like DC
Costs of widely prescribed drugs jumped up to 5,241 percent in recent years, joint investigation shows
The “They Had Their Minds Made Up Anyway” Excuse
There’s Hamilton, the hit musical and Hamilton, the city. Angry social media users confuse the two
North of Dixie: Civil Rights Photography Beyond the South
How to Hide $400 Million
Progressives: Please stop doing this very annoying thing (agreed)
The Revolution Will Not Be Staffed: How Big Organizing Can Take Down Trump
Why People Turn to Dictators

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