Links 2/8/16

Links for you. Science:

Bacteria-fighting antitoxins offer remedy to antibiotic resistance
The Salmonella In Silico Typing Resource (SISTR): An Open Web-Accessible Tool for Rapidly Typing and Subtyping Draft Salmonella Genome Assemblies
Twitter Nerd-Fight Reveals a Long, Bizarre Scientific Feud
Spread of bee disease ‘largely manmade’
The Zika questions that science needs to answer


blogroll amnesty day is here again!!!
Chamber of Commerce Lobbyist Tom Donohue: Clinton Will Support TPP After Election
How the Homeless Population Is Changing — and Becoming Much More Vulnerable
Understanding the Trump/Sanders Constituencies: Inequality Is Something the Elites Did
The Clinton System
Why Chinese Factories Fare Poorly in the U.S.
Too poor to retire and too young to die
Cheap cab ride? You must have missed Uber’s true cost
A Non-Neoliberal Woman President Is Not One of the Choices
The rise of the Sagebrush Sheriffs: How rural ‘constitutional’ peace officers are joining the war against the feds.
Taking Away The Punchbowl
Dismissing Sanders: Democratic Condescension and the Mythic Political Grown-up
Hillary Clinton Pledges Not To Cut Social Security Benefits
How abortion opponents secretly bought a Va. abortion clinic to deceive women

Posted in Uncategorized | 1 Comment

Night Riders

Observed on 18th Street NW, between Swann and T, Dupont Circle, D.C.:

Bat mobile

Bat mobile

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What Does ‘Reproducibility’ Mean?

Drugmonkey does a fine deconstruction of the latest Amgen/Nature paper, so I won’t rehash the whole thing here (go read it; the comments really blow up the details of the replications). But a key point is best summarized by Drugmonkey:

…I have long suspected many of these alleged replication failures claimed by Amgen are of the lack-of-generalization variety. A drug company of course wishes they can take a single hot basic science result and turn that into a human medication. The fact this doesn’t work out is not a failure of the original paper to replicate. And ffs the overblown translational claims of your typical Glam authors doesn’t change this reality.

It raises some real questions about what the reproducibility crisis is about. While there are some obvious cases, such as the ESP studies, where this is a statistical assessment issue, that seems to be conflated with ‘generalizability’–that is, if I change my study system slightly (different organisms or strains, slightly different methods, etc.) and I don’t observe the ‘same’ result (or a much weaker result), did the study fail to reproduce? Given real constraints of time and money, it’s often not feasible to replicate a previous experiment and conduct your own follow-on experiment as well.

I’ve spent much of my career in an open-data field–and the grunt work of my day job, in part, consists of trying to replicate other people’s results using their data (pipeline development, etc.). Even using the same data, slightly different processing and analysis steps can yield different results (though what ‘different’ means is open to discussion). Reproducibility isn’t a trivial thing to assess, since the real issue is how much irreproducibility is tolerable.

What bothers me about the reproducibility discussion is that, for the most part, we’re not discussing what reproducibility would and should mean, but rather it’s more along the lines of ALL TEH SCIENTISMZ ARE BROKEN! Which makes for great pundity thinky-pieces, but doesn’t really help us do science within the real-world constraints that scientists experience.

I will now go outside and yell at clouds.

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Links 2/7/16

Links for you. Science:

USDA Imposes Stricter Limit On Salmonella Bacteria In Poultry Products
Implications of the Brazilian report on pre-Zika microcephaly
How Scared Should You Be About Zika?
Want to be ethical in science? Speak up.
Joe Felsenstein on the ‪#‎parsimonygate‬ Twitter uproar


90% of what goes on at The New Yorker can be explained by Vulgar Marxism
Why Common Ground Between Left and Right Is Not Necessarily Shared
The NYT needs a mathematics editor
Explaining Why Federal Deficits Are Needed
Why is Twitter’s pop-out feature such a disaster?
Trans-Pacific Partnership Being Sold With Bogus Economic Models
Hillary Clinton Wants You to Believe She’s Tough on Wall Street. She’s Not.
Wife crashes her own funeral, horrifying her husband, who had paid to have her killed
Bill Clinton’s Legacy Haunts the Democratic Debate (and this doesn’t even get to the racism and sexism underlying welfare reform–which Clinton supported in her “deadbeats” speech)
The NYPD is Kicking People Out of Their Homes, Even If They Haven’t Committed a Crime
Hillary brought her own Goldman Sachs lobbyist to Dem debate (Electable!)
Remembering The Slocum Massacre
Iowa Caucus Morning After: Apologize for This, Jackasses
Poll: Most voters are ready for a political revolution to redistribute wealth
Suburban Annexation is a Bailout
A Future History of the United States
18 cities in Pennsylvania reported higher levels of lead exposure than Flint
Ken Stabler, a Magnetic N.F.L. Star, Was Sapped of Spirit by C.T.E.
The Trans-Pacific Partnership threatens our liberty

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“My Kind of Misogyny”

Amber A’Lee Frost (boldface mine):

And isn’t that the simpler explanation of left dissent from Team Clinton? It’s not that critics of Hillary are largely misogynist or even that they’re obsessed with political purity. It’s that she’s a proven neoliberal warhawk, a Wall Street sycophant, and a consistent enemy of the poor.

It’s a strange sort of “misogynist” who condemns Clinton for her endorsement of “welfare reform,” which eviscerated a social safety net that primarily benefited women and children. And who are these misogynists who question Clinton’s time on the board of Wal­mart, a company known for its mass exploitation, particularly of women? What a misogyny that decrees the women of Iraq deserve lives free of American war! There’s a misogyny that advocates for childcare, healthcare, free university parental leave? O brave new world, that has such misogynists in it!

I’ve made this point before, but Clinton partisans have made a really big mistake in two ways. First, they act as if opposition to Clinton is largely ‘BernieBro driven’, as opposed to based on serious criticism. Second, the condescending hectoring about electability (more about that in a future post) does nothing to address legitimate concerns about her history, including her full-bore advocacy for welfare reform. Which is to say, deadbeats. Who, if the unofficial house organ of the Clinton administration, The New Republic, was to be believed, looked like this:
Continue reading

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Links 2/6/16

Links for you. Science:

The Bugs Behind The Bed Bug Genome: New research came from a famous bed bug lineage
Deep-sea ‘purple sock’ provides clues to early life
The Zika conspiracies have begun
Look Somewhere Else for Romance
If you fail to reproduce another scientist’s results, this journal wants to know


The Left
4 Ways Utah is Dealing with Overly-Wide Streets
Oregon standoff: Bundy occupation leaves scars behind
The Democrats Effectively Tied in Iowa, But Sanders Won the Future (and the condescension from too many Clinton supporters only exacerbates things)
What Bernie Sanders Has Already Won
Twilight of the Superpredators (wrote about this here; Hillary Clinton used superpredator rhetoric)
New OECD tax agreement improves transparency — but the US doesn’t sign and the US press won’t tell you
Why Hillary Clinton’s razor-thin Iowa win is really a crushing defeat (the key thing is that, as I’ve been saying all along, conservatives realize Clinton is vulnerable on the cronyism/corruption charges)
Chicago Professor Resigns Amid Sexual Misconduct Investigation
Everyone Is Wrong About the Bernie Bros: How a necessary critique of leftist sexism deteriorated into a dumb flame war
Is TPP dead if Sanders becomes President?
D.C. Will Form Disability Advisory Committee to Improve Snow Response
How class could eventually remake the Democratic Party
Flint Probably Has Bigger Problems Than Lead Pipes
American capitalism has failed us: We’re overworked, underemployed and more powerless than ever before
Bernie Sanders and the New Populism
A public backlash against the Malheur occupiers also suggests American sympathy for those who work for the US Forest Service, the Bureau of Land Management, and the US Fish and Wildlife Department.
Wealthy Donors Pump Millions Into Sanders’ Campaign In Last-Ditch Effort To Destroy His Credibility (funny)
Sanders Beats Clinton 49-49: The Real Story Behind the Iowa Numbers
New Yorker Joins Open Season on Bernie Sanders

Posted in Lotsa Links | 3 Comments

This Seems Socially Disruptive

The U.N. made a statement (boldface mine):

The United Nations on Friday urged countries hit by the dangerous Zika virus to let women have access to contraception and abortion…

“How can they ask these women not to become pregnant, but not offer… the possibility to stop their pregnancies?” spokeswoman Cecile Pouilly told reporters…

But UN human rights chief UN rights chief Zeid Ra’ad al-Hussein said this warning meant little in countries that ban or heavily restrict access to reproductive health services like contraception and abortion.

“The advice of some governments to women to delay getting pregnant ignores the reality that many women and girls simply cannot exercise control over whether or when or under what circumstances they become pregnant, especially in an environment where sexual violence is so common,” Zeid said in a statement.

“In situations where sexual violence is rampant, and sexual and reproductive health services are criminalised, or simply unavailable, efforts to halt this crisis will not be enhanced by placing the focus on advising women and girls not to become pregnant,” he said.

Instead, he insisted that governments must “ensure women, men and adolescents have access to comprehensive and affordable quality sexual and reproductive health services and information, without discrimination.”

This, his office pointed out, includes contraception — including emergency contraception — maternal healthcare and safe abortion services.

This is like catnip for wingnuts. The only thing missing are black helicopters piloted by Planned Parenthood workers.

I told you this would be a social problem (whether it’s actually a significant medical problem is unclear).

Posted in Blastocyst Liberation | Leave a comment