Links 2/17/17

Trump_finetunedmachine
Links for you. Science:

Sea Turtles Are in Much Worse Shape Than Previously Thought
The anti-vaccine movement is growing dangerously stronger
Broad Institute prevails in heated dispute over CRISPR patents
How the New Climate Denial Is Like the Old Climate Denial
Robert De Niro and RFK Jr. have joined forces to push vaccine nonsense

Other:

Is Trump a Populist?
Don’t Blame Oroville on Environmentalists
A last chance to add life to Seaport
The Christian woman who defended Obamacare says she actually wants a single-payer system
“Not Wanted” Jason Chaffetz
Senate Doesn’t Have Plans To Block D.C.’s Death With Dignity Law
President* Trump Can’t Escape This Time
Just Elect Keith Ellison Already
Trump voters deserve understanding and consideration — but not more than any other Americans
The Washington National Cathedral Was Lit Last Night
Democrats bracing for town hall protests directed at them ask Bernie Sanders for help
“Civil Rights Groups” Throw Public Under the Bus on Net Neutrality for Their Big Telco Donors
In California Farm Country, Trump’s Deportation Threat Looms Large
Feds cite D.C. charters for high suspension rates, particularly for black students
Theresa Kereakes’ Intimate Portraits Capture Punk’s Latino Roots in 1970s LA
Republicans Must Own Trump; “Reformers” Must Own DeVos
Persuade
Can “institutional inertia” save the EPA?
Beauty and the Beast: Donald Trump as the Interior Decorator in Chief

Posted in Lotsa Links | Leave a comment

PacBio Finally Makes A Move It Desperately Needed To Make

While everyone hunts for the Holy Grail of human genomic sequencing (and other large genome critters), I’ve noted before there’s an obvious, if less sexy, market:

…microbial genomes are cheap, fast, and you can provide epidemiological relevant information to clinical laboratories, hospital networks, and public health departments. I’m not arguing that we will or should sequence everything–and today that’s not feasible–but in two or three years, I don’t see any technical hurdles to routine microbiological surveillance in hospitals. This is something already being done, just with mid-20th century technology.

And I wrote that four years ago, before programs like GenomeTrakr (genomic food-borne microbial surveillance) really got off the ground. We’ve arrived. While Illumina sequencing is very cheap (though the price versus the cost depends greatly on your cost structure model), it’s not likely to get that much cheaper or faster–right now, the major costs are personnel, DNA preparation, and the machine itself. Illumina-sequenced genomes also have problems with contiguity: that is, it’s often hard to tell if genes are linked to each other, especially the clinical relevant stuff, like virulence and antibiotic resistance genes, which are often found on plasmids* that are hard to assemble (#NotAllResistanceGenes…).

However, PacBio is very good for bacterial genomes. Compared to Illumina, it doesn’t produce very much sequence–a problem for large genomes (like boring humans). But bacterial genomes are small, so the technology produces enough sequence per run (we’ll return to this in a moment). PacBio’s large read size means that it’s very possible to assemble bacterial chromosomes and plasmids in their entirely–or at least in a very small number of pieces. The problem, until now, is that, for a single bacterial genome, PacBio produces too much sequence, to the point where the reagent cost (‘the sequencing cost’) is very high per bacterial genome (>$1,000 per bacterial genome).

So PacBio finally released a protocol that enables multiplex sequencing–the ability to sequence multiple bacterial genomes at one time:

This document describes a procedure for multiplexing 5 Mb microbial genomes up to 12-plex and 2 Mb genomes up to 16-plex, with complete genomes assemblies (<10 contigs). The workflow is compatible for both the PacBio RSII and Sequel Systems. 10kb SMRTbell libraries are constructed for each sample through shearing and Exo VII treatment before going through the DNA Damage Repair and End-Repair steps. After End-Repair, barcoded adapters are ligated to each sample. Following ligation, samples are pooled, treated with Exo III and VII, and then put through two 0.45X AMPure® PB bead purification steps. Note that size-selection using a BluePippin™ system is not required. SMRTLink v4.0 is utilized to demultiplex and assemble the genomes after sequencing….

For this procedure, the required total mass of DNA, after pooling, is 1 – 2 μg. Therefore, the required amount of sheared DNA, per microbe, going into Exo VII treatment is 1 μg divided by the number of microbes. For example, in a 12-plex library, 1 μg ÷ 12 microbes = 83 ng of sheared DNA is needed for Exo VII treatment.

Translated into English, you can sequence 12 E. coli at once, or 16 Camplyobacter. This makes the sequencing cost per bacterium very affordable. The quality of these genomes, if they’re similar to previous PacBio bacterial genomes, is quite high, both in terms of contiguity (figuring out where the genes are relative to each other) and sequence accuracy (the latter, as best as I can tell, is still a problem for Oxford Nanopore).

This is a good move for PacBio, and a pretty interesting development for bacterial genomics, especially if you’re interested in plasmids and genome architecture.

Plasmids are small, ‘mini-chromosomes’ that often can move from bacterium to bacterium, and which can also carry antibiotic resistance genes–making them medically important (though other plasmids are equally cool). Like bacterial genomes, they are a circle of DNA (in most cases…)

Posted in Genomics | 4 Comments

Links 2/16/17

Trump_tweetingphone
Links for you. Science:

Scientists discover pollution 10,000 meters below the ocean’s surface in the Mariana Trench
5 possible futures for the EPA under Trump
How a minor committee became a ‘weapon’ of the climate wars
A millionaire’s mission: Stop hospitals from killing their patients by medical error
This Beetle Bites an Ant’s Waist and Pretends to be Its Butt

Other:

As a Christian, I defended Obamacare. But I really support single-payer.
Self-Described Liberals And Democrats Had Lots of Gay Friends
The DNC road show came to Baltimore
The Forgotten History of U Street
Universities didn’t “turn left”; they stayed committed to rational thought. It was the right which turned imbecile.
From a friend in Texas, the real results of anti-immigrant policy
A Political Opening for Universal Health Care?
This Is Not America
House committee moves to block D.C.’s assisted-suicide law (when you make Rep. Issa look good, you’re doing something very wrong)
This is what school buses looked like in 1934
Hundreds Of Washingtonians Plot To Keep Meddlesome Congress’s ‘Hands Off D.C.’
Sympathy For The Staff
Management team at Kramerbooks quits as new owner’s changes take hold
Mass sexual assaults by refugees in Frankfurt ‘completely made up’
AMERICA’S DUMBEST TRAITORS
Trump, asked about anti-Semitism, brags about election victory
Should Democrats team up with Wall Street to fight Trump? Hell no.
Some are wondering why historical comparison this cartoon tries to make is so wrong-headed. Let me try to explain.

Posted in Lotsa Links | Leave a comment

A Small Example Of The Scientific Infrastructure Crisis: The Karst Edition

Despite what is commonly depicted in books, television, and movies, the state of much of our scientific infrastructure is threadbare:

One of the ridiculous things about many depictions of science in TV and movies is the notion that there’s this huge infrastructure: shiny labs (which are always neat and spacious), high-tech this and that, and an army of workers to solve a problem. The reality is that much of our scientific knowledge in any subdiscipline is held by a few people who are operating on shoestring budgets with inadequate resources. To put it bluntly, we often lose considerable knowledge and materials when an older faculty member or researcher dies or retires (in my own subdiscipline of microbiology, there are several valuable collections that would be lost if a single freezer broke for an extended length of time).

Today’s example has to do with the unique and rapidly vanishing limestone karst habitat in Cambodia (boldface mine):

Cambodia has almost no botanists and the study of plants in the country came to a standstill from 1970 to 1992 during an extended period of war and unrest punctuated by the trauma of the Khmer Rouge takeover from 1975 to 1979.

The country’s main herbarium is a single room at the Royal University of Phnom Penh. It houses about 12,000 specimens, many of which have not been inventoried and are simply piling up on shelves. They are meant to be kept cool and dry by two air-conditioners, but one air-conditioner is broken and there is no money to fix it.

“You talk about a herbarium in another country and it should be very big, but this is just one room,” said Ith Saveng, who runs the university’s Center for Biodiversity Conservation. “We hope to expand to another room within the next two years.”

Rare plants found in karsts have to be shipped to Vietnam so better-trained scientists can do the precise work of matching species to species.

A small amount of money could very easily have a huge effect on our understanding of biodiversity. But, as we’ve noted many, many, many times, much of our scientific infrastructure is very fragile.

And we are long gone and forgotten, it’s these sorts of facilities that are future generations’ patrimony.

Posted in Funding, Museums etc., Plants | 2 Comments

Links 2/15/17

Trump_killmoosensquirrel
Links for you. Science:

Watch how the measles outbreak spreads when kids get vaccinated – and when they don’t
She felt a ‘crawling sensation.’ Doctors found a live cockroach in her skull.
The tragic story of Soviet genetics shows the folly of political meddling in science
NASA launched an unprecedented study of Greenland’s melting. Now, the data are coming in
Here’s why India is struggling and failing to control tuberculosis

Other:

The Gorsuch gambit
Chinese factory replaces 90% of human workers with robots. Production rises by 250%, defects drop by 80%
Milk is the new, creamy symbol of white racial purity in Donald Trump’s America
How We Can Thrive Under Trump: A Muslim’s Letter to His Jewish Neighbors
Who Benefits From Trump’s Chaos? Elites have always used a climate of fear to push their own agendas
It’s Not Foreigners Who are Plotting Here: What the Data Really Show
Syria has secretly executed thousands of political prisoners, rights group says
Trump says sanctuary cities are hotbeds of crime. Data say the opposite.
ONE MORE GROUP THE TRUMPERS DELIBERATELY OFFENDED
When The New York City Subway Was The Most Dangerous Place On Earth
Beware of Self-Censorship
It’s time for the lamest lie in U.S. politics to go away
Who Uses the ACA? Trump Voters.
Cancel dinner plans. Send ‘nerd prom’ to the history books.
The big lesson of Trump’s first 2 weeks: resistance works
South of the border, Mexicans are puzzled by Trump’s relentless and pointless antagonism
How Trump’s policies and rhetoric are forging alliances between U.S. Jews and Muslims
A Stern warning
Breitbart loses advertising deals with 935 companies due to grassroots campaign

Posted in Lotsa Links | 2 Comments

In Bipartisan Fashion, Congress ‘Fixes’ Its Own Postal Service Screw Up

Consider this a case study in how Democrats lose.

Years, the august solons of the U.S. Congress decided that the U.S. Postal Service (‘USPS’) would be forced to fund 75 years of retirement funds over a period of ten years–something virtually no business could do. This is all the more galling as USPS probably paid $50 to $100 billion more than it should have to retirement funds in the first place.

As a result of this financial chicanery, USPS has been ‘losing massive amounts of money’, even as it operates in the black. I’ve never figured out why Democrats went along with this, but Republicans love this because it gives them an opportunity to reward corporate privatizers (we must outsource to save money, even though that rarely works) as well as the opportunity to pound postal workers and their unions.

So the House panel which oversees USPS has released this gem of a bill (boldface mine):

Now, with bipartisan legislation being considered in the infamously partisan House, hopeless no longer describes the USPS’s future. It’s not fixed yet, but the Postal Service Reform Act of 2017 provides a degree of optimism that for many years was absent.

“We’re actually going to get to the finish line and get a bill on the president’s desk,” Committee Chairman Jason Chaffetz (R-Utah) told the hearing. “I’d like to see that as a bipartisan reform proposal that we can all get behind and champion. I didn’t get everything I wanted, Congressman (Elijah E.) Cummings didn’t get everything he wanted, but that’s the nature of coming up with a compromise without compromising your principles.”

Anything Rep. Chaffetz, High Lord of the District of Columbia, touches is going to be shit. We know this. Moving along…

We’re faced … with 10 consecutive years of financial losses at the Postal Service, totaling some $62 billion. The United States Postal Service isn’t at ‘a’ crossroad, it’s at ‘the’ crossroads,” Chaffetz said. “It’s up to this Congress to address the challenges facing the Postal Service, its customers, the businesses that rely on it, and the taxpayers who will bear the burden if we fail to act.”

Much of what the bill would do is in the weeds of postal finances, dealing with the nitty-gritty of health benefits for employees and retirees, pensions, governance and contracting. Postmaster General Megan J. Brennan said the provision requiring postal retirees to fully participate in Medicare is key because that “would essentially eliminate our unfunded liability for retiree health benefits,” which has been a major driver of postal doldrums.

The National Active and Retired Federal Employees Association (NARFE) objected to this proposal, saying it would mean a monthly increase in Medicare premiums of at least $134 for postal retirees. “All for health insurance coverage many postal retirees do not want, may not be able to afford, and have previously chosen not to take,” said a letter to the committee from NARFE President Richard G. Thissen.

Keep in mind, when we alter retirees’ benefits–which were part of the contract they signed–we are retroactively inflicting a pay cut on them years after they have retired, for no reason other than a bullshit financial crisis. Bidness ‘leaders’ seem to know the real score:

In a demonstration of the exceptional unity around this bill, even the Coalition for a 21st Century Postal Service (C21), an organization of mailing industry trade associations and companies, endorsed the legislation, including the postage increase.

“To put it bluntly, mailers do not welcome rate increases generally, including this one. They are bad for business,” said Art Sackler, C21’s manager. “Nonetheless, we accept the necessity in this unique set of circumstances for the one-time across-the-board 2.15 percent increase … as, from our perspective, a necessary evil to assure longer-term postal financial stability.”

So Democrats, once again, were outmaneuvered by Republicans, and then Democrats knuckled under and screwed their supporters, a large union (which is disproportionately minority to boot). Winning!

It is a mystery why Democrats have a hard time getting voters to turn out. It really is.

Posted in Conservatives, Democrats, Fucking Morons, USPS | Leave a comment

Links 2/14/17

Trump_OutLikeFlynn
Links for you. Science:

The new face of US science
Federal Wildlife And Land Managers Say They Fear For Their Safety
Scientists Make Progress Toward a Safe, Effective Zika Vaccine
Scientists Are Arguing About Whether The March For Science Will Be Too Political
Patients treated by foreign-educated doctors are less likely to die, study finds

Other:

The Big Reason Whites Are Richer Than Blacks in America: Inheritance matters a lot more than previously thought. Guess who’s getting the lion’s share.
The Long, Strange History of Non-Citizen Voting
Why Is Trump Adviser Wearing Medal of Nazi Collaborators?
President Trump’s racist time machine
Democratic Party Policies Actually Hurt the Working Class
Donald Trump And The Crazy Rich
Japanese Street Style Magazine FRUiTS to Shutter After 20 Years Citing Lack of Cool Kids
Taking Corruption International
South Dakota GOP Repeals Anti-Corruption Act Passed By Voters
House Republicans Vote to End Rule Stopping Coal Mining Debris From Being Dumped in Streams
Historic black cemeteries seeking the same support Virginia gives Confederates
Here’s What Happens When You Wear Giant JNCO Jeans In 2016
And Then the Breitbart Lynch Mob Came for Me: For 15 years, I’ve spoken out against executive overreach. But in the Trump era, even theoretical criticism puts a target on your back
‘A Sense of Dread’ for Civil Servants Shaken by Trump Transition
See Photos From the World’s Oldest Operating Photo Studio
Gerrymandering is the biggest obstacle to genuine democracy in the United States. So why is no one protesting?
We sent @Amy_Hoggart to Scotland to discuss resisting oppression with people who are born crotchety.
The forgotten New Yorker who changed the ‘80s music scene

Posted in Lotsa Links | Leave a comment