Cavalcade of Mammals

Links for June 2019

Larotrectinib approved for the treatment of metastatic solid tumors with NTRK fusion (inhibitor of TrkA, TrkB, and TrkC).

1 in 5 Cops Had Posted Racist, Violent Content on Facebook

Reminder of a what a shit human Dinesh D’Souza’s is

The Wonderful World of Free Market Drugs by Dean Baker

China Miéville’s rejected Iron Man pitch

Genetic changes to improve humans from George Church’s lab

cǎonímǎ 草泥马 Grass-mud horse tank man. Mascot of Chinese netizens fighting for free expression, symbolizing defiance of Internet censorship.

A teachable moment in why Uber/Lyft can never replace public transportation. That Uber was oblivious enough for this self-goal explains why their stock will soon be worth less than monopoly money. link


Trove of leaks show that Brazil’s “anti-corruption” task force was secretly trying to oust Lula and install a far-right strongman


Links for May 2019

How Single-Family Garages Can Ease California’s Housing Crisis: Given the affordable housing crisis, California cities should encourage single-family homeowners to convert garages into apartments and accessory dwelling units.

How long do vaccines last? The surprising answers may help protect people longer.
Recent studies show vaccines for flu, mumps, pertussis, meningococcal disease, and yellow fever also lose their effectiveness faster than official immunization recommendations suggest.

True Crimes. Why it’s important to name names when discussing the climate catastrophe. by Billy Wilson.

Syphilis Is Spreading Across Rural America.
Back in 1999, the Centers for Disease Control and Prevention had a plan to eradicate the sexually transmitted disease that totaled over 35,000 cases nationwide that year. While syphilis can cause permanent neurological damage, blindness or even death, it is both treatable and curable. By focusing on the epicenters clustered primarily throughout the South, California and in major urban areas, the plan seemed within reach.

Instead, U.S. cases topped 101,500 in 2017 and are continuing to rise along with other sexually transmitted diseases. Syphilis is back in part because of increasing drug use, but health officials are losing the fight because of a combination of cuts in national and state health funding and crumbling public health infrastructure.

Esther Lederberg and Her Husband Were Both Trailblazing Scientists. Why Have More People Heard of Him? Like many female scientists, Esther Lederberg saw her achievements overshadowed by a man’s. Now there’s a movement to tell their stories. by Katy Steinmetz.

She discovered lambda phage, invented replica plating.

Statistical Guidance on Reporting Results from Studies Evaluating Diagnostic Tests – Guidance for Industry and FDA Staff

Undercover with New York Nazis by Michael McCanneM

Your Gas Stove Is Bad for You and the Planet: To help solve the climate crisis, we need to electrify everything. by Justin Gillis and Bruce Nilles

In 2008, Johns Hopkins scientists urged doctors to advise parents of asthmatic children to get rid of their gas stoves or at least install powerful exhaust hoods.

How Margaret Dayhoff Brought Modern Computing to Biology

To combat rising U.S. prescription drug prices, let’s try competition. by Michael Kades

The Myth of Fingerprints. by Clive Thompson
Nonetheless, the reliability of fingerprinting today is rarely questioned in modern courts. One exception was J. Spencer Letts, a federal judge in California who in 1991 became suspicious of fingerprint analysts who’d testified in a bank robbery trial. Letts was astounded to hear that the standard for declaring that two prints matched varied widely from county to county. Letts threw out the fingerprint evidence from that trial.

Universal Health Care Might Cost You Less Than You Think: We don’t think of the premiums we already pay as taxes, but maybe we should. by Matt Bruenig

2 Rules for Building Comfortable Stairs
rise plus run (r+R) should equal 18 inches.
And twice the rise plus (2r+R) the run should be 25 inches.

From Digby

Wireless LEDs Aren’t A First, But You Can Make Your Own
X-base | Wireless LED Lighting and Display System Kickstarter 2018

Why American Costs Are So High for building transit (4X – 10X rest of world)

The Human Antivenom Project by Kyle Dickman

Understanding the Basics of Cardiopulmonary Exercise Testing

Cardiopulmonary exercise testing and its application

The World’s Most Annoying Man: Steven Pinker is selling Reason™, not reason… by Nathan J. Robinson





Carbon capture

The basic problem with carbon capture is energy, and energy is cost. When coal or oil is burned, heat and CO2 are produced. CO2 is a pretty low energy form of carbon. Turning it into something solid (calcium carbonate, graphite or coal) requires a lot of energy. Also, when CO2 is made by burning fossil fuels it disperses, and re-concentrating it requires energy. That’s why carbon capture proposals often include using exhaust gas, grabbing the CO2 before it disperses. The other main type of capture I’ve seen proposed takes the CO2, concentrates it to high pressure, and pumps it underground (and hopes it stays there). Compressors take a lot of energy, and so do pumps if the CO2 needs to be piped hundreds of miles to a place where it can be pumped underground.

The key number for carbon capture is, how much energy is required relative to the amount generated by burning the fossil fuel? I’ve never seen articles about it touting this number. A quick look shows one assessment being 30% – 35% of the energy (Zhang et al, 2014), another figures the production cost of electrcity with carbon capture being 62% – 130% higher (White et al, 2012, Table 6) Another article looks at the harder case, CO2 capture from air, and estimates the cost at $1000/ton CO2 (link). Burning the coal to generate a ton of CO2 (1/3 of a ton coal) generates about $80 of electricity.

So the best case cost of carbon capture–from power plant exhaust gas–is dismal, 25%, 75%, maybe over 100% of the value of the electricity. This number will translate directly to increased fossil fuel energy costs (+30%, +100%, etc.) if fossil fuel companies are required to capture the majority of the CO2 pollution they generate.

All the carbon capture projects are basically stalling actions. The fossil fuel companies pay small $$ to put together a pilot plant (or better yet, get the govt to fund it), run tests for years, but never implement CO2 capture on a coal or gas energy plant. This had been a very successful approach for the fossil fuel industry, they’ve managed to stall things for 50 years already!

CRISPR

The CRISPR gene editing system is a major technical advance. It does open up the near term possibility of making a few small changes to a human embryo’s DNA, but I don’t find that particularly interesting or alarming.

What makes CRISPR better than previous tech for gene modification is that it works at high efficiency–1% to 60% with very high specificity. I read a recent paper testing CRISPR on human embryos that reported 50% effectiveness. Given a handful of embryos to work with, there is a very good chance of making a single change in one embryo.

We have very little knowledge or technology for making positive changes to animals which is a huge limitation to genetic ‘engineering’. Mostly what is understood are disease causing (or predisposing) genetic variants. So a single change (maybe in a few years, a handful of changes?) can be made to a human embryo. There are other limits to modifying human embryos apart from lack of knowledge. The more time an embryo or human embryonic stem cell is cultured, the more it is manipulated, the greater the chance of something going wrong, and the child being born with problems. This tech is great for manipulating animals in the lab. If many or most of them have the genetic change, great! If some are born with defects, cull them, or breed another generation and use those in experiments (often the first generation has non-genetic defects that breed away). But these are huge problems if you are working on humans, because things that increase the risk of getting a damaged child are not desirable.

Long term (100-1000 years), when increases in understanding of biology make improvements (or significant changes of any sort) in humans possible, I think what we’ll see is that the people with the least concern for child welfare will be the most willing to experiment on them.

The really exciting possibilities CRISPR opens up is in genetic treatment of human disease in the tissues of kids and adults. There is delivery tech (well tested viral vectors, and a host of other methods) that can get CRISPR into a good percentage of cells (10% to 50+%) in many tissues, and once there, CRISPR will edit a good fraction of those cells. For many diseases, fixing a genetic defect in 1%, 10% or 20% of cells is enough to treat the disease, so genetic treatment of host of diseases is now possible. Things like hemophilia, some muscular dystrophy, maybe Huntington’s Disease, metabolic diseases, Parkinson’s disease, and on and on. There will be a lot of exciting advances turning that ‘possible’ into actual treatments for different diseases over the next decade or two.

The other major effect of CRISPR tech is that it makes animal experimentation faster and cheaper, and will accelerate basic biological research. We still don’t know what the majority of indivdual genes do, let alone how they work in complexes and networks in cells.

Links for February 2019

Bizarre Paintings Of Mecha Robots And Werewolves Attacking East European Peasants Of The Early 20th Century by Polish artist Jakub Rozalski
2019 Sequencing Tech Speculations: Will We Actually See New Entrants?

Novel Benzodiazepine-Like Ligands with Various Anxiolytic, Antidepressant, or Pro-Cognitive Profiles, link.
-Improves mood and age-related memory loss.

Under the Boot: Max Boot’s conversion narrative proves one thing—he hasn’t changed a bit. by Lyle Jeremy Rubin

Kompromat: Or, Revelations from the Unpublished Portions of Andrea Manafort’s Hacked Texts. by Maya Gurantz

Is Sunscreen the New Margarine? by Rowan Jacobsen

It was already well established that rates of high blood pressure, heart disease, stroke, and overall mortality all rise the farther you get from the sunny equator, and they all rise in the darker months. Weller put two and two together and had what he calls his “eureka moment”: Could exposing skin to sunlight lower blood pressure?

Sure enough, when he exposed volunteers to the equivalent of 30 minutes of summer sunlight without sunscreen, their nitric oxide levels went up and their blood pressure went down.


A Brad DeLong explains why it’s time to give democratic socialists a chance

“The baton rightly passes to our colleagues on our left.”


Paul Krugman Asked Me About Modern Monetary Theory. Here Are 4 Answers: Deficit levels, interest rates and the tradeoff between fiscal and monetary policy. by Stephanie Kelton

Stephen Wolfram: Seeking the Productive Life: Some Details of My Personal Infrastructure

The MBA Myth and the Cult of the CEO
CEOs don’t play much of a role in driving stock price performance, and the “aligned incentives” of equity incentive pay don’t change behavior in any way that benefits shareholders. The “best and brightest” — those executives with the most dazzling CVs and track records — don’t perform any better than less credentialed executives.

Harmony of Means and Ends: “theory of politics” by Cosma Shalizi

Socialists Win Big in Chicago: In city elections this week, progressive candidates shocked the Democratic machine. by Miles Kampf-Lassin

Review of Whiteshift by Eric Kaufmann
Kaufmann focuses on the “ethno” part [in ethnonationalism], arguing that mainstream politicians need to more openly cater to white concerns about cultural and demographic change if they wish to beat back the far-right tide.

Potluck Economics from Existential Comics


Number of unauthorized immigrants in the U.S. declined over the past decade

US_immigration_2019

Conversion of the solar fuel from norbornadiene to quadricyclane uses sunlight, reversed by a catalyst to release heat. ref, news.

Sleep is still a mystery.

Mac OSX Bash Profile

Recent US election results:
2016 President:
Donald J. Trump 63.0 million votes
Hillary R. Clinton 65.8 million votes

In 2018, Americans got some of what they want:
Democratic House candidates 59.0 million votes
Republican House candidates 50.3 million votes

Links for January 2019

Video of house
Gear design: Gearotic
Bike horse clopping
National Association of Watch & Clock
Watchmaking info
Cardboard Dinosaur PuzzleT-Rex Dinosaur Puzzle With Different Sizes and Positions
Bacteria In Worms Make A Mosquito Repellent That Might Beat DEET
How to Close the Democrats’ Rural Gap by Claire Kelloway


How Russian Money Helped Save Trump’s Business. After his financial disasters two decades ago, no U.S. bank would touch him. Then foreign money began flowing in. By Michael Hirsh

Sequencing an Ashkenazi reference panel supports population-targeted personal genomics and illuminates Jewish and European origins

Sequencing an Ashkenazi reference panel supports population-targeted personal genomics and illuminates Jewish and European origins

Shai Carmi et. al., Nature Communications volume 5, Article number: 4835 (2014)

Abstract

The Ashkenazi Jewish (AJ) population is a genetic isolate close to European and Middle Eastern groups, with genetic diversity patterns conducive to disease mapping. Here we report high-depth sequencing of 128 complete genomes of AJ controls. Compared with European samples, our AJ panel has 47% more novel variants per genome and is eightfold more effective at filtering benign variants out of AJ clinical genomes. Our panel improves imputation accuracy for AJ SNP arrays by 28%, and covers at least one haplotype in ≈67% of any AJ genome with long, identical-by-descent segments. Reconstruction of recent AJ history from such segments confirms a recent bottleneck of merely ≈350 individuals. Modelling of ancient histories for AJ and European populations using their joint allele frequency spectrum determines AJ to be an even admixture of European and likely Middle Eastern origins. We date the split between the two ancestral populations to ≈12–25 Kyr, suggesting a predominantly Near Eastern source for the repopulation of Europe after the Last Glacial Maximum.

pdf, suppl

Pan-cancer network analysis identifies combinations of rare somatic mutations across pathways and protein complexes

Pan-cancer network analysis identifies combinations of rare somatic mutations across pathways and protein complexes
Mark D M Leiserson et. al., Nature Genetics volume 47, pages 106–114 (2015)

Abstract

Cancers exhibit extensive mutational heterogeneity, and the resulting long-tail phenomenon complicates the discovery of genes and pathways that are significantly mutated in cancer. We perform a pan-cancer analysis of mutated networks in 3,281 samples from 12 cancer types from The Cancer Genome Atlas (TCGA) using HotNet2, a new algorithm to find mutated subnetworks that overcomes the limitations of existing single-gene, pathway and network approaches. We identify 16 significantly mutated subnetworks that comprise well-known cancer signaling pathways as well as subnetworks with less characterized roles in cancer, including cohesin, condensin and others. Many of these subnetworks exhibit co-occurring mutations across samples. These subnetworks contain dozens of genes with rare somatic mutations across multiple cancers; many of these genes have additional evidence supporting a role in cancer. By illuminating these rare combinations of mutations, pan-cancer network analyses provide a roadmap to investigate new diagnostic and therapeutic opportunities across cancer types.

pdf, suppl

Links for Dec 2018

Frank Wilhoit: The Travesty of Liberalism
Conservatism consists of exactly one proposition, to wit:
There must be in-groups whom the law protectes but does not bind, alongside out-groups whom the law binds but does not protect.

Silicon Valley’s Chinese Dream: Tech elites, weary of democracy, look to the East by Jacob Silverman
Trump Fans Sink Savings Into ‘Iraqi Dinar’ Scam

An Alternative History of Silicon Valley Disruption

   “Temp: How American Work, American Business, and the American Dream Became Temporary’ by Louis Hyman
   “The Value of Everything: Making and Taking in the Global Economy” by Mariana Mazzucato
   “Winners Take All: The Elite Charade of Changing the World” by Anand Giridharadas

Create a living will without a lawyer

Interpreting 23andMe, Ancestry SNP array results: Promethease, SNPedia
Four Days Trapped at Sea With Crypto’s Nouveau Riche by Laurie Penny
How to Convince MAGA Cretins to Fear Climate Change
Paper craft, including two by Haruki Nakamura
Kamikara – Mechanical Origami, book by Haruki Nakamura, in Japanese — Kami no karakuri – Kamikara de Asobo!
Wood clock plans and kits
Clayton Boyer Clock Designs
Aleksandar Hemon: Fascism is Not an Idea to Be Debated, It’s a Set of Actions to Fight
   In the comments: Bertrand Russell’s 1962 letter to fascist Sir Oswald Mosley

LEGO Star Wars Ultimate Millennium Falcon 75192 Building Kit (7541 Pieces)
Ramesh Ponnuru: Recession Is a Far Larger Threat Than Inflation
Commented:
We’re in the strange situation where the Fed, Republican economists, and related commentators all want to keep the economy juiced and growing for another year and a half to two years. I expect that will be the unspoken factor in Fed decisions and the wonkosphere, they’ll all sound more reasonable than normal for the period. I expect the Fed will begin to think a Democrat in WH is likely in 2020, and will steer the next recession to 2020-2021.

The Woman Who Cared for Hundreds of Abandoned Gay Men With AIDS by David Koon

Functional medicine: Reams of useless tests in one hand, a huge invoice in the other. by David Gorski


REVIEW ESSAY: Principles for Dummies by Matthew Walther

Principles: Life and Work by Ray Dalio

On the first page of his best-selling memoir, Ray Dalio unburdens himself of the opinion that he is “a dumb shit.” Nothing in the ensuing six hundred or so pages convinced me that I should dissent from this verdict.