Cavalcade of Mammals

Links for Sept 2019

I now publish #MeToo stories on my blog, for free. Here’s why. by Michael Balter. Academic sex crimes.

I Support Unions, Just Not This On. Liberalism in a nutshell… by Nathan J. Robinson

Come With Us If You Want to Live. Among the apocalyptic libertarians of Silicon Valley by Sam Frank
Designing the perfect society, without any consideration for pesky, disagreeable people.

Hubble finds C
60 in space, helps solve interstellar mystery

The Day One Agenda. The Next Administration: Using Presidential Power for Good by David Dayen

Glass slump 1

Two test pieces. One a 10 cm square, the other a 12 cm square. For both, arranged 3 mm colored pieces over a 3 mm clear base, filled in gaps with medium clear frit. Tacked down the larger pieces with craft glue. COE 90.

300F 60′
600F 60′
900F 60′
1000F 35′
1480F 60′
960F 60′
800F 60′

Cleaned up frit that had fallen off and stuck to the edges with a Dremel.

Slump smaller square over a 10 cm bowl. Drape larger square over a 10 cm bowl upside down suspended on two small posts. Put kiln paper over the bowls to prevent sticking.

300F 60′
600F 60′
900F 60′
1000F 40′
1250F 40′
960F 120′
880F 24′
800F 24′

Links for August 2019

Middle Eastern food in Chicago, link

Supercentenarians and the oldest-old are concentrated into regions with no birth certificates and short lifespans by Saul Justin Newman, BioRxiv

Interesting post on C.S. Lewis and Fred Hoyle arguing by writing books at each other. I had never run across Ossian’s Ride. link

The Role of Deliberate Practice in the Acquisition of Expert Performance. (1993). K. Anders Ericsson, Ralf Th. Krampe, and Clemens Tesch-Romer pdf

“crackpots” who were right: the conclusion

How Life Sciences Actually Work: Findings of a Year-Long Investigation by Alexey Guzey, link. Some insights.

Open Borders Made America Great. For most of U.S. history, all immigrants were undocumented. It’s a fact Democrats should embrace. by Aaron Freedman, link

The three technologies bioinformaticians need to be using right now. by biomickwatson, link
BioConda/Docker/Singularity, SnakeMake/NextFlow, Cloud computing

Encyclopedia of Chicago History, link
Ancient Indian Earthworks in the Chicago Region

Links for July 2019

Republican terrorist threats shut down Oregon legislature, link

Concluding they can’t win the vote, Republicans abandon democracy, link

Grover Cleveland’s Sex Scandal: The Most Despicable in American Political History by Charles Lachman

Some Notes on Chinese Communist Party Internal Resilience by Bill Markle (10 part post on Chinese government)

The Truth About Chlorinated Chicken review – an instant appetite-ruiner
Britain fears low US food standards will come to Britain post-Brexit

Cave debris may be the oldest known example of people eating starch:
Charred material found in South Africa suggests humans digested starch long before farming

Looks like the paleo diet will need to be updated with potatoes

Guantánamo’s Darkest Secret: The U.S. military prison’s leadership considered Mohamedou Salahi to be its highest-value detainee. But his guard suspected otherwise. by Ben Taub
People are imprisoned for decades at Guantánamo Bay because it would be embarrassing to the military to admit there was never a reason to hold them. Also, they were tortured.

GM fungus rapidly kills 99% of malaria mosquitoes, study suggests. by James Gallagher

Birdbath mosaic, link

Use a teflon spatula to remove warranty sticker without leaving the ‘void’ mark: youtube
Science division of White House office left empty as last staffers depart, link

Slide mounting options, link

“A Tall Tail” by Charles Stross

EquiFax hacking settlement–apply for $125-$425. Affects most US adults. link

Senescent cells exhibit depletion of metabolites from nucleotide synthesis path- ways. Stable isotope tracing with 13C-labeled glucose or glutamine revealed a dramatic blockage of flux of these two metabolites into nucleotide synthesis pathways.  Blocking the pathway in replicative cells induces senescent phenotype.
Inhibition of nucleotide synthesis promotes replicative senescence of human mammary epithelial cells. May28, 2019.  JBC. Alireza Delfarah, Sydney Parrish, Jason A. Junge, Jesse Yang, Frances Seo, Si Li, John Mac, Pin Wang, Scott E. Fraser, and X Nicholas A. Graham. DOI10.1074/jbc.RA118.005806. 

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!


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.