True's beaked whale.jpg

Western spotted skunk

Hooded skunk

Yellow-throated Marten

Wolverine

Links for October 2015

October 7th, 2015

More guns means more people shot
How to sequence and assemble a large eukaryote genome with long reads in 2015
Convert between RefSeq and Ensembl Transcript
Ion Torrent S5, $65k, between Proton and PGM in capability, 200bp reads in 2.5 hrs

Podcasts:
Stuff You Should Know
Stuff You Missed in History Class
HOW TO DO EVERYTHING
Skeptics’ Guide to the Universe

50 despicable things George W. Bush did before and after 9/11
Oak leaf mites bite humans this year

Beer:
Practical Porter
Beer Styles: Making a Porter Recipe

Links for September 2015

September 4th, 2015

Japanese zoning. Allow mixed land use by design, up to a maximum use for each zone. Contrasted with US Euclidian zoning.
India’s Subterranean Stepwells
Solidarity Squandered by Rick Perlstein. The attacks brought us together until we let them turn us against each other–and damn near everyone else.
Article on the culture of Iceland and how it intersects with the 2008 bankruptcy crisis, “Wall Street on the Tundra” J
by MICHAEL LEWIS, APRIL 2009

Illinois good hiking spots
Pics of a WWI German sub (sunk and recovered by the British–all Steampunk
Rethinking government debt by Frances Coppola. Covers the economics of money and debt.
God damn letter sent to Abraham Lincoln
Virus GBV-C protects somewhat against AIDs

Links for August 2015

August 1st, 2015

Colourlex: pigments and paintings
Dietary pesticides (99.99% all natural) (pdf)

The toxicological significance of exposures to synthetic chemicals is examined in the context of exposures to naturally occurring chemicals. We calculate that 99.99% (by weight) of the pesticides in the American diet are chemicals that plants produce to defend themselves. Only 52 natural pesticides have been tested in high-dose animal cancer tests, and about half (27) are rodent carcinogens; these 27 are shown to be present in many common foods. We conclude that natural and synthetic chemicals are equally likely to be positive in animal cancer tests. We also conclude that at the low doses of most human exposures the comparative hazards of synthetic pesticide residues are insignificant.

“Racism and Science Fiction” by Samuel R. Delany
Genetics of color, COLOUR AND PATTERN CHARTS
Sarah Hartwell

Info on college costs from the National Center for Education Statistics (NCES)
A genome-wide analysis of putative functional and exonic variation associated with extremely high intelligence. Spain et. al., 2015. Molecular Psychiatry

Although individual differences in intelligence (general cognitive ability) are highly heritable, molecular genetic analyses to date have had limited success in identifying specific loci responsible for its heritability. This study is the first to investigate exome variation in individuals of extremely high intelligence. Under the quantitative genetic model, sampling from the high extreme of the distribution should provide increased power to detect associations. We therefore performed a case–control association analysis with 1409 individuals drawn from the top 0.0003 (IQ >170) of the population distribution of intelligence and 3253 unselected population-based controls. Our analysis focused on putative functional exonic variants assayed on the Illumina HumanExome BeadChip. We did not observe any individual protein-altering variants that are reproducibly associated with extremely high intelligence and within the entire distribution of intelligence. Moreover, no significant associations were found for multiple rare alleles within individual genes. However, analyses using genome-wide similarity between unrelated individuals (genome-wide complex trait analysis) indicate that the genotyped functional protein-altering variation yields a heritability estimate of 17.4% (s.e. 1.7%) based on a liability model. In addition, investigation of nominally significant associations revealed fewer rare alleles associated with extremely high intelligence than would be expected under the null hypothesis. This observation is consistent with the hypothesis that rare functional alleles are more frequently detrimental than beneficial to intelligence.

In the modern Republican Party, making sense is a secondary consideration. Years of relentless propaganda combined with extreme frustration over the disastrous Bush years and two terms of a Kenyan Muslim terrorist president have cast the party’s right wing into a swirling suckhole of paranoia and conspiratorial craziness. There is nothing you can do to go too far, a fact proved, if not exactly understood, by the madman, Trump.


First octopus genome published: California two-spot octopus, Octopus bimaculoides


Pentagon tiling discovery.

pentagon tiling examples


Hugo awards 2015!
Yea, the asshole muckers lost! Nice to see Orphan Black win.

What the alternate Hugo Ballot would likely have been Good source for my TO READ list.


Flying Spaghetti Monster propaganda materials

HTTP error codes in cat gifs

Scientists who found gluten sensitivity evidence have now shown it doesn’t exist. Follow up study by Peter Gibson at Monash University in Australia to his 2011 paper

Links for July 2015

July 3rd, 2015

Short and succinct argument for removing ten Commandments from public spaces.
Orac on ‘integrative medicine’
Recommended economics books by Brad DeLong
Lyme disease, common and dangerous
Trump’s short and long cons
The myths of bioinformatics software
Were Republicans really the party of civil rights in the 1960s?
History of British slave ownership

Protein in dinosaur fossils, new paper

June 12th, 2015

A second group has found protein preserved in dinosaur fossils. I wouldn’t call this solid yet, but it is encouraging. This hit the news in September 2009

Fibres and cellular structures preserved in 75-million–year-old dinosaur specimens

Abstract
Exceptionally preserved organic remains are known throughout the vertebrate fossil record, and recently, evidence has emerged that such soft tissue might contain original components. We examined samples from eight Cretaceous dinosaur bones using nano-analytical techniques; the bones are not exceptionally preserved and show no external indication of soft tissue. In one sample, we observe structures consistent with endogenous collagen fibre remains displaying ~67 nm banding, indicating the possible preservation of the original quaternary structure. Using ToF-SIMS, we identify amino-acid fragments typical of collagen fibrils. Furthermore, we observe structures consistent with putative erythrocyte remains that exhibit mass spectra similar to emu whole blood. Using advanced material characterization approaches, we find that these putative biological structures can be well preserved over geological timescales, and their preservation is more common than previously thought. The preservation of protein over geological timescales offers the opportunity to investigate relationships, physiology and behaviour of long extinct animals.
Nature Communications 6, Article number: 7352, 09 June 2015

Links for June 2015

June 10th, 2015

Pseudoscience: IgG Food Intolerance Tests
William Thompson, the Savannah, Georgia Daily Morning News editor who designed the Confederate flag describes its racist meaning
What the rich want, everyone in the US gets. Survey data
Making Leavers machine lace
Why early Chlamydia vaccines failed (and lowered resistance to Chlamydia)

TGF-β1 inhibitor stimulates stem cell division in old mice

May 20th, 2015

RepSox, a TGF-β1 inhibitor, promotes stem cell growth and enhances neurogenesis and muscle regeneration in old mice. Neurogenesis occurs primarily in the dentate gyrus of the hippocampus, and this is where the authors find it. No functional tests are shown.

The compound, 2-(3-(6-Methylpyridin-2-yl)-1H-pyrazol-4-yl)-1,5-naphthyridine or RepSox (PubChem) has been mentioned in half a dozen studies as a drug that promotes stem cell proliferation. Compound sells for research use at $50 / gram.

<p>Systemic attenuation of the TGF-β pathway by a single drug simultaneously rejuvenates hippocampal neurogenesis and myogenesis in the same old mammal. Hanadie Yousef, Michael J. Conboy, Adam Morgenthaler, Christina Schlesinger, Lukasz Bugaj, Preeti Paliwal, Christopher Greer, Irina M. Conboy, David Schaffer
Oncotarget. May 06, 2015. (pdf)

Links for May 2015

May 11th, 2015

Analysis: Over Half of All Statements Made on Fox News Are False
Lokiarchaeota, an archea, is the closest relative to eukaryotes
Carl Zimmer on the biological mathematics of long bamboo flowering cycles (120 years!)
Paramagnetic fluid

Fixing a Shark SV75 mini vaccum

April 27th, 2015

Bad batteries–vaccum has 13 sub C NiCD cells. Tested voltage on the individual cells and replaced 6 bad cells.

The vaccum still wouldn’t charge–checking the charging circuit board showed a crack in a trace near the edge where the indicator LED is located. A bit of solder fixed it, and now it is charging.

FYI, the main IC on the circuit board is a ABOV MC96P0202, a 8-bit OTP CPU.

Average Number of Recessive Lethal Mutations Carried by Humans

April 26th, 2015

Recently Gao et. al. published “An Estimate of the Average Number of Recessive Lethal Mutations Carried by Humans”. They studied a Hutterite group in South Dakota, highly inbred (63 founders 13 generations ago). From serious genetic diseases common in this population, they determine the number of deleterious variants present in the founders. They find that 0.29 recessive lethal alleles per haploid genome. Since some lethals manifest before birth, they double the estimate to 0.58.

This gives an expected 1.8% increased chance of a genetic disease from two first cousins.

Gao, Z., Waggoner, D., Stephens, M., Ober, C. & Przeworski, M. Genetics 199, 1243–1254 (2015).