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Protein in dinosaur fossils, new paper

Friday, 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

Wednesday, 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

Wednesday, 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

Monday, 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

Monday, 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

Sunday, 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).

Links for April 2015

Wednesday, April 1st, 2015

NPR Enables The Anti-Worker Movement
Economics blog: Beat the Press (Dean Baker)
Purple frog
Ultrasound Alzheimer’s treatment fully restores memory function. pub link. Worth following up in a year
Welfare that the well off get
Medzhitov / Galli theory that allergies are a response to toxic chemicals
Family firms
Survey of gun researchers: having a gun increases your risk

Links for March 2015

Thursday, March 5th, 2015

Ending the Creditor’s Paradise
First detailed microscopy evidence of bacteria at the lower size limit of life (0.2 um, 1/150th size of an E. coli) (paper)
Best Feminist Books For Younger Readers
Cold-brewed chocolate
A Chladni plate experiment–visualizes complex resonance patterns
Fuse glass in a microwave and metals
Variant annotation: ANNOVAR vs VEP: McCarthy et. al., 2014, pdf, suppl.
Blog post with a comparison: State of Variant Annotation: A Comparison of AnnoVar, snpEff and VEP by Andrew Jesaitis
TIP – Troubles in Paradise (history of creationist argumentation)
The Irrationality of Alcoholics Anonymous–using naltrexone to treat alcoholism
Krugman reports on the Republican budget proposal
A Scientist’s Guide to Citizen Science

Links for February 2015

Tuesday, February 3rd, 2015

Comic: Phoebe and Her Unicorn
Illumina sequencer comparison: XTen, HiSeq 2500, NextSeq 500, MiSeq
NextSeq 500, an odd choice
How fast is your flash? Measuring high-speed flashes
Plans for an air-gap flash
The Infection Schedule versus the Vaccination Schedule by Mark Crislip. Comparing the antigens in a vaccine to the number a person responds to in ordinary life.
Elysium Health (Guarente) has a NAD precursor + sirulin targeting anti-oxidant, $2/day
VAX! A game about epidemic prevention.
Roald Dahl on Olivia, writing in 1988. “MEASLES: A dangerous illness.”
UPC codes for a product, inexpensive from a reseller
USB id for a product, inexpensive from a reseller
NGS machine comparison

2015 Nebula award speculation

Origin of the $ sign

Converting files avi to mp4

Measles vaccine nonsense

Sunday, February 1st, 2015

I was sent a link to a blog post, “This Mama Isn’t Scared of the Shmeasle Measles” by Megan Heimer.

I’ll run through the post in a minute, it contains a whole lot of nonsense. First, some links to reliable info:
CDC measles info
CDC Manual for Surveillance of VPD: Chapter 7: Measles
Measles week posts by an immunologist

Now, on to the post…

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