Cavalcade of Mammals

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)


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)


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
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.

Links for November 2018

Chicago police search arrests
Chicago Police Department BAIL BOND MANUAL

Shetland sheep

“A Shetland ram was kept by United States President Thomas Jefferson for several years in the early nineteenth century. Unlike modern Shetlands (but like some related breeds) this ram had four horns. He was kept with about 40 other sheep on President’s Square in front of the White House. In the spring of 1808, it attacked several people who had taken shortcuts across the square, injuring some and actually killing a small boy.[8] Having been moved to Jefferson’s private estate at Monticello, the ram was eventually killed after having killed several other rams: it was described by Jefferson as “this abominable animal”.[8] Such aggressive Shetland rams, however, are unusual.[9]”

Candice Delmas, A Duty to Resist: When Disobedience Should Be Uncivil (2018)
QAnon’s true believers are devastated as the conspiracy theory goes down in flames
How to Stock a Biology/Genetics Lab
Justin Teng’s Personal Go Book Collection and Guide
Timothy Denevi, author of “Freak Kingdom,” details how Hunter S. Thompson “is really good at trying to see what’s necessary and not, in terms of justice.” by Erin Keane


STAR-Fusion is a program that detects RNA fusions events in RNA-Seq data. According to the paper describing the program, STAR-Fusion is much better than the dozen or so other callers under active development.

Still, reading the paper left me with some questions. As descried by the authors, STAR-Fusion is not just a good caller, but the best caller by a wide margin. See Fig 3A. The next nine best callers have AUC values of 0.5 to 0.3, but STAR-Fusion has a value of 0.8 in the author’s testing.

And what is the source of this incredible result? The authors are silent on the subject. They don’t know, or perhaps didn’t notice how remarkable their achievement is, and so don’t remark on it. The description of the STAR-Fusion algorithm seems very similar to the algorithms used by every other RNA fusion caller. Some do better than others, so details of implementation must matter.

So what is the critical advance STAR-Fusion makes? Is better sequence alignment key? Is the filtering approach? The paralog handling seems like it cuts down on false positives, is this key? Discovering the critical factors for RNA fusion calling would be an important result.

Or are the performance results in the paper dependent on the synthetic test data set the authors use? Will subsequent papers comparing STAR-Fusion to other methods find that it is only average, or sub-par?

Links for October 2018

Video of tagged individual mouse cells during embryo development. The video gets good at 2:20. It even includes a TARDIS (of sorts).

Conservatives’ self-delusion on race: How the right created the illusion of colorblindness. By Joshua Tait

House GOP Bill Cuts Legal Immigration By 1.4 Million Over 20 Years
Trump-era GOP cares more about the national origin and race of immigrants than how they got here.
Presidential Campaign Slogans
Trump’s Caravan Hysteria Led to This by Adam Serwer

Archaeorhynchus spathula, a dinosaur that is an early ancestor of birds, had bird-like lungs! In bird lungs, air makes a circuit rather than going in and out like in mammals. link, bird lungs

Wisconsin’s $4.1 billion Foxconn boondoggle

Thermo Nicolet IR200 Spectrometer

Thermo Nicolet IR200 Spectrometer investigation

Requires a custom power brick, multiple pins. Could not find power specifications. Power bricks do not seem to be available.

Laser was removed from this unit. This is a HeNe laser used “provies the reference signal for triggering data collections and measuring the stroke of the moving mirror.”

Dessicant spot indicates that the dessicant was exhausted. Dessicant appears to be a standard pack. Recharged dessicant in 250F oven for three hours. I’ll try to preserve the optics, I may be able to reuse them.

Requires ENCOMPASS or OMNIC software. I was able to find an OMNIC iso. Untested.

“The interferometer window in your spectrometer is made of KRS-5…” KRS-5 is thallium bromoiodide (TlBr-TlI). KRs-5 (TlBr-TlI) is a gorgeous red crystal commonly used for attenuated total reflection prisms for IR spectroscopy. It is also used as an infrared transmission window in gas and liquid sample cells used with FTIR spectrophotometers in place of Potassium Bromide (KBr) or Cesium Iodide (CsI) for analysis of aqueous samples that would attack KBr or CsI optics. It has a wide transmission range and is virtually insoluble in water. It is a useful alternative to AgCl since it is not photo-sensitive and for ATR applications it will transmit well beyond the 18 micron useful range of ZnSe.

Background on FT-IR:
Nicolet brochure

Unit with case removed:

IR mirror on the left. The right side module looks like a detector:

Back of detector module:

Dry optics compartment:

Dry optics compartment:

Laser diode?:

Corner mirror and flat mirror:

Second corner mirror on solenoid:

Nicolet IR100 and Nicolet IR200 User’s Guide
Nicolet 4700 or Nicolet 6700 User’s Guide
OMNIC User’s Guide, v7.4 Transport Kit User’s Guide
Also have “OMNIC- for TIR.iso”
Could not find a service manual.

The 2000 election and voting systems

After the 2000 ‘hanging chad’ election, the Election Commission report concluded that about 10% of votes are never counted or miss-counted. The Republican President and House didn’t much care, threw a few billion at the states some counties replaced the punch card machines w/ electronic voting machines. It made things worse. The election results are still untrustworthy, but in many places there’s no paper record to check but there is a poorly designed and poorly secured software program counting the votes. And yet worse, these voting machine companies are all private, and keep their software a secret, so there is no way to audit the software or check the election results. In the *rare* cases where security researchers have inspected the software and computerized voting machines, they have always proved easy to break into and subvert. Same with the centralized websites counting and recording the votes. Complete failure of democracy.

XKCD comic

Links for Aug 2018

LED bulbs are as cheap as incandescents
Goodbye To Harlan Ellison
Very Short Stories
Sundown Towns history
Wimshurst machine, kit
Fabricating Reflectors for Displaying Multiple Images, pdf
Climate change and China–too hot, flooded
Sanders Medicare for all proposal would save $2T over first 10 years.
Media portray these tales of perseverance as uplifting and inspirational. They’re actually horror stories.
Write in PDFs in Linux
My ancestry test revealed a genetic bombshell
Better command line tools
The end of the oceans
Colliding stars will light up the night sky in 2022
NAD precursor as anti-aging drug (Basis from Elysium Health)

Is Iron Man made of Lego?

Solving the Autism Puzzle

Elevian: daily injections of a protein called GDF11 can promote “the body’s ability to restore itself”

The company builds on research findings several years ago that if the bloodstreams of young and old mice are connected together, it seems to rejuvenate the older ones. … In a 2015 study, for example, scientists at Novartis found that GDF11 levels do not fall with age and that the protein actually inhibits rather than promotes muscle regeneration.

The alt-right is drunk on bad readings of Nietzsche. They don’t understand him. By Sean Illing
Cactus seeds supplier