True's beaked whale.jpg

Western spotted skunk

Hooded skunk

Yellow-throated Marten

Wolverine

Idea: steampunk clock

April 2nd, 2014

Have the time displayed by colored liquids in glass tubes, either a column of liquid or a large segment. The time tube can be straight or circular.

Move the liquid by a mechanism where brass gears compress a bellows. The brass mechanism would be driven by a microcontroller.

Links for April 2014

April 1st, 2014

Tess, software for designing tesselations
FBI suppression of peaceful activists
True Bugs posters
Truth about vaccines
Private equity companies in business as slumlords
Outbreaks sourced to labs
Peter Baker’s Days of Fire hackery
Handmade kalliroscope
Crab-ble – A Table That Walks
Nanopore sequencing
The Meaning of Oaths and a Forgotten Man by Lt. Col. Robert Bateman
DIY fog curtain
Pyro Board: A Two Dimensional Ruben’s Tube
Wave simulation java applets
Obama Declares Obamacare Victory
Books to read: Joan Robinson’s “Introduction to Modern Economics” (1973)
Magnet platforms moved by circuit board coils
Crude demonstration of 2D linear motor

Idea: make a microcentrifuge using RC motors

March 30th, 2014

The motors made for RC planes and cars are high speed and high power.

For example, the Turnigy Trackstar 1/10 12.0T 3300KV Brushless Motor, $23 specs are:
Kv: 3300
Max Voltage: 15v
Max current: 35amps
Watts: 550
Resistance: 0.0221Ohms
Max RPM: 50000

The load on a microfuge will be greater–22 tubes x 1.5 ml can be roughly 44g, figure a 100g total load with the rotor. So slower than max, but still quite fast.

High power ESC modules are sold to run these motors. So they take DC power, and a servo like signal (PWM), +5, GRD.

So a 10k RPM microfuge can be made with one of these motors + ESC, a servo for locking the lid, and a microcontroller to run it, take speed / time settings, and monitor and show the RPMs on a display.

Power could be from a PC power supply or a dedicated supply.

Links for March 2014

March 5th, 2014

1 pixel moon
Guide to Convincing Parents to Vaccinate their Children
Boosting the signal: THE SMALL TOOLS MANIFESTO FOR BIOINFORMATICS
Zero senators per state
Why the Fed hates inflation
Progressive Caucus’s Better Off Budget
Levels of analysis of religion, Atran, Boyer & Wilson
Whistleblower Reveals Favoritism Toward the Rich, Robo-Signing at the IRS
Top 5 Bioinformatics papers
Measles spreading in the US
The Sober Truth: Debunking the Bad Science Behind 12-Step Programs and the Rehab Industry by Lance Dodes (Author), Zachary Dodes
Autism risk

New public health measures

March 2nd, 2014

Could new measures substantially improve public health?

What would be the effect if, say, 90% of the country wore filter masks for one week, and concentrated on washing hands?

Infection is a chain, one individual infects one or more others, and an infection gets passed on. That is how disease persists–for most infectious agents, not in one person for months on end, but passed serially every few months as an individual gets infected, and over a few weeks mounts an immune response and fights it off.

An infectious agent requires a basic reproduction factor, an R0, of more than one. If R0 > 1, an infection is growing more common, if R0 < 1, an infection is disappearing. For more diseases, for infection to persist it must spread.

Currently there are constant but weak efforts to reduce the spread of infection–encouraging the sick to stay home and hand washing. Vaccines for influenza. But what if a serious effort was made? A big effort could not be sustained, at least not in the US culture.

But what would be the effect of a large, short effort? If infection transmission can be stomped down for a short period, but long enough to break the chain of infection, it might have a large effect on public health. I wonder if this has been modeled?

Setting up libcutter

February 28th, 2014

On Ubuntu 12.04.

Downloaded from https://github.com/vangdfang/libcutter/.

It was hard to compile, requiring libsvg and several other libraries.
I added to the include directories:

CMakeLists.txt

include_directories(${PROJECT_SOURCE_DIR}/include/ ${PROJECT_SOURCE_DIR}/include/pub /usr/include/freetype2)

Download keys.h from: http://www.jestinstoffel.com/files/keys.h


#ifndef KEYS_H
#define KEYS_H
#define MOVE_KEY_0 1194338851ul
#define MOVE_KEY_1 1563510831ul
#define MOVE_KEY_2 992311905ul
#define MOVE_KEY_3 913389615ul

#define LINE_KEY_0 809461859ul
#define LINE_KEY_1 1902406960ul
#define LINE_KEY_2 1198081403ul
#define LINE_KEY_3 1832133993ul

#define CURVE_KEY_0 0x7D316E22ul
#define CURVE_KEY_1 0x4A4A7133ul
#define CURVE_KEY_2 0x5A3C5C5Ful
#define CURVE_KEY_3 0x78613A61ul
#endif

Full set of keys:

KEY0 - 0x272D6C37, 0x342A6173, 0x3663255B, 0x2B265A4D
KEY1 - 0x7D316E22, 0x4A4A7133, 0x5A3C5C5F, 0x78613A61
KEY2 - 0x47302A23, 0x5D31482F, 0x3B257A61, 0x3671382F
KEY3 - 0x303F6863, 0x71646D30, 0x4769457B, 0x6D342569
KEY4 - 0x45356650, 0x3A386D69, 0x575A7037, 0x335F357D
KEY5 - 0x343A2148, 0x614F3925, 0x753F6953, 0x47463626
KEY6 - 0x3F62626D, 0x7E555F44, 0x7E29425A, 0x52246268
KEY7 - 0x47302A23, 0x342A6173, 0x4769457B, 0x335F357D

Replaces include/pub/keys.h

./util/draw_svg ./util/svg_tests/Mini_DIY_circuit.svg /dev/ttyUSB0

Test run, worked!

Other options:
Freecut — Firmware replacement, haven’t tried.
Licut –Tried binaries and program compiled from source, did not work.

Cricut dissection, discusses the default blank cartridge.
ATX Hackerspace cricut page
Repair info
Build-to-spec Cricut Hacks Wiki (recovered from the Internet Archive)

Links for February 2014

February 4th, 2014


Firefly’s 15 Best Chinese Curses (and How to Say Them)

If at First You Don’t Succeed: A short history of the Republicans’ 48 attempts to repeal Obamacare. By NEERA TANDEN
Origin of America the Beautiful
Syphilis: Then and Now. Researchers are zeroing in on the origin of syphilis and related diseases, which continue to plague the human population some 500 years after the first documented case. By Kristin N Harper, Molly K. Zuckerman, and George J. Armelagos
Misunderstanding Orange Juice as a Health Drink: Juice is, nutritionally, not much better than soda. How did U.S. consumers come to believe that oranges, in any form, were an important part of a healthy diet? by Adee Braun
The Vampire Squid Strikes Again: The Mega Banks’ Most Devious Scam Yet By Matt Taibbi
From & Friends: Failing upward at the Democratic Leadership Council with Al From. by Rick Perlstein
Oxford Nanopore MinION early data review
Chicago food inspection reports are online
Ten Terrific Resources for Writing Space-Based Hard Science Fiction
Honey Badger
Recent history of political murder in Argentina: An Interview with Uki Goñi by Jessica Sequeira
Panda’s Thumb tears apart “The Politically Incorrect Guide to Darwinism and Intelligent Design Review”
DNA-encoded libraries for drug discovery
Coiled fishing line as muscle fiber
How to Write About Tax Havens and the Super-Rich: An Interview with Nicholas Shaxson
Boltzmann’s Anthropic Brain
The Deep State and its vulnerability

Do vaccines prevent disease?

January 13th, 2014

Here’s an interesting graph comparing disease prevalence before vaccines and now:
disease pre and post vaccination

This is quite a strong correlation, but how do we know that vaccines caused the diseases to become so rare? Did vaccines causes disease incidence for all these diseases to bottom out, or is it something else, say a coincidence, or maybe all diseases are just disappearing because Americans are healthier today?

So more information is needed. The first thing to consider is that all infectious disease hasn’t gone away. The cold is still as common as ever. Kids still get sore throats and ear aches. There are also the ones I don’t think about or haven’t heard of, like RSV, croup, Fifth disease. And looking at adults, clap, HPV, and gonnorhia are at epidemic levels. So infectious disease is still very common, but the worst diseases have become rare–the ones for which general vaccination is practiced .

Another line of evidence that vaccines are what stomped out the targeted diseases is the timing. They didn’t all disappear at once, not even close. What was observed is that each disease dropped off after widespread vaccination became common.

Here’s a study that looked at incidence for several disease in the US over decades: pdf

If you look at page 4, they summarize incidence over time for 8 diseases. At the top they summarize incidence. The colored section of the graph is detailed regional data. The grey vertical bar shows when widespread vaccination was introduced–a different year for each disease. After the vaccine is introduced, the disease incidence goes way down. Note that for smallpox, it was better vaccines replacing ones started in the 1800’s, so no grey bar is shown.

Here’s a simpler graph of measles from the CDC site:
CDC measles
measles incidence in the US

So it isn’t general health or healthier people with immune systems that prevent disease causing a gradual decline in infectious disease. Instead, the incidence of a specific disease drops when the vaccine is introduced.

Rotavirus

And here’s one of the new vaccines–for rotavirus. Nearly all kids used to get it: “four of five children in the US had symptomatic rotavirus gastroenteritis, one in seven required a clinic or emergency department (ED) visit, one in 70 was hospitalized”. The vaccine was introduced in 2006 and the disease has already become much less common: CDC Surveillance of Rotavirus

clinical lab rotavirus findings
See fig 4 especially.

So what I conclude from these lines of evidence is that the introduction of widespread vaccination for a disease causes it to become much, much less common.

Dinosaur coloration

January 9th, 2014

In the last decade or so, dinosaurs have started being depicted as brightly colored. The reason for the trend of brightly colored dinosaurs in movies is that in recent years techniques for identifying pigments from fossils have been developed, using electron microscopy and ion bombardment mass spectrometry.

News report: Ancient Pigments Unearthed: Fossilized skin reveals the colors of three extinct marine reptiles by Ed Yong. The Scientist, January 8, 2014
Original article: (Abstract) Skin pigmentation provides evidence of convergent melanism in extinct marine reptiles. Lindgren et. al., Nature 08 Jan 2014

and news report: Pictures: Dinosaur True Colors Revealed by Feather Find, Chris Sloan, National Geographic Daily News
Original article: Zhang et. al., 2010

Fossil color studies were pioneered by Jakob Vinther at Yale

No doubt movie speculation is running far ahead of the science, but these are the discoveries that unleashed the trend of brightly colored dinosaurs. At this point, it is reasonable to think dinosaurs are as brightly colored as birds or reptiles are today, and in some cases the coloring of specific species is known.

Ideas: sensors

January 2nd, 2014

Further notes on using digital camera sensors as high density multimodal sensor arrays.

1) Detect loading / strain using a module incorporating a strain sensor (e.g. the resistive type used in scales and strain gauges) to a diode. The diode is coupled to a fiber optic line that takes the signal to the camera.spectrometer.

2) Position sensors. Use an arc of partially clear plastic that has a light at one of the ends at the arc edge. A fiber optic line at the oriented normal to the arc gathers light that takes the signal to the camera. As the joint moves, the plastic arc moves and distance between the light and the fiber optic changes. This change is converted to a position.

For joints with 360 rotation, the arc of plastic is replaced by a disk. The light source is placed at the center, and an opaque radial line gives each position of the disk a different light intensity.

3) Touch sensors. Use my previous idea of an array of sensors embedded in a squishy and translucent layer with one or more light sources. Touch distorts the light path of direct or reflected light between the light source(s) and sensor in reproducible ways. The set of sensors is trained to recognize the pattern of light formed by different touches. The pattern may also be changed by movement of the surface, for example if the array of sensors covers a hand, and could bed used to detect hand position.

4) An array of fibers can be placed to collect light from a spectrometer. An array of spectrometers can be developed using this approach, as the camera can collect light from several 1D fiber optic arrays.