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Archive for January, 2014

Do vaccines prevent disease?

Monday, 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.


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

Thursday, 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

Thursday, 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.

Links for January 2014

Thursday, January 2nd, 2014

Cars above 50 MPG
Acupuncture found to be ineffective Bao et. al., 2013. Cancer Genetics, ppt
Collection of great posts on the pathology of the Repubs
10 million Americans now have health insurance due to Obamcare/ACA (6.4 million + 3.1 million < 26 on parents plans + direct signups
Genomics predictions for 2014
Debunking global warming denial: Is the CO2 absorption window saturated?
Scarleteen: sex ed for the real world
What happens when patients know more than their doctors? Experiences of health interactions after diabetes patient education: a qualitative patient-led study, Snow et. al., BMJ Open 2013
NSA and surveillance: Jacob Appelbaum’s talk on the NSA at 30c3 computing conference
Refuting arguments against the minimum wage: Greg Mankiw Battles the Minimum Wage (Dean Baker)
Growing Up Unvaccinated By Amy Parker
Dragon watches you
Contagious Diseases in the United States from 1888
to the Present. Panhuis et. al., 2013 NEJM
blog post
9 Childhood Illnesses: more common than you think.
Cat ceiling playground
OpenROV: DIY underwater robots
Brad DeLong post with recommended books on effective govt service
Maps of preventable disease outbreaks
US Political Party Platforms
Whatever Happened to Republican Feminists? by Jo Freeman (1996)
It’s not Ike’s Party anymore by digby
Metal Clay!!
The Bountiful Breweries of the United States of America poster Pop Chart Lab

ABI 377 Teardown

Thursday, January 2nd, 2014

I picked up two ABI PRISM 377 DNA sequencers. These are the last generation of slab gel sequencers.
ABI 377

ABI 377

With the front open, you can see the place where the gel gets mounted.

gel door open

The left side opens, and the bottom cover comes off. The laser can be seen at the bottom, and some of the power supplies on the left.

Open cabinet

Here is the laser, a Uniphase Argon laser, 0.5W 2214-40MLA 1998.


The power supply modules are located on the left side. On the top left is the laser power supply. The electrophoresis power supply is on the left in the middle. To the right of it is the power distribution center–plugs for the laser and electrophoresis power supplies, and the blower motor. On the bottom at the left is the blower motor. In the middle at the bottom the top of a mirror module that bounces the laser back to the right at the level of the bottom of the gel. On the right at the bottom, the servo motor that moves the detector unit along the bottom of the gel.

left side

Here’s the laser power supply. The laser is not plugged in.
laser power supply

Close up of the laser power supply, Uniphase 2114B-40MLA 12A:
laser power supply

The power distribution center labels: J41 DC Power Supply Max 4000W J40 Heater and Pump Control

The electrophoresis power supply: Spellman P/N X2094 Rev. E4 Model No PTV5P300X2094
230V 5A, output 0-5kV, 0-60mA.

Here is a closeup of the servo: Telcomm brushless servo motor

On the back side of the machine behind the top panel is this circuit board, the control, data processing, and interface board.

main board

Two interesting chips on the board, a FPGA and a pair of voltage converters.

The FPGA is a Xilinx XC3064A

The voltage converter.
voltage converter

On the left of the main board is region with cooling lines:
pump area