Monthly Archive: October 2009

Evolution of the glucocorticoid receptor

Interesting letter about the evolution of the glucocorticoid receptor from Joe Thornton, a biologist at the University of Oregon. Thornton’s lab has figured out some of the details on how this receptor evolved. Thornton’s writing this because creationist Behe is passing off a mangled version of his work as evidence for ‘intelligent design’.

The first Discover magazine blog post gives a good overview of what Thornton’s lab learned about the glucocorticoid receptor.

GR receptor pathway

Stepper motor controller

Stepper motors are easier to control than servos, but they typically produce lower power. A number of people have built stepper motor run CNC projects, so for small or mid-size CNC control they work.

I have three bipolar stepper motors, but seven 6-wire unipolar steppers plus other unipolar steppers with other wire counts so it makes sense to design a unipolar stepper controller.

A unipolar stepper has three coils all of which get driven in the same direction by PWM signals amplified and isolated by a driver circuit. Because the drive current is always in the same direction an H-bridge is not required, rather a simpler driver can be used.

The simplest way to drive the stepper is to activate each coil in turn slowly enough that the motor has time to move a step before the next step is given. A smoother and more power efficient method called microstepping uses PWM to transition gradually from one step to the next (Microchip App Note). This requires four signals from the PIC to the driver. The PIC18F4x31 chips can output 8 PWM signals and so could drive two motors.

An intelligent driver with integrated stepping like the Allegro SLA7070MR ($7) at only requires a direction and step signal. A PIC16F88 has 16 IO lines, enough to drive 4+ unipolar steppers, and PIC18 or PIC30 can run 4+ unipolar steppers plus has PWM lines to drive additional hobby servos. The PIC18 can have a USB interface and so could run a CNC by itself.

A more robust stepper controller interfaced to an SLA70xx driver would have a RESET pin, a common one running to all the drivers, and M0 line monitoring the each stepper, and shared M1 and M2 lines running to all the drivers, so three common lines, and three per driver, so fifteen for four motors. Then figure each axis would have a pair of end stop switches, so four input lines for those, and one input line for a big STOP button. So altogether 20 IO lines for four axis control.

Two IO lines are required for USB. The PIC18F46K20 ($3), a 40-pin DIP, has 36 IO lines, four of which can be PWM and several A/D input lines. This PIC could run four axes and have separate lines for USB, in circuit programming, and still have lines available to run PWM hobby servos, input temperature, etc.

Some CNC setups have centering switches, so that could be useful. Other CNC systems use the axis end stop switch to find their initial position.

Stepper and servo motor control

So I have a box of motors scavenged from old electronic equipment. The first step was figuring out what I have.

I have four identical Pittman servo motors with attached optical encoders. They have two leads for motor control and four leads for the encoders, Vc, Gnd, quadrature A & B signals. So these motors need a sophisticated servo driver that can do PID (Proportional, Integral, Derivative) control. Basically the controller senses motor movement and direction by counting encoder tick marks and then juices the motor in the desired direction using a PWM (Pulse Width Modulation) applied driver voltage.

It’s common to run the these servos with PIC18 chips ($4.50). They have a built in quadrature encoder reader and can be programed to do PID.

Then the low power PWN signal gets run through a power driver like the L298 ($2.60). Here’s a well-documented L298 project. The L298 can driver two servo motors. A LMD18200 H-bridge ($12.50) is another power driver option, used in the Jeffery Kerr boards. Here’s a project using a PIC16 and the LMD18200 driver. The Allegro A3953 is another driver option.

Typically one PIC16 or PIC18 would control each servo motor. The recent dsPIC33 chips ($3.00) have dual encoders and should be able to run two servos. These chips came out in 2008 so I haven’t found any projects on the web describing dual servo projects.

The PIC18 and dsPIC33s are available as DIPs or as SMDs. They can interface to a computer through USB and so can be controlled directly, though connecting them to a programmable controller, a PIC, a BASIC stamp, an Arduino, etc is more common.

Hobby servos are much easier to drive and a single PIC18 can drive several, six to eight depending on the chip variation. Typically a hobby servo would not need a driver as the PWM is its control signal.

Mouse coat colors

Here’s a web page at the The Jackson Labs site showing the most common mouse coat color mutations [link].

Here is white-bellied agouti with head blaze, greyish coat:

white-bellied agouti


In a passing during a discussion of the lack of a system for naming viral strains and diseases, Greg Laden mentions that Ebola was named after the town in Zaire/Congo where it was first found.

That has to depress the local real estate market!


I put my spokePOV back on my bike now that it is getting dark early. Here are a few photos:

spokePOV biohazard
spokePOV ghost
spokePOV star

Maybe I’ll try something animated next…

Bird flu–humanity gets lucky

H1N1 flu is going around this year, an especially bad flu to which few people under 35 have much immunity. A bad flu year, but not in the same class as the 1918 flu.

The bird flu had potential to be very deadly, potentially as bad as the 1918 flu. The bird flu, an avian influenza A (H5N1) virus strain that emerged in Asia in 2003 had potential to turn into a very deadly human flu. A flu virus emerged that spread as an epidemic in birds or several species. Then it passed to humans–several times–and was very deadly, 60% fatal. While deadly, the virus that humans got was either wouldn’t transmit between people or did so only with great difficulty. Small clusters of people, usually of families that worked or lived with birds, came down with bird flu.

Bird flu needed only one or two mutations to become capable of causing a worldwide pandemic. It needed to pick up the property of easy contagion, human-human transmission. The first steps to contain bird flu in Asia failed. It spread around the world in wild and domestic bird populations and sometimes infected other animals. It has become endemic in bird populations this gives the virus many opportunities to infect humans and pick up mutations to allow it to spread in people.

Flu virus particle

So far we’ve been lucky, and the H5N1 avian influenza hasn’t turned into a fast spreading human flu epidemic. Perhaps this flu virus is a dead end of sorts and is incapable of jumping to humans. It does keep getting chances and infecting the occasional person so the CDC and WHO continue to monitor it. It has had many chances to become a human epidemic and so far hasn’t, and as time it becomes less likely to jump to humans. It looks like we got lucky.

We didn’t get so lucky with the capacitor plague…

Bill Watterson cartoons

Making Light pointed me to this site of collected Bill Watterson art. It includes cartoons drawn for his college paper, political cartoons, one offs to decorate interviews, some album art, and more. It must really suck for cartoonists, having to draw a cartoon for free to go with an interview.

Watterson drawing

Creationism talk by Dave Eakin

A UK Bible study group hosted a talk tonight by Dave Eakin, an Associate Professor in the Department of Biological Sciences at Eastern Kentucky University (EKU). I didn’t know quite what to expect coming in to the talk–was Eakin going to explain some biology to the Bible study group or was this going to be bog standard creationism? The talk turned out to be standard old Earth creationism. What an embarrassment he is to EKU!

An MP3 recording of the talk is available here.

I made notes during the talk, they give a flavor for it. My comments are in brackets:

3 groups: biblers, people with set minds…

Comments about apoliticalness and open mindedness.

Cartoon: candle representing science, “Hit it with the Bible”.

Chain of being cartoon.
He mentions he had a creationisty poster at the KAS meeting and no one gave him guff about it.

3 theories of evolution:
1. chemical evolution (abiogenesis)
2. general evolution “an extrapolation of Darwin’s natural selection”
3. natural evolution = special evolution [seems to be a ref to microevolution]

Behe’s Black Box book. [Darwin’s black box: the biochemical challenge to evolution
By Michael J. Behe]

It’s hard to tell if things are designed.
Creationists are blackballed, McCarthyism-type environment for creationists.

Paley-like are arguments are too simple/wrong, but Behe is more sophisticated [not clear how].
Watch, mouse trap, flagellum
[clotting cascade, eye, Krebs]
Trials for cats. [????]

Graduate of U. of Louisville! [figures!]

No one can solve these problems

Color blindness slide?
Can make it clear by increasing contrast…
“Evidence doesn’t support theories, theories support evidence” –Dr Dave.
Big Bang not current, has been replaced by String Theory

CSI example, making the point that evidence can be made to support whatever theory a person wants.

If 60,000 people believe a lie, it’s still a lie.

All his sick evolutionist friends ask him to pray for them.

Quote: when fossils are known all no more guessing. [missed the cite]

We doesn’t know everything so we know nothing.

Absence of life in pre-Cambrian, organisms suddenly appear, and…

Picture of single-celled microfossils, asks if anyone believes them.
Makes fun of certainty of Ph.Ds.

Something new from Discover mag, image of tree of life from single-celled organism.
Pisoliths from pre-oxy atmosphere Earth (pre 2.3 billion years), but they only occur in presence of oxy.
[Casting doubt on what we know.]

Stephen Jay Gould had a young Earth Creationist student. [meaning unclear…]
Quote from Gould, from Evolution’s Erratic Pace, Natural Hist May 1977, at 12, 14. about no transitional forms.

Erase all the lines from tree of life because we don’t know anything for sure.

Never presented Creationism in class. Wants student to think for themselves.
Quote from Colin Patterson (April 10, 1979) on how we don’t have any transitional fossils.
Quote by Tom Bethell in Harper’s February on how no one is willing to publicly talk about ‘questions’.

But what about Archaeopteryx? Small, unimportant. Just a reptile.
Eakin has reviewed many/most biology textbooks.
Says Archaeopteryx is often misrepresented, over interpreted.

Some point about lack of learned behavior in reptiles.
Figures of bird physiology. Pectoral muscles in bird/reptiles.

How did scales evolve into feathers? Unknown, too hard to imagine. [Evo-dev has been providing answers about this.]

How did birds start to fly? An irreducible jump.
We know in our hearts that transitional forms can’t happen.

Faith is… “the substance of things hoped for, the evidence of things not seen.”

My battery ran down at this point and the sound cut off the last minute or two of his talk and the extended Q&A afterward. He mentioned the audience was very respectful and had given him his say. Bible groups must usually be a rough audience!

In the Q&A, he also said that he had talked to many biologists and that 10-20% were creationists of some variety but unwilling to publicly talk about it. This is quite silly, an argument from popularity. Also it’s nonsense. Anonymous surveys of biologists have been done and almost no biologists are creationists. A 1987 Newsweek article reports a survey found 0.14% of earth scientists and biologists are creationists, and a survey reported in CSI pegs the number at 1-2 in about 2000, about 0.1%.

It was sad to find out that EKU has a creationist teaching biology. Oh, the poorly served students!

Most surprising was that Eakin gave his whole talk without ever describing the theory of evolution, in any of its forms, either the simple Darwinian version or the Modern Synthesis. His talk was instead the poorly thought out basket of criticisms of evolution with no case made for anything else. I’ve heard this described as common in creationist talks.

Eakin started his talk saying that evidence is never conclusive, that there’s always doubt, and that we can’t be sure of anything. I thought that would be the theme of his talk before he swerved into ordinary creationism.

Eakin’s talk was at least a decade out of date. One topic was Behe’s book and the argument of ‘irreducible complexity’. Eakin doesn’t seem to know that Behe’s featured examples, the flagellum and the eye, have been shown to have evolutionary precursors where part of the ‘irreducible’ structure exists and functions.

Eakin mentions Archaeopteryx and then makes an extended argument that the evolution of reptile ancestors into birds is impossible but doesn’t seem to know that additional transitional birds have been discovered, or the recent evidence of the relationship between scales and feathers.

Eakin also briefly mentioned his impression that few transitional horse fossils are known, and mentioned that the linear, gradual depiction of horse evolution was admitted by biologists to be false. This hoary creationist canard leaves so much out as to be plain dishonest. Eakin should known better.

In the early part of the 20th century, depictions of horse evolution presented a linear, gradual picture of horse evolution, but soon after more and more horse fossils were discovered and filled in a picture of horse evolution as a branching bush with over a score of Genera, many coexisting and all but a few now extinct. has a good page on this, though Stephen Jay Gould’s essay “Life’s Little Joke” collected in Bully for Brontosaurus is a better read. There are many transitional horse fossils, and the branching tree of horse evolution has been widely known for 70+ years.

The talk ended with a series of quotes from evolutionary biologists about the lack of transitional fossils and the difficulty of drawing conclusions. This was standard creationist quote mining, quite a laugh.

Eakin is a graduate of U of L. I know that won’t surprise anyone at UK.

Where’s Phil Agre?

Phil Agre ran the Red Rock Eater mailing list for many years, it was active during the 90’s. I think I started reading it in the late 90’s. The emails ran down to a trickle in 2002, in part I think due to Phil getting a permanent position at UCLA. The mailing list archive indicates it ran up to Jan 2005.

Phil Agre’s mailing list in essence was one of the first blogs. The content was mainly links and commentary by Phil with occasional longer essays. He was one of the best people thinking about what the internet could be used for and how it was changing the world.

After 2002, the Red Rock Eater list went into abeyance then seemed to have stopped for good. Phil Agre seems to have dropped off the net. In this comment thread a UCLA student says he was ill. I fear it is very serious to keep him off line so long.

His essays, “Advice for undergraduates considering graduate school” and “How to be a leader in your field” are internet classics.

Here is an essay I found interesting titled What Is Conservatism and What Is Wrong with It?

Update: He’s literally missing. This site is run by friends looking for him.
Update 1/31/09: UCLA police talked with him. He’s alive, though not well.