Cavalcade of Mammals

What would be required to set up an inexpensive system for hobbyists to experiment with biology? Consider PCR for example. PCR requires heat stable polymerase, primers, nucleotides, buffer.

The DNA polymerase is easy to purify from E. coli carrying the plasmid. Grow bacteria containing plasmid expressing Taq DNA polymerase, boil, spin down denatured proteins, and you are left with the DNA polymerase.

Primers can be bought inexpensively–$0.35 per base, a pair of 18-mers cost less than the shipping. Though they are inexpensive only if one set gets used repeatedly.

The cost of buffer (NaCl, MgCl₂, Tris) is negligible.

Nucleotides are expensive up front, $150 for a set of dNTPs (dATP, dCTP, dGTP, dTTP), but this works out to about $0.06 per 50 ul PCR reaction.

Can nucleotides be prepared by a hobbyist? Nucleotides are easy to obtain-DNA is a major constituent of cells and is easy to purify. DNA + DNAase = dAMP, dCMP, dGMP, and dTMP. How can the trinucleotides be regenerated?

One route is to do it enzymatically using
polyphosphate:AMP phosphotransferase (PPT) and adenylate kinase (AdK) with polyphosphate (polyP) as the energy source (Resnick and Zehnder, 2000). It is not clear how the trinucleotide product would be separated and purified. Presumably different enzyme pairs could be used to regenerate the other dNTPs from the monophosphates.

These other enzymes could be cloned in E. coli expression vectors and purified either by tagging them with His₆ and using a Ni or Co resin. Or by cloning heat-stable isoforms from one of the extremophiles and using a one-step boiling purification like that used for Taq polymerase.

Update: Bochkov et al., 2006 describe a method of preparing dNTPs from digested DNA. DNA is digested with DNAase and Nuclease S₁. DNAase chews DNA into show oligonucleotides and the nuclease breaks them down to single dNMPs.

Then a crude extract of E. coli is prepared that contains the kinases to convert dNMPs to dNTPs along with the acetokinase. The kinases use ATP. ATP must be regenerated, and this is done using acetokinase with acetyl phosphate ($30/g) as an energy source. Combined dNMPs were converted to dNTPs with at least 86% regeneration and separated from reactants by chromatography on a Dowex 1×2 anion exchanger. The conversion was followed by thin-layer chromatography.

For PCR it may be possible to use a crude purification of nucleotides, but purification protocols would need to be developed and tested.

Last October, NASA’s LCROSS mission slammed a spent rocket booster then the LCROSS spacecraft itself into the moon. No debris plume was seen from Earth, but observations from LCROSS of the booster hitting indicate the presence of water on the moon. How much water? Most news accounts don’t say, but the Science magazine article does.

100 kilograms of water was detected from an impact that created a crater estimated to be 20 m wide and 3 meters deep. So 100 kg water in about 500 m³ of regolith = 0.1 g/kg. (Googled a reference giving 2.3 to 2.6 g/cm³ as lunar regolith density).

The article gives a higher estimate for water, 0.1% to 10%, higher than my crude 0.01% estimate. Which is great–enough water to extract easily and live off. Best news for space exploration in thirty years!

(Credit: NASA)

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.

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.

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:

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!

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.

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…

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.

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]
Eye
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. Talkorigins.org 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.

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.