Saturday, October 31, 2009

Post with the Most

Tom Paine's Ghost is excited to announce 
a composition competition.

A $100 cash prize will be awarded for the most aesthetically powerful multi-media blog post.

Post content is limited only by the bounds of imagination.
Keep in mind Tom Paine's Ghost was founded amidst a battle to defend freedom of the press and we hope to echo that theme throughout our pages.

Submissions will be selected and judged on the basis of four criteria:

1. Clarity
2. Originality
3. Integration (at least three forms of media must be utilized, images, text, movies (you tube or vimeo), audio, etc.)
4. Power (the post's ability to motivate readers to action).

Submissions will be accepted until the summer solstice - June 21st, 2010. Please submit a link to your post in the comments section below along with a short note explaining why you feel your post  meets the criteria.  Selected submissions will be linked in a submission post here at TPG and voted on by our panel of citizen judges. The winner will be announced on July 4th, 2010 and will be notified by email. Whether this is your first post or your one thousandth all submissions will be reviewed.

You may also submit your post in an email to

The above scene is one of ten panels that adorn the double doors to the octagonal building known as the baptistry in the center of Florence, Italy. In 1401 a competition was held among the sculptors of the day for the privilege of creating these doors. Doors Michelangelo would later dub the "gates of paradise." The use of point perspective and heightened human realism marked the end of the dark ages and the beginning of the Renaissance. As we emerge from eight years of darkness perhaps a competition in the context of New Media can facilitate the evolution of our communication.

~Cheers to revolution via evolution!

For your Perusing Pleasure

The editor of Boneshaker - Evan P. Schneider - has a nice piece in here about his experience as "Landfill" in this year's Tour de Fat.

The Biochemistry of Halloween: Installment II

Mothers and fathers watched the shriveled toes of a poor beggar swing from the gallows. They placed their faith in God that the death of this unfortunate person might take away the torment, fits, and visions  that plagued their children. That somehow through supernatural forces the sensations of ants crawling underneath skin, delusions of bursting into flames, and frenzied shrieks of terror in the night would cease. As the the seasons brought new harvests the number of swinging bodies dwindled. But bouts of bewitchment would visit the same locales for centuries.

This was a typical scene in the medieval villages that lined the dank Rhône and Rhine River valleys following the seam of modern-day Germany and France south through Switzerland to the Italian boarder. Here and in other curiously coincidental micro-climates all over Europe something dark and treacherous lurked in the fields.

During the cold, wet growing seasons a deep maroon colored fungus Claviceps purpurea reared its ugly sclerotium amongst the ears of rye. Looking much like the rooster's spur the killer was given the french name - erogot. When rye was milled the flour could contain up to 30% ergot by dry weight. And so it goes that the biochemistry of bewitchment had its origins under the millstones of fifteenth century Europe.
During this age the peasantry ate an enormous proportion of the darker cheaper rye bread; upwards of three pounds a day. As the alkaloids synthesized by the ergot made their way into the blood and brains of those apparently seized by demons, the unaffected were left to assume they had been bewitched. The linguistic fossil preserved in the very word - seizure - describes the uncontrolled fits the affected displayed. A condition known at the time as "St Anthony's fire"  (aka Ignis Sacer) did not become known as ergotism until 1853 when the clinical connection to the mycotoxins was finally made.

Mycotoxins contained in ergot infested rye caused two distinct varieties of ergotism. These toxins are known as the ergot alkaloids and the two classes each have separate physiological effects - gangrenous or convulsive ergotism. Ergotamine, a powerful vaso-constrictor preventing blood flow to the extremities, is the main culprit in gangrenous ergotism.  Whereas ergine and lysergic acid hydroxyethylamide cause convulsive ergotism. These lysergic acid compounds have 10% the activity of the infamous psychoactive drug -LSD.  Both LSD and the ergot alkaloids induce hallucinations by a similar and yet poorly understood mechanism.  Structurally similar to serotonin these compounds bind serotonin receptors in the brain. It is not known how this induces hallucinations but it is thought that agonist activity to serotonin releases higher concentrations of the neurotransmitter glutamate in the brain's cortex exciting neurons in random ways.  This would explain the varied psychological effects reported by individuals under the influence of this class of drugs.

By their activity these compounds were known long before their chemical makeup was uncovered. Ergotamine had been used for nearly two centuries in midwifery to stop hemorrhaging after birth and also to induce abortion. In the first half of the 20th century the other ergot alkaloids were probed for other uses such as blood pressure and migraine treatments.  A young chemist named Albert Hofmann working for Sandoz pharmacueitcal company in Basel, Switzerland literally stumbled across LSD while performing organic synthesis of ergot alkaloids.  His wild bicycle ride is a story of scientific lore worthy of its own post.

But here we are focused on the science behind medieval bewitching. The connection between ergotism and witch trials was first proposed by Linda Caporael in 1976 where she hypothesized in the Journal Science that Ergot could have been the real world cause of the supposedly supernatural events that transpired in the village of Salem, Massachusetts in 1692.  
In her paper  Caporael outlines the evidence for convulsive ergotism being the scourge that set off the string of hangings accompanying the infamous witch trials.  Mainly she points out that the symptoms of ergotism, -spasms, the sensation of ants crawling under skin, and the feeling of being disemboweled - were all recorded by the court clerk when taking the testimony of the affected teenage accusers.  Indeed the very fact that the accusers were female and in their teens also implicates ergotism as these are the most susceptible individuals in any community where there is an outbreak.  Lastly, she turns to the geographic distribution of the bewitchment. Here she reconstructs a map of Salem village where she hypothesizes that a contamination of grain grown on the eastern bank of the Wolleston river could have been the only source of ergot and still affected all the families involved.
Less than a year after her paper was published skeptical scientists came in to refute her claims.  Spanos and Gottlieb assert that Caporael is incorrect in her hypothesis and they give several reasons. They  report that more towns people should have shown signs of convulsive  ergotism, that the afflicted girls did not testify to to having exactly the same kind of symptoms expected form classic ergotism, and that the town most likely did not have a vitamin A deficiency that normally accompanies convulsive over gangrenous ergotism.  Reading these rebuttals there is no hard evidence in either direction.

Despite this  disagreement Caporael's work inspired Mary Matossian to conduct further investigations into the possible connection between witch trials and ergotism outbreaks throughout the middle ages up until the 19th century.  In her book Poisons of the Past Matossian lays out an incredibly convincing argument that outbreaks of ergotism indeed correlate to increased incidence of witch trials.  She explains how tree ring data taken by x-ray measurements of tree ring density compiled for every year from 1269 - 1977 C.E. can be compared to an annual index of number of witch trials with statistical correlation in southwestern Germany and the Swiss alps. 
Years where the growing season was cool and wet correspond to thicker tree rings and therefore seasons in which the amount of fungus growing amongst the rye was high.  These long wet seasons directly preceded autumns with more witch trials. Like the medieval trials the Salem affair was also preceded by two years of unusually cold spring weather. Though there is evidence for a connection between ergot and witch trials in both Salem and the multitude of trials that took place in Europe throughout the middle ages, evidence is stronger for the later. In 2000 Alan Wolf writing from the Harvard Medical School further put the cabash on the Salem ergotism hypothesis.  But if Carporeal had never posed the question the work of Matossian may never have been conducted.

Further evidence for medieval outbreaks of both gangrenous and convulsive ergotism in Europe during the 16th century can be taken from a contemporary reporter.  Transcending language and centuries the oil paintings of Pieter Bruegel the Elder give us an unusually clear window into recent human history.  In the ergot alkaloid figure above a painting titled "the beggars" depicts peasants in what is now Belgium in the mid 1500's begging for food with stubs for limbs.  Considering the geography and timing of these depictions it is not difficult to imagine that these poor souls are suffering from gangrenous ergotism.  Following his brush further we see in the 1562 painting below the story of Dull Gret or "Mad Meg" as she is known in English.  Leading a band of paranoid peasant women she storms the gates of hell, armed with cooking utensils, fearful that Spanish soldiers will pillage her village.   "Mad Meg" of Flemish folklore may be under the influence of lysergic acid compounds found in Ergot!

When the imagery of Bruegel is conjured into mind one can't help but wonder if generations of creative medieval  minds weren't  unwittingly dosed with background levels of the psycoactive components of Ergot.

As samhain approaches it would do us good to contemplate the possibility that some of the most infamous characters of all hallows eve my indeed have had very real biochemical origins.

I would like to thank Nick Clark for our many discussions and collaboration on this topic and George Hudler for his kind advice and additional references.

Caporael, L. (1976). Ergotism: the satan loosed in Salem? Science, 192 (4234), 21-26 DOI: 10.1126/science.769159  

Schweingruber, Fritz H., BrÄker, Otto U. & SchÄr, Ernst (1979). Dendroclimatic studies on conifers from central Europe and Great Britain Boreas, 8, 427-452  

Friday, October 30, 2009

Holy Wolfram Alpha!

Here Stephen Wolfram introduces a new kind of search engine.

The idea is to take all the math that has ever been conjured by humanity and build it into a search engine such that any person out there on the world wide web can type in any question and have this search engine send back a "search results" page with that question analyzed by all relevant mathematical tools.

In the introduction you can see and be mesmerized by some of the complex functions wolfram alpha is capable of.  Brilliant! To say the least.

It seems this is an attempt by Stephen Wolfram to answer Hans Rosling's call to action made at TED in 2006.

Why didn't this exist when I took P-Chem?
Thanks Nate for the heads up!

Thursday, October 29, 2009

Defining Demon

St. Anthony tormented by demons
by Martin Schongauer ~1480s

n his book Demon Haunted World Carl Sagan claims that the word "demon" comes from the Greek word for  "knowledge" yet in looking around the internet to verify this I am unable.  Some explanations make more sense than others. I would think it logical that it somehow has a root in common with the word "Deity" say in the Greek word "deiwos" that originally meant a shining or bright light.  But how does this then translate to knowledge?  Does anyone out there know the source Carl Sagan used to claim that the word demon comes from the Greek word for knowledge?

Sunday, October 25, 2009

You Can't Burn Blogs!

According to this telegraph article a pastor in North Carolina will celebrate All Hallows Eve with a good ol' bonfire fueled by books!

“We are burning books that we believe to be Satanic,” said Pastor Marc Grizzard.

Friday, October 23, 2009

6.02 x 10^23 HAPPY MOLE DAY

At 6:02 tonight join in celebration of National Mole Day. I'm all about making this an international holiday but the relevence to this particular date only make sense in the context of the American way of writing out the time and date (6:02 10/23).

Little Guys Under Attack!

Activate team internet! Boycott Hansen Beverage!!! They are using their Goliath-style corporate might to bully a tiny Vermont brewery. The brewery named one of their beers the "Vermonster" so Hansen Beverage Inc. claims this is a copyright infringement on their "Monster" energy drinks. Now I know most TPG readers cringe at the thought of buying a Monster energy drink in the first place but, take it to the next level. Hansen Beverage A California company and the parent company of Monster sure does a good job putting up the facade of green-friendliness, but underneath those green scales lies a real corporate monster! Join in the Hansen Beverage Boycott!!! 

Check out Jim Hightower's piece on this topic.

Or outwit them.  Ben and Jerry's could sue Hansen Beverage as they used the name Vermonster years ago for their giant tub of ice cream!


Still think we should continue the boycott to send a message to any corporation thinking about pulling a move like that!

Sunday, October 18, 2009

Fundamental: Open Access

If we had a mission statement here at TPG the words "open access" would be in the text.

Open Access 101, from SPARC from Karen Rustad on Vimeo.

Lazy Sunday in Llama land

Friday, October 16, 2009

The Fun Theory


In honor of Federico García Lorca.
Without whom I would never have had the pleasure of memorizing the following poem in 10th grade Spanish class. Thank you Señora Perrin. It took this news and re-reading of the poem for me to realize how tragic and eerily foretelling the text really is.

Lejana y sola.

Jaca negra, luna grande,
y aceitunas en mi alforja.
Aunque sepa los caminos
yo nunca llegaré a Córdoba.

Por el llano, por el viento,
jaca negra, luna roja.
La muerte me está mirando
desde las torres de Córdoba.
¡Ay que camino tan largo!
¡Ay mi jaca valerosa!
¡Ay que la muerte me espera,
antes de llegar a Córdoba!

Lejana y sola.

Single Molecule in Sight

A few weeks ago I traveled from my home in Fort Collins down to Golden, Colorado to hear Vladamir Lunin from the Institute of Mathematical Problems of Biology in Pushchino, Russia give a lecture on x-ray crystallography at the the National Renewable Energy Lab (NREL). He spoke about how to improve the three dimensional map of a crystal structure by applying Fourier-transforms and other mathematical operations to crystal diffraction data.  Ab initio phasing as it is known.

This was a talk from first principles as Dr. Lunin built the talk from an explanation of electrons and waves all the way to showing the audience 0.8 ångström resolution data. At this high level of resolution one is able to see the shape of electron orbitals of the atoms in the molecule under investigation (you can believe your quantum mechanics teacher - they weren't just making that stuff up). He also showed some images of low density lipoproteins LDLs (which are massive molecules) at low resolution.  This was all very impressive work but I wanted to know what this distinguished crystallographer thought of the so-called intrinsically disordered proteins. The more than 80% of Eukaryotic proteins that are not  "well behaved" in the context of crystallography.

When I asked him how to deal with understanding the structure of these seemingly un-crystalizable proteins he first mentioned NMR as an alternative technique but then quickly said that he thought single molecule investigation was the wave of the future. He was cautious in this assumption saying that these techniques seem to be perpetually "under development" and rarely give a clear picture of what is actually going on.  My mind immediately went back to the spring of 2007 when I took part in a class put on by graduate students as a series of seminars covering different single molecule techniques in biochemistry.  Here I talk about how I first learned of Steven Chu while preparing my talk on optical trapping for this course.  Recently, because of Vladamir's talk and also discussions of this paper appearing in the August 28th issue of Science I have had renewed hope that the large gap in our understanding of biochemical mechanisms between events visible under a microscope and those accessible by crystallography might actually be filled in. As a  prime example look at the incredible resolution achieved by scientists working for IBM in Zurich on visualizing a pentacene molecule.


Researchers attached a single molecule of carbon monoxide to the gold tip of the scanning arm of an atomic force microscope and probed the surface of this molecule of carbon and hydrogen.  The angles of the bonds between the carbon are in plain sight and the individual hydrogen atoms are there! Notice the apparent electron density at the outer rims of the two ends of the pentacene.  I wonder if this is a product of the imaging or if the increased density represents slowing electron traffic as they round the turns.

To anyone who has opened up an organic chemistry textbook and thought of the straight black lines as just part of some mad scientist's imagination this image gives us all reason to do a double take and affirm our collective comprehension of the "atomic theory" as a theory based in the real world rather than buried in obscure wave equations. This image amongst many takes the uncertainty out of the "uncertainty principle" and affixes it as a representation of electrons frozen in time.

Gross, L., Mohn, F., Moll, N., Liljeroth, P., & Meyer, G. (2009). The Chemical Structure of a Molecule Resolved by Atomic Force Microscopy Science, 325 (5944), 1110-1114 DOI: 10.1126/science.1176210

Lunin, V., Lunina, N., Ritter, S., Frey, I., Berg, A., Diederichs, K., Podjarny, A., Urzhumtsev, A., & Baumstark, M. (2001). Low-resolution data analysis for low-density lipoprotein particle Acta Crystallographica Section D Biological Crystallography, 57 (1), 108-121 DOI: 10.1107/S0907444900014608

Tuesday, October 13, 2009

Monday, October 12, 2009

Being born in Western New York State I would like to take this day and honor the wisdom of the League of the Iroquois. In the midst of harvest season I take time to give thanks to the three sisters.

Thursday, October 8, 2009

First Snowfall in the Fort

Da Vinci Rocks!

Thursday, October 1, 2009

Infectious Enthusiasm

Should scientists speak their minds?

Yesterday Dave Munger, an editor at, picked up on a post I had written for Tom Paine's Ghost about the implications of increased biofuel production in the United States. Munger furthered the discussion in an e-cover story published on Seed Magazine.

In the article he cites me as the one who drew his attention to the story then proceeded to ask the question of whether or not I have the right to insert my opinion. He ponders what role scientists should play in making policy decisions in light of newly uncovered facts.
"Shouldn’t scientists just be interested in giving us the facts, staying removed from policy decisions and letting the general public and politicians decide how to act? Doesn’t becoming an advocate introduce bias into the scientific process, potentially tarnishing results?"
I see what he is doing in trying to get a conversation started but his premise that working scientists should stay removed from policy decisions assumes that scientists themselves are  A.) not part of the general public and B.) not politicians.   These are both false assumptions. Our country started with a bunch of statesmen scientists interesting in forming a democracy.  I will never forget the words tacked to my undergraduate research mentor's office cork board.  It was a card from the ACS quoting Thomas Jefferson ~ "Science is my passion, politics my duty."  For some reason in the 21st century the idea of a scientifically literate politician has escaped the bounds of possibility in the United States which I see as a travesty.  Angela Merkel - the high chancellor of Germany got her doctorate in Quantum chemistry for crying out loud and we in the United States have this notion that scientists should stay out of politics?  Maybe that explains why the city of Munich alone produces more solar generated energy than the entire United States of America!  

Getting back to Dave's article. The facts are the facts are the FACTS.  No human has the ability to change these. I here argue that scientists should not be robots with binary brains sorting the infinite number of yes no answers floating out there in the universe but should actively use their brains to form opinions about the observations to drive the conversation of science and let those ideas survive or die according to the same evolutionary sieve our own genes pass through. Memetic cultural selection within the confines of scientific method.

Let me illustrate what I believe the role of the scientist should be with two images. The image on top is a protein called MeCP2 run out on a 12% SDS polyacylimde gel with apparent molecular weight of 71.5 kD (actual 53 kD)  while the image on the bottom is a cropped painting by Mark Rothko.  As an observer you would not be able to identify the one on top and you might be able to tell the one on the bottom but not unless you happened to have seen that painting before.  I can tell you that the band on top is MeCP2 protein but you have to believe me.  I can show you how I sequenced the plasmid, expressed, and purified the protein from E. coli and ran it through mass spec and loaded 10 micrograms onto this particular gel. But in the end you have to believe me that this is what I say it is.  And I say it is what it is because I believe in the central dogma of biochemistry.  I can not observe this nano scale assembly line with my eyes but I believe it because the stifling evidence for it has been explained very clearly, many times, by many apt mentors.  Interpretation of observation, in my mind, is THE central role of a scientist.   And if that interpretation is false then it will eventually be overturned by a better explanation.  That is at the heart of the the scientific method. In fact an idea must be falsifiable upon emergence for it to qualify as a scientific idea at all. When a human mind takes two or more ideas and synthesizes some conclusion from these data it must have the potential to be proven wrong! That is why truths such as earth's spherical shape and evolution by natural selection are so significant. They have survived the test of time. 

To say that scientists should not be involved in policy decisions sounds like something right out of George W. Bush's play book. Rule number one - keep any and all brains out of decision making offices. Yeah that seemed to work out great for the planet.

I would like to bring up a counter point to Munger's. Shouldn't there be more positive encouragement for scientists to publicly speak their minds?  A lot of government funded scientific researches have an invisible gag order on them politically.  Last April  Dr. Craig Martens of the  Rocky Mountain Lab in Hamilton, MT visited Colorado State, his Alma mater.   During the lunch after his seminar we were talking about politics and he mentioned that the National Lab there requested that all employees take off any political bumper stickers from their personal vehicles during election season.  This sounded mad to me.  He also told me that employees are prohibited from getting involved with city government in Hamilton.  Again to me  - madness.  Yes, just as a good journalist should stay objective, so must a good scientist but this does not mean he/or she should feel restricted in expressing thoughts.  Besides, new psychological research indicates that being an activist is good for vitality.

As Frances Moore Lappé said at the sustainable living fair in in Fort Collins, Colorado last week -
"When you feel the need to say something but it seems controversial think of that heart pounding anxiety you get in front of a crowd as 'inner applause'"  

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