Saturday, October 20, 2012

Thursday, October 18, 2012

A Big Problem in Science Publishing

In the following video a prominent medical doctor, author, and anti-anti vaccine activist named Ben Goldacre rails against a big problem in the way scientific data is published. His point is that only exciting and dramatic results get published. Because of this reality all those boring negative results that show no difference between experimental and control groups do not get published.

Take a simple experiment... a bunch of different scientists ask - does drug X work at curing a particular disease? So they get people to volunteer. They give half the people drug X and the other half a sugar pill (placebo). Now say there are 10 different studies set up just like this but only 5 show any difference in the group that took drug X. The studies that show that drug X "works" will get published while those that do not show the drug to have any effect will not get published. Why is this a problem? because the deciders at your bedside (aka doctors) will only see the papers with positive results, while never knowing that there were a bunch of unpublished studies that show drug X to be ineffective. This is a disservice to patients and doctors alike and does not help anyone.

The onus is on publishers to publish everything no matter how un-sexy the result. There is no reason in the internet-age that all results can not be archived in a universally searchable data-base. Doctors and patients need the whole picture when they make decisions, not just the bright shiny bits editors choose for them!

Wednesday, October 17, 2012

The Onion stabs TED talks in the face!

GMO Cancer Study in Rats - Sketchy Science

Listen to the following interview with science-writer and Yale University professor Carl Zimmer to see how the release of the recent study from France that claims genetically-modified corn causes increased rates of tumors in a special breed of rats is misleading.

Saturday, October 13, 2012

Witches, tree-rings, and LSD

In the moonlight 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 "witch" might take away the torment, fits, and visions that plagued their children. That somehow through supernatural forces the sensations of ants crawling underneath their 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 valleys for centuries.

This was a typical scene in the medieval villages that lined the Rhône and Rhine rivers. Here, and in other curiously coincidental micro-climates all over Europe something dark and treacherous lurked in the farm fields.

During the cold, wet harvest seasons a deep purple 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; upwards of three pounds a day. As the chemicals made 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 fungus was finally made.

Mycotoxins are poisons produced by fungi and mold. The variety of mycotoxins contained in ergot-infested rye cause two distinct varieties of ergotism - gangrenous or convulsive ergotism. Ergotamine, a powerful vaso-constrictor, prevents blood flow to the extremities and is the main culprit in gangrenous ergotism.  Whereas ergine and lysergic acid hydroxyethylamide cause convulsive ergotism. These lysergic acid compounds found in the ergot fungus have similar effects on the human brain as the 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 alternative medical 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 ergotism being the scourge that set off the string of hangings accompanying the infamous witch trials in Salem.  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.
Caporael's work inspired historian 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 throughout the medieval period.  She explains how tree ring thickness measurements 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 in which 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.

I was and still am utterly fascinated by the potential connection between a nefarious fungus and the waves of witch trials throughout the middle ages. So fascinated that I have continued seeking further evidence for this biochemical culprit in primary sources.  As I have said, the mid-wives of medieval Europe knew how to use ergot to treat hemorrhaging after birth, but did they know they could use this fungus to induce abortion? Surely they must have, and this would only have placed them higher on the list of public enemies by church rulers. Interesting observation, but how can I use this bit of information to test the claim that the presence of ergot in the diet of medieval peoples lead to witch trials?

There was a guide-book to hunting witches written in Germany in 1486 and approved by the papcay - the Malleus Maleficarum. Translated to English from Latin this means "the hammer of the witches."
The main purpose of the Malleus was to attempt to systematically refute arguments claiming that witchcraft does not exist, discredit those who expressed skepticism about its reality, to claim that witches were more often women than men, and to educate magistrates on the procedures that could find them out and convict them.
Might I use this primary text to hunt for clues connecting ergot to geographic regions affected by witchcraft?   Ergot can induce abortion in humans, right? Well, ergot in rye can also induce abortion in cattle. With this fact in mind I went to the text of the Malleus which is available through Google Books and project Gutenberg. When I searched in the book for the word "cattle" I found several references and even a whole chapter on how witches injure cattle in various ways. To my astonishment, there was even mention of bewitched cattle spontaneously aborting their calves! To the witch-hunters and inquisitors of the middle ages this phenomenon was a sign of witchcraft but the reality was most likely a rotten rye crop!

Thanks for reading! I hope you liked this story. If you did please share it! I would like to make this part of a storytelling series I am planning on you tube. Stay tuned here in the coming weeks for more biochemistry of Halloween content! You can subscribe to Tom Paine's Ghost at the link in the upper-right sidebar. If you like what you read here please make a donation of any size so I can continue to do what I love :)  Donate button also in the sidebar.

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  

The Story of Storytelling

Sunday, October 7, 2012

Congressman - evolution and bing bang "lies from the pit of Hell!"

Rep. Paul Broun (R-Georgia) is seen in the video below saying that evolution, embryology, and the big bang are “lies straight from the pit of Hell”. The scariest part of this is that he is a current member of the Science Committee of the House of Representatives! No wonder we are lagging international in science education. We have young earth creationists operating at the upper echelons of our federal government!

Where the Buffalo Roam

Took this photo in the Black Hills of South Dakota last week.
Chubby prairie dog. Black Hills, SD.
Black Hills, Chippy
Herd chillin' in Theodore Roosevelt National Park, ND.
North Dakota natural gas boom. Drill baby drill.
Wild horse!
This guy was standing near a herd in Theodore Roosevelt National Park on the western edge of North Dakota. Accidentally took photo with camera on a night setting. I like the contrast though.

Saturday, October 6, 2012

Super Slo-mo Slinky in HD Glory

Nightfall: minute physics explains

Good Morning Hippie!

I woke up this morning to an interesting comment posted here at Tom Paine's Ghost. My old friend Troy decided it was time to let me know how appalling my support for Obama is. Troy is a good guy, a hard worker, a veteran, a family-man and a friend. I have a lot of respect for him and I am glad he has decided to engage in discourse here with us. Troy is mainly responding to a video I posted of the speech Obama delivered to the United Nations just a few weeks after the attacks on the US embassy in Libya. I will re-post his entire comment here and add my rebuttals in this green font as I think of them. Feel free to jump in and add to the conversation. OK, here we go...

Kris, Kris, Kris, for a “Freethinker’s Cove” I’m afraid you check your brain at the door and allow your far-left ideology and infatuation with Obama to rule over reality and reason!

I agree, the first 5-10 minutes of Obama’s speech was admirable and I appreciated listening to the short biographies of the Americans who lost their lives in the service of our country. But he quickly losses me when he starts making excuses for Muslims:

“Let us remember that Muslims have suffered the most at the hands of extremism.”

Really? What about the thousands of Americans who died at the hands of Muslim extremists on 9/11(
2,606 people died in New York City in the World Trade Center and on the ground, 125 died at the Pentagon, and 44 people died in Shanksville, PA.) and their family members or the thousands of soldiers who have died from Muslim extremists to give Iraq (4,488 dead US Troops) and Afghanistan (1,957 dead US troops) a fresh start from tyranny and repression. What about the family members of the deceased still suffering from their losses? 

Each and every human life lost in war is deplorable. I am not saying and I don't think Obama is saying that a Muslim mother who loses her son in war suffers any more or less than an American mother who loses her son. Consider this, it has been estimated that anywhere from 28,000 to 42,000 people have lost their lives in Syria alone since the beginning of the civil war there in 2011, LAST YEAR. So lets take the US deaths from 9/11 and the wars in Iraq and Afghanistan and add them together = 9,220. Do I think Obama could have used more precise language when saying "that Muslims have suffered the most at the hands of extremism" Yes, I do. And being a bean counter when it comes to human life is a terrible thing to do. Every human life is invaluable, But I hardly consider the statement you quoted as Obama apologizing to moderate Muslims. He was attempting to give the world some perspective on the consequences and geography of terrorism.

Is it really enlightenment and tolerance to make excuses and apologize for these people? I think it is the highest form of enlightenment and tolerance to empathize with any group of people that is different from your own. I agree the Muslim community as a whole suffers from the extremists that use their religion for power. If you agree with this then you agree with what Obama said in the speech to the UN. The moderate Muslim’s in this world have to outnumber the extremists by millions. I don’t see them policing their own nearly enough if ever (What about Turkey? They still belong to NATO, have a strong military, and have a record of using military force against bad neighbors- ex: last week and Syria). Why doesn’t Obama apologize to America about his failed economic policies  or his failure to protect our citizen’s in foreign embassies?

What’s even worse is that the whole video excuse is a farce and a distraction from the fact that the Obama Administration dropped the ball on securing the US Embassy in Libya. I agree with this, just as I agree that the Bush administration dropped the ball on securing the World Trade Center on 9/11 But I am not a conspiracy theorist. I can sit here and complain all day that more was not done to prevent 9/11 but that does not mean I think Bush somehow caused 9/11 to happen, just as I do not think Obama somehow caused the attacks on the US embassy in Benghazi to happen. Terrorism exists and we need to be vigilant. I agree with this stance. Do you really think that a spontaneous riot would conveniently erupt on 9/11 from a video that was posted on the internet back in July? If that is the case Bill Maher’s “Religulous” would have started WWIII sometime in the past few years don’t you think? I don’t remember any backlash from that movie.

Liberalism, progressivism, whatever you want to call it, is zapping all the motivation, inspiration, ingenuity and drive out this country. The Obamaphone Lady in Cleveland, OH is a great example of where this country is heading under the leadership of President Obama:

Four years ago I would never have imagined myself thinking that I wish George W. Bush was still in office, but here I am thinking just that. It is appalling to me to see you idolizing Barack Obama like you do. Kris, where’s the hope and change he promised? Where’s the transparency (Here , the honesty and the openness? I have seen nothing but lies, deception and closed doors for the past four years. It is disgusting to me to see the President of the United States let other countries tell us what to do, especially China and Russia, or make excuses for my country in the name of tolerance and good-will. Kris, you’re an intelligent man. Why is it so hard for you to open your eyes and see the wrong this administration is doing to our country? What really has this man done in the past four years as president? (Yes, what has Obama done?) Please don’t answer with he killed Osama…

I tried to be as good as possible, I promise! I just hate to see an old friend wander down the wrong path. I appreciate your concern :) Miss you brother. How is your new family?

Friday, October 5, 2012

Night Skies - Yosemite

Colbert on "Pulpit-Freedom Sunday"

Stephen Colbert takes his satire to a whole new level here. He can hardly keep his contempt for Jim Garlow and his anti-church-and-state-separation mentality.

Wednesday, October 3, 2012

Fate or Feedback: is the microbiome driving our behavior?

Once upon a time there was an unsuspecting ant on the rainforest floor somewhere in Thailand. Marching along single-file between his brothers he was minding his own business, when he suddenly cocked his head and sniffed a moldy kind of smell. Thinking nothing of it, he kept on walking but soon found himself compelled to get out of line and began wandering off into the forest alone. He felt disoriented, confused, not knowing what was happening to him. 

Our tiny friend then found himself at the base of a towering leafy plant. Looking up at the massive translucent leaves he began to climb. Higher and higher he climbed up the central trunk, passing branch after branch, all the while loosing any idea of where he was or what he was doing. Once he reached a height where the air was thick with humidity he stopped climbing and began to walk out onto a leaf. Over the edge of the leaf he could see the long homeward-bound procession of his brothers far below. But before he could make another move he felt an overwhelming urge to bite down on the central vein of the leaf where he found himself perched. As he bit down he felt all the energy in his tiny body flow to the muscles in his head and mandibles and he bit harder than he had ever bit before. His life flashed before his eyes and in an instant he was dead, frozen. 

What has happened to our little ant friend?

Just a few days after the ant's demise a long grey tube began to grow from inside his head, eventually puncturing the top of his ant-skull it continued to grow into a large mushroom. As soon as the fruiting body had fully unfurled tiny spores were released from the cap and sprinkled like snow, slowly down over a fresh line of brother ants where the entire sordid tale began anew.

This is a true story. As you can see, this fungus has hijacked the ant's body turning it into a zombie of sorts, bending the ant's behavior to work exclusively for the benefit of the fungus.This is not the only example of this kind of fucked up relationship in nature. There is nematode worm that lives part of it's life cycle inside the guts of birds. When the birds poop in the jungle, ants eat the poo and with it the nematode larva. Inside the ant's stomach the nematode enters the next phase of its life cycle causing the ant's abdomen to swell and turn bright red. The round red ants look like ripe local berries to hungry birds and the cycle starts again.  Crazy!

Humans are still plagued by extreme parasites as well. The killer gut bacteria Clostridium difficile (widely known as C. diff) causes 14,000 deaths in the US annually according to the Centers for Disease Control. The extreme diarrhea symptomatic of C.diff.  can cause patients to loose a third of their body weight or more. As C.diff usually proliferates in the wake of long antibiotic regimes it is often resistant to antibiotics.  At the same time C. diff. ferociously out-competes the diversity of benign bacteria (part of the microbiome) that regularly inhabit the ecosystem inside the human gut. 

Fear not! A radically simple and effective treatment has emerged for this problem. Fecal transplants! That's right, people get so desperate when they have lost 80+ lbs and are too weak to walk they will try anything. But this shit actually works! Doctors get a "donor" to poop into a container, then they mix it up into a slurry with some water, and deliver the slurry to the colon with a colonoscopy-style tube, or... the doctors can also deposit the donor's poop slurry through a nose-tube into the stomach. I almost just barfed typing that out.  Usually the fecal "donor" is a spouse or a parent, and four out of five patients who receive this poop infusion are cured on the first go!

It is hard to think of near-fatal diarrhea as a behavior but, strictly speaking, it is. The point I want to make by bringing up C.diff infection is that a human behavior - extreme diarrehea - can be changed by a fecal transplant. A transfer of the microbial garden from one field to another can literally change the culture.

So far I have examined extreme examples of behavior modification by parasites. They are extreme in the sense that the victims pay with their lives, but what if there were a whole lot more of these relationships than we ever thought? Relationships in which the host's behavior only had to be manipulated slightly to help the parasite. What if much of human behavior is largely dictated by the the non-human denizens of our bodies? One out of ten cells making up  a person's body are actually of the species Homo sapiens. The rest? Fungus, bacteria, mites, protozoa and a whole ecosystem of diverse fauna. The question is, how democratic is the human body in decision making? Do the peptides secreted by your gut bacteria help decide what to eat, who to mate with, when to fight and when to run?

Enter Toxoplasma gondii, a protozoa that has just such subtle effects on human behavior. In an article published in the European Journal of Personality researchers report that human beings inoculated with these tiny creatures are more outgoing socially, have a higher rate of car crashes, and become less and less conscientious the longer they carry the parasite (especially men).  The shocking part of this study was the number of people who host this little bug - 22.4% of the US population over the age of 12! T. gondii is generally thought to be benign unless present in pregnant women or infants where it can cause damage to developing tissue.  The protozoa is so small during the stage of its life cycle when it lives inside humans it actually penetrates the cells, living in heart and brain tissues. As it replicates it can form benign cysts in the heart and brain... yuck!  The prevalence of T. gondii is underscored by it's signature behavioral modification - extroversion.  By rendering its host more outgoing it increases the likelihood it will spread to additional hosts. Diabolical! Are there any benefits to knowing this? could someone with chronic shyness inoculate themselves with this bug and make themselves more sociable? Might we extract the biochemical mechanism this bug uses and just make an extroversion drug instead? Who knows! Time will tell.  

To me, it is interesting to ponder how deep this connection between medical ecology and human behavior will play out. Are we, like the ant at the beginning of this story, bouncing like a pin-ball between the needs and desires of tiny creatures that call our bodies home?

By writing out these thoughts I want to get my readers thinking about behavior and the unseen factors that influence it. You know that person at work who really gets on your nerves with the constant close-talking? Maybe it's not their fault. May they're acting on a whim of one of their microbial free-riders. Maybe this is true for a lot of human traits. Will we identify more human behaviors that operate under direct feedback by bacteria? fungus? protozoa? cats? dogs? Can we "fix" people by modifying their microbial clouds? Should we? How will super-cheap gene sequencing affect social dynamics?

I do not have the answers to these questions. Maybe you do. Is this a worthy line of scientific inquiry? Share your thoughts below or find me on twitter @thorsonofodin.

Written by Kristopher Hite

1.) Andersen SB, Gerritsma S, Yusah KM, Mayntz D, Hywel-Jones NL, Billen J, Boomsma JJ, & Hughes DP (2009). The life of a dead ant: the expression of an adaptive extended phenotype. The American naturalist, 174 (3), 424-33 PMID: 19627240  

2.) Khoruts A, Dicksved J, Jansson JK, & Sadowsky MJ (2010). Changes in the composition of the human fecal microbiome after bacteriotherapy for recurrent Clostridium difficile-associated diarrhea. Journal of clinical gastroenterology, 44 (5), 354-60 PMID: 20048681  

3.) Jitka Lindová1,, Lenka Příplatová,, & Jaroslav Flegr (2012). Higher Extraversion and Lower Conscientiousness in Humans Infected with Toxoplasma European Journal of Personality, 26 (3), 285-291 DOI: 10.1002/per.838

Obama addresses the World

The President of the United States addressed the United Nation's General Assembly last week in New York City. Though the speech was covered by the mainstream news networks, it was by no means emphasized. In my opinion this 30-minute speech was the most historic speech President Obama has delivered and I think will go down in history as a shining moment.  Famed biographer Doris Kearns Goodwin taught me that the Gettysburg address was barely noticed when Lincoln first delivered it. Few but the attendees in the front row could hear Lincoln's spoken words. Most of the crowd were not even paying attention to him but talking amongst themselves, much like contemporary people get distracted talking amongst themselves over social networks and so on. Don't let this historic speech pass you by. You can watch it right here on Tom Paine's Ghost! 

P.S. I will be live-blogging the Presidential Debate from Colorado today. Tune in here at 9PM eastern, 7PM mountain time tonight!