What can be done with CRISPR-Cas9 Technology?

Kayaks block Shell Oil Rig in Seattle!

Worn Wear - A Traveling Patagonia Repair Shop!

@Patagonia rep patching my jacket with tenacious tap for free @newBelgiumBrewing with the Holler Playing in the background!

A photo posted by Kristopher Hite PhD (@odinsravens) on Apr 23, 2015 at 3:30pm PDT

Watch a Grizzly Bear get an MRI

Well wishes for Lucy a 3-year-old grizzly from the Montana Grizzly Encounter who received an MRI today #GoCougs
— WSUVETMED (@WSUvetmed) January 17, 2014

The story.

CLARITY - looking inside the brain

I stumbled across this video yesterday while bouncing around Twitter. Mitch Waldrop had posted the video a few months ago. The technology displayed here is dubbed CLARITY - a new method for looking inside animal tissues. In this case brains. It takes the grey mass you normally think of when you think "brain" and turns it into a jellyfish-like consistency, see-through and all. CLARITY was developed by a team of interdisciplinary researchers at Stanford University lead by Karl Deisseroth. I am constantly amazed at the pace of progress we are witnessing in biomedical science. Just brilliant!

Lyrebird repertoire includes chainsaw

I know the resolution on this clip is low but it is completely worth watching. The Australian Lyrebird sings a song of irony for the world to hear. A clear feedback loop in the forest and a beauty to behold.

3D Printing Life: Molecular Paleontology and the Potential for Anthropogenic Panspermia.

Here we see Austen Heinz of Cambrian Genomics describing the method and potential future applications of 3D printing living things.
 

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.

Pronghorn

Night Skies - Yosemite

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

Richard Feynman lectures at Cornell 1964

Big thanks to fellow blogger Jennifer Ouellette for sharing this wonderful lecture on gravity by Richard Feynman at Cornell University recorded in 1964. The preservation of the spirit of great teaching displayed by Feynman is, in my opinion, a testament to the archival value of YouTube.

What is the Higgs field?

Could it be that Healthcare in the United States is approved AND the Higgs boson is discovered in the same week? Maybe.

I am watching with great anticipation this week as my favorite physicists tweet their way all the way to Switzerland for a big announcement from CERN at the Large Hadron Collider.

Sean Carrol, physicist and blogger just tweeted he was boarding a plane bound for CERN and several prominent physicists notorious for not keeping their mouth's shut have been bursting at the seems awaiting the announcement expected this Wednesday July 4th.

UPDATE: Peter Higgs, the theoretical physicist who originally imagined his namesake particle is also en route to CERN!  

All this indicates some new data about the Higgs boson has been collected and is ready for public display.

If you are unfamiliar with this particle it is at the crux of all matter in the universe - hypothetically.

The following video is the least woo-woo explanation I can find out there describing what the Higgs field may be. High praise to the creators for not mentioning the "God Particle" once. Tough to resist the trendy pop-culture label.

The Paradox Behind the PRKCA Gene

A guest-post by Phillip Moore

The PRKCA gene is a paradox of sorts in that it has been identified by European researchers to improve memory, but also to increase the risk of post-traumatic stress disorder (PTSD). The magazine Nature just recently released a fascinating article that highlights the curse of possessing a good memory in certain traumatic situations. Let's examine the important details of this study conducted by Dominique de Quervain of the University of Basil in Switzerland and then explore future work that must be done to better understand the PRKCA gene.

Brief Details of 3-Part Study

Dominique de Quervain and his colleagues recruited 700 healthy young European volunteers in order to obtain their DNA samples to analyze the sequence of their PRKCA gene. This gene is just one of many known to impact our emotional memories. The researchers displayed emotionally disturbing images to the participants and then soon after asked them to write brief descriptions of the images. The participants either carried two copies of the A allele or two copies of the G allele, both of which are variants within the PRKCA gene. Those participants who carried two copies of the A allele remembered the most details about the traumatic images, while participants who carried two copies of the G allele remembered the least.

The researchers then recruited 394 other participants to perform the same task while undergoing brain imaging. The study also confirmed that variations in the PRKCA gene impact emotional memory. The brain imagine scans revealed that the A allele was affiliated with enhanced activity in the lateral and medial prefrontal cortex, both of which are regions involved in the encoding of memories.

Finally, the researchers explored the distribution of the A allele among the 347 survivors of the 1994 Rwandan genocide who fled the civil war. This results of this study were consistent with the other two studies in that survivors who possessed two copies of the A allele were almost twice as likely to suffer from PTSD.

Moving Forward

The PRKCA gene is just one of many known to influence our emotional memories. It is important to examine the role that other genes play in shaping our memories. Massive genomic studies will likely reveal a multitude of other gene variants associated with the greater risk of developing PTSD. Also, more research must be done to understand exactly why the A allele leads to differences in brain activity during the process of memory encoding.

The research conducted by Dominique de Quervain and his colleagues really demonstrates that a good memory can be both a blessing and a curse.

Phillip Moore is an online instructor and coordinator for The College City. As a molecular biologist, Phillip was very interested in this European based study and wants to conduct his own research on the PRKCA gene.

Underneath the Waterfall

Matteo is with us. The magic of reality is pouring through this video. I hope his energy rubs off on you on this fine spring day here on our pale blue dot!

Inside the Climate-Change-Denial Playbook

Last week I posted a video of Senator James Inhofe interviewed by Rachel Maddow. In this interview Inhofe makes assertions that made my jaw drop. Namely, that environmental lobbying groups out-spent oil-and-gas lobbyists by over a billion dollars in 2009.  He even sites Nature Magazine as the source for this "fact." A "fact" that he clearly got wrong by grossly misrepresenting and confusing the numbers.

The opinion piece in question can be viewed here. The numbers reported by the editors are as follows; $272 million spent by oil-and-gas lobbyists opposing cap-and-trade in 2009 while $229 million spent by environmental groups lobbying for cap-and-trade legislation. By claiming that environmental lobbyists spent nearly a billion dollars more than oil-and-gas lobbyists while the article clearly states that environmental groups spent 43 million dollars less, Inhofe is guilty of an egregious falsehood. 

Incidentally, Inhofe also describes Nature as a "very liberal publication." This struck my as particularly hilarious as the vast majority of the material written about in Nature is derived from primary research conducted in laboratories all over the world.  It has the highest impact factor of any academic journal and publishing in said journal is the most competitive endeavor a scientist can undertake.  In all my life I have not seen a single member of the US congress argue about the scientific reporting in Nature Magazine unless it threatened their bottom-line. You don't see Inhofe arguing over the liberal or conservative way in which the crystal structure of Malaria parasite proteins are described. Imagine hearing a senator argue - Yes, the cysteine-rich Duffy-binding-like domains of the parasite's erythrocyte binding protein actually only bind to right-leaning cell surface receptors - COME ON!

I want to emphasize that the article Inhofe refers to is a brief OPINION piece, not a full-on research article. It is an opinion written by the editors encouraging their audience to read a report made by a professor at American University in Washington, DC named Matthew C. Nisbet. The title of professor Nisbet's article is - Climate Shift: Clear Vision for the Next Decade of Public Debate.  

While reading professor Nisbet's response to Inhofe's misuse of his report I came across a very interesting paragraph describing the playbook of the climate-change-deniers.  The following paragraph makes clear that there is an orchestrated effort among some conservatives in Washington to frame climate-change consistently in a severely anti-science manner.  

"During the 1990s, based on focus groups and polling, Republican consultant Frank Luntz helped shape the climate skeptic playbook, recommending in a strategy memo to lobbyists and Republican members of Congress that the issue be framed as scientifically uncertain, using opinions of contrarian scientists as evidence. He also wrote that the “emotional home run” would be an emphasis on the dire economic consequences of action, impacts that would result in an “unfair burden” on Americans if other countries such as China and India did not participate in international agreements.^"

Using anti-science tactics is intolerable to me and I feel sad for the people of this county who are fooled by charlatans like James Inhofe.  They are making a mockery of this republic and it makes me want to scream!

---

Did you like this article? If so please help out my blog however you can. You can donate as much or as little as you like, even just a few pennies. By supporting Tom Paine's Ghost you are helping me bring interesting topics to your beautiful eyes :) Click the MuCash button below. Thanks!

Science in the Constitution of the United States of America

Section 8, Clause 8 of the United States Constitution reads -  

"To promote the Progress of Science and useful Arts, by securing for limited Times to Authors and Inventors the exclusive Right to their respective Writings and Discoveries"

This bit codified prose is pressing on my mind.  Is it possible that promoting the "Progress of science" now requires a new approach different to that agreed upon over two centuries ago?

World Science Festival 2011

Hello from New York City. For all you faithful Tom Paine's Ghost readers out there you may have noticed a marked decline in my actual written-word of late.  Apologies as I was composing my dissertation and being distracted with flowering aloe plants good music and LOVE all at the same time.  Having defended my dissertation and driven a few thousand miles I am here in New York City to live-blog the 2011 World Science Festival.

I am a big fan of the overall mission of this festival which is...

"The Mission of the World Science Festival is to cultivate and sustain a general public informed by the content of science, inspired by its wonder, convinced of its value, and prepared to engage with its implications for the future."

Keep your eyes here at Tom Paine's Ghost and catch me blogging for the official WSF blog over the next few days!

PS - please excuse grammatical and spelling mistakes for the time being. I am of the philosophy that content is more important than the frame it is presented in. I promise I will  go back and tidy it up after I come up for air sometime next week but for now you get my thoughts raw!

Date. Interrupted.

Greatness on Parade

23 Feet

23 Feet Trailer from Allie Bombach on Vimeo.