Science of Halloween: Biochemical Culprits

Teabaggers are officially crazy!!!!!!!! EVERYONE VOTE - STOP THEM!

The horror! This fills me with remorse that this is part of the country we share.

This land is your land this land is my land.

FOR CRYING OUT LOUD WAKE UP AMERICA!!!

Biochemistry of Halloween: Vampires!!!

This is a RE-POST from the Halloween series. Highly relevant as fellow graduate student Nick Clark and I will be presenting this along with discussions of witches and zombies TODAY at the Park Hill Library in Denver. We were asked to give this presentation by the CSU Alumni Association almost a year ago. It is a free event with a raffle for some CSU garb and other treats. Nick ad I will be providing the tricks :) This whole thing was born out of a conversation Nick and I were having in the lab one October morning 3 years ago. Glad to see it grow into such an event!

We've even got some MSM buzz going on here here and here!

"A Candle in the Dark"

Teeth lengthened by receding gums glow in the shaded valleys of the Carpathian basin. The genetic milieu of the Visigoths, Huns, Carpians, and Slavic peoples have swirled over centuries as granite crags pushed populations into shallow gene pools. A ghoulish thing of legend emerged from Transylvania and has since soaked literature and pop-culture with a reddish froth. Science and medicine have given us reason not to fear for our necks in a story that is truly stranger than fiction...

The glowing teeth mentioned earlier occur because of an accumulation of light sensitive molecules called porphyrins in victims of a rare genetic disease. Porphyria affects one of the steps in heme production. A heme is the chemical group that holds iron atoms in their proper position in hemoglobin (the protein of blood). The name "porphyria" came from the Greek words for purple and pigment. Victims of this disease have an uncanny similarity to historical descriptions of vampires and phenotypes of this disease have been suggested as possible explanation for the origin of vampire legends.

Mal-formed porphyrin molecules accumulate in affected people's skin and teeth. When activated by light these molecules activate oxygen molecules into destructive radicals that can wreak havoc on surrounding tissue. When exposed to light individuals appear to be burned with caustic lesions left on their skin. Enter: Nosferatu's pale countenance shrieking in terror as the sun rises.

Though no blood-lust is reported by sufferers some historians speculate that drinking the blood of animals may have been attempted as a folk remedy in treating the disease. It has since been proven that the heme molecule is in fact robust enough to survive digestion indicating that replenishing mal-formed blood molecules by drinking blood may indeed help those that happen to exhibit anemia in conjunction with porphyria. When watching vampire movies the whole garlic premise never made any sense to me. Why couldn't you use mushrooms, or cinnamon, or toothbrushes to scare away vampires? What was it about garlic. With the Porphyria hypothesis in mind it makes sense however. Garlic has vasso-dilator chemicals and is reported to exacerbate the affects of porphyria. Sufferers may have learned to avoid it indeed!

In the genetically secluded valleys of Transylvania it is not hard to imagine disorders like these occurring more than expected in a diverse population. Before the renaissance and the spread of the scientific revolution a vampire myth may have grown from accounts of these individuals with their glowing long teeth, aversion to sun and garlic, and maybe even sucking blood in the night!

Thanks Nick for your help with this!!! stay tuned for the next installment of the Biochemistry of Halloween when we talk about Haitian Zombies!

Things You Think

Brian Jones presents a huge TESLA COIL

I am Iron Man. Thanks for the heads up on this one Jared!

darwin deez - DNA

Guest Post: Gandhi was right about Christians

I attended my first meeting for Freethinkers of Northern Colorado today at the Dazbog coffee shop on North Mason Street in Fort Collins, CO.  They meet there the third Sunday of each month at 10 AM. An invigorating conversation was had by all. During the discourse the Loveland Art Hoopla was discussed at length. I speak of the unfortunate incident in which a Mz. Kathleen Folden from  Kalispell, Montana waltzed into the Loveland Museum Gallery, took out a crowbar and smashed open a display containing a print composed by Stanford University professor Enrique Chagoya. The print, titled "The Misadventures of the Romantic Cannibals" depicts the head of jesus on the body of a clothed prostitute who has a young man pressing his head on her thigh with his tongue out. You can see the print here. 

To me, the most entertaining aspect of the media coverage of this fiasco has been the apparent inability of certain news correspondents to look at and consider art for themselves, let alone place it in any societal context. I find it incredibly funny and sad that all the people complaining about this art (FOX news correspondents especially) have apparently not looked at the entire piece with their own eyes but are merely going off of hearsay. In their report that aired before the art was attacked they bemoaned the piece saying - "I wonder what would have happened to the art were it Mohammed depicted in a sex act?"

Funny they should say this. If you look at the bottom row of panels you see Mohammed knelt and praying at the foot of a bed where two pigs in bikinis are dancing. I'm quite sure this means Chagoya is an equal opportunity blasphemer and probably will be called an artistic genius for this!   

A fellow first-time attendee to the meeting spoke up and said he had written an op-ed piece that had yet to be printed in the local paper. I offered to put it up here at Tom Paine's Ghost. So here you go.  A guest post from a fellow free-thinker of Northern Colorado.

Gandhi was right about Christians

By  Joe Martin

Mahatma Gandhi said, "I like your Christ, I do not like your Christians. Your Christians are so unlike your Christ." Kathleen Folden is a perfect example of what he meant.

While I don't expect the average bumpkin to understand abstractions such as artistically expressed messages about society or its institutions, neither do I expect them to start swinging a crowbar to express their indignation at a less than flattering depiction of their religion's sacred cow.

Freedom of speech is fine for religious nutjobs like Folden as long as they don't find that expression to be offensive, in which case you find equally unstable zealots in Washington, attempting to smash the Plexiglas protecting the Constitution. Protection of offensive speech is the very reason for that clause of the First Amendment. Nobody hacks to pieces artistic expressions that they like.

Sadly, this is well within the range of crimes against the greater society of which modern activist Christians are capable on their march to turn America into a theocracy.  It is no less reprehensible than the Muslim riots that happened in reaction to the Danish newspaper cartoon.

It has been suggested that similar art depicting Mohammed or more contemporary figures in the same manner would not have been considered for display. I can’t speak for what the museum would or would not accept for display; but I know I would welcome such work.

Religion does not deserve special protection against offensive artistic expression. Nobody has an inalienable right to not be offended.

Scary Data Contest!

Do you have Frightful Data?

Enter it and win prizes !!

Entry Deadline:  Friday, October 29^th – NOON

Send your data to kristopherhite@gmail.com

Prizes will be awarded for:

Best Costume * Creepiest Gel * Genius Mad Scientist Award

 * Best in Show *

Refreshments will be served

 Sponsored by your friends at Planet Protein

Decision of the Judges is Final

BARP Goes the Weasel!

By Kristopher Hite

Looking back at discoveries of the past year the one that sticks out above all others to me was the identification of a single protein; a bacterial actin homologue dubbed BARP - Bacterial Actin Related Protein. The brilliance of this discovery comes from its directly contributing to our understanding of evolution, overturning decades of dogma, and providing a shiny new teaching tool.  The discovery was published in late 2009 as part of a massive sequencing project to fill in gaps of knowledge among bacterial and archael genomes.

With all the other sexy and more controversial stories about evolution - Ardi, Ida and so on, why do I pick this one? Aside from my biochemical inclination I thought this little piece of biological hardware deserved more exposure.  Though the paper was covered and lead author Jonathan Eisen interviewed for the nature podcast, it received relatively little coverage on the science blogs. Yes, the prolific science writer Carl Zimmer wrote a nice summary for the New York Times but the BARP bit is mentioned only briefly. I don't know if anyone realized what a great tool this discovery is to hammer even more nails in the coffin of the "irreducible complexity" argument for intelligent design. 

In January 2010 I had the pleasure to sit down and interview Eugenie Scott - executive director of the National Center for Science Education (NSCE).  As she explained the history of science education in the United States we came to an agreement on what one "take home" message should be for the average high school student - that all living things on earth share common ancestors, that all species have a common descent. This point may not seem earth-shattering to comprehend but I think many in America fail to realize the significance of this fact. The procession of science has uncovered an armory of teaching tools - fossilized trilobites, floating whale hip bones, and common DNA sequences. The more is known about the inner workings of the natural world the easier it should be for students to see and accept the facts. What then is the barrier to getting students to accept take-home messages like common descent? I would posit that fundamentalist opposition to evolution and the idea of the rapture have more than a little to do with it. Proponents of intelligent design often use a phrase coined by Lehigh University professor Michael Behe - irreducible complexity - in their defense of a necessary designer. This was a large part of Behe's arguments against teaching evolution as fact in the Kitzmiller vs. Dover, PA landmark court case.

Behe defines an irreducibly complex system as one "composed of several well-matched, interacting parts that contribute to the basic function, wherein the removal of any one of the parts causes the system to effectively cease functioning." Brown University Biology Professor Ken Miller uses the analogy of a mouse trap to explain away irreducible complexity. Yes, all components of a mouse trap are necessary for overall function but each component can be have alternate uses.

In the logical chronology of evolution complexity emerges incrementally by the acquisition of functional structures that appear by chance and remain due to conferred advantage. Behe has tried over and over to use the molecular structure of the bacterial flagellum as an example of an irreducibly complex system.  In response Ken Miller did an excellent job explaining how the components of bacterial flagella could emerge incrementally.

So what IS actin and how does its showing up in a bacterial specimen add to the arsenal of teaching tools against irreducible complexity?

actin filament

As you move your cursor around this page your muscles are contracting and relaxing, your brain is sending signals along tiny electrified strands called axons guiding these contractions. Among the myriad things that make this possible is the little protein called actin.  Deriving its name from the word "activating" actin enables muscular motion, provides train tracks inside each cell for directional transportation of other tools, and gives shape to most cells in your body.  Like oddly shaped legos these tiny building blocks bind to each other and form long filaments that grow and shrink.  A mesh-work of actin filaments push on the perimeter of each cell establishing shape.  Those long axons I mentioned before are extensions of brain cells (neurons). During development neurons send out these long extensions and it is the mesh-work of actin that leads the charge enabling all those millions of electronic connections between brain and body to form. 

The gene that codes for this little protein exists without much variation in all eukaryotic organisms. Eukaryote means simply "true nucleus." The distinction is made because the more ancient but still surviving bacteria do not have "true nuclei" they are therefore dubbed prokaryotes. The moment at which the first eukaryote appeared on earth marked the beginning of an explosion of diversity, and a fundamental branch point in the phylogenetic tree of life.

(Haliangium ochraceum)

 Unlike the carefully crafted nuts and bolts you can pick up at the hardware store cellular machinery is not designed for a purpose, it just appears by duplication, mutation, or other spontaneous variations of genetic material.  If it works it is retained, if its merely eating up metabolic resources it usually goes extinct.  This represents an important variation on pure chance that the process of evolution carries with it.  Richard Dawkins has illustrated the power of evolving systems to accumulate positive variation in his classic "Weseal" thought experiment. Self-replicating systems have the ability to retain random variation in their code by copying themselves. When a variation carries a positive effect for the code carrier (organism) then that carrier is more likely to make more copies of that advantageous variation.  New variation is possible because there are usually redundant bits of cellular machinery.  This is exactly what we see in the case of BARP.

If you asked any professor of cell biology any time prior to a year ago "Do bacteria contain a gene for actin?" they would, without hesitation, say "of course not." It was understood that the gene for actin was one that separated eukaryote from prokaryote. Bacteria have an unrelated gene  - MreB - that has a scaffolding function. They don't need actin.   Now it is shown that the gene for actin may have shown up in  marine bacteria (specifically the one named Haliangium ochraceum) prior to the evolutionary branch-point. If this is the case it means that actin was later recruited to its now prolific function giving shape and motion to eukaryote cells. Actin was not designed then implemented like machined parts in human created contraptions. According to this research it probably appeared by chance in marine bacteria, served some other unknown function, then just happened to work later on in evolution.  This, I think, is why many mechanical engineers have an aversion to studying the slimy, oozing, organic structures in nature. They are inherently messy and imperfect.  This is because they are not designed! They are the result of chance events captured inside self-replicating systems - us included.

This post has been submitted to the NESCent competition for a travel award for the ScienceOnline 2011 un-conference January 13-15 in North Carolina’s Research Triangle Park.




  




Wu, D., Hugenholtz, P., Mavromatis, K., Pukall, R., Dalin, E., Ivanova, N., Kunin, V., Goodwin, L., Wu, M., Tindall, B., Hooper, S., Pati, A., Lykidis, A., Spring, S., Anderson, I., D’haeseleer, P., Zemla, A., Singer, M., Lapidus, A., Nolan, M., Copeland, A., Han, C., Chen, F., Cheng, J., Lucas, S., Kerfeld, C., Lang, E., Gronow, S., Chain, P., Bruce, D., Rubin, E., Kyrpides, N., Klenk, H., & Eisen, J. (2009). A phylogeny-driven genomic encyclopaedia of Bacteria and Archaea Nature, 462 (7276), 1056-1060 DOI: 10.1038/nature08656

"Success of the Smelliest"