Biochemistry of Halloween: Installment 1

By Kristopher Hite

"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!

Fashionable Science

from Nature 455 23 October 2008
Epigenetic (adjective.)

Helen Pearson

No one denies that epigenetics is fashionable: its usage in PubMed papers increased by more than tenfold between 1997 and 2007. And few deny that epigenetics is important. What they do disagree on is what it is.

“Epigenetics is a useful word if you don't know what's going on — if you do, you use something else.”

Adrian Bird

A lot of money can ride on whether a researcher is, or is not, studying epigenetics: the US National Institutes of Health (NIH) this month started handing out US$190 million as part of its epigenomics initiative and other countries are pouring funding into the area. (The NIH is careful to define the epigenetics it is paying for as including both heritable and non-heritable changes in gene activity, something that Ptashne describes as "a complete joke".) Bird says he remains in favour of a relaxed usage. "Epigenetics is a useful word if you don't know what's going on — if you do, you use something else," he says.

It's Alive!

"They are hunks of dead flesh sewn into the walking corpse of the Republican party"

A visit from Barack

A subtle point ringing out at the beginning

Palin vs Science

WOW!!!
The level of ignorance displayed here surpasses anything I have heard slip out of George W. Bush's mouth yet. Modern genetics is built on the work done on Drosophila Melanogaster aka "fruit flies." This is the same ignorance that perfuses so many minds attached to bodies that vote. The fear and ignorance on display here explain much of the reason the epidemic of evangelism has spread so fervently in the United States over the past several decades. A union of scientists should coalesce around this soundbite of stupidity and rally with all their might against Sarah Palin, I kid you not!



Yeah who cares about understanding the biochemical mechanisms of disease? If someone gets sick or is born with a congenital defect it was God's will. Right?

Who are these people and why do they have any political clout at all?
And what happened to Renaissance statesmen/women?

Thomas Jefferson once said "Science is my passion, politics my duty."
This philosophy is worth reviving!!!

See Keith's take on this.

Ferrell is back!!!

Obama to Speak in Fort Collins, CO Sunday October 26th

Mr.Obama will be in Fort Collins, Colorado this Sunday for a rally at the "oval" at Colorado State University. Admission is on a first come first served basis. The gates open at the corner of West and University Ave. at 1:30 PM. Mr Obama will speak at 3:30 PM. RSVP here.

Listen to Larry

"He sends shivers down my spine talking about that destruction and makes my eyes water. I love seeing old timers who you think would be set in their ways, a republican type, go against the government and protest to what they are allowing. I cant believe the government considers him a threat to national security! I am glad to see he is still out there educating people on what is going on in the environment as the government allows more and more coal extraction and development. That is not the long term solution at all. And since energy is a huge issue in this election, I hope to see his work pay off."
~Jo

My America

A special comment by Keith Olbermann


Also too see Jon's mathematical explanation of this phenomenon

What Tom Paine's Ghost is all about!

What this country needs is more free speech worth listening to.
- Hansell B. Duckett

Powell Delivers Resounding Obama Endorsment

The most poignant logic I have heard from any military or political leader.



While General Powell described the mother of a fallen soldier standing over his grave an overwhelming wave of goosebumps ran through me.

Then...

The the dragon spewed fire!!!



But a hero put out the flames!

Bluegrass on the Brain

The nexus of science and art exists in the head of Eddie Adcock. Literally. This Virginia native made his career as a banjoist in Nashville,TN, but during recent years tremors in his right hand and arm prevented him from strummin' and pickin' the way he used to. Surgeons at Vanderbilt University have since stepped in and helped him with that. During brain surgery Eddie was pickin' away as surgeons placed an electric generator with electrodes into the left hemisphere of Eddie's brain. Through a hole they drilled in his head they wiggled the electrodes around until his pickin' improved. This story is a secular miracle brought to the world through the scientific method. A miracle does not have to involve blind faith. It can be a perfectly explainable event with a wonderfully successful outcome. May this symbiosis of art and science crescendo into a modern Renaissance. Stories like these make me think that non-fiction today is better than any science-fiction ever written.

Palin as herself on SNL

The entirety of the Fey - Palin exchange!



and act 2



The build-up to this Palin performance might be even more funny than the skits themselves. Below is the "word salad" the governor served up when asked how she felt about her much anticipated SNL debut. I first read this quote here

“Oh, man. I'm excited for tomorrow night, I have no idea what to expect because I haven't seen any scripts or anything else yet, but it will be fun. The opportunity to show American television watchers anyway that you get to have a sense of humor through all of this or even just this really would be wearin’, tearin’ on you, so an opportunity to show that sense of humor and that side of all of this, I look forward to it.”
-Sarah Palin 10/17/2008

I have never been 100% perfect at "on the spot" English speaking, but I do believe the inability to place pronouns and adjectives in coherent sentence structures demonstrates serious deficiencies in normal neural network architecture.

Obama Roasts McCain at Alfred E. Smith Dinner

Watch Out Colbert!

Voting by Mail Changes the Game in Colorado

Every fall in Fort Collins, CO the city holds the "New West Fest," a celebration of local music, art, and business. Here we see the "new west" emerge as a crucial factor in the 2008 presidential election. While many rural areas in the east (like my hometown - Boomertown, NY) have experienced a brain-drain for decades, places like Fort Collins, CO are on the receiving end of that flowing gray matter. I am pleased to see that this demographic, the 20 something college educated "New Wester," is being realized as a genuine political tour de-force.

Folks born between 1978-2000 have been dubbed "millennials" and we number around 95 million. Compare this to the roughly 73 million "baby-boomers" that have held sway over American politics since the mid 1960's. Our political weight is finally being felt. Whether our youth or our apathy held us back in 2004, it does not matter, we have now in 2008 united behind certain shared values that have grown up with us, and it is apparent in this election. We are the generation that grew up watching "Captain Planet" on Saturday mornings, and remember movies like Fern Gully and Land Before Time. The ghost of Jim Henson still whispers the moral of the story in our ears at night. We like thinking and planning green.

Millennials have also been called "Generation We" for our unprecedented cooperativity enabled by the internet. The world has grown a nervous system and we are the neurons. Our blog posts, our Facebook pokes, our text messages, our i-reports are the electro-chemical bursts giving life to a new global organism. The financial firestorm is manifestation of the mental breakdown of this organism while it reconciles the differences so exaggerated during the last eight years. The Markos Moulitsas' and the Bill O'Reilly's of the world have stretched the rubber-band of the polis so far to either side that it is crashing back to center and we are having to redefine and reassign value. May the millennials deliver on their promises and bring conscious evolution to the halls of Washington.

My God?

When I first saw a clip from the video below on Countdown with Keith Olbermann I thought it was a joke. I thought this video actually came from an extremest religious group backing McCain. I was dumbfounded when I saw that this was the bona fide invocation delivered at a McCain rally in Davenport, Iowa last Saturday.



Reverend Arnold Conrad here spreads the notion of the "other." The idea that "he's not like us, so he must appeal to the other." This is unabashed ignorance. I would think that the pious of this nation would condemn his blasphemy when he tells god what to do. I bet God didn't know his "reputation" was riding on this election. Reverend Conrad what exactly are the "various reasons" that the "other" religions of the world would want an Obama victory? Desire for peace over war? Energy policies that actually emphasize renewable resources? A leader who will listen to them?

This instance of misguided self-righteousness is a symptom of the certainty that plagues the American Evangelical movement. This certainty is what lead the United States into preemptive war, and is the same type of malicious certainty suicide bombers have in their minds at the moment of detonation. The certainty that "my God" is better that yours.

In the fall of 2004 I was in my senior year at college in New York State. I would drive every weekend back and fourth across the 200 mile stretch of interstate 86 between Fredonia and Ithaca, the part of the state known as the southern tier. I would often leave Ithaca before the sun came up on Monday morning to return to Fredonia for my 9 A.M. instrumental chemistry class. During the three weeks leading up to the presidential election that year I noticed something that I hadn't in all my drives along that beautifully bucolic stretch. Loping through the Allegheny hills, an ear-grating malice oozed from the radio stations. I could swear that some FCC authority had increased power to these provincial stations to spread lies about John Kerry. Over and over on these otherwise benign stations I heard graphic descriptions about how John Kerry was a baby-killer and hated America. Stern voices came over the airwaves warning people of the impending doom of a Kerry victory.

After the election I was not able to pick up some of the stations that broadcast during that time. My hope is that the inter-connectivity of society has grown past the point of no return and that the internet will act as the disinfectant that makes the fear promulgated by the Arnold Conrads of the world powerless.

iReporter's Find

I generally don't go for this sort of thing - anecdotal and biased - but there are some good quotes in there.



"[Palin] turned it into the armpit of Alaska. Everyone thinks so."

"...instead of exploit [Alaska] and sap every bit of money out of [Alaska] that you can possibly, and leave it like this empty shell. You know what I mean?"

"You can't play catch-up in the White House. You know?"

Obama and McCain on higher education

Barack Obama proposes an excellent plan for higher education, the American Opportunity Tax Credit. This plan would allow students to exchange 100 hours of community service for a $4,000 Tax credit. Any student that has ever looked for a part time job to fund their college education knows that it is impossible to compete with this rate of $40/hour! This would pay for 2/3 of the average annual tuition at a 4 year public college and would completely cover community college tuition. This plan would be an addition to existing government funding opportunities. The greatest part of this plan is the increased integration of students into the community for mutual benefit. Community internships add considerable value to a student's education. Providing this opportunity to more students is a truly nobel and excellent policy for strengthening students and communities.

McCain's plan for higher education, is focused on simplifying tax credits and financial aid application by "consolidating programs." However, Obama trumps McCain in simplification reform by eliminating the financial aid application process altogether, allowing parents to simply check a box on their income tax forms.

McCain's education policy includes a 250 million dollar program that will increase post-secondary opportunities for high school students by providing tax credits for online college preparatory courses (SAT/ACT).

Obama's education policy supports an infrastructure for preparing high school students with college outreach programs (GEAR UP, TRIO and Upward Bound). Obama also proposes a "Make College a Reality" policy that would actively encourage enrollment in AP classes and provide grants to high school students seeking resources at community colleges not available at their high schools.

McCain proposes 250 million so that "States can use these funds to build virtual math and science academies to help expand the availability of AP Math, Science, and Computer Sciences courses, online tutoring support for students in traditional schools, and foreign language courses." This program would provide important resources for many under-privileged schools and students. Although not specifically listed under McCain's higher education policy, McCain proposes to "target $500 million in current federal funds to build new virtual schools and support the development of online course offerings for students. These courses may be for regular coursework, for enhancement, or for dual enrollment into college." I am in support of increasing and developing online tools that enhance traditional education and provide students with more options. However, I am concerned that this would be seen or encouraged as an alternative to traditional post-secondary education instead of enhancing it, especially for students with funding issues. Student/mentor relationships and the vast support networks for students are critical in the retention of students and in their growth! Why the online-centric approach?

In short, Obama's higher education policy includes support programs for high school students and an element integrating college students within the community, adding value to a students education and benefiting the community. In stark contrast, McCain's policy involves an online education approach that would be great in enhancing education but is not a viable policy to supplant broad reform for student support programs.

Awaken!

It is time to awake from your slumber America! As citizens of this great country it is our responsibility to demand more of politics and of politicians, of ourselves and of our neighbors. Apathy and ignorance afflict America like a festering infection. It is time for the common citizenry to step forth like the immune system it is designed to be and combat this infection.

If you are unsure where to begin, start with friends, family and coworkers. If you are not moved by mainstream politics, engage in discussion of any issue that compels you! If you are sick of mainstream politics portrayed by the media, become the media of your own politics! Political forums are everywhere. If you are opposed to existing forums, create your own!

Keep in mind that political progression is not based on preaching to the choir. Political progress is based upon insightful discussion and reasoning, thoughtful consideration and deliberation, compassion and compromise between people with different perspectives. Never assume that people have already made up their minds and that your thoughts will fall on deaf ears! Don't be deaf! Instead of wielding an arsenal of sound bites and talking points, wield an arsenal of research!

Keep in mind that engaging in political debate is an inherently frustrating activity and the utility of your labor may not be instantly recognizable. Resist the futility of anger and hostility in this endeavour and foment tolerance and understanding. Politics as a whole is an infinite process with unfathomable connectivity and consequence. The failure of a single individual to participate in the process will result in disequilibrium of the entire political system!

Engaging in politics is a duty. Federal, state and local policy impacts every aspect of all of our lives! No one is exempt!

End the Culture Wars!

Anyone who took high school history will remember this image. This was one of the first political cartoons to appear in the American colonies calling for unification. Created by Benjamin Franklin it was first published in the Pennsylvania Gazette on May 9, 1754. The contemporary relevance of this image is striking. Though today it might be simplified even more. The snake could be made into 50 bits colored in red and blue.

The Bailout! The Rescue!
Raising taxes! Rolling back the tax breaks!
Occupying Iraq! Liberating Iraq!
Killing an unborn child! Ending a pregnancy!

Well Which is it?
- It' all about framing the issue.
Politics in the United States has boiled down to who promotes the shortest most powerful sound bite. If we are going to avoid a collapse the likes of the Roman, Ottoman, or the Persian empires we have got to be willing to use reason above and beyond party lines. Reason is a unifying force that needs to be reclaimed with a vengeance. Though politicians are guilty of the empty rhetoric that has stuck us in the mire of partisanship, much of the blame must be shouldered by a complacent citizenry. Below Steven Pinker gives us some insight into why.





As I've said before, the financial crisis is a great place to start coming together. There are no clear party politics surrounding this crisis because the damage caused by this affects us all. It is fitting that Americans need go little further than their currency for wisdom regarding this mess.

E PLURIBUS UNUM! Indeed!

On an unlikely stage a Rhodes scholar holds up the candle of reason and begins the end of the culture wars.

Matthew 25 Network

A women's right to abort pregnancy is a fundamental right. I support this fundamental right! I will be voting NO on Colorado's Amendment 48! Amendment 48 is an attempt to change the legal definition of a person.

I must preface my next thoughts by acknowledging that I am about to be guilty of engaging in a series of broad generalizations, so that I might make a point. Even if you find these generalizations to be disagreeable, I ask that you please continue reading. I have encountered many pro-lifers who are close-minded hypocrites that lack the ability of consideration and simply regurgitate religious teachings "without flinching." Many pro-lifers that sound the murder drum and make a stance of supporting the UNBORN, are often the same people that do nothing to support those BORN into challenging situations themselves and do not support legislation that would help families in challenging situations (i.e. the same people that vote republican). That being said, I have struggled to find many exceptions, let alone a massive movement of exception. The exceptions have now stepped forward.

At a time when America is increasingly polarized on so many issues such as this, and a great majority of American citizens choose to either strictly adhere to party lines or to ignore politics altogether, I have discovered a political action committee that is a breath of fresh air. Check out this group's stance on abortion and more importantly the manner in which they are approaching their cause at the link above.

Before you judge this group, I urge you to PLEASE rise above the talking points of pro-life and pro-choice, regardless of your stance, and make a genuine effort to employ reasoning. Please hear this group out by visiting their website at the Matthew 25 Network and learn more about them! They are a pro-life, pro-Obama committee that understands that overturning Roe vs Wade would be very dangerous and that the legal status of abortions would not impact abortion rates. This committee is backing Barack Obama because of his policies that will provide support for women and families, provide affordable healthcare for every American and help the impoverished (i.e. policies that will encourage alternatives to abortions in a non-invasive way that preserves a women's right to choose)!

I commend this group for their efforts, their cause and their couragesness. Regardless of their personal religious beliefs, this group is stepping up to help their brothers and sisters, their neighbors, their country. This is an independent political action committee that will be "targeting Christian voters on Christian radio stations with a Christian message." While I may not agree with this group from a religious standpoint, I have a great respect for the manner in which they are approaching their cause. Most importantly, this group understands that Barack Obama is the best choice for America. For the sake of America's future, may the Matthew 25 Network convince many in their target audience of this same conclusion.

REMembering in Sleep

In his seminal book "The Interpretation of Dreams", Freud toyed with the meaning of dreams and because of his work, we will never look at cigars the same way (we could also thank William Clinton for that). Yet despite his influence, Freud largely missed the mark because he could not see inside the "black box" of the mind. But we can. This blog is about what happens when we dream.

Dreaming, in humans, largely occurs during two periods of sleep: during slow-wave sleep (SWS) and during rapid-eye movement (REM) sleep. These two periods of the sleep cycle are also present in rats, birds, and monkeys, but I am not going to try to convince you that they dream the same way we do. It is enough to know that what occurs in our brains during these two stages of sleep also occurs in theirs (both at the level of single-cell recordings and EEG). (However, if you have a dog, you might swear that he's chased a squirrel or two in dreamworld)

In order to understand what happens inside a rat's brain during sleep, it is necessary to first understand what happens when they're awake, specifically when they are learning. In a brain region known as the hippocampus (part of Sagan's reptilian brain), unique cells called "place-cells" respond to unique spatial positions, much like how road signs indicate your position in a city.

To understand this better, imagine a linear track in which a rat can navigate. While the rat is navigating, unique place-cells will respond at specific positions on the track. Place-cell A might respond best when the rat is at the left-most edge of the track and not respond at any other position on that track. Place-cell B, on the other hand, might respond to the right-most edge of the track, but will fail to respond to other positions. Other place-cells would respond to regions in the middle of the track and so forth; in the end, a complete "map" of the rat's running could be reconstructed from all place-cell-responses. If the rat were running left-to-right on the track, place-cell A would respond first, followed by other place-cells (in the middle of the track), and finally end with place-cell B. We will identify these particular sequences of place-cell-responses as "temporal-sequences".

Temporal sequences are not intrinsically generated and require training to learn and memorize them. That is, before entering the linear-track, place-cell A would not even have a position-preference. However, after running the linear-track, place-cell A would NOW respond only to the left-most edge of the track, and this position-specificity can be retained for days. In the end, the temporal-pattern of place-cell-responses acts as a unique memory trace.

Now, back to the original idea. During slow-wave sleep (SWS) and REM sleep, these memory traces (ie: temporal sequences) are replayed in the hippocampus (as the rat lays motionless). Even more amazing, temporal sequences of cell-activity are also replayed in other brain regions such as the visual cortex and the prefrontal cortex (responsible for converting memories from the short-term to the very-long-term). The point is that sleep-related replay is observed in various and distinct brain regions, and the playback is coordinated between these regions.

A Hebbian paradigm of learning endorses a use-it-or-lose-it model of long-term learning and sleep-related replay has been suggested as a method for "using it". Neurologically, sleep-related replay is not very different from mental-rehearsal when awake. These "activities" have been suggested to facilitate the conversion of short-lived memories to long-lived ones.

If you think humans are exceptional to rats in this, you'd be wrong. Sleep-related memory-replay has also been observed in humans (epilepsy patients with deep-brain electrodes), and even more, memory-recall is better for subjects allowed to experience SWS or REM sleep than subjects who are prevented.

So, sleep well readers. You might have learned something.

Igniting Passion for Free Press, Advocacy and Activism.

Last September the Colorado State University school newspaper, The Rocky Mountain Collegian, ran an editorial with a heading that garnered immediate national attention. Ultimately, the editorial heading resulted in many citizens calling for the editor-in-chief of the Collegian to resign and others signing a petition urging that the editor-in-chief be fired. In the spirit of advocacy and activism, I would like to reference you to a blog account of Kristopher Hite's thoughts on his experience with this situation.

The photo of Kristopher Hite shown above, engaging in debate with the college republicans student group, appeared in the Rocky Mountain News on September 27, 2007 with a story entitled "300 at CSU urge firing of editor."  It is from this experience that our blog, Tom Paine's Ghost, would be born.

Biological Politics

Perusing the vender booths at the annual sustainable living fair here in Fort Collins, CO a few weeks ago I came across a quote that still resonates in my head.

"It is not the strongest of the species that survives, nor the most intelligent that survives. It is the one that is the most adaptable to change."

- Charles Darwin

Improving nature's design?

This morning I came across a ScienceDaily article online highlighting the potential dangers of consuming green-tea supplements.  In extreme excess the normally protective compounds found in green tea were reported to result in liver, kidney, and intestinal toxicity.  There is a large body of evidence suggesting a positive correlation between green tea catechins and cardiovascular health, as well as many other health benefits.

It is very hard to improve on what nature has to offer with respect to diet and perhaps many other areas of human endeavour.  A simple cup, or even 5 cups, of green or white tea a day would provide all of the benefits without any risk.  In preparing a concentrated green tea supplement, the human animal has failed to improve on nature's design. Earth is the greatest and most glorious biological experiment of which I am aware. We should try to learn from this experiment as much as possible.  Today's lesson, dosage!

As a biological scientist, I am amazed at the the fragility and resiliency of life, often times in the same instance. If we fixate on either of these characteristics of life, we will become susceptible to the other. Life is abound with apparent contradictions. Oxygen enables life on earth, it is also the reason why we age and often why we die. Biological compounds that inhibit cancer and are often essential to biological functions, actually promote cancer at high doses in many cases. The balance of contradiction is important from both a biological and a philosophical standpoint.  As a moderate extremist, this is as much a blog to myself as it is a reflection of an important idea.

Live From New York it's Thursday Night

Our generation doesn't watch TV on TV anymore so I missed the fact that SNL was actually broadcast live on Thursday this week. McCain walking around aimlessly in front of the camera was also pointed out by Jon Stewart this week.

"No Ma'am" - John McCain

When your campaign asserts that Senator Obama "pals around with terrorists," this is the type of poison you harvest. If the last 8 years has taught us anything it should be that living in fear does not work for America. Freedom includes freedom from fear. Refuse to be made afraid!!! Listen to John McCain, Barack Obama is a good man.

Obama/McCain Income Tax Proposals Compared

Here are the Obama and McCain income tax policy proposals side by side, according to the Tax Policy Center, a joint project of the Urban Institute and the Brookings Institution, as published in the Washington Post. Check out the striking differences between the two proposals!

Notice that the bottom 3 tax classifications represent 60% of all taxpayers. While the top 2 classifications represent 1.1% of all taxpayers. Under John McCain's tax plan, the citizens who are in dire need of income tax breaks and would benefit the most from them, would not receive significant income tax reductions.

Fun with Google

As someone very intellegent pointed out to me the "b" and the "s" keys are not even close to each other on a keyboard.

In light of the recent news that hundreds of absentee ballots were sent out to voters in New York State's Rensselaer County reading "Barack Osama" I did a little exercise. I typed the question "Is Barack Obama muslim?" into the Google search engine. I'm glad to see that some very smart people wrote a very concise web page explaining this. Here is the top hit if you don't feel like doing it yourself.

For those of you who missed episode 14

I think I know why this one wasn't there...

see the rest here

Something From Nothing

Behold! A Beautifully Bountiful Beta Barrel

Green Fluorescent Protein - The discovery and development of this biochemical flashlight was awarded the Nobel prize in chemistry this week. Three great brains were awarded the Nobel for GFP, Osamu Shimomura, Martin Chalfie and Roger Tsien.


Osamu Shimomura (Woods Hole, Mass) - First isolated the protein from the outer bell of the crystal jellyfish in Washinton state in 1962.


Martin Chalfie (Columbia) - First used GFP to tag a protein in a living system (the model organism c. elegans). This method of tagging recombinant proteins then observing them is cells and whole organisms has become one of the most common techniques in bio-medical research.


Roger Tsien (UC San Diego) - Developed a whole rainbow of fluorescent proteins. This allows multiple proteins to be tagged at once and distinguished in living systems.

The observations made possible by the advent of GFP as a molecular candle are by all means amazing and good. However, I could not help but cringe when I saw the picture below of two adolescent Macaque primates who had been genetically modified with a bad Huntington's disease gene tagged with GFP. This image was published in a research paper in the Journal Nature - spring 2008. This represents an image issue science has had since the late 20th century as socially irresponsible.

Thoughts on Kristopher Hite's "Healthful Incentive"

I would like to extend the "genetic versus environment" consideration and the idea of genetic determinism philosophically. I think destiny and choice are really one in the same :-) I don't think the idea of destiny weakens choice, I think destiny empowers it.

Dr. David Servan-Schreiber makes a great point about the impact of habits and environmental conditions on cancer. Unarguably, these two variables are major determinants for cancer risk. I would argue that there is a genetic component to habituation and that on an evolutionary timescale genetics "impacts" specific environmental conditions where individuals find themselves, the converse scenarios would also be true.

In regard to people with the realization that lifestyle changes (diet, exercise, etc.) will greatly reduce their risk of cancer, some will make significant changes in their lives, while others will not! Why? Whether by choice or destiny the outcomes are the same. Scientists are trained in and often focused on the mindset of how not why! Again, are these really one in the same?

Habits are interesting beasties. They impact our lives more than most will ever know. Habits affect the way we think and the way our life will "go." I make a point to recognize my habits so that I can change things up as frequently as possible. An awareness of our habits and their deconstruction stimulates the brain, opens the mind to new perspectives and is very refreshing.

Cheers to stimulating Thursday afternoon blog posts :-)

USA is Saudi Arabia of Wind Power.

Too good to be true? Maybe, but maybe not. Read more about it here.
I like this "plan" and I hope we can make this our new Manifest Destiny. An energy infrastructure conversion as our means for emerging form this depression sure sounds a lot more peaceful than what got us out of the last one.

Tao Te Ching: Chapter 71

Written in the 6th century B.C. by Lao Tsu with three English translations show here.

Chapter 71:

Not-knowing is true knowledge.
Presuming to know is a disease.
First realize that you are sick;
then you can move toward health.
The Master is her own physician.
She has healed herself of all knowing.
Thus she is truly whole.


Knowing ignorance is strength.
Ignoring knowledge is sickness.
If one is sick of sickness, then one is not sick.
The sage is not sick because he is sick of sickness.
Therefore he is not sick.


To know and yet think we do not know is the highest attainment; not to know and yet think we do know is a disease.
It is simply by being pained at the thought of having this disease that we are preserved from it.
The sage has not the disease. He knows the pain that would be inseparable from it, and therefore he does not have it.

Healthful Incentive

As a fan of Steven Pinker I have come to appreciate his supposition that personality is mostly determined by genetics. He argues convincingly against the idea of the "Tabula Rasa" or the blank slate when it comes to perceiving newborns. He argues that a person's genetic makeup automatically provides them with a pre-programed set of potentials (in the form of wired neural networks), that the environment then acts on to form overall personality. The point is best illustrated in studies of twins separated at birth who share uncanny personality traits even when they have never met. This is illustrated in the above cartoon by Charles Addams. After reading Pinker's book "The Blank Slate: The Modern Denial of Human Nature" I was convinced of this assertion. As I am still. However, it is dangerous to extend this way of thinking to all facets of human life. It perpetuates the chilling echoes of eugenics and gives people the hopeless feeling of being stuck in a world of genetic determinism.

This is not the case with many ways in which our phenotypes brush up against the outside world. I had this realization in two waves over the past 24 hours. First as I watched a man who had spent the last 8 years weighing over 300 pounds loose 180 pounds in a matter of a few months on the show the biggest loser, and second when I read this article about how the cancer epidemic in the west might be curbed by lifestyle changes. The most powerful message in this article is that genes people are born with only affect 15% or fewer instances of cancer. By changing our lifestyles we can dramatically lower our risk of cancer.

Dr. David Servan-Schreiber: "The most recent studies show that: 15 percent at most of all cancers are due to genetic factors - and only partially. Eighty-five percent are not. Nonetheless, cancer strikes families: a notable study published in the New England Journal of Medicine showed that children adopted at birth who were born of parents who died of cancer before age 50 presented the same level of cancer risks as their adoptive - not their biological - parents. What is transmitted from generation to generation are habits and environmental conditions. Not the genes responsible for cancer."

A Vastly More Articulate Sarah

Recently I also wanted to have one of those old giant wooden radios and listen to a friendly voice explain all this complicated Banking hullabaloo in terms I could understand. Here is the closest I could get. The take home message is - DON'T PANIC!!!

"And that Spirit of Prophecy, Also" - Sarah Palin.

When the going gets tough... Laugh

White & Nerdy from waymoby on Vimeo.

Flippin' Hilarious

The Great Schlep from The Great Schlep on Vimeo.

Everything is going to be OK... But it's not.

Thanks for the heads up on this one Rob!

Debate Simulcast

Highlights -
As an example of "wasteful" government spending McCain cites Obama's request for federal money to repair a Chicago planetarium's overhead projector. In other words he thinks talking about about this --->
is important enough to mention when the economy is "cratering." This speaks to how out of touch McCain is with the world outside the bubble of his 7 houses. Also, I see it as ironically metaphorical that he talks about a science museum's overhead projector with disdain. This is a tool of education - a light - an instrument of understanding. You know, the type of thing Bush and McCain fear the most. If McCain and Palin are elected we might have it taught in public schools that the earth is 6,000 years old. Kids don't need planetariums, because if they knew how many light-years wide our galaxy is their brains would explode from confusion.

McCain on Obama's nuclear policy - "He said it had to be safe... or somethin like that."

(I'm paraphrasing in all quotes below )

On Science...
McCain - "Government research projects should be turned over to the private sector."
Obama - "The computer was invented within a government research project."

On Health Care...
McCain - "If Obama's health care plan passes he will fine struggling single moms struggling to insure their kids."
again using fear to take a jab at Obama's character.
"I don't know but I may need hair plugs."
yeah I'm sure the people at serious health risk because of the state of
health care in the US were rolling around on the floor at that one.

On Foreign Policy...
McCain - Trying to quote Teddy Roosevelt - "Talk softly and carry a big stick"
Obama - Softly correcting him "SPEAK Softly" - This is the actual verb Teddy used.

The Gloves Are Off

In the following montage put together by the Talking Points Memo Blog, the sweeping arms of the GOP draw on doubt about Barack Obama's character. The seeds of doubt were first sewn in the slanderous e-mails that passed around the country a little over a year ago. Remember that e-mail you got from your cousin or your aunt that accused Obama of being unpatriotic, Muslim, and refusing to say the pledge of allegiance, or swear into office on a bible? Those were all patent falsehoods that infected the minds of countless Americans. Now, the attack dogs are out in full force. To me, they are just exposing themselves as the combative hawks they have become under the delusional world of the George W. Bush administration. Like the greedy investment bankers selling off their stocks to the demise of the rest of the market, these political pit bulls are squandering what little character they have left at a cost to their party. The way they repeat the name "Bill Ayers" comes across with the rhythm of a battle drum for a McCain campaign loosing ground. As I watched this I thought I recognized representative Blackburn from Tennessee. Then I remembered were I had heard her voice before. See the second video below for a testament to Rep. Blackburn's priorities.

Fractals in Your Frappuccino

When the Rabbi pours the milk into the coffee we witness a fractal pattern emerge. Researchers at Kyushu university in Japan recently described that pattern mathematically. The spirals are caused by a battle between gravity and surface tension that plays out at the boundary between the two liquids. Read more in the most recent issue of Nature.

Ideas Worth Spreading

Though the talk below by Jonathan Haidt is the most germane to recent posts there are several talks posted at the TED (Technology entertainment design) website worth viewing. Topping my list are

1.) Hans Rosling - The best stats you've ever seen
2.) Blaise Aguera y Arcas: Jaw-dropping Photosynth demo
3.) Jeff Han - Unveiling the genius of multi-touch interface design
4.) Steven Pinker - Chalking it up to the blank slate

An abundance of oil dulls the imagination

This thought came to me as I perused the pages of this popular science magazine from 1919. This fascinating set of blog posts shows that science magazines have had many iterations of the same sensational ideas pass through them over the generations. It seams that when we all know what we will use to fuel our means of transportation we don't really care how things work but rather that they work at all. When there is a dearth, centuries old ideas well up once again as in the article on "Electricity from wind and waves."

OK... Let's talk about relevant track records.

What Would a Maverick Do?

O'BAMA and his Mama - It's All in the Genes

Meet Obama's family starting with his mom - Anne Dunham (her first name was actually Stanley after her father - he obviously wanted a boy) I can see the resemblance in Anne's chin ears and lips.
Some other twinkling lights on this family tree include Barack's great great great grandfather Falmouth Kearny, an Irish Farmer that settled in Indiana after escaping Ireland's Potato blight, and the Frenchman Mareen Duvall. The later genetically links Barack to President Harry Truman and Vice President Dick Cheney. Barack and Dick are 9th cousins three times removed if you can believe it. The other interesting thing about Barack's family tree is the extent and depth of its American roots. There are records of his ancestry back to 1694 within the United States, and several of his male ancestors fought in the Revolutionary War. How dare Sarah Palin tell voters that this dyed in the wool American "pals around with terrorists." Go back to Alaska (the 47th most populous state in the Union by the way).

Brian Williams stays neutral on Letterman

I don't know... you don't know... and no man or woman who is, was, or ever will be knows.

President George W. Bush has said that the United States is engaged in a battle between good and evil. Many faithful people have agreed. My question is; how can the battle end without massive bloodshed? Only when we collectively realize that the real battle is not between good and evil, but between reason and irrationality. The end to this battle starts in United States by having reasonable discussions with our fellow Americans. The only sustainable manner in which to secure and defend the United States is to raise generations of rational citizens who value logic above emotion in the face of adversity.

When enemies in a conflict are painted as inhuman evil doers it lets a warrior feel less about killing them. In order to acquire more resources and therefore more power, empires need warriors that won't have psychological qualms with killing people. Portraying enemies as pure evil helps deal with these qualms. Terrorists attacks and retaliatory military responses are the violent manifestation of the "battle between god and evil." The men that committed both suicide and mass homicide on September 11th 2001 were poisoned by the delusion that they would be rewarded in the afterlife with their scriptural promises of virgins in heaven because, in their eyes, their deaths were honorable as they were carrying out jihad against the infidel. A Christian warrior in the Middle East in 2008 filled with the idea that his or her actions there will be rewarded in the afterlife is affected by the same delusion.

Thomas Paine was mocked by his contemporaries and later called a “dirty little atheist” by Theodore Roosevelt (I tend to like Teddy in general, but I think he got this one wrong). The fact is that Thomas Paine was not an atheist. None of the founding fathers were. They like many Renaissance people before them knew that certainty marks the beginning of the end of empires. They were deists who derive the existence and nature of God from reason, and refuted claims of supernatural events such as those described in the scripture of all holy books. They did not set out to found an American Empire, but rather a new order of the ages. "Novus Ordo Seclorum" as is enunciated in the great seal of the United States. A new world order in which freedom and equality are the foundation of a government empowered by the people, not nobility and not theocracy. Certainty comes from dogma and many churches survive and thrive among generations of other dying cultural trends because of the ease and comfort it gives the faithful. There is no need to think about issues if what is right and wrong has already been decided for you by a church. Certainty is what blinds fanatics. Certainty let the middle ages hinder centuries of scientific progress. Certainty put Galileo in house arrest. Certainty burned nearly all of Gregor Mendel's scientific works. Certainty caused the Holocaust.

In 2008 Americans need to choose knowledge over certainty more than ever. As we watch our sea levels rise, our population outpace our food production, and our children go on 21st century holy wars, we stand at a tipping point between a sustainable future and a self-fulfilling prophecy of anthropogenic end-times.

As a American who has watched the debate set aflame between atheists and the faithful during the past decade I have to agree with Bill Maher more than I do Richard Dawkins (as much as that pains me as a scientist). When the idea of "God" can have as many different meanings as there are sentient beings on earth then it is pointless to go on a secular crusade against that amorphous blob, that continuum of changing perceptions. It is much more effective to attack the root of self righteousness. It is more effective to tackle certainty. To introduce skepticism. The most glistening example I can think of from recoded history is the story of Johannes Kepler. From faithful follower of the gospels of Christ to someone who saw the imperfections in the heavens and was able to explain them with a scientific theory. These should be the bedtime stories we read our children. The stories of discovery. Certainty precludes hope from earthly life, while the unknown provides an infinity of potential discoveries. Skepticism and doubt are prerequisites for freedom, without these tools freedom is just another word.

What Happened?!?

Clean Water Action

I am now a supporting member of the Clean Water Action citizen's organization with my small but meaningful donation.  CWA fights for sound water policy that encourages conservation and other cost effective alternatives which seek to protect watersheds and the environment.  CWA contributes an impressive 70.1 % of donations towards program expenses to protect America's water. Apathy is weakening this great country of ours.  Find something you care about and get involved, become an activist!

The Kitchen Garden

"You can fix all the world's problems in a garden!"
Geoff Lawton

Biden = Human Being... Palin = Plastic Parrot

Shame on you America!

The vice presidential candidate debate, or debacle last night was a complete mockery of the US political system. I am absolutely amazed that Sarah Palin is actually a vice presidential candidate. While this complete failure of a debate reinforced my hope that Barack Obama and Joe Biden will emerge victorious on Tuesday November 4th, it actually made me ashamed to be a citizen of this great country. Is this the best the US political system is capable of? It is very clear who dominated this "debate," it is also very clear that there was only one legitimate participant. Sarah Palin simply avoided the moderator's questions most of the time and the moderator made no attempt to "moderate" the debate in this respect. What is the point of even asking a question if Sarah Palin is allowed to talk about whatever she pleases? It is completely absurd that last night's showing was passed off as a debate! Even in her "topic of choice speeches," Sarah Palin struggled to display the ability to formulate any rational thought and seemed capable of merely tossing out buzz words, often times in a completely incoherent manner. This is certainly not an isolated incident, check out the poetry of Sarah Palin. Human nature may have many of us laugh at her comments, when it may actually be more appropriate to cry. Check out the treatment of Sarah Palin's logic and decor in this New Yorker article by George Saunders. Very laughable, until you realize this is a vice presidential candidate of THE UNITED STATES of AMERICA, then the shame sets in. America!? You are ignorant by choice! Please wake up from your slumber!

Neurobiology of Stress

This documentary is a collaboration between Stanford University and National Geographic. Two startling conclusions are made in the film: acute stress can actually shrink neurons in the hippocampus, and people with chronic exposure to stress can remediate the physiological effects by having social meetings where they can vent and talk about their angst. More information here. Check if the documentary is playing on your local PBS station here.

How Does a Namibian Fog Basking Beetle get Water?

This miraculous creature is capable of harvesting moisture in the desert air by condensing H₂0 on its abdomen then tilting his body towards his mouth when he needs a drink. I first heard about this
here. One of the fellas you hear in the BBC podcast is Michael Pawlyn, not to be confused with Michael Pollen (One of my favorite contemporary writers). The British Michael can be seen in the video below sharing some more insight into the logic of biomimicry. Enjoy!

Architectural Biomimicry

As the old adage goes "Form Follows Function." In the case of green buildings our cities might be the more beautiful for it. The "treescraper" pictured below is a glistening example.

Going Big

This edition of "This American Life" is both extremely inspiring and informative. Truly a brain stimulator!

BBC special narrated by Richard Dawkins: The Genius of Charles Darwin

Remember Miss South Carolina 2007?