Wednesday, September 30, 2009

David Sloan Wilson wants to bury a bad idea

To me Wilson is  most poignant with this remark.
"Evolution helps explain all behaviors. The idea that evolution explains selfishness well and altruism poorly is so dead that it is beginning to smell. Can we please bury it now? Evolution explains the full range of behaviors, from extreme selfishness to extreme altruism. What evolves in any particular case depends upon the underlying environmental conditions, which are fairly well specified by now. No one should be surprised anymore by the raw fact that kindness exists in nature. The frontier of science has moved on to a more refined set of questions."
With this in mind I think it still possible to move forward with the argument that it behooves humanity to learn from successful survival strategies in nature if we hope to achieve actual sustainability in terms of current  global zoological/botanical survival. Humans avoiding extinction by helping each other and our phylogenetic cousins avoid extinction as well.

Tuesday, September 29, 2009

Monk's Hood in the Morning

Monk's Hood - aka wolfsbane, Devil's helmet, or blue rocket on display on the big south trail along the Poudre River.

Blogging Brings Life to Biology Class

Stacey Baker, a high school biology teacher on Staten Island, New York is using the internet in an extreme way to make science exciting for her students and the rest of the world. Brilliant!

A pupil of Ms. Baker informs us about transpiration!

Monday, September 28, 2009

The "Theorum" of Evolution

By Kristopher Hite

Within the first pages of Richard Dawkins' newest book - The Greatest Show on Earth; the evidence for evolution the author continues on his life-long spree of neologisms by coining a new term for expressing the concept of evolution. Dawkins proposes a change from calling it the "theory of evolution" to the "theorum of evolution." This is not to be confused with a mathematical THEOREM spelled with an e but is chosen to give a more specific slant and weight to a particular meaning of the word "theory" in the context of evolution. This particular meaning being a systematic set of ideas that account for a body of facts. Dawkins is trying to provide the lexicon with a word that differentiates the meaning provided in the last sentence from the secondary definition of the word "theory" which is a "speculative conjecture, or idea" giving the impression that, used in this sense, an idea is merely a concept or "only a theory." This second definition is often used by intelligent design proponents to basically give the false impression that the concept of evolution has not been proven.

Well it has, and the most stark evidence for descent with modification driven by natural selection that chemical biology can currently provide lies in the genetic code. Comparing sequences of DNA we are able to see that certain sequences match and others partially match in mammoths and mice, frogs and dogs, and in some genes even humans and plants. We can see in the code what is known as molecular phylogeny. We see in matching strings of As Ts Gs and Cs that every organism is living at the tip of a theoretical branch in an ancient tree of life with a central trunk from which we all descended through countless generations of successfully prolific ancestors. To give an example, the genes that dictate the human body plan (Hox genes) are also present in all major branches in the "animal" part of the tree. It has been shown by comparative molecular phylogenetic analysis that these genes arose before the Cambrian explosion about 530 million years before any kind of hominid creature roamed the earth.

Great, but why should we care? Why should anyone not making their living in a biologically inclined academic setting need to understand the "theorum" of evolution?

Humans are uniquely positioned in the animal kingdom to predict and outmaneuver the inherent screening process that normally facilitates natural selection among all other organisms. On a single person scale, I myself would not be alive today were it not for the maneuvering of medical technology. When I was born I inhaled part of the afterbirth and had to have my lungs pumped right away. On a global scale, the natural selection screen of limited fossil fuels is rapidly approaching and regardless of your thoughts on the evidence for global climate change, survival in the face of resource depletion requires that we understand how evolution by natural selection works if we hope to overcome and outsmart the brutality of resource wars.

In the above movie when I talk of a "peaceful survival strategy" being the most successful. I should qualify that further by saying a cooperative and empathetic strategy will out-compete a selfish and aggressive strategy. This is demonstrated by the algorithms of Robert Axelrod explained in great detail in the later chapters the Selfish Gene while the parameters of those strategies are further explored in this paper.

Serendipitously, in a review (which I had not read until after composing this post) of the new book The Age of Empathy by Frans De Waal some of the concepts that I just mentioned are fleshed out even more. The review was aptly titled Survival of the Kindest and apperaerd in SEED magazine last week.  Check it out for yourself.

This post has been submitted to the NESCent competition for a travel award for the ScienceOnline 2010 un-conference in Durham, NC, January 14‐17th, 2010.

To the Judges. I realize that this post is less than the 750 word minimum set as a standard by the competition, but I would argue that because of the video the post actually far exceeds 750 words. there is no specification in the rules that the 750 words had to be all in written format.

Axelrod, R., & Dion, D. (1988). The Further Evolution of Cooperation Science, 242 (4884), 1385-1390 DOI: 10.1126/science.242.4884.1385
Gehring WJ, Kloter U, & Suga H (2009). Evolution of the Hox gene complex from an evolutionary ground state. Current topics in developmental biology, 88, 35-61 PMID: 19651301

Sunday, September 27, 2009

Legacy of Darwin - Intelligent Design Conference

This Halloween the shepherd project in cooperation with focus on the family and the discovery institute is putting on a forum on intelligent design - The Legacy of Darwin Intelligent Design Conference in Castle Rock, Colorado. As we Coloradans brace to be descended upon by a slew of intelligent design (ID) proponents the following debate recorded at Seton Hall in 1997 contains two of the ID figureheads that are coming (Behe, Berlinski) and is worth review. Ken Miller's introduction provides a wonderfully concise set of points that have yet to be refuted and continue to defend the concept of descent with modification in American courts!

Friday, September 25, 2009

HIV Vaccine

By now you have probably heard the news.  HIV has been cured.  Well not quite but there are some promising results. In a press release put out by the NIH modest preventative effects were reported according to a clinical study done in Thailand funded by the NIH.

Cutting to the chase, the results are as follows: 74 of 8,198 people who received placebo shots became infected, while 51 of the 8,197 people who received the vaccine did not. It can be inferred from these results that the risk of being infected with HIV was reduced by 31% because of the vaccine. Though the numbers are significant and the test group is gigantic random effects can not be ruled out in explaining the difference of 23 individuals between placebo and vaccinated test groups. Cautious optimism is advisable however.

I've watched this story unfold in the mainstream with FOX just putting up the headline "Breakthrough" with a graphic of a syringe, more tempered coverage has come from CNN, but THE BEST coverage of this story comes from a top-notch radio program airing on BBC4 - Material World with Quentin Cooper. I don't think there is a quicker wit on the airways anywhere on the planet. Either Quentin has an amazing team of writers or he himself is gifted with an incredible talent for come backs and other lightning fast witticisms. Check out the entire program here. The following clip from WSJ is also a descent source on this story.

Speaking of Pollan

Today I had a Michael Pollan inspired lunch. Spinach salad with full-fat feta a tiny bit of cut smoked salmon, walnuts, and raisins dressed with balsamic vinaigrette. Trying to follow the guidelines in his In Defense of Food. All ingredients were purchased in bulk from King Soopers, NOT WHOLE FOODS, and many items were on sale including a 1 lb container of baby spinich for US $2.99 that has lasted me all week!

Thursday, September 24, 2009

The Botany of Desire

Catch the whole episode Wednesday, October 28th on your local PBS station.

Wednesday, September 23, 2009

Swimming in Ethanol's Ethos

The Arizona Chemical wood pulp mill in Panama City, Florida sits within a stone's throw of the Gulf of Mexico.

Hey there TPG readers, CHECK THIS OUT!!! This article has been translated to Hatian Creole.  I am both flattered and impressed at this unsolicited dissemination of TPG material. Quite cool :)

By Kristopher Hite

Walking on a balance beam, the idea of ethanol powering America's future took a shove from the scientific community this week. A new study published in the Journal of Environmental Science and Technology indicates that no matter the starting material whether it be corn kernels or wood chips, switch grass, and corn stover (all forms of cellulose), the environmental impacts of more ethanol, and other so called biofuels, in the gas tanks of America will mean increased environmental damage. Specifically, this study discusses the expanding "dead zone" in the Gulf of Mexico. Nutrient run-off from increased farm fertilizers being applied to crops throughout the Midwestern United States will drain into the gulf and cause larger algal blooms. This, in turn, will rob the water of dissolved oxygen killing fish, crustaceans, and other gulf-water inhabitants.

Here we have a case of clashing federal mandates. The EPA has required that steps be taken to reduce the size of the Gulf's dead zone while congress passed the Energy Independence and Security Act (EISA) in 2007 which requires the production of 36 billion gallons of biofuels by 2022. These two orders just will not jive with current agricultural practices.

Multinational biofuel manufactures are sitting pretty with the current federal mandate written in the fine print of the EISA but the citizenry need access to the knowledge buried in this recent paper to hold these companies accountable for the their potential environmental impacts. To the credit of cellulose-derived ethanol the amount of nutrients running off into the gulf would be reduced by 20% if all ethanol were to be derived from cellulose vs. corn. But either scenario will undoubtedly kill more organisms living in the gulf and increase the area of the dead zone.

Ethanol as a fuel source for transportation, home heating, and industry continues to be a double edged sword. After taking flack for driving up tortilla prices in Mexico there was a shift to talking up cellulosic ethanol in lieu of corn ethanol, but with evidence like this being presented it makes the process a harder sell. But who needs to make a sale when you've already made a long term deal with the feds?

From an applied research side I am encouraged to seek out the cutting edge of cellulosic ethanol manufacturing technology so that mandated production is done in the least wasteful way. This research lays inside fungal genomes. Scientists continue improving enzymes produced by millions of years of evolution by tweaking the amino acid sequences and increasing efficiency and stability of some very useful enzymes, in the case of deriving ethanol from the woody parts of plants (cellulose) these enzymes are called cellulases. They break down the long chains of linked sugars that constitute cellulose. By manually changing the single amino acids and then testing thermal stability and conversion efficiency scientists are able to make the process of ethanol production more efficient. Recent research in the Journal of Biochemistry reports this process in action. By demonstrating that single amino acid substitutions, in the context of a chain of hundreds of amino acids, can stabilize enzymes dramatically a group from Cal-Tech proves that human manipulation of genes can, in fact, improve the efficiency of our transition to a home-grown renewable energy economy. The Carnot's and Tesla's of this age are hard at work at this biochemical frontier.

I am torn on this issue as I can see two futures coming of all this. One in which we have attained energy independence and are free to refine our energy equilibrium to the point of balance with the ecosystems in which we live. Or the other where our environment has completely eroded and we have no choice but to fight amongst each other for the scant resources still available. The technologist in me says "onward" while the environmentalist says "onward, but mindfully." In either scenario the ideal of efficiency is a positive one that can be easily applied locally by individuals adopting more mindful habits.

Note:  This blog post was picked up by an editor at SEED magazine and turned into and e-cover story - The Dead Zone Dilemma.   In this article Dave Munger questions my optimism and my advocacy as a scientist. In so doing he is questioning some basic tenets of scientific inquiry.

He asks - "Shouldn’t scientists just be interested in giving us the facts, staying removed from policy decisions and letting the general public and politicians decide how to act? Doesn’t becoming an advocate introduce bias into the scientific process, potentially tarnishing results?"

After contemplating these questions I responded in a post titled "Should Scientists Speak their Minds?"

Stumble Upon Toolbar

Heinzelman, P., Snow, C., Smith, M., Yu, X., Kannan, A., Boulware, K., Villalobos, A., Govindarajan, S., Minshull, J., & Arnold, F. (2009). SCHEMA Recombination of a Fungal Cellulase Uncovers a Single Mutation That Contributes Markedly to Stability Journal of Biological Chemistry, 284 (39), 26229-26233 DOI: 10.1074/jbc.C109.034058
Costello, C., Griffin, W., Landis, A., & Matthews, H. (2009). Impact of Biofuel Crop Production on the Formation of Hypoxia in the Gulf of Mexico Environmental Science & Technology DOI: 10.1021/es9011433

Evo Rap

Had to let this meme undergo a duplication event. Courtesy Pharyngula

Tuesday, September 22, 2009

Green Mountain gets deeper green

One of my favorite companies continues to impress me. Green Mounatin Roasters has finished installing a 572 panel solar power array on their plant in Waterbury, Vermont. An alliance between Green Mountain Coffee Roasters, the State of Vermont's Clean Energy Development Fund and Green Mountain Power enabled this high up-front cost project to manifest.

I'd like to see this kind of collaboration happen in my home state of Colorado. Seems like businesses and cities around here talk about being green a lot but when it comes down to getting up the solar panels or wind turbines self-interest prevails and projects get halted. From a home owner's perspective the incentives are still left to be seen. Xcel energy gives no rebates to potential and eager home owners who wish to install solar panels if there is a tree partially shading their roof! Think about the amount of sun that is hitting my roof in Colorado vs. the amount hitting this factory in Vermont or any city in Germany for that matter. And the energy tyrants at Excel have the audacity to deny subsidies because of shade trees! Drives me batty.

The case of Green Mountain Coffee is a great example to follow. Perhaps we in Colorado on the frontier of the "New Energy Economy" can learn a few things about cooperative collaboration from this company.

Read more about this at Greenbiz.

Monday, September 21, 2009

10th Annual Sustainable Living Fair

Photos by Kristopher Hite
Valet bike parking upon arrival!

Zero Hero Waste Stations

New shirt!
Need food.

Green Ride

Panda Bikes

Matter Bookstore cleans up.

Two years of Tom Paine's Ghost

By Kristopher Hite

I am writing today to celebrate two years passing since the seed of Tom Paine's Ghost was planted. Planted as my heart pounded reading the CNN coverage of a printed-word fiasco happening right here on the campus of Colorado State University in Fort Collins, Colorado. If you want to read the origin story in its entirety I spewed it out here in almost unbearable detail the day after my involvement was over.

If you want the short version I'll lay it out here.

At exactly midnight September 21st 2007 the editorial board at the Collegian Newspaper decided to publish in large font "Taser this... FUCK BUSH" on the opinion page of their student run periodical. Instantly this set ablaze a national media firestorm. Was it a breech of decorum? Yes. Rude, asinine, immature? Yes. Justified. I think so! Now that we are all lounging in Obamaland we too easily forget how George W. Bush and his cronies really did rob the entire planet of so much and in so little time. 8 years beginning centuries of conflict and making any kind of climate remediation that much more difficult.

Even though the text was profane and literally absurd it accomplished something. Four words elicited a response both positive and negative out of an otherwise complacent student body of nearly 30,000. Colorado State University and Fort Collins, Colorado for too long had enjoyed a kind of happy delusion. Being named the top place to raise a family and the number one small city to live in the United States we were running the risk of becoming completely void of personality and submitting to the corporate developers and house farms that continue to propagate to the south. The "F... Bush" editorial fiasco was like a large turd sitting in the side walk at city park. Yes it was disgusting, but we couldn't pretend it wasn't there. We could not keep pretending everything was just dandy in our country when we had a tyrant at the helm. We needed to clean that up!

For pointing this out the Editor in Chief at the Collegian - J. David McSwane - was put in the hot seat. With a petition started by the college republicans he ran the risk of loosing his job at the hands of the "board of student communication." To combat this threat I began circulating a petition to save his job. We collected several hundred more signatures in 2 days than they had in 4.

In the end he kept his job and basically got a written slap on the wrist for his breech of professionalism. A typical bureaucratic handling of free speech/free press issues by the powers-that-be seen lately in our own congress regarding the Joe Wilson outburst.

McSwane will get upset with me for saying this but I felt obligated to lend a hand in this situation after learning how he had won a Peabody award for investigative journalism while in high school. He basically shut down all army recruiting in the entire country for a week so that recruiters could have a lesson in ethics. As my best friend was, at the time, stationed in Iraq and had been recruited before this intervention I felt connected to McSwane though I had never before met him. Through his student paper he was able to change one small part of the system. This reiterates my belief that single voices can and do change the world. In fact, they are the only instruments that can.

Wells Meets Welles

Meeting of Minds

Friday, September 18, 2009

Returning the Rainbow

By Kristopher Hite

Red-Green color blindness is caused by a deficiency in opsin genes. These genes code for photoreceptor proteins positioned in the cone cells of the eye's retina. When light hits these proteins a tiny molecule buried inside the protein called retinal (aka vitamin A) changes its shape by swinging its bond angles and begins a signal transduction cascade. The signal of "red" or "green" is passed from this single "g-coupled" protein receptor along the optic nerve and eventually to the brain's visual cortex where the mind perceives the hue of that specific wavelength of light. This gene for this opsin resides on the X chromosome which means colorblindness has a higher incidence in males as females have two chances to get a good copy while men only have one.

A paper published this week in Nature describes research that essentially cured colorblindness in monkeys. This cure is miraculous because A.) it was done using gene therapy and B.) it was given to adult monkeys not monkey embryos. The researchers took a virus, inserted the corrected copy of the opsin gene into the virus' genetic material then locally injected the virus near the monkey's deficient retina where the virus proceeded to "invade" and insert the correct copy into the genomes of the retinal cells. Lo and behold, the monkeys were able to see color for the first time in their lives!

The researches say if they are able to hone the technique to where it is as safe as Lasik surgery it may one day be applied to humans. Research like this raises some questions as to enhancing our natural abilities. If we extrapolate this technique to brain proteins we need to ask some tough questions. If we knew of a gene that could make a human brain work more efficiently, thus making the individual smarter, should we allow people to have "corrected" brain genes injected? If Joe Millionaire could afford this but Joe six-pack could not should the government step in to avoid the rise of a genetic cast system paralleling the present day financial cast system? The prospect of broadly applied corrective gene therapy really is the pinnacle goal of so much bio-medical research, specifically when it comes to inborn errors of metabolism and other very clear single gene, single disease situations. But who will guide society through the slippery slope of choosing which genes are worthy of correction. Work continues on the "can we" side but I think all citizens regardless of their scientific background need to take part in the "should we" conversation. If this is not a healthy conversation I fear that very useful and beneficial gene therapy treatments will be the proverbial baby in the bathwater when the anti-GMO, anti-vaccine masses catch wind of these kind of available "treatments."

What do you think about this? Listen to the primary researcher - Jay Neitz - discuss the experiments in the following Nature podcast.

Mancuso, K., Hauswirth, W., Li, Q., Connor, T., Kuchenbecker, J., Mauck, M., Neitz, J., & Neitz, M. (2009). Gene therapy for red–green colour blindness in adult primates Nature DOI: 10.1038/nature08401

Thursday, September 17, 2009

Obama Calls a Spade a Spade

Worth 16 minutes and 24 seconds

This represents the future of film!

Wednesday, September 16, 2009

Darwin STILL to controversial for America!


This well put together Hollywood-caliber movie about the life of Charles Darwin (BORN 200 YEARS AGO) is still too controversial for the USA. According to the Telegraph "Creation" - a film about Charles Darwin - has failed to find a US distributor. Are we really that provincial? This is an OUTRAGE!

100 Years of Color

Taken in 1909 this scene along the Ostrechina river in Russia is one of many color photographs on display at the Newsweek website this week. These are some of the earliest color photographs in existence. Among the images is one of the only known color photographs of Leo Tolstoy! As we move through history the importance of outstanding recording is highlighted by these rare crisp glimpses into the past.

Tuesday, September 8, 2009

Science is Real. By They Might be Giants

Biking made easier in NYC

Caught my ear today. As a former resident of Greenwich Village I' like to think Paine would be proud.

Limeriks of Learning

Two biochemically inspired limericks by Kristopher Hite

The proteosome proceeds to forage
transforming proteins to porridge
if ubiquitin tagged
Then subsequently bagged
catabolized and placed into storage

Hec1 and Nuf2 unite
together coiled-up tight
microtubule bound
never coming unwound
to align all the chromosomes right

inspired by the following research...

Yao, T. (2000). Cyclization of Polyubiquitin by the E2-25K Ubiquitin Conjugating Enzyme Journal of Biological Chemistry, 275 (47), 36862-36868 DOI: 10.1074/jbc.M006050200

GUIMARAES, G., DONG, Y., MCEWEN, B., & DELUCA, J. (2008). Kinetochore-Microtubule Attachment Relies on the Disordered N-Terminal Tail Domain of Hec1 Current Biology, 18 (22), 1778-1784 DOI: 10.1016/j.cub.2008.08.012

Sunday, September 6, 2009

beauty in the everyday

I turned on the radio this morning to change-up my usual internet and coffee regime. After fuzzing through the noise and stopping at all the clear channels I realized all of the old media outlets (TV, radio, and newspapers) are finally and completely filled with junk. Avarice in advertising has marginalized the main-stream to the point of irrelevance. I came back to the internet by typing in scienceblogs to the "google machine" and the first thing I saw was this wonderfully zen video about the ephemeral moments that we all let go by without a second reflection. After watching I realized there is no turning back. Web 2.0 will only continue to get better and bring us people-powered content that is tailored to our unique interest-profiles. Simply beautiful.

Thanks to Bioephemera for passively passing this along.

Saturday, September 5, 2009

More Tour de Fat

Photos by Kristopher Hite

Tour de Fat 2009

Photos by Kristopher Hite.
The annual Tour de fat bike parade put on by New Belgium Brewery. Creativity galour on display at City Park in the Fort Collins, Colorado version of this carnival on wheels. Ride on!

Wednesday, September 2, 2009

Heat Moon

Took this picture from my back yard in Fort Colins, CO on Monday night. Posting it to honor the work of William Least Heat Moon, author of the book I'm currently reading Blue Highways - Journey into America.

A Lesson

Tuesday, September 1, 2009

Great Conversation

This past May as I sat in the audience at the Unity Church in Boulder, Colorado listening to Michael Pollan speak about food and the negative global impacts of cheap food for Americans I could not help but think him a bit pretentious. I do have incredible respect for his cause and his scholarly work in clearly explaining the whole story when it comes to the American food web, but asking cash-strapped regular folks to spend more on food pangs of self-righteousness.

The conversation that follows (below) provides a contrasting opinion to Pollan's but I do have to say Charlotte Allen sounds a bit too far out on the opposite slant. Her argument that the environmental problems associated with products made in China are China's problem is isolationist, selfish, and flat out juvenile. Geographical separation does not mean that our global resources/responsibilities are not shared.

Still, this conversation is one I find myself having with my own organic-food-loving friends. Right here in Fort Collins this very evening our local food co-op is having a community meeting to decide whether or not to buy into a national food co-op in order to get better prices on bulk organic products. Are we selling out to save a buck when we should be thinking about the farmers next door just scraping by as it is? In a population whose percentage of church-goers is dwindling (which I have no problem with) we have to ask ourselves as humanists where should we put our tiny bit of extra income if we have any at all that is. A convincing argument could be made to keep it as local as possible. How do we do that most effectively?