David Sloan Wilson wants to bury a bad idea

UPDATE on The "Theorum" of Evolution: David Sloan Wilson has posted a response to the review of The Age of Empathy on SEED.

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.

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!

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

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!

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!

The Botany of Desire

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

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?"

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