Wednesday, March 28, 2012
Fruiting Bodies!
Sunday, February 20, 2011
Evolution of a line
"A Sequence of Lines Consecutively Traced by Five Hundred Individuals is an online drawing tool that lets users do just one thing - trace a line. Each new user only sees the latest line drawn, and can therefore only trace this latest imperfect copy. As the line is reproduced over and over, it changes and evolves - kinks, trembling motions and errors are exaggerated through the process. A Sequence of Lines Consecutively Traced by Five Hundred Individuals was first created as a tool to be used in conjunction with Amazon’s Mechanical Turk - an online labor market. Mechanical Turk workers were paid 2 cents to trace a line."
Monday, January 31, 2011
EGYPT
~ President Barack Obama
Sunday, November 14, 2010
Wednesday, November 10, 2010
Friday, November 5, 2010
ABOUND SOLAR
He said...
"We hit the knowledge to acquire this consort and create continuance in this process. If things go substantially and business markets are cooperative, as we intend toward the latter conception of incoming year, we strength study an IPO"
If I can translate to English, I think he is saying that the technology they have developed has finally proven cost effective enough to warrant further expansion and possibly a public offering of stock. I'm not sure what language he is speaking in the last sentence but it seems positive.
The take home message? Keep your eye out for this company going public soon. Why?
Look at their biggest rival First Solar. This is what it did within the first year after going public.
$25 to over $300 a share in just over a year.
Thursday, November 4, 2010
Wednesday, October 13, 2010
BARP Goes the Weasel!

With all the other sexy and more controversial stories about evolution - Ardi, Ida and so on, why do I pick this one? Aside from my biochemical inclination I thought this little piece of biological hardware deserved more exposure. Though the paper was covered and lead author Jonathan Eisen interviewed for the nature podcast, it received relatively little coverage on the science blogs. Yes, the prolific science writer Carl Zimmer wrote a nice summary for the New York Times but the BARP bit is mentioned only briefly. I don't know if anyone realized what a great tool this discovery is to hammer even more nails in the coffin of the "irreducible complexity" argument for intelligent design.
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| actin filament |
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| (Haliangium ochraceum) |
If you asked any professor of cell biology any time prior to a year ago "Do bacteria contain a gene for actin?" they would, without hesitation, say "of course not." It was understood that the gene for actin was one that separated eukaryote from prokaryote. Bacteria have an unrelated gene - MreB - that has a scaffolding function. They don't need actin. Now it is shown that the gene for actin may have shown up in marine bacteria (specifically the one named Haliangium ochraceum) prior to the evolutionary branch-point. If this is the case it means that actin was later recruited to its now prolific function giving shape and motion to eukaryote cells. Actin was not designed then implemented like machined parts in human created contraptions. According to this research it probably appeared by chance in marine bacteria, served some other unknown function, then just happened to work later on in evolution. This, I think, is why many mechanical engineers have an aversion to studying the slimy, oozing, organic structures in nature. They are inherently messy and imperfect. This is because they are not designed! They are the result of chance events captured inside self-replicating systems - us included.
This post has been submitted to the NESCent competition for a travel award for the ScienceOnline 2011 un-conference January 13-15 in North Carolina’s Research Triangle Park.Wu, D., Hugenholtz, P., Mavromatis, K., Pukall, R., Dalin, E., Ivanova, N., Kunin, V., Goodwin, L., Wu, M., Tindall, B., Hooper, S., Pati, A., Lykidis, A., Spring, S., Anderson, I., D’haeseleer, P., Zemla, A., Singer, M., Lapidus, A., Nolan, M., Copeland, A., Han, C., Chen, F., Cheng, J., Lucas, S., Kerfeld, C., Lang, E., Gronow, S., Chain, P., Bruce, D., Rubin, E., Kyrpides, N., Klenk, H., & Eisen, J. (2009). A phylogeny-driven genomic encyclopaedia of Bacteria and Archaea Nature, 462 (7276), 1056-1060 DOI: 10.1038/nature08656
Monday, January 25, 2010
Eugenie Scott Interview
Thursday, November 5, 2009
Saturday, October 31, 2009
The Biochemistry of Halloween: Installment II
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| The moon through the cottonwood trees on the Oval at Colorado State University Photo credit - Kristopher Hite |
By Kristopher Hite updated and edited - 10/30/2025
Mothers and fathers watched the shriveled toes of a poor beggar swing from the gallows. They placed their faith in God that the death of this unfortunate person might take away the torment, fits, and visions that plagued their children. That somehow, through supernatural forces, the sensations of ants crawling underneath skin, delusions of bursting into flames, and frenzied shrieks of terror in the night would cease. As the seasons brought new harvest,s the number of swinging bodies dwindled. But bouts of bewitchment would visit the same locales for centuries.| A sclerotium of Claviceps purpurea on a wheat frond. Photo credit - Dominique Jacquin |
HUDLER, GEORGE W. Magical Mushrooms, Mischievous Molds. Princeton University Press, 1998. JSTOR, https://doi.org/10.2307/j.ctvs32r8v. Accessed 30 Oct. 2025.
Schweingruber, Fritz H., BrÄker, Otto U. & SchÄr, Ernst (1979). Dendroclimatic studies on conifers from central Europe and Great Britain Boreas, 8, 427-452
Monday, September 28, 2009
The "Theorum" of Evolution
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
Sunday, March 15, 2009
ABOUND SOLAR
The company formerly known as AVA Solar has unveiled a new name - ABOUND SOLAR.
The vision of W.S. Sampath, Abound Solar is based in Fort Collins, Colorado and is embarking on large scale production of low-cost thin-film solar panels. Dr. Sampath is as much a hero as anyone could hope to find in this world. The idea of harnessing the abundant radiant energy that bathes our planet is not a new invention; in fact within the evolution of Earth’s biosphere it is a most ancient innovation. Human-made solar panels have been around long enough that the truly awesome globe-changing promise they offer has almost been forgotten. Perhaps the most precipitous obstacle for the coming of age for solar energy has been affordability.
For over 15 years, Sampath has nurtured a vision to develop technology enabling low-cost production of thin-film solar cells. By reducing production costs, sun-derived energy will be significantly more affordable. In essence, he has fulfilled that dream and will produce solar energy at approximately $1 per Watt bringing the cost down from $13 a Watt achieved by traditional silicon solar cell systems.
The story of this company is a literal ray of sunshine in the midst of the darkest economic times our generation has ever seen. The story of Abound Solar provides great hope accompanying the promise of renewal our president likes to speak of so frequently. The impact this will have on a global scale sends shivers through my fingers. When a child can educate him/herself anywhere in the world by illuminating a book with energy from the sun, even as darkness falls democracy and free thought will prevail. As Thomas Jefferson said "where the press is free, and every man able to read, all is safe." A world full of illuminated minds is a safe world. Barriers to affordable energy keep stone aged philosophies alive on our globe today and as Nikola Tesla foretold, only equal access will remedy that.
Freeing ourselves from the current addiction to fossil fuel represents perhaps the greatest challenge in our world today. Will Abound Solar be the company to rise to the challenge and bring solar energy capabilities to the masses? Time and the market will answer this question. But, Abound Solar certainly has the hope and support of Tom Paine's Ghost.
It has been an inspiration to witness a man with such noble intentions turn a dream into reality on such a scale. As Thomas Paine might say - May the merit of our ideas rather than the weight of history pull us from the brink on which we find ourselves.
SOURCE: Solar Industry Magazine, PV-tech.org
Stay tuned to TPG for further updates through Google, Yahoo, or directly.
Saturday, March 14, 2009
Gaia Cleansing
The idea that Earth's biosphere operates cooperatively as a singular superorganism (also known as Gaia theory) has gained footing as more than just a new age worldview since its formation by James Lovelock and Lynn Margulis in the late 1960's. With the publication of James Lovelock's book Gaia - a New Look at Life on Earth the idea that life would go on with or without humanity began trickling into general consciousness.
Forty years later Lovelock is not optimistic about the future of humanity in the face of inevitable global climate change. A year ago he was quoted in the Guardian as believing that "global warming is now irreversible, and that nothing can prevent large parts of the planet becoming too hot to inhabit, or sinking underwater, resulting in mass migration, famine and epidemics." He highly doubts the efficacy of green initiatives saying it is really all too little too late.
When we go to the grocery store on our bikes and fill up reusable grocery bags with organic veggies are we simply rearranging the deck chairs on the titanic? No one who has made these life changes wants to concede that. But at least we have new leadership that might steer us away from the iceberg. If the desire to make small lifestyle changes spreads to a large enough scale perhaps some environmental mitigation will manifest. In the meantime it might be worth investing in planning "cities of the future" so we might have rafts of survival when southwest Asia runs out of glacial melt water and the Mediterranean gets flooded by Greenland falling into the north Atlantic.
Maybe all the houses left empty by the financial meltdown can be left vacant and be readied for the billion plus climate refugees that might be displaced in the near future. In the face of inevitable catastrophe James Lovelock tells a reporter to "Enjoy life while you can. Because if you're lucky it's going to be 20 years before it hits the fan." Cheers to that! We all need to eat drink and be merry regardless of the negative drivel that oozes from the television screen.
What do you think about Lovelock's outlook?
Free Energy
For the sake of making the hidden abundance of energy on earth more widely known we present a part of the popular film Zeitgeist addendum.
Disclaimer. Admittedly the Zeitgeist films feel like left wing propaganda but there seem to be some valid points embedded within a cloud of preachyness.
Lighting a 60 Watt bulb for 1 hour uses 216,000 Joules. One zetaJoule is 1,000,000,000,000,000,000,000 Joules. this amount of energy could light one 60 Watt bulb for every human on earth continuously for 79 years.
Monday, February 23, 2009
Post with the Most on Tom Paine's Ghost

The above scene is one of ten panels that adorn the double doors to the octagonal building known as the baptistry in the center of Florence, Italy. In 1401 a competition was held among the sculptors of the day for the privilege of creating these doors. Doors Michelangelo would later dub the "gates of paradise." The use of point perspective and heightened human realism marked the end of the dark ages and the beginning of the Renaissance. As we emerge from eight years of darkness perhaps a competition in the context of New Media can facilitate the evolution of our communication.
Tom Paine's Ghost is excited to announce the first annual TPG Composition Competition.
A $100 cash prize will be awarded for the most aesthetically powerful multi-media blog post.
Post content is limited only by the bounds of imagination. Keep in mind Tom Paine's Ghost was founded amidst a battle to defend freedom of the press and we hope to echo that theme throughout our pages.
Submissions will be selected and judged on the basis of four criteria:
1. Clarity
2. Originality
3. Integration (at least three forms of media must be utilized, images, text, movies, audio, etc.)
4. Power (the post's ability to motivate readers to action).
Submissions will be accepted until April 2, 2009. Submit entries by email to Tom Paine's Ghost. Please submit HTML for your post within the body of the e-mail. If you would like to submit a link to your own blog please write a three to four sentence primer to be published on TPG along with your link. Selected submissions will be posted here at TPG and voted on by our panel of citizen judges. The winner will be announced on April 22, 2009 and will be notified by email. Whether this is your first post or your one thousandth all submissions will be reviewed.
Cheers to revolution via evolution!
Sunday, February 22, 2009
Jihad against junk food
I have been waiting for a hero in the US to stand and fight for more healthful food in schools. Whenever I engage in conversation on this topic the archetype of Jamie Oliver and his "feed me better" campaign in Brittan comes up. Read his manifesto where he outlines a strategy for putting fresh local ingredients into the cafeteria. Talk about people powered media, Mr. Oliver encourages children to use their cell phone cameras to take pictures of the their school lunches and post them on his site. Internal checks to ensure the reform is happening on the ground. This could happen in the US, but living in the breadbasket of the world we have some of the largest food production lobbies on the planet. Look what we are up against.
Saturday, January 17, 2009
The Pennsylvania Constitution of 1776
On the birthday of Benjamin Franklin I think it appropriate to review a particularly progressive collaboration between he and Thomas Paine - the Pennsylvania Constitution of 1776. This document is considered by some historians to be the most "democratic" legislation to emerge from revolutionary America. This was the first legislation drafted that directly echoed the Declaration of Independence and further enunciated and protected the freedom of every person to "natural rights" including the right to worship "according to the dictates of their own conscience." Also, the language of this document presents a situation wherein all men, no matter race or creed were free to vote. This being penned in 1776 was a little too radical for the time. In 1790 it was amended by conservatives in that state to be more inline with the other state's constitutions.
From the preamble it is clear that this document serves as a universal template for an evolving government. It also highlights the balance of consciousness Ben Franklin and Thomas Paine had. Though they did not agree on the extent to which to renounce religion themselves they did understand the significance of embedding religious freedom in the legal genome of posterity's government.
"We, the representatives of the freemen of Pennsylvania, in general convention met, for the express purpose of framing such a government, confessing the goodness of the great Governor of the universe (who alone knows to what degree of earthly happiness mankind may attain, by perfecting the arts of government) in permitting the people of this State, by common consent, and without violence, deliberately to form for themselves such just rules as they shall think best, for governing their future society; and being fully convinced, that it is our indispensable duty to establish such original principles of government, as will best promote the general happiness of the people of this State, and their posterity, and provide for future improvements, without partiality for, or prejudice against any particular class, sect, or denomination of men whatever, do, by virtue of the authority vested in us by our constituents, ordain, declare, and establish, the following Declaration of Rights and Frame of Government, to be the CONSTITUTION of this commonwealth, and to remain in force therein for ever, unaltered, except in such articles as shall hereafter on experience be found to require improvement, and which shall by the same authority of the people, fairly delegated as this frame of government directs, be amended or improved for the more effectual obtaining and securing the great end and design of all government"
Read the rest here.
Thursday, October 16, 2008
Voting by Mail Changes the Game in Colorado
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.





