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Our pages are dedicated to the dissemination of Free Thought and the stimulation thereof. We are focused on the discussion of innovative, progressive and revolutionary ideas with topics ranging from politics to poetry, from science to religion.
The interwebs are exploding right now with buzz about a paper published in the Journal of Cosmology authored by a NASA scientist - Richard B. Hoover. The title of the controversial paper published online late last Friday is Fossils of Cyanobacteria in CI1 Carbonaceous Meteorites.
Hoover claims to have found evidence of extra terrestrial life.
This isn't a new claim. This evidence comes by microscopic observation of a freshly fractured meteorite that landed on earth in 1864........ Read more »
Hoover, Richard B. (2011) fossils of cyanobacteria in C11 carbonaceous meteorites. Journal of Cosmology. info:/
To sell a bottle of Champagne as "bubbly" a vendor must ensure that the wine has absorbed between five and six atmospheres of carbon dioxide. To anyone who has ever popped the cork on champagne you know there is enough force there to do some serious damage to an innocent bystander in the event of poor aim.
Viruses spend part of their existence as a kind of bottle (capsid) with a message inside (DNA or RNA). The message inside carries the code or blueprint to make more viruses, more message........ Read more »
Yu, J., Moffitt, J., Hetherington, C., Bustamante, C., & Oster, G. (2010) Mechanochemistry of a Viral DNA Packaging Motor. Journal of Molecular Biology, 400(2), 186-203. DOI: 10.1016/j.jmb.2010.05.002
Moffitt, J., Chemla, Y., Aathavan, K., Grimes, S., Jardine, P., Anderson, D., & Bustamante, C. (2009) Intersubunit coordination in a homomeric ring ATPase. Nature, 457(7228), 446-450. DOI: 10.1038/nature07637
I'm giving myself ten minutes to do this. To write whatever storms into my mind then hit post.
I think the archaic revival might run into some barriers. Like starvation, no communication, and other electrical difficulties if it embraces the Abbey-esque Luddite philosophy entirely.
As much as I want to get onto that other boat I think I will just slip between the hulls and end up swimming by myself among the sea-monsters, bullets whizzing past my head with bubbles trailing behind in dark ........ Read more »
Sedel F, Baumann N, Turpin JC, Lyon-Caen O, Saudubray JM, & Cohen D. (2007) Psychiatric manifestations revealing inborn errors of metabolism in adolescents and adults. Journal of inherited metabolic disease, 30(5), 631-41. PMID: 17694356
Altintoprak AE, Ersel M, & Bayrakci A. (2009) An unusual suicide attempt: a case with psychosis during an acute porphyric attack. European journal of emergency medicine : official journal of the European Society for Emergency Medicine, 16(2), 106-8. PMID: 19262206
Mandoki MW, & Sumner GS. (1994) Psychiatric manifestations of hereditary coproporphyria in a child. The Journal of nervous and mental disease, 182(2), 117-8. PMID: 8308532
By Kristopher Hite
Looking back at discoveries of the past year the one that sticks out above all others to me was the identification of a single protein; a bacterial actin homologue dubbed BARP - Bacterial Actin Related Protein. The brilliance of this discovery comes from its directly contributing to our understanding of evolution, overturning decades of dogma, and providing a shiny new teaching tool. The discovery was published in late 2009 as part of a massive sequencing project to f........ Read more »
Wu, D., Hugenholtz, P., Mavromatis, K., Pukall, R., Dalin, E., Ivanova, N., Kunin, V., Goodwin, L., Wu, M., Tindall, B.... (2009) A phylogeny-driven genomic encyclopaedia of Bacteria and Archaea. Nature, 462(7276), 1056-1060. DOI: 10.1038/nature08656
Before the event took place there was much consternation abuzz on the blogosphere over the cast of characters chosen to speak at the Faith and Science event held as part of the 2010 World Science Festival. Sean Carrol of Cosmic Variance being the first vocal critic with Richard Dawkins and Jerry Coyne re-posting Carroll's critique on their respective homepages. Other discussions of the event can be seen at Thoughts from Kansas, Uncertain Principles, and evolutionblog. The panel inclu........ Read more »
Newberg A, Pourdehnad M, Alavi A, & d'Aquili EG. (2003) Cerebral blood flow during meditative prayer: preliminary findings and methodological issues. Perceptual and motor skills, 97(2), 625-30. PMID: 14620252
Campbell CS. (2010) What more in the name of god? Theologies and theodicies of faith healing. Kennedy Institute of Ethics journal, 20(1), 1-25. PMID: 20506692
T. G. Dobzhansky, a prominant evolutionary biologist once said...
"Nothing in biology makes sense except in the light of evolution"
Recently, I received a request from a Tom Paine's Ghost reader to answer some questions about public perceptions of evolution. The questions, along with my responses follow.
Reader: How is evolution relevant to the lives of everyday people?
TPG: I will here talk about medicine, childhood obesity, and sex.
The first topic that springs to mind when I think ........ Read more »
Miller, J. (2006) SCIENCE COMMUNICATION: Public Acceptance of Evolution. Science, 313(5788), 765-766. DOI: 10.1126/science.1126746
By Kristopher Hite
A few weeks ago I traveled from my home in Fort Collins down to Golden, Colorado to hear Vladamir Lunin from the Institute of Mathematical Problems of Biology in Pushchino, Russia give a lecture on x-ray crystallography at the the National Renewable Energy Lab (NREL). He spoke about how to improve the three dimensional map of a crystal structure by applying Fourier-transforms and other mathematical operations to crystal diffraction data. Ab initio phasing as ........ Read more »
Lunin, V., Lunina, N., Ritter, S., Frey, I., Berg, A., Diederichs, K., Podjarny, A., Urzhumtsev, A., & Baumstark, M. (2001) Low-resolution data analysis for low-density lipoprotein particle. Acta Crystallographica Section D Biological Crystallography, 57(1), 108-121. DOI: 10.1107/S0907444900014608
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 "the........ Read more »
Gehring WJ, Kloter U, & Suga H. (2009) Evolution of the Hox gene complex from an evolutionary ground state. Current topics in developmental biology, 35-61. PMID: 19651301
The Arizona Chemical wood pulp mill in Panama City, Florida sits within a stone's throw of the Gulf of Mexico.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 the wood chips, switch grass, and corn stover (all forms of cellulose), the environmental........ Read more »
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 , 2147483647. DOI: 10.1021/es9011433
Red-Green color blindness is caused by a deficiency in opsin genes. These genes codes for photoreceptor proteins of the same name positioned in the cone cells of the eye's retina to receive photons (light). When light hits these photoreceptor proteins a tiny molecule buried inside changes its shape by swinging its bond angles and begins a signal transduction cascade. The signal of "red" or "green" is passed from this tiny "g-coupled" protein receptor along the optic nerve and eventually to the b........ Read more »
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
Two biochemically inspired limericks by Kristopher Hite1.)The proteosome proceeds to foragetransforming proteins to porridge if ubiquitin tagged Then subsequently baggedcatabolized and placed into storage2.)Hec1 and Nuf2 unitetogether coiled-up tight microtubule bound never coming unwoundto align all the chromosomes rightinspired by the following research...Yao, T. (2000). Cyclization of Polyubiquitin by the E2-25K Ubiquitin Conjugating Enzyme Journal of Biological Chemistry, 2........ Read more »
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
Imagine stepping onto a vast green field. A closer look and you notice circular patches of white grass speckle the landscape. If you know what you are looking at these biological signals might save your life as you proceed. TNT leaching from buried landmines activate plants with an engineered ability to "degreen" in the presence of specific molecules. Though these sentinals have yet to be deployed on the battlefield it is not hard to imagine a technique like this being used to save lives. A cl........ Read more »
Antunes, M., Ha, S., Tewari-Singh, N., Morey, K., Trofka, A., Kugrens, P., Deyholos, M., & Medford, J. (2006) A synthetic de-greening gene circuit provides a reporting system that is remotely detectable and has a re-set capacity. Plant Biotechnology Journal, 4(6), 605-622. DOI: 10.1111/j.1467-7652.2006.00205.x
And in science this can be the biggest barrier to moving forward. If we can't show an event happening how do we know it is happening at all? Since the 1950's a large gap between what we can see under microscopes and what we can see when we crystallize things (i.e. DNA) has existed. The gap has historically been in the range of tens to hundreds of nanometers leaving many macromolecular events taking place inside every living cell on earth in a black box; inaccessible to the human eye and ther........ Read more »
Lee, J., Hong, B., Kim, W., Min, S., Kim, Y., Jouravlev, M., Bose, R., Kim, K., Hwang, I., Kaufman, L.... (2009) Near-field focusing and magnification through self-assembled nanoscale spherical lenses. Nature, 460(7254), 498-501. DOI: 10.1038/nature08173
The locksmith that uncovered the keys to genetic manipulation - Wener Arber - expressed some of his thoughts on the nature of natural selection last week at the Annual Meeting of Nobel Laureates at Lindau, Gernamy. P.Z. Meyers at Pharyngula critically reviews his synthesis and takes a particularly skeptical view of his conclusions.The main conclusion Arber makes is that genomes contain a duality of genes that affect mutation rates and therefore the rate of evolution. On one hand there are genes........ Read more »
Strand, D., & McDonald, J. (1985) is transcriptionally responsive to environmental stress . Nucleic Acids Research, 13(12), 4401-4410. DOI: 10.1093/nar/13.12.4401
The fact that this bombshell of a fossil was unleashed in the pages of PLoS One says more than something about the future trends of scientific publication and the open access philosophy!Dubbed Darwinius masillae this arboreal quadruped lived in the trees of an ancient rain forest now buried under present day Germany. This is the most complete early primate fossil ever unearthed.Bora has more on this wonderful specimen over at the Blog Around the Clock. and PZ runs down the phylogenetic "tech-s........ Read more »
Franzen, J., Gingerich, P., Habersetzer, J., Hurum, J., von Koenigswald, W., & Smith, B. (2009) Complete Primate Skeleton from the Middle Eocene of Messel in Germany: Morphology and Paleobiology. PLoS ONE, 4(5). DOI: 10.1371/journal.pone.0005723
DNA Origami goes 3DImagine sitting down at your computer, typing out a message, and then having that message translated into a tiny self-assembling machine. In essence, this is what a group of Danish German and American researchers have done. Using short bits of DNA to link up distant regions throughout a very long single strand of DNA these folks were able to build six square walls and have them assemble, on their own, to form a sealed box. What's more, they were able to affix several molecul........ Read more »
Andersen, E., Dong, M., Nielsen, M., Jahn, K., Subramani, R., Mamdouh, W., Golas, M., Sander, B., Stark, H., Oliveira, C.... (2009) Self-assembly of a nanoscale DNA box with a controllable lid. Nature, 459(7243), 73-76. DOI: 10.1038/nature07971
Planted together corn, beans, and squash form a "holy trinity" of cooperative growth. By living in close quarters they provide each other with physical protection and nutritional abundance. As the corn emerges high above the others the stalk provides a living scaffold the beans can coil their vines around as they seek the sun. Meanwhile at ground level the squash act as living mulch by preserving moisture under shady leaves and monopolizing sunlight that might otherwise go to nefarious weeds. ........ Read more »
HERMANN, J., PARKER, S., BROWN, B., SIEWE, Y., DENNEY, B., & WALKER, S. (2006) After-School Gardening Improves Children’s Reported Vegetable Intake and Physical Activity. Journal of Nutrition Education and Behavior, 38(3), 201-202. DOI: 10.1016/j.jneb.2006.02.002
Life is written in a language of chemical sentences. In 2006 a group of researchers began the process of engineering new letters to be incorporated into the genetic alphabet. The naturally occurring genetic alphabet is made up of 20 chemical letters (amino acids). These letters are arranged in the correct order by molecular machines, called ribosomes, into words that make sense (proteins). There are words of all sizes that perform key functions in all organisms, from two letter hormones to the........ Read more »
Xie, J., & Schultz, P. (2006) A chemical toolkit for proteins — an expanded genetic code. Nature Reviews Molecular Cell Biology, 7(10), 775-782. DOI: 10.1038/nrm2005
Whenever evidence is presented for global climate change on a millennial time scale the method of choice seems to be polar ice. By measuring carbon dioxide in the tiny gas bubble captured in ice core strata from Antarctica researchers can generate graphs depicting earth's annual inhalation/exhalation of carbon dioxide for thousands of years. Al Gore famously displayed these results in an Inconvenient Truth while riding a hydraulic scissor lift next to his presentation showing how dramatically........ Read more »
Conroy, J., Restrepo, A., Overpeck, J., Steinitz-Kannan, M., Cole, J., Bush, M., & Colinvaux, P. (2008) Unprecedented recent warming of surface temperatures in the eastern tropical Pacific Ocean. Nature Geoscience, 2(1), 46-50. DOI: 10.1038/ngeo390
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