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Discussion of all things science with a focus on clarity, rationality and enthusiasm. Discussion topics: Natural Science, Biology, Evolution, Paleontology, Geology, Science Education
Johnny
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by Johnny in Ecographica
...undermining the normal life-processes of the host’s cells, viruses are detriments to health; however, more than just illness can remain in the wake of the virus’s biological sabotage. Sometimes included with the observable symptoms of an ailment are other characteristics of viral infection that serve to promote the spread of disease. The genes that such a virus splices into a host cell’s mainframe can code for phenotypes that manipulate unwitting vectors into exposing themselves – purely for the benefit of the virus... Read more »
Mauck, K., De Moraes, C., & Mescher, M. (2010) Deceptive chemical signals induced by a plant virus attract insect vectors to inferior hosts. Proceedings of the National Academy of Sciences. DOI: 10.1073/pnas.0907191107
by Johnny in Ecographica
...the invasive could theoretically replace the native with little ill effect to the ecosystem; the invasive could fill the niche left void by the out-competed native plant without disrupting the energetics of the plant community as a whole. BUT, at the same time, a newly arrived invasive species may have a distinct advantage over a native transient because it is completely foreign to the ecosystem. For example, being unrecognized by its new environment the invasive may, for a period of time, be buffered against attack by herbivores, parasites and other stressors that may be actively reducing the fitness of the locals. ... Read more »
Simberloff, D. (2010) Invasions of Plant Communities – More of the Same, Something Very Different, or Both?. The American Midland Naturalist, 163(1), 220-233. DOI: 10.1674/0003-0031-163.1.220
by Johnny in Ecographica
A recent blog post at National Public Radio’s “Cosmos And Culture” by astrophysicist Adam Frank has raised my hackles. The post, titled “The Evolution Debate Is Over; It's Time To Move Forward,” argues that “it's time to put the prejudices that drag down discussion between science and the domains of human spiritual endeavor aside.”
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Sedikides, C. (2009) Why Does Religiosity Persist?. Personality and Social Psychology Review, 14(1), 3-6. DOI: 10.1177/1088868309352323
by Johnny in Ecographica
According to Utah State Representative Mike Noel, global climate change is a conspiracy theory. He insists that the whole idea of shifting climates was put together by the world’s biologists, climatologists and other scientists as an elaborate effort to control his sex life.Speaking to climate change, Republican Mike Noel (at left) explained recently that, “This is absolutely, in my mind, in fact a conspiracy to limit population not only in this country but across the globe."Being both a Republican and an enthusiast of the equestrian arts, Noel isn’t the type to quietly lie down and let the lefties fondle his reproductive liberties! To the contrary, he has been an outspoken proponent of Utah’s House Joint Resolution 12; a proposition that aims to stop the Environmental Protection Agency from establishing policies that reduce carbon dioxide. Noel’s good friend, Republican Kerry Gibson, sponsored Resolution 12 because… Well…Well, because there’s a global conspiracy going on!Here are a few proofs of the conspiracy as listed in House Joint Resolution 12:1. “…Climategate, indicate[s] a well organized and ongoing effort to manipulate and incorporate "tricks" related to global temperature data in order to produce a global warming outcome…”2. “…there has been a concerted effort by climate change alarmists to marginalize those in the scientific community who are skeptical of global warming by manipulating or pressuring peer-reviewed publications to keep contrary or competing scientific viewpoints and findings on global warming from being reviewed and published…”3. “…the Intergovernmental Panel on Climate Change (IPCC), a blend of government officials and scientists, does no independent climate research but relies on global climate researchers”4. “…the climate change "gravy train," estimated at more than $7 billion annually in federal government grants, may have influenced the climate research focus and findings that have produced a "scientific consensus" at research institutions and universities”In addition to deducing the above listed ‘hard facts,’ Noel and Gibson also arranged for a hired gun to testify as an expert witness at Utah’s legislative proceedings. The hired gun was non other than the infamous Roy “shunned by the system” Spencer, a climatologist from Alabama whose work has been continuously rejected by the scientific community – yet further evidence of the conspiracy!Checking Roy's facts during the proceedings was a group of 18 scientists from Brigham Young University. The group unanimously concluded that he was full of crap and even “patently false.” Accordingly, they put their findings into an open letter (available here), which each scientists signed. The letter was mailed to the State legislature in hopes of dissuading them from passing the resolution.What was the result of this unified effort?Republican chairman of the Utah farm group Randy Parker publicly demanded a formal apology from Brigham Young University. Parker in part stated that, "I guess the bottom line here, from my perspective, is that science is an open process of ongoing research and debate, and a group of scientists should not make these kinds of statements about another scientist…” (Note: I couldn’t agree more with this sentiment. The art of debating without debating is under-appreciated.)So unfortunately, it looks as though Mike Noel, Kerry Gibson, and Randy Parker’s fight for breeding rights has paid-off for the republicans. House Joint Resolution 12 passed committee yesterday morning. The state of Utah is about to tell the Federal Government that climate change is nothing but a conspiracy theory, take the EPA regulations and shove 'em!This should be great for tourism: Welcome to Utah – the State of Denial!References & Credits:Sovacool, B., & Brown, M. (2009). Scaling the policy response to climate change Policy and Society, 27 (4), 317-328 DOI: 10.1016/j.polsoc.2009.01.003Chris Vanocur-ABC Channel 4Judy Fahys- Salt Lake TribunePhoto: Mike Noel
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Sovacool, B., & Brown, M. (2009) Scaling the policy response to climate change. Policy and Society, 27(4), 317-328. DOI: 10.1016/j.polsoc.2009.01.003
by Johnny in Ecographica
According to Utah State Representative Mike Noel, global climate change is a conspiracy theory. He insists that the whole idea of shifting climates was put together by the world’s biologists, climatologists and other scientists as an elaborate effort to control his sex life.
... Read more »
Sovacool, B., & Brown, M. (2009) Scaling the policy response to climate change. Policy and Society, 27(4), 317-328. DOI: 10.1016/j.polsoc.2009.01.003
by Johnny in Ecographica
If I had a nickel for every time a biologist told me that tree plantations are nothing but “biological deserts” I’d be a rich man!
Well, at least a rich-er man anyway…
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Paquette, A., & Messier, C. (2010) The role of plantations in managing the world's forests in the Anthropocene. Frontiers in Ecology and the Environment, 8(1), 27-34. DOI: 10.1890/080116
by Johnny in Ecographica
Birds undertake a re-conquest of the ground following the KT Extinction and ultimately find themselves on Darwin's dinner plate.... Read more »
Phillips, M., Gibb, G., Crimp, E., & Penny, D. (2009) Tinamous and Moa Flock Together: Mitochondrial Genome Sequence Analysis Reveals Independent Losses of Flight among Ratites. Systematic Biology, 59(1), 90-107. DOI: 10.1093/sysbio/syp079
by Johnny in Ecographica
...the paper is saying that the introduction of ACQUIRED CHARACTERS into the germline of a lineage has lead to GENETIC NOVELTIES with the demonstrated ability to translate to the expressed PHENOTYPE of an ANIMAL, thus acting as a source of INNOVATION... Read more »
Horie, M., Honda, T., Suzuki, Y., Kobayashi, Y., Daito, T., Oshida, T., Ikuta, K., Jern, P., Gojobori, T., Coffin, J.... (2010) Endogenous non-retroviral RNA virus elements in mammalian genomes. Nature, 463(7277), 84-87. DOI: 10.1038/nature08695
by Johnny in Ecographica
An irreducibly complex rant using developmental biology (arrested development) to connect the shortfalls of the Greek Philosopher Socrates to failed creationist arguments; includes a detailed account of a parasitic worm’s lifecycle (Alaria marcianae), and of course, endangered Florida Panthers and Mexican axolotls… A well rounded post!
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Davies, S. (2003) Developmental plasticity in schistosomes and other helminths. International Journal for Parasitology, 33(11), 1277-1284. DOI: 10.1016/S0020-7519(03)00161-9
Foster, G., Kinsella, J., Sheppard, B., & Cunningham, M. (2009) Transmammary Infection of Free-Ranging Florida Panther Neonates by Alaria marcianae (Trematoda: Diplostomatidae). Journal of Parasitology, 95(1), 238-239. DOI: 10.1645/GE-1749.1
by Johnny in Ecographica
Research published today... tediously analyzing the genomes from multiple generations of the plant Arabidopsis thaliana, scientists from the Max Planck... Sanger scientists published work in which the rate of mutation in humans was estimated at around...... Read more »
Ossowski, S., Schneeberger, K., Lucas-Lledo, J., Warthmann, N., Clark, R., Shaw, R., Weigel, D., & Lynch, M. (2009) The Rate and Molecular Spectrum of Spontaneous Mutations in Arabidopsis thaliana. Science, 327(5961), 92-94. DOI: 10.1126/science.1180677
by Johnny in Ecographica
Whiptails and fencers scurry and make haste,
cross White Sands their paths converge and pace.
Tho' differing by both origin and type,
their causal genotypes follow trace.
Independent mutations had aligned,
and were by adaptation refined.
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Rosenblum, E., Rompler, H., Schoneberg, T., & Hoekstra, H. (2009) Molecular and functional basis of phenotypic convergence in white lizards at White Sands. Proceedings of the National Academy of Sciences. DOI: 10.1073/pnas.0911042107
by Johnny in Ecographica
Shield pennywort represents but one of about a hundred different species that belong to the Genus Hydrocotyle, a.k.a the ‘water pennyworts.’ Though often found listed as members of the Apiaceae Family, the Hydrocotyle group is now included in the ‘Ivy Family’ (Araliaceae). The genus as whole enjoys a worldwide distribution; however, the Facultative Wet H. verticillata is native to the Americas where can be found occupying floodplains, swamps, ditches, and just about anywhere with moist soils.... Read more »
CHANDLER, G., & PLUNKETT, G. (2004) Evolution in Apiales: nuclear and chloroplast markers together in (almost) perfect harmony. Botanical Journal of the Linnean Society, 144(2), 123-147. DOI: 10.1111/j.1095-8339.2003.00247.x
by Johnny in Ecographica
What are males good for? ... mitochondrial genomes of a freshwater snail species in order to compare the rates at which genetic mutations accumulate during sexual and asexual reproduction.
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Neiman, M., Hehman, G., Miller, J., Logsdon, J., & Taylor, D. (2009) Accelerated Mutation Accumulation in Asexual Lineages of a Freshwater Snail. Molecular Biology and Evolution. DOI: 10.1093/molbev/msp300
by Johnny in Ecographica
...published a letter in which other California based scientists have extrapolated the shifting niche model in order to estimate the anticipated ‘velocity’ of temperature change across different biomes...or through the advent of novel life-history strategies, the ability of an organism to accommodate ecological variability is essential.... Read more »
Loarie, S., Duffy, P., Hamilton, H., Asner, G., Field, C., & Ackerly, D. (2009) The velocity of climate change. Nature, 462(7276), 1052-1055. DOI: 10.1038/nature08649
by Johnny in Ecographica
...recent experiments into the coevolution of male and female duck genitalia...provided evidence of ducks being actively engaged in a sexually antagonistic arms race...equipped with artificial duck vaginas, mineral oil and a high speed video camera. ... Read more »
Patricia L. R. Brennan, Christopher J. Clark and Richard O. Prum. (2009) Explosive eversion and functional morphology of the duck penis supports sexual conflict in waterfowl genitalia. Proc. R. Soc. B. info:/
by Johnny in Ecographica
Recent research conducted out of UC Berkeley and Penn State University has quantitatively demonstrated that mammal diversity in North America has plummeted since the arrival of humans about 13,000 years ago. ... Read more »
Carrasco, M., Barnosky, A., & Graham, R. (2009) Quantifying the Extent of North American Mammal Extinction Relative to the Pre-Anthropogenic Baseline. PLoS ONE, 4(12). DOI: 10.1371/journal.pone.0008331
by Johnny in Ecographica
...lineage of Iva frutescens specifically, proximity to tidally influenced waters has selected achenes with a tolerance for saltwater and a proven ability to stay afloat while in a non-dormant condition. In fact, research published just this year has shown that the achenes of Iva frutescens can stay ... Read more »
Elsey-Quirk, T., Middleton, B., & Proffitt, C. (2009) Seed flotation and germination of salt marsh plants. Aquatic Botany, 91(1), 40-46. DOI: 10.1016/j.aquabot.2009.02.001
by Johnny in Ecographica
While in field last week, I encountered a species of fungus with a rather unique set of morphological and ecological characteristics. The aptly named ‘stinkhorn’ fungus (Clathrus columnatus) belongs to the Phallaceae Family of fungi and produces a distinctive gelatinous spore mass that gives off a lovely perfume. Well, lovely to insects anyway, to me it reeked of rotting meat and dung. The stinkhorn’s ‘aroma’ serves as an attractant for flies and other insects vital to the fungus’s lifecycle. In the process of munching on the glebra (spore mass) insects gather the fungus’s reproductive spores on their bodies and in their digestive tracts, these spores are then transported and dispersed once the insects have gotten their fill and part ways. Although my nose took offense to ... Read more »
Tuno, N. (1998) Spore dispersal of Dictyophora fungi (Phallaceae) by flies. Ecological Research, 13(1), 7-15. DOI: 10.1046/j.1440-1703.1998.00241.x
by Johnny in Ecographica
Another Science Lesson from Rick Santorum...
I think that I ruffled Rick Santorum’s feathers. Last week I published an article in which Christian fundamentalist and presidential hopeful Rick Santorum was used as a metaphor to dispel one of the commonly held misconceptions about biological evolution.... Read more »
Scott, E. (2009) Science Standards Evolve. Evolution: Education and Outreach, 2(3), 538-540. DOI: 10.1007/s12052-009-0153-0
by Johnny in Ecographica
An article just published to Nature has turned the world of evolutionary biology topsy-turvy!Or, so they’d like us to believe…The paper’s authors Chris Venditti, Andrew Meade and Mark Pagel have devised a new model that shows that evolution is not driven by natural selection or through the accumulative effects of random genetic drift. Rather than incremental and gradual change, their study suggests that the vast bulk of speciation results from rare stochastic events. They call this new theory “punctuated equilibrium” – NO WAIT! They don't...Actually, they don’t call it punctuated equilibrium, which is strange because that’s what it looks like to me… What’s even stranger is that neither Niles Eldredge nor Stephen Jay Gould’s names appear anywhere in the paper – including the references.Through phylogenetic analysis of 101 different plant, animal and fungi groups the researchers established that - what I’m going to call - the punctuated equilibrium model is the most parsimonious fit for explaining the branch lengths of the studied taxa.Although, this ‘rediscovery’ of what’s been known for about the last 30-years may not seem too earthshaking, I’m confident that (with Nature’s help of course) creationists around the world will be harvesting quotes from the article and its associated news release.Check out these lines:Quotes from Nature’s accompanying news release-“New species might arise as a result of single rare events, rather than through the gradual accumulation of many small changes over time, according to a study of thousands of species and their evolutionary family trees.”“This contradicts a widely accepted theory of how speciation occurs: that species are continually changing to keep pace with their environment, and that new species emerge as these changes accrue.”“The team's findings might stir things up in the world of evolutionary biology.”It really goes against the grain because most of us have this Darwinian view of speciation," says Pagel. "What we're saying is that to think about natural selection as the cause of speciation is perhaps wrong."Quotes from around the web-"A new study published in Nature contradicts the commonly-held belief that most species evolve gradually through sexual selection in response to subtle changes in their environment." (SOURCE)"This new theory is likely to be quite controversial, as it goes against the Darwinian view of evolution that most people are familiar with. "It really goes against the grain because most of us have this Darwinian view of speciation," says Pagel. "What we're saying is that to think about natural selection as the cause of speciation is perhaps wrong." (SOURCE)'The surprise is that this model is not compatible with the idea that lots of small events combine to bring about speciation,' he adds. (SOURCE)"Our research indicates that the idea that new species occur by gradually becoming more and more adapted to their particular niches, is not true. In fact, we have found that new species appear due to rare random events that seem to simply just happen." Pagel (SOURCE)Quotes from the study -“The Red Queen describes a view of nature in which species continually evolve but do not become better adapted. It is one of the more distinctive metaphors of evolutionary biology, but no test of its claim that speciation occurs at a constant rate has ever been made against competing models that can predict virtually identical outcomes, nor has any mechanism been proposed that could cause the constant-rate phenomenon.”“This model predicts a constant rate of speciation, and provides a new interpretation of the Red Queen: the metaphor of species losing a race against a deteriorating environment is replaced by a view linking speciation to rare stochastic events…”“Speciation is freed from the gradual tug of natural selection, there need not be an ‘arms race’ between the species and its environment, nor even any biotic effects.”“If the original Red Queen model had a ‘whiff’ of a species running out of breath from the accumulation of many detrimental biotic effects, and then being ‘knocked off’ by the next event, the interpretation we propose is different. Species do not so much ‘run in place’ as simply wait for the next sufficient cause of speciation to occur.”“This means that researchers seeking to develop explanatory theories of speciation should focus their attention on the size of the catalogue of sufficient causes (speciation factors)shared by a group of organisms, rather than on special driving forces or how these forces might combine.”Venditti, C., Meade, A., & Pagel, M. (2009). Phylogenies reveal new interpretation of speciation and the Red Queen Nature DOI: 10.1038/nature08630
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Venditti, C., Meade, A., & Pagel, M. (2009) Phylogenies reveal new interpretation of speciation and the Red Queen. Nature. DOI: 10.1038/nature08630
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