Month: April 2015

Posted on April 30, 2015May 22, 2015 Articles Evolution Literacy, Editorials The Standard Times, Video

A Secular Humanist’s Plea for Dzhokhar Tsarnaev’s Life

New England Science Public – An Initiative for the Public Understanding of Science – on Twitter @EvoLiteracy – @gpazymino – ResearchGate – Academia.edu

A Humanist’s Plea for Dzhokhar Tsarnaev’s Life

[click on subtitle to be redirected to The Standard Times]

“…the Tsarnaev brothers were internet-self-taught jihadi-aspirants, erratic online consumers of radical Islam; no less dangerous or accountable. But obviously their dysfunctional upbringing, combined with individual failures, made them prone to recruit each other and act criminally… Even so, “Jahar” belongs more in jail than in the execution chamber… Incarceration counters more rationally [his] alleged desire to die as martyr… And, as a humanist, I plea for a life.”

Jahar Tsarnaev illustration by Jane Flavell Collins

Dzhokhar Tsarnaev in Court, Boston; illustration by Jane Flavell Collins

As a secular humanist, I oppose the death penalty, but have no sympathy for Dzhokhar Tsarnaev’s self-inflicted condition in which his execution is probable. After all, a jury found him guilty of killing three people and injuring 260 when he and his brother, Tamerlan, deliberately detonated pressure-cooker bombs at the Boston Marathon of 2013. And guilty was Dzhokhar found on 30 counts, 65 offenses, including the murder of an MIT Officer. Still, as a college educator, another element in my plea, I think that the juvenile, subordinate-sibling and neither-so-bright Dzhokhar deserves imprisonment rather than death. Incarceration counters more rationally Dzhokhar’s alleged desire to die —in his mind— as martyr.

I was in North Carolina, at Duke University, attending an academic event at the National Evolutionary Synthesis Center, when I learned that Dzhokhar Tsarnaev (the name was not initially released), student at UMass Dartmouth, had been identified as one of the marathon bombers, and that the Tsarnaev brothers were being hunted by the police. The previous day, April 18, I had met with colleagues at NESCent and, although our dialog was mostly about the upcoming “Evolution Education and the Underserved Catalysis Meeting,” sponsored by the National Science Foundation, we were all troubled by the events in Boston.

Whit Hat and Black Hat Suspects as per the FBI

“White Hat” and “Black Hat” subjects, as depicted by the FBI. Soon after detonating pressure-cooker bombs at the Boston Marathon, on April 15, 2013, the Tsarnaev brothers (Dzhokhar and Tamerlan) were being hunted by the police.

The following morning, when I returned to our sessions at NESCent, a conspicuous silence awaited: almost everyone was devouring the news about the Tsarnaevs. More than their identities, their faces and actions had been exposed on TV. I broke the ice by sharing that I had also become aware that one of the suspects (“white hat,” as identified by the FBI in the surveillance videos) was a student at my own campus —I never knew him. Stillness and discomfort continued as we gradually drifted toward the purpose of our panel: promote the participation of minorities in science careers, specifically evolutionary biology.

I must admit that I remained multitasking for two consecutive days: contributing to the NESCent–NSF discussions and, simultaneously, checking emails from UMass Dartmouth and monitoring the media. Snapshots of the “white-” and “black-hat subjects” plus visuals of the UMassD grounds appeared everywhere.

The momentary embarrassment that Dzhokhar Tsarnaev caused me was, of course, minuscule in contrast to the pain and suffering he and his brother inflicted on people, families, the majestic city of Boston and the country that homed the Chechen-Avar-Tsarnaev kin of refugees. Overnight, the brothers, particularly Dzhokhar, became front-page nourishment —in a dreadful manner— for the world’s news outlets. By August 2013, Rolling Stone magazine doubled its sales after featuring “Jahar” on its cover; Adweek awarded it “Hottest Magazine Cover of The Year.”

Dzhokhar’s deplorable conduct, prior and post the marathon’s blasts, will certainly influence the jury’s final judgment of his wicked psyche: capital punishment or confinement. Yet, justice can be served by not vanishing the quasi-adolescent killer, and by rather relying on the legal system itself to convey a message —human rights, even for brutal felons— and teach a lesson —ultimate civility. Lock him up, as pleaded by some of the victims’ families, although not all, nor a majority.

Bruce Hoffman, Director of the Center for Security Studies at Georgetown University, characterized the Tsarnaev brothers as “jihadi autodidacts,” and this assessment might be accurate. In fact, out of the 30 counts in which Dzhokhar was found responsible, including conspiracy to use and possession of a weapon of mass destruction (pressure cookers and pipe bombs), possession and use of a firearm, bombing of a place of public use, conspiracy to and malicious destruction of public property, carjacking, and violent crime (murder), none related to militant participation in organized domestic or international terrorism. Largely, the Tsarnaev brothers were internet-self-taught jihadi-aspirants, erratic online consumers of radical Islam [self radicalized]; no less dangerous or accountable. But obviously their dysfunctional upbringing, combined with individual failures, made them prone to recruit each other and act criminally.

Illustration of Jahar Tsarnaev by Josie Jammet The Boston Globe

Dzhokhar Tsarnaev, illustration by Josie Jammet (click on image to enlarge). “Jahar didn’t try very hard to conceal his drug-dealing, keeping a scale in his dorm room desk and bagging marijuana with the door open” (Credit “The Fall of the House of Tsarnaev“)

Again, I have no sympathy for Dzhokhar Tsarnaev. Before his explosive act in Boston, he was indeed a 19-year-old petty law offender, with no deep political or religious ideology, who probably did not deserve to be in a university, although his high school years seem to have been more promising (his teachers and wrestling-team coach remember him fondly). But, in college, he was a “high-volume pot dealer” (weekly profit $1,000) as depicted by The Boston Globe’s “The Fall of the House of Tsarnaev,” detached from studying, indolent, borrower of a pistol from his best buddy (the very Ruger P95 9mm semiautomatic co-used with Tamerlan to kill Officer Sean Collier), which Dzhokhar needed to “rip” his weed customers.

Illustration of Boston Marathon Trial by Jane Collins

Judge George O’Toole speaks during the penalty phase of the trial of convicted Boston Marathon bomber Dzhokhar Tsarnaev – Illustration by Jane Flavell Collins – Boston com

Resources: videos and in-depth analyses

Boston Marathon Bombings – History Channel

Inside the Hunt for the Boston Bombers – National Geographic

Manhunt Boston Bombers – NOVA PBS

Timeline of the bombings, manhunt and aftermath – CNN

Boston Marathon Bombing Trial – The Boston Globe Metro

Dzhokhar Tsarnaev Has the Most Ferocious Lawyer in America Defending Him – Vanity Fair Law and Order

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Evolution Stands Faith Up: Reflections on Evolution’s Wars By NOVA Publishers, New York Soft Cover. Find it at Barnes & Noble, Amazon.com, Amazon UK.

“This is an inspiring, readable collection of essays of reflective value to everyone. Paz-y-Miño-C points to the vain attempt by many to try and accommodate scientific rationalism with supernatural beliefs. They are simply incompatible. The author has a marvelously eloquent style of writing, full of inspiring metaphors and lateral observations that reinforce connections to the foundations of scientific inquiry and to biological evolution in particular. These thoughtful essays… are inspiring… [and] help clear the fog in our communities and arm our neighbors [with arguments] against theistic anti-science, medical quackery and other irrational nonsense.” – Greg M. Stott, PhD, Geoscientist with the Ontario Geological Survey, Canada.

“Paz-y-Miño-C doesn’t ask the reader to ‘believe’ in evolution. He provides overwhelming evidence, clearly written, that shows how scientific inquiry leads to important and practical results, while superstition and faith lead nowhere. Although we may not be able to reason someone out of what they were never reasoned into, the author presents a roadmap for those whose minds are open to discover the wonders and beauty of science.” – Herb Silverman, PhD, author of Candidate Without a Prayer: An Autobiography of a Jewish Atheist in the Bible Belt. — READ MORE at EvoLiteracy Mini Reviews.

Posted on April 29, 2015 EvoLiteracy News, Scientific Literacy, Video

EvoLiteracy News 4 29 2015

Today’s EvoLiteracy News include: First, the discovery of a vegetarian T. rex- phylogenetic relative from Chile. Second, “bird accent” [vocalization] variation as function of elevation, a study of mountain chickadees. And, third, an extensive map documentation of seismic risks in North America. The special treat includes a superb video reconstruction of Hubble’s cosmic images, with links to historical photos in celebration of the telescope’s 25th anniversary. Enjoy! — GPC.

Was T. rex cousin a vegetarian? Plant-eating theropod Chilesaurus from the Late Jurassic period of Chile. Nature.

Chilesaurus diegosuarezi Illustration by Gabriel Lío – Nature Magazine

A phylogenetic relative of Tyrannosaurus rex, recently discovered in Chile, fed on plants about 140 million years ago, in the Late Jurassic. Novas et al. (total 10 coauthors) summarize their study as follows: “Theropod dinosaurs were the dominant predators in most Mesozoic era terrestrial ecosystems. Early theropod evolution is currently interpreted as the diversification of various carnivorous and cursorial taxa, whereas the acquisition of herbivorism, together with the secondary loss of cursorial adaptations, occurred much later among advanced coelurosaurian theropods. A new, bizarre herbivorous basal tetanuran from the Upper Jurassic of Chile challenges this conception. The new dinosaur was discovered at Aysen, a fossil locality in the Upper Jurassic Toqui Formation of southern Chile (General Carrera Lake). The site yielded abundant and exquisitely preserved three-dimensional skeletons of small archosaurs. Several articulated individuals of Chilesaurus at different ontogenetic stages have been collected, as well as less abundant basal crocodyliforms, and fragmentary remains of sauropod dinosaurs (diplodocids and titanosaurians).” For complete article go to Nature.

Mountain chickadees from different elevations sing different songs. Can “bird accents” change with elevation? Royal Society Open Science.

Mountain Chickadee Image by Tringa Photography

Authors Carrie L. Branch and Vladimir V. Pravosudov summarize their research as follows: “Song in songbirds is widely thought to function in mate choice and male–male competition. Song is also phenotypically plastic and typically learned from local adults; therefore, it varies across geographical space and can serve as a cue for an individual’s location of origin, with females commonly preferring males from their respective location. Geographical variation in song dialect may reflect acoustic adaptation to different environments and/or serve as a signal of local adaptation. In montane environments, environmental differences can occur over an elevation gradient, favouring local adaptations across small spatial scales. [Branch and Pravosudov] tested whether food caching mountain chickadees, known to exhibit elevation-related differences in food caching intensity, spatial memory and the hippocampus, also sing different dialects despite continuous distribution and close proximity. Male songs were collected from high and low elevations at two different mountains (separated by 35 km) to test whether song differs between elevations and/or between adjacent populations at each mountain. Song structure varied significantly between high and low elevation adjacent populations from the same mountain and between populations from different mountains at the same elevations, despite a continuous distribution across each mountain slope. These results suggest that elevation-related differences in song structure in chickadees might serve as a signal for local adaptation.” For complete research go to Royal Society Open Science.

2014 Update of the United States National Seismic Hazard Maps. Research just released by the US Geological Society.

2014 Update of the US National Seismic Hazard Maps – Click on USGS or map for access to complete report

Petersen et al. (total 17 coauthors) summarize their research as follows: “The national seismic hazard maps for the conterminous United States have been updated to account for new methods, models, and data that have been obtained since the 2008 maps were released (Petersen and others, 2008). The input models are improved from those implemented in 2008 by using new ground motion models that have incorporated about twice as many earthquake strong ground shaking data and by incorporating many additional scientific studies that indicate broader ranges of earthquake source and ground motion models. These time-independent maps are shown for 2-percent and 10-percent probability of exceedance in 50 years for peak horizontal ground acceleration as well as 5-hertz and 1-hertz spectral accelerations with 5-percent damping on a uniform firm rock site condition (760 meters per second shear wave velocity in the upper 30 m, V_S30). In this report, the 2014 updated maps are compared with the 2008 version of the maps and indicate changes of plus or minus 20 percent over wide areas, with larger changes locally, caused by the modifications to the seismic source and ground motion inputs. ” For complete report and maps go to USGS.

Video:

Celebrating the Hubble Telescope 25th Anniversary with an amazing video released by NASA: “This visualization provides a three-dimensional perspective on Hubble’s 25th anniversary image of the nebula Gum 29 with the star cluster Westerlund 2 at its core. The flight traverses the foreground stars and approaches the lower left rim of the nebula Gum 29. Passing through the wispy darker clouds on the near side, the journey reveals bright gas illuminated by the intense radiation of the newly formed stars of cluster Westerlund 2. Within the nebula, several pillars of dark, dense gas are being shaped by the energetic light and strong stellar winds from the brilliant cluster of thousands of stars. Note that the visualization is intended to be a scientifically reasonable interpretation and that distances within the model are significantly compressed.”

Also, you can read the interesting article “How the Hubble Telescope cheated death,” published in Nature, plus the “Top 10 Hubble Images.”

Posted on April 23, 2015 EvoLiteracy News, Video

EvoLiteracy News 04 23 2015

Today, EvoLiteracy News picks are about sexual dimorphism –apparently driven by female mate choice– in Stegosaurus dinosaurs. Also, research just published about editing DNA in human zygotes has generated numerous editorials in science journals (we’ll hear more about it in the upcoming months). The Hubble Telescope celebrates its 25th anniversary. And a powerful video by Stated Clearly Animations on “What is The Evidence For Evolution” — GPC.

Stegosaurus illustration by Karen Carr (click on image)

Sexual Dimorphism in the Plated Dinosaur Stegosaurus? Yes, why not. Study just published in PLoS ONE.

Author E. T. Saitta summarizes the research as follows: “Conclusive evidence for sexual dimorphism in non-avian dinosaurs has been elusive… [D]imorphism in the shape of the dermal plates of Stegosaurus mjosi (Upper Jurassic, western USA)… is most likely a sexually dimorphic feature. One morph possessed wide, oval plates 45% larger in surface area than the tall, narrow plates of the other morph. Intermediate morphologies are lacking as… analysis supports marked size- and shape-based dimorphism… Taphonomy of a new quarry in Montana (JRDI 5ES Quarry) shows that at least five individuals were buried in a single horizon and were not brought together by water or scavenger transportation. This new site demonstrates co-existence, and possibly suggests sociality, between two morphs that only show dimorphism in their plates. Without evidence for niche partitioning, it is unlikely that the two morphs represent different species. Histology of the new specimens in combination with studies on previous specimens indicates that both morphs occur in fully-grown individuals. Therefore, the dimorphism is not a result of ontogenetic change. Furthermore, the two morphs of plates do not simply come from different positions on the back of a single individual. Plates from all positions on the body can be classified as one of the two morphs, and previously discovered, isolated specimens possess only one morph of plates. Based on the seemingly display-oriented morphology of plates, female mate choice was likely the driving evolutionary mechanism rather than male-male competition. Dinosaur ornamentation possibly served similar functions to the ornamentation of modern species…” For complete study go to PLoS ONE.

Gene Editing in Human Zygotes? Again, yes, and we’ll hear more debate about this type of research in the social media and science editorials.

Editing Human DNA at the Zygote Level. Image from Shutterstock (Nature).

Liang et al. (total sixteen authors) just published an article in the journal Protein & Cell about DNA-engineering in human zygotes, specifically of genes involved in blood disorders. The authors summarized the research as follows: “Genome editing tools such as the clustered regularly interspaced short palindromic repeat (CRISPR)-associated system (Cas) have been widely used to modify genes in model systems including animal zygotes and human cells, and hold tremendous promise for both basic research and clinical applications. To date, a serious knowledge gap remains in our understanding of DNA repair mechanisms in human early embryos, and in the efficiency and potential off-target effects of using technologies such as CRISPR/Cas9 in human pre-implantation embryos. [Liang et al.] used tripronuclear (3PN) zygotes to further investigate CRISPR/Cas9-mediated gene editing in human cells. [The authors] found that CRISPR/Cas9 could effectively cleave the endogenous β-globin gene (HBB). However, the efficiency of homologous recombination directed repair (HDR) of HBB was low and the edited embryos were mosaic. Off-target cleavage was also apparent in these 3PN zygotes as revealed by the T7E1 assay and whole-exome sequencing. Furthermore, the endogenous delta-globin gene (HBD), which is homologous to HBB, competed with exogenous donor oligos to act as the repair template, leading to untoward mutations. [The] data also indicated that repair of the HBB locus in these embryos occurred preferentially through the non-crossover HDR pathway. Taken together, [the study] highlights the pressing need to further improve the fidelity and specificity of the CRISPR/Cas9 platform, a prerequisite for any clinical applications of CRSIPR/Cas9-mediated editing.” For complete study go to Protein & Cell; for criticisms go to Nature (Chinese Scientists Genetically Modify Human Embryos).

According to Nature magazine, Liang et al. “attempted to modify the gene responsible for β-thalassaemia, a potentially fatal blood disorder, using a gene-editing technique known as CRISPR/Cas9… [The researchers] injected 86 embryos and then waited 48 hours, enough time for the CRISPR/Cas9 system and the molecules that replace the missing DNA to act — and for the embryos to grow to about eight cells each. Of the 71 embryos that survived, 54 were genetically tested. This revealed that just 28 were successfully spliced, and that only a fraction of those contained the replacement genetic material… [The researchers] also found a surprising number of ‘off-target’ mutations assumed to be introduced by the CRISPR/Cas9 complex acting on other parts of the genome. This effect is one of the main safety concerns surrounding germline gene editing because these unintended mutations could be harmful. The rates of such mutations were much higher than those observed in gene-editing studies of mouse embryos or human adult cells.” For more discussion go to Nature.

25 years of The Hubble Telescope. One of NASA’s amazing scientific achievements… An acute eye on the cosmos!

After twenty five years in operation, and five servicing missions (1993, 1997, 1999, 2002, 2009), NASA’s Hubble Telescope continues to send images of impressive quality. Here is NASA’s overview of The Hubble Telescope (for detailed information go to NASA’s Hubble):

Hubble has made more than 1.2 million observations since its mission began in 1990.

Astronomers using Hubble data have published more than 12,800 scientific papers, making it one of the most productive scientific instruments ever built.

Hubble does not travel to stars, planets or galaxies. It takes pictures of them as it whirls around Earth at about 17,000 mph.

Hubble has traveled more than 3 billion miles along a circular low Earth orbit currently about 340 miles in altitude.

Hubble has no thrusters. To change pointing angles, it uses Newton’s third law by spinning its wheels in the opposite direction. It turns at about the speed of a minute hand on a clock, taking 15 minutes to turn 90 degrees.

Hubble has the pointing accuracy of .007 arc seconds, which is like being able to shine a laser beam on a dime 200 miles away.

Outside the haze of our atmosphere, Hubble can see astronomical objects with an angular size of 0.05 arc seconds, which is like seeing a pair of fireflies in Tokyo from your home in Maryland.

Hubble has peered back into the very distant past, to locations more than 13.4 billion light years from Earth.

The Hubble archive contains more than 100 Terabytes, and Hubble science data processing generates about 10 Terabytes of new archive data per year.

Hubble weighed about 24,000 pounds at launch and currently weighs about 27,000 pounds following the final servicing mission in 2009 – on the order of two full-grown African elephants.

Hubble’s primary mirror is 2.4 meters (7 feet, 10.5 inches) across.

Hubble is 13.3 meters (43.5 feet) long — the length of a large school bus.

For collection of images go to Hubble Gallery.

Video Animation: this time “What is the evidence for Evolution?” by Stated Clearly Animations

Posted on April 14, 2015 EvoLiteracy News

EvoLiteracy News 04 14 2015

Today’s EvoLiteracy News are sushi-, ultra-small nano-lanterns-, and bird-malaria related. The “Wasabi Receptor” protein has been 3D-characterized (watch video); the technology offers insights for possible drug-design to manage pain. “Nano-lanterns” genetically engineered to illuminate inside cells. Plus, recent studies of bird blood parasites, including avian malaria, suggest a likely center of speciation (high diversity) and endemism in Malawi. And a treat: watch a cool animation by TED Ed about ‘How we think complex cells evolved’ via endosymbiosis — GPC.

“Wasabi Receptor” research featured in journal Nature. Yes, it is about the inseparable and irritant sushi companion!

Wasabi and ‘wasabi receptor’ 3D images. Click on image for links to UCSF press release.

The article, authored by Paulsen and four other collaborators, most currently affiliated with the University of California San Francisco, is titled Structure of the TRPA1 Ion Channel Suggests Regulatory Mechanisms. The UCSF press release highlights the research as a “First Look at ‘Wasabi Receptor’ Brings Insights for Pain Drug Development… Protein’s Structure Will Guide Hunt for New Treatments of Inflammation-Induced Pain…”

“TRPA1, the newly visualized protein resides in the cellular membrane of sensory nerve cells. It detects chemical agents originating outside our bodies —pungent irritants found in substances ranging from wasabi to tear gas— but is also triggered by pain-inducing signals originating within, especially those that arise in response to tissue damage and inflammation.”

The authors formally summarize the science as follows: “The TRPA1 ion channel (also known as the wasabi receptor) is a detector of noxious chemical agents encountered in our environment or produced endogenously during tissue injury or drug metabolism. These include a broad class of electrophiles that activate the channel through covalent protein modification. TRPA1 antagonists hold potential for treating neurogenic inflammatory conditions provoked or exacerbated by irritant exposure. Despite compelling reasons to understand TRPA1 function, structural mechanisms underlying channel regulation remain obscure. Here we [Paulsen et al.] use single-particle electron cryo-microscopy to determine the structure of full-length human TRPA1 to 4A resolution in the presence of pharmacophores, including a potent antagonist. Several unexpected features are revealed, including an extensive coiled-coil assembly domain stabilized by polyphosphate co-factors and a highly integrated nexus that converges on an unpredicted transient receptor potential ( TRP)-like allosteric domain. These findings provide new insights into the mechanisms of TRPA1 regulation, and establish a blueprint for structure-based design of analgesic and anti-inflammatory agents.” For original scientific paper go to Nature.

Below, watch 1:10-min ‘Wasabi Receptor’ video released by UCSF:

Ultra small “nano-lanterns” genetically engineered to illuminate cell structures and study them from the inside out. Work published in the Proceedings of the National Academy of Sciences.

Time-lapse dual-color luminescent imaging of cyan and orange colored cells. Click on image to watch video.

Takai et al. (total nine coauthors) titled their article Expanded Palette of Nano-lanterns for Real-time Multicolor Luminescence Imaging. The authors highlight the significance of their findings as follows: “The application of luminescence imaging has been limited mainly by the two drawbacks of luciferases: low brightness and poor color variants. [Takai et al.] report the development of cyan and orange luminescent proteins approximately 20 times brighter than the wild-type Renilla luciferase. The color change and enhancement of brightness were both achieved by exploring bioluminescence resonance energy transfer (BRET) from enhanced Renilla luciferase to a fluorescent protein, a technology that [the researchers] previously reported for the development of the bright yellowish-green luminescent protein Nano-lantern. These cyan and orange Nano-lanterns along with the original yellow Nano-lantern enable monitoring of multiple cellular events, including dynamics of subcellular structures, gene expressions, and functional status, such as intracellular Ca²⁺ change.” For complete study and video images go to PNAS.

The summarized article’s abstract reads: “…The brightness of these cyan and orange Nano-lanterns… allowed [Takai et al.] to perform multicolor live imaging of intracellular submicron structures. The rapid dynamics of endosomes and peroxisomes were visualized at around 1-s temporal resolution, and the slow dynamics of focal adhesions were continuously imaged for longer than a few hours without photobleaching or photodamage. In addition, [the researchers] extended the application of these multicolor Nano-lanterns to simultaneous monitoring of multiple gene expression or Ca²⁺ dynamics in different cellular compartments in a single cell.” Read more in PNAS.

79% of Malawi’s birds infected with blood parasites. High parasite diversity and endemism suggest Malawi’s ecosystems might have been the center of avian malaria origins; PLoS ONE.

Lutz et al. (total eight coauthors) titled their article Parasite Prevalence Corresponds to Host Life History in a Diverse Assemblage of Afrotropical Birds and Haemosporidian Parasites. The authors tested the hypothesis that life history traits of Afrotropical birds predict rates of parasitism by haemosporidian parasites (including Plasmodium, Haemoproteus and Leucocytozoon). Lutz et al. included in their analyses “traits known to be associated with host-vector encounter rates (for example, nest type, nest placement and flocking behavior).” They “combined taxonomic sampling of host species from a wide variety of habitats and life histories in Northern Malawi with the application of PCR-based methods to detect rates of parasitism.” In addition, Lutz et al. documented an “unprecedented prevalence of Plasmodium, Haemoproteus and Leucocytozoon infections across a broad range of birds belonging to 16 orders, 50 families, 100 genera, and 152 species.”

Mosquito biting a bird’s eye, where skin is exposed. Avian blood cell infested with Haemoproteus (center of image).

“Birds with closed cup nests experienced increased rates of Plasmodium infection and decreased rates of Haemoproteus infection, whereas cavity-nesting birds experienced increased rates of Leucocytozoon infection” But, perhaps most significantly, the authors found that “Haemosporidian prevalence in birds from… Malawi [was] higher than… other tropical regions… The results suggest that the Afrotropics is an area of high… endemicity and diversity… Southeastern Africa is… an important region in which to investigate… host-parasite associations, speciation, and the evolution of malaria parasites and other closely related haemosporidians.”

Lutz et al. formally summarize the research as follows: “Avian host life history traits have been hypothesized to predict rates of infection by haemosporidian parasites. Using molecular techniques, we tested this hypothesis for parasites from three haemosporidian genera (Plasmodium, Haemoproteus, and Leucocytozoon) collected from a diverse sampling of birds in northern Malawi. We found that host life history traits were significantly associated with parasitism rates by all three parasite genera. Nest type and nest location predicted infection probability for all three parasite genera, whereas flocking behavior is an important predictor of Plasmodium and Haemoproteus infection and habitat is an important predictor of Leucocytozoon infection. Parasite prevalence was 79.1% across all individuals sampled, higher than that reported for comparable studies from any other region of the world. Parasite diversity was also exceptionally high, with 248 parasite cytochrome b lineages identified from 152 host species. A large proportion of Plasmodium, Haemoproteus, and Leucocytozoon parasite DNA sequences identified in this study represent new, previously undocumented lineages (n = 201; 81% of total identified) based on BLAST queries against the avian malaria database, MalAvi.” Read complete open access study in PLoS ONE.

Video: How we think complex cells evolved – Adam Jacobson TED Ed Lessons – Imagine you swallowed a small bird and suddenly gained the ability to fly … or you ate a cobra and were able to spit poisonous venom! Well, throughout the history of life (and specifically during the evolution of complex eukaryotic cells) things like this happened all the time. Adam Jacobson explains endosymbiosis, a type of symbiosis in which one symbiotic organism lives inside another.

Posted on April 7, 2015April 7, 2015 EvoLiteracy News

EvoLiteracy News 04 07 2015

Today’s EvoLiteracy picks are quite fun: First, a note about Neil deGrasse Tyson’s participation at this year’s UMass Amherst Undergraduate Commencement. Neill will be speaking to 5.5k undergrads on May 8th. Second, three new species descriptions –just published yesterday, April 6– of lizards in the genus Enyalioides, by colleagues at the Museum of Zoology QCAZ at the Pontifical Catholic University of Ecuador (yes, my undergraduate “Alma Mater”). And, third, a cool animation by TEDEd about how geckos defy gravity! Enjoy – GPC.

Neil deGrasse Tyson to be Commencement Speaker at UMass Amherst.

Neil deGrasse Tyson Photo Richard Shotwell

Dr. Neil deGrasse Tyson to be Commencement Speaker at UMass Amherst, on May 8, 2015 – Photo Richard Shotwell

Astrophysicist Neil deGrasse Tyson, Director of the Hayden Planetarium in New York City, will be this year’s keynote speaker at the Undergraduate Commencement of the University of Massachusetts Amherst. Dr. Tyson will address 5,500 students receiving bachelor’s degrees, as well as family and friends, on May 8th.

The UMass Amherst press release states: “Dr. Tyson’s professional research interests include star formation, exploding stars, dwarf galaxies and the structure of the Milky Way. He most recently became executive editor and on-camera host for Cosmos: A Spacetime Odyssey, the 21st century reboot of Carl Sagan’s landmark television series. The show ran 13 episodes and appeared in 181 countries and in 45 languages –on the National Geographic Channels. Cosmos has been nominated for 13 Emmy Awards, including Outstanding Documentary.” Read detailed story at UMass Amherst News & Media Relations, and The Boston Globe.

More from Ecuador and Peru: Colorful New ‘Dwarf Dragons’ Found in South America.

From Nat Geo: “Wood lizards are among the largest and most colorful lizards in South American forests, making their discovery even more notable. It took a decade for scientists to identify the reptiels, which are commonly called wood lizards. They are the Alto Tambo wood lizard (Enyalioides altotambo), rough-scaled wood lizard (E. anisolepis), and Rothschild’s wood lizard (E. sophiarothschildae). The discovery brings the total number of wood lizard species to 15. That’s nearly twice the number of species known in 2006—giving this group of South American reptiles one of the fastest discovery rates of the past decade.”

The study, authored by Omar Torres-Carvajal, Pablo J. Venegas and Kevin de Queiroz was published yesterday, April 6, 2015, in ZooKeys. The authors summarize the research as follows: “The discovery of three new species of Enyalioides from the tropical Andes in Ecuador and northern Peru is reported. Enyalioides altotambo sp. n. [new species] occurs in northwestern Ecuador and differs from other species of Enyalioides in having dorsal scales that are both smooth and homogeneous in size, a brown iris, and in lacking enlarged, circular and keeled scales on the flanks. Enyalioides anisolepis sp. n. [new species] occurs on the Amazonian slopes of the Andes in southern Ecuador and northern Peru and can be distinguished from other species of Enyalioides by its scattered, projecting large scales on the dorsum, flanks, and hind limbs, as well as a well-developed vertebral crest, with the vertebrals on the neck at least three times higher than those between the hind limbs. Enyalioides sophiarothschildae sp. n. [new species] is from the Amazonian slopes of the Cordillera Central in northeastern Peru; it differs from other species of Enyalioides in having caudal scales that are relatively homogeneous in size on each caudal segment, a white gular region with a black medial patch and several turquoise scales in males, as well as immaculate white labials and chin. A molecular phylogenetic tree of 18 species of hoplocercines is presented, including the three species described in this paper and E. cofanorum, as well as an updated identification key for species of Hoplocercinae.” For complete study and images go to ZooKeys, and for popular media article go to NatGeo.

Above: Holotype of Enyalioides altotambo. Photo Luis A. Coloma.

Above: Paratype of Enyalioides altotambo. Photo by Luis A. Coloma.

Above: Holotype of Enyalioides anisolepis. Photo by Omar Torres-Carvajal.

Above: Holotype of Enyalioides sophiarothschildae. Photo by Pablo J. Venegas

How do geckos defy gravity? Watch a cute video, with some serious information by TEDEd Lessons Worth Sharing.

From TEDEd: “Geckos aren’t covered in adhesives or hooks or suction cups, and yet they can effortlessly scale vertical walls and hang from ceilings. What’s going on? Eleanor Nelsen explains how geckos’ feet allow them to defy gravity.” Watch the video produced by TEDEd Lessons Worth Sharing.

Posted on April 4, 2015April 5, 2015 Book Reviews, EvoLiteracy News, Recommended Books

Mini-reviews of Evolution Stands Faith Up: Reflections on Evolution’s Wars

By NOVA Publishers, New York Soft Cover. Find it at Barnes & Noble, Amazon.com, Amazon UK

In preparation for “the sequel”… Here are some mini-reviews of Evolution Stands Faith Up: Reflections on Evolution’s Wars. I thank Greg M. Scott, Herb Silverman, Jeff Podos, Jan A. Pechenik, George A. Lozano and Stan Braude for their generous statements about the book – GPC. More in-depth reviews are posted at EvoLiteracy Book Reviews.

“The sweet spot of this collection of essays is the interface of science, history and literacy. Paz-y-Miño-C is, in essence, a champion of rationalism and a passionate defender of literacy standards. His essays deftly weave hard survey data and memorable turns of phrase with evocative imagery… While the essays in this collection are vast in coverage —from climate change to energy policy, stem cell research, vaccinations and, especially, evolution— a clear underlying theme emerges: [the author’s] goal is no less than to counter, through the lens of history and the majesty of rationalism, social forces that sanction ignorance, celebrate denial and… continue to diminish our global status in the fields of science and technology.” Jeff Podos, PhD, Professor of Biology, University of Massachusetts Amherst, USA.

“Paz-y-Miño-C is a firm believer in evolutionary processes. He would like to see decisions made on the basis of facts, not unsupported opinion. He abhors and fears irrational thinking, especially ‘the views of those who see evil in truth and menace in the realities discovered by science.’ He marvels at the intricacy and diversity of life, and how it came about through natural selection… and is clearly frustrated by the unwillingness of so many to see the beauty and majesty in this view of the world and all that it explains.” – Jan A. Pechenik, PhD, Professor of Biology, Tufts University, USA, author of The Readable Darwin: The Origin of Species, as Edited for Modern Readers.

“Many scientists would probably agree that the struggle against creationism as an alternative to science is a war that must be waged. However, we all know it is a difficult fight… After all, how does one produce a coherent, logical and intelligent argument against an opponent whose very aim is to create confusion, to deny reality, and to promote ignorance? Few among us have the audacity. With this book, Paz-y-Miño-C establishes himself as a clear, lucid, and refreshingly candid fighter of creationism and defender of evolution.” – George A. Lozano, PhD, Estonian Centre of Evolutionary Ecology, Estonia.

“Too many of our colleagues work so hard to appear open minded that their brains seem to have fallen out. When they teach our students that they can pick and choose when to be logical, critical thinkers, they are modeling the type of reasoning that leads to the politics of convenience and its bridesmaids: racism, sexism, and the whole host of xenophobias. Paz-y-Miño-C is a prolific essayist, he does not pull any punches, but when he cuts to the core of an argument, he does it with the flare of a true artist.” – Stan Braude, PhD, Professor of Practice in Biology, Washington University in St. Louis, USA.

Posted on April 3, 2015April 5, 2015 EvoLiteracy News, Excerpts from scientific articles, Scientific Literacy

EvoLiteracy News 04 03 2015

Atlanta Educators Convicted in School Cheating Scandal. Judge ordered them jailed immediately. From The New York Times.

Atlanta Educators Might Go to Jail photos Kent D Johnson

Donald Bullock, a former Atlanta testing coordinator, and Sharon Davis Williams, a former research team director, after judge Jerry W. Baxter ordered the educators jailed immediately. Photo by Kent D. Johnson.

As an educator –although, mostly college– this story is both distressing and sad for me since I support high standards in education, at the same time that consider public schools to be underfunded and in constant need of financial and public support. The historical sequels of neglect and segregation -in the region- might also explain the complexity of this case, but the evidence presented to the court seems unequivocal — GPC.

Alan Blinder, who writes for The New York Times, examines the “largest cheating scandal in the nation’s history, [in which] a jury convicted 11 educators —a mixture of Atlanta public school teachers, testing coordinators and administrators— for their roles in a standardized test cheating that tarnished a major school district’s reputation and raised broader questions about the role of high-stakes testing in American schools.” The defendants (11 of 12) were convicted of racketeering, a felony that carries up to 20 years in prison.

Judge Jerry W. Baxter ordered most of the educators jailed immediately, and they were led from the courtroom in handcuffs. “Defense lawyers, some of whom were clearly angered by Judge Baxter’s decision to jail the educators, immediately began planning appeals and said they were stunned by the verdicts,” reports journalist Alan Blinder in his NYT article. “I don’t like to send anybody to jail,” Judge Baxter said. “It’s not one of the things I get a kick out of. But they have made their bed, and they’re going to have to lie in it, and it starts today”… Read complete story in The New York Times. For a local perspective and updates since 2008, see report in The Atlanta Journal Constitution, for an international take see The Guardian.

“Little-Foot” older than “Lucy.” New technology dates skeleton 3.67 million years old. What does it mean for hominid evolution?

Little Foot Skull 2.67 Million Years Old

The skull extracted from the cave breccia. Photo by Jason Heaton. Click on image for higher resolution.

“Little Foot is a rare, nearly complete skeleton of Australopithecus first discovered 21 years ago in a cave at Sterkfontein, in central South Africa. The new date places Little Foot as an older relative of Lucy, a famous Australopithecus skeleton dated at 3.2 million years old that was found in Ethiopia. It is thought that Australopithecus is an evolutionary ancestor to humans that lived between 2 million and 4 million years ago.” Read Purdue University press release in EurekAlert! Or see the original article in the journal Nature.

The Little Foot skeleton represents Australopithecus prometheus, a species very different from its contemporary, Australopithecus afarensis (“Lucy”), and with more similarities to the Paranthropus lineage. The dating relied on a radioisotopic technique, which uses radioisotopes within several rock samples surrounding a fossil to date when the rocks and the fossil were first buried underground.

“…Australopithecus africanus and Paranthropus did not all have to have derived from Australopithecus afarensis [Lucy]… This new date [Little Foot’s 3.67 my] is a reminder that there could well have been many species of Australopithecus extending over a much wider area of Africa…”

The authors of the study, Granger et al. (total of 6 coauthors), who just published their results in Nature, summarize the work as follows: “The cave infills at Sterkfontein contain one of the richest assemblages of Australopithecus fossils in the world, including the nearly complete skeleton StW 573 (Little Foot) in its lower section, as well as early stone tolls in higher sections. However, the chronology of the site remains controversial due to the complex history of cave infilling. Much of the existing chronology based on U-PB and paleomagnetic stratigraphy has recently been called into question by the recognition that dated flowstones fill cavities formed within previously cemented breccias and therefore do not form a stratigraphic sequence. Earlier dating with cosmogenic nuclides suffered a high degree of uncertainty and has been questioned on grounds of sediment reworking. Here we use isochron burial dating with cosmogenic Al-26 and Be-10 to show that the breccia containing StW 573 did not undergo significant reworking, and that is was deposited 3.67 ± 0.16 My ago, far earlier than the 2.2 My flowstones found within it. The skeleton is thus coeval with early Australopithecus afarensis in eastern Africa. We also date the earlies stone tools at Sterkfontein to 2.18 ± 0.21 My ago, placing them in the Oldowan at a time similar to that found elsewhere in South Africa at Swartkans and Wonderwerk.” For complete study go to Nature.

Posted on April 1, 2015 EvoLiteracy News

EvoLiteracy News 04 01 2015

Happy Wednesday, April 1st, everyone!

Today, my picks for EvoLiteracy News are summarized in the following questions: Do liberal politicians smile more sincerely (= genuine happiness) than conservative politicians (= apparent happiness)? Does growing up in a deprive-from-resources environment (poverty) affect human brain development? How do sexual and natural selection interact when driving the evolution of plumage-coloration in birds? Below are the answers. Plus, don’t forget to visit the Photography Page of Evolution Literacy, which includes images of wildlife, landscapes, museums, monuments and cities from many countries, go to EvoLiteracy Photos.

Liberal Politicians Smile Sincerely… Conservatives Not So Much. Conservatives report, but liberals display, greater happiness. Science Magazine.

Wojcik et al. (total of 5 coauthors) summarize their study as follows: “Research suggesting that political conservatives are happier than political liberals has relied exclusively on self-report measures of subjective well-being. Wojcik et al. show that this finding is fully mediated by conservatives’ self-enhancing style of self-report and then describe three studies drawing from “big data” sources to assess liberal-conservative differences in happiness-related behavior. Relative to conservatives, liberals more frequently used positive emotional language in their speech and smiled more intensely and genuinely in photographs. The results were consistent across large samples of online survey takers, U.S. politicians, Twitter users, and LinkedIn users. Wojcik et al. findings illustrate the nuanced relationship between political ideology, self-enhancement, and happiness and illuminate the contradictory ways that happiness differences can manifest across behavior and self-reports.” See study in Science Magazine.

Poverty Does Affect Brain Development. Family income, parental education and brain structure in children and adolescents. Nature Neuroscience.

Noble et al. (total of 25 coauthors) write: “Socioeconomic disparities are associated with differences in cognitive development. We investigated relationships between socioeconomic factors and brain morphometry, independently of genetic ancestry, among a cohort of 1,000+ typically developing individuals between 3 and 20 years of age. Income was associated with brain surface area. Among children from lower income families, small differences in income were associated with relatively large differences in surface area, whereas, among children from higher income families, similar income increments were associated with smaller differences in surface area. These relationships were most prominent in [brain] regions supporting language, reading, executive functions and spatial skills; surface area mediated socioeconomic differences in certain neurocognitive abilities. These data imply that income relates most strongly to brain structure among the most disadvantaged children.” For access to complete article go to Nature Neuroscience.

Natural and sexual selection act on different axes [“directions”] of variation in avian plumage color. Science Advances.

Authors Peter O. Dunn, Jessica K. Armenta and Linda A. Whittingham summarize their research as follows: “The bright colors of birds are often attributed to sexual selection on males, but in many species both sexes are colorful and it has been long debated whether sexual selection can also explain this variation. Dunn et al. show that most evolutionary transitions in color have been toward similar plumage in both sexes, and the color of both sexes (for example, bright or dull) was associated with indices of natural selection (for example, habitat type), whereas sexual differences in color were primarily associated with indices of sexual selection on males (for example, polygyny [one male mating with several females] and large testes size). Debate about the evolution of bird coloration can be resolved by recognizing that both natural and sexual selection have been influential, but they have generally acted on two different axes [= “directions”]: sexual selection on an axis of sexual differences and natural selection on both sexes for the type of color (for example, bright or dull).” See complete article in Science Advances.

Birds of Paradise — Photos by Tim Laman. Click on image to be redirected to ‘Birds of Paradise’ at NatGeo

Dunn et al. explain that “Darwin’s theory of sexual selection was based on his observations of the bright colors of males, which he thought were preferred by females and led to a mating advantage for more colorful males. Wallace, on the other hand, pointed out that in many species, females are as ‘gay and brilliant’ as the male, and he suggested that dichromatism [the “two colors,” one in males, the other in females] evolved as a consequence of nest predation favoring more cryptic females.” The authors “examined both male and female plumage color in relation to 10 indices of natural and sexual selection to test whether dichromatism was primarily due to sexual selection, as Darwin proposed, whereas the color of both sexes was primarily due to natural selection [Wallace’s proposal].”

The Answer Is Both: Dunn et al. concluded that “Both natural and sexual selection have influenced the evolution of bird coloration, but in many respects, they have acted on two different axes [ = “directions”]: sexual selection on an axis of sexual differences and natural selection on an axis of color (for example, dull or bright) in both sexes. Thus, debate about the causes of variation in bird coloration may be resolved by recognizing that natural and sexual selection have generally acted on two different axes.” Science Advances.

Note: Sexual dimorphism driven by sexual selection is a wide spread phenomenon, documented in the fossil record; below, Parasaurolophus (male and female), a hadrosaurid dinosaur from the end of the Cretaceous (Art by Pavel Riha). The topic ‘sexual selection’ was addressed extensively by Charles Darwin in ‘The Descent of Man, and Selection in Relation to Sex‘ (1871), and by Alfred R. Wallace in ‘Tropical Nature, and Other Essays‘ (1878).

Reviews of Evolution Stands Faith Up: Reflections on Evolution’s Wars.

Paz-y-Mino-C_Book_Cover_Evolution_Stands_Faith_Up_JPEG

Available at NOVA, Barns & Noble, Amazon.com, Amazon UK

“…Shot-gun marriages between evolution and faith have never worked, despite the tradition of pointing the barrel at evolution’s head. The truth is that evolution likes it single. Free, with no stoppers of thought or restrains on logic. And when lured unknowingly into the altar by those who see facts and fiction compatible, evolution has consistently stood belief up and walked away, sometimes run, toward its secular turf… [The] dream of arranging evolution’s wedding with belief will remain dormant for as long as evolution is awake.” Provocative, intriguing, a contemporary and concise analysis of the clashes between science and faith: In this book, Guillermo Paz-y-Miño-C examines the societal sequels in public education, the future of America’s science and academia of believing in a deity. For this evolutionary biologist, educator and public speaker, “science is [the only] refined device for resolving ordinary curiosity and a powerful liberator of superstition. He thinks of science as “the subsistence kit to defeat re-emerging fundamentalism” in the world. With a journalistic style in short, yet documented essays, Paz-y-Miño-C encourages the reader to question “faith healing,” the “silly” forecast of Armageddon on two occasions in 2012 (after postponing the first engagement), or the “wrongly called” The God Particle, which scrambles fiction with facts. He considers “belief” to be a “disruptor,” which delays and stops the correct comprehension and acceptance of evidence. He alerts us about the threats of rejecting science, our African and ape evolutionary ancestry, and the epidemic growth of anti-intellectualism among decision makers, whose interest in replacing “curiosity-driven science” with profitable laboratory-bench work to secure sales of “science products” will drive the “culture of discovery in America” to vanish. But this author also contrasts his inner “frustration in attempting to reverse, at least around [his] immediate circle of influence, such trend…” with essays in which his contagious passion for science emerges. In his prose, Paz-y-Miño-C ignites our imagination to “take off from the roof of the Boston Museum of Science and its Charles Hayden Planetarium, while flying in a helicopter that, after metamorphosing into a spaceship, leaves Earth to immerse us into galactic infinitude.” Or to hike among sea lions, while they rest on the Galapagos shores, and feel as Darwin did the magnificence of nature. Or to contemplate the night sky from the top of the largest volcano in the World, Mauna Kea, in Hawaii, and accept the fact that, one day in the distant future, all its telescopes —or their remains— will drift away on their carrier, the late “Big Island,” and sink in the Pacific when the summit of Mauna Kea succumbs to erosion, hence following the drowning fate of the Hawaiian Islands. This open-ended book assures: “Once embraced by all, this truly universal language —scientific rationalism/empiricism and evolution— shall lead us to a more cohesive understanding of nature and of our amazingly diverse human condition. Humanity’s ultimate challenge will be to collectively embrace reality, with no stoppers of thought or restrains on logic.” (Imprint: Novinka).