2015 Nobel Prize in Chemistry Goes to Curiosity-Based Research

By Guillermo Paz-y-Miño-C PhD — © 2015

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

Nobel Prize in Chemistry Goes to Curiosity-Based Research

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

“…Mutations are essential to evolutionary change; they provide the genetic variability that lineages of organisms need to persist over the eons. At the same time, evolution has equipped our cells with repairing mechanisms to fix, edit DNA errors that can be detrimental…”

If completely stretched into a single, long molecular chain, the DNA of a human cell would measure about two meters. During our lifetimes, our bodies would replicate enough DNA that, theoretically, it could be extended from Earth to the Sun, and back, 250 times. Ample opportunities to accumulate 37 trillion mutations while re-copying the genetic material.

D - DNA Repair image by Tom Ellenberger

DNA-repair, image by Tom Ellenberger, Washington University in St. Louis.

Yet, evolution has equipped our cells with repairing mechanisms to fix, edit such DNA errors. And this year’s Nobel Prize in Chemistry has been awarded to Tomas Lindahl (Sweden), Aziz Sancar (Turkey) and Paul Modrich (US) precisely for discovering and characterizing –independently— these processes.

What I admire most in these investigators is their obsessive pursue of knowledge during a vigorous exploration of the intimacy of our inner molecules. As Modrich puts it “curiosity-based research is so important; you never know where it is going to lead.” And it did lead them from almost extraneous observations of the harmful effects of UV-light on the DNA of bacteria to –four decades later— its applications to our current understanding of cancer, neuro-degenerative disorders and ageing. Another lesson for today’s academic administrators infatuated with worshiping the science-for-profit model.

All began in the 1920s when American geneticist Hermann Muller (Nobel Laureate in Physiology or Medicine, 1946) found that X-rays could harm bacterial cells. By the 1940s, it was known to scientists that UV-light also had mutagenic effects on most cells. Interestingly, despite radiation-induced damage in bacteria, laboratory colonies continued to persist, which led researchers to infer that these organisms had repair-mechanisms to reinstate the internal chemistry. In 1944, DNA was recognized as the material of heredity and UV-light as a deteriorating agent of its structure.

“…What I admire most in these investigators is their obsessive pursue of knowledge during a vigorous exploration of the intimacy of our inner molecules… [Their] story only grows in beauty…”

The first breakthrough in DNA-repair mechanisms was unexpected: Albert Kelner (US) discovered that, in response to UV-induced cellular damage, bacterial enzymes could reverse the process by using –surprisingly— light, and capturing its energy-particles (photons), which excite electrons in the enzymes’ functional parts, thus jump-starting their repairing engines. The process was termed photo-reactivation and the enzymes photolyases. The story only grows in beauty.

Keep in mind that DNA is built of four “bases,” called adenine A, guanine G, cytosine C and thymine T. Under ordinary circumstances, A always pairs with T, and G with C, hence forming the steps of the DNA’s double helix, which is usually depicted as a staircase. In 19741976, Tomas Lindahl studied a frequent mutation in which G, rather than pairing with C (as G-C), had, as partner, the base U (uracil), a constituent of other molecules in the cell. Why? C and U are very similar, but when C loses some of its parts, due to predictable chemical contingencies, it can resemble U more closely. Thus DNA would temporarily accept the pairing G-U, but the cell would fix it by enzymatically chopping off U and restoring the correct coupling G-C. And Lindahl mapped, so elegantly, this entire process, which was labeled single-base excision repair. Later, it became part of the cell’s toolbox for DNA repair mechanisms, of which numerous have been described.

A - Base Excision Repair

Illustration: Johan Jarnestad – The Royal Swedish Academy of Sciences (click to enlarge).

In a separate study, Aziz Sancar experimentally manipulated with UV-light-induced mutations and characterized how the cell could fix errors via an alternative pathway, termed multiple-base excision repair, which included cutting off several bases, not only one, as described by Lindahl. Sancar knew that UV-light could make T behave strangely and pair with its homologue (T-T), rather than with A, as it normally does (T-A).

Let us imagine two parallel rows of DNA sequence in which the top one is G,C,T,T,C,G. Its complementary, bottom, pairing (following the rule A-T and G-C) would be C,G,A,A,G,C. However, UV-light damage can induce the Ts on the top row to pair with each other, as T-T, rather than with their corresponding As in the bottom, as T-A and T-A. Thus creating a bump loop on the top row (T-T), leaving the As in the bottom unpaired.

In 1983, Sancar plotted the entire mechanism of repair of the T-T mutation, which included multiple enzymes responsible for accurately cutting and restoring 12 bases in the top row of DNA, five prior and five post T-T. An amazing work.

B - Nucleotide Excision Repair

Illustration: Johan Jarnestad – The Royal Swedish Academy of Sciences (click to enlarge).

By 1989, Paul Modrich had unveiled a third mechanism, which involved the fixing of DNA sequence mismatches, which randomly emerge during cell divisions. A process called DNA mismatch repair. It included even larger stretches (beyond 12 bases) of folded DNA, which specific enzymes would cut and restore to the correct sequence (watch VIDEO).

C - Mismatch Repair

Illustration: Johan Jarnestad – The Royal Swedish Academy of Sciences (click to enlarge).

What is the value of curiosity-driven research? Because cancer, neuro-degeneration and ageing start with DNA damage, almost all we understand about them –including drug treatment— relies on the basic science of DNA repair mechanisms. — © 2015 by Evolution Literacy all rights reserved.

E - DNA Repair cartoon

DNA Repair during evolution… Image from public domain Google Images

Suggested Readings:

Historical paper by Tomas Lindahl published in Nature 1993: Instability and decay of the primary structure of DNA.

Press Release from the Royal Swedish Academy of Sciences: the 2015 Nobel Prize in Chemistry

Scientific Background on the 2015 Nobel Prize in Chemistry: Mechanistic Studies of DNA Repair, compiled by the Class for Chemistry of the Royal Swedish Academy of Sciences.

Popular Science Background: DNA Repair – Providing Chemical Stability for Life.

History of the Nobel Prize in Chemistry 1901 – 2015.

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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.comAmazon UK.

Paz-y-Mino-C_Book_Cover_Evolution_Stands_Faith_Up_JPEG

“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.

“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.

Evolution Controversy and the Incompatibility of Science and Religion

Published in The International Journal of Science in Society — Paz-y-Miño-C & Espinosa (2015). Evolution Controversy: A Phenomenon Prompted by the Incompatibility between Science and Religious Beliefs. Int. J. Sci. Soc. 7(2). ISSN 1836-6236. -May 14, 2015.

Why do people hesitate to embrace evolution? What triggers the controversy evolution-and-science versus creationism? What factors characterize the evolution wars? Will the conflict evolution-and-science versus religiosity ever end? In a latest study published in the International Journal of Science in Society, Guillermo Paz-y-Miño-C and Avelina Espinosa address these questions under the conceptual framework of the Incompatibility Hypothesis, which the authors have proposed  — EvoLiteracy.

In previous publications, ranging from 2009 to 2014, Paz-y-Miño-C & Espinosa have formally examined the Incompatibility Hypothesis (IH), a conceptual, theoretical framework to explain the foundations of the “evolution wars,” as well as the societal struggles between science and faith. In their most recent article, published in The Int. J. Sci. Soc. Vol. 7 No. 2 (May 14, 2015), the authors state:

Evolution Controversy Int J Sci Soc May 14 2015 Paz-y-Mino-C Espinosa

Click on image to enlarge

“The observable phenomenon in society, which we aim at examining academically, is the controversy over acceptance of evolution, the conflicts that emerge when facts organized in a rational interpretation of the empirical reality (i.e. the science of evolution) challenge belief-based answers to questions about the origin of the universe and life. [The incompatibility proposal] IH is an ultimate-level [of analysis] hypothesis, rather than a proximate one. IH explains the cause of the controversy, its fundamental reason. IH addresses directly the inquiry: what elicits the controversy evolution-and-science versus creationism? And it offers an educated answer: their intrinsic and opposing approaches to assess reality, i.e. science by means of testing hypotheses, falsifying and/or testing predictions and replication of experiments; creationism, in contrast, via belief in supernatural causality.”

The authors acknowledge and value alternative approaches to examining the evolution controversy, which they consider “proximate levels of analysis of the [societal conflicts], including the detailed and simultaneous characterization of multiple factors that can influence an individual’s acceptance of evolution and scientific evidence, e.g. religious beliefs, pro-life beliefs and political ideology; or political activity, political and religious conservatism, knowledge about evolution and its relevance, creationist reasoning, evolutionary misconceptions, and exposure to evolution; or religious affiliation, frequency of attendance to religious services, college academic level, exposure to evolution in high school, and college major.” The authors themselves have examined some of these variables in their research, however, they highlight that “from a research program perspective, the proximate-level studies, or descriptions of the evolution controversy, are auxiliary in essence, while IH [plays the role of] a central hypothesis, as a guiding ultimate level of [scrutiny].”

Here is the abstract of the 2015 study:

“The incompatibility between science and the belief in supernatural causation helps us understand why people do not accept evolution. Belief disrupts, distorts, delays or stops (3Ds + S) the acceptance of scientific evidence. Here we examine the evolution controversy under three predictions of the incompatibility hypothesis:

Cover Int Journal Science Society Paz-y-Mino-C and Espinosa 2015

Click on image to be redirected to the International Journal of Science in Society

(1) Chronological-conflict-and-accommodation, which explains the historical re-emergence of antagonism between evolution and religion when advances in science continue to threaten the belief in supernatural causation; in such situations, creationists’ rejection of and subsequent partial acceptance of the new scientific discoveries are expected.

(2) Change in evolution’s acceptance as function of educational attainment, which explains the positive association between acceptance of evolution and level of education.

And (3) change in evolution’s acceptance as function of religiosity, which explains the negative association between acceptance of evolution and level of religious beliefs.

We rely on an ample assessment of the attitudes toward evolution by highly-educated audiences (i.e. research faculty, educators of prospective teachers, and college students in the United States) to characterize the associations among understanding of science and evolution, personal religious convictions, and conservative ideology. We emphasize that harmonious coexistence between science and religion is illusory. If co-persisting in society, their relationship will fluctuate from moderate to intense antagonism.”

The complete article, which includes 23-pages, 11 figures and 59 references, can be downloaded —for free— from the International Journal of Science in Society. Click on the images below to enlarge, or go to the journal website to download the PDF.

Figures Evolution Controversy Paz-y-Mino-C and Espinosa IJSS 2015

Suggested Readings where The Incompatibility Hypothesis is discussed:

BOOK small format - Measuring the Evolution Controversy 2016Book: Paz-y-Miño-C., G & Espinosa, A. 2016. Measuring the Evolution Controversy: A Numerical Analysis of Acceptance of Evolution at America’s Colleges and Universities. Cambridge Scholars Publishing, Newcastle, United Kingdom. ISBN (10): 1-4438-9042-1, ISBN (13): 978-1-4438-9042-7. The publisher has made available a “VIEW EXTRACT” (in PDF), which includes the first 30-pages of the book: Cover, Table of Contents, Acknowledgments, Preface, Chapter ONE and the beginning of Chapter TWO. For PDF of color illustrations go to Image Resources of Didactic Relevance. — Mini Reviews: “Isaac Newton is said to have been a seriously religious man. Yet it is primarily due to Newton’s influence that science, unable to test propositions concerning the supernatural, focuses instead on finding natural causes for natural phenomena. Thus science is not a “belief,” but rather an epistemology aimed at understanding the natural world. In their welcome book, Paz-y-Miño-C and Espinosa succinctly draw the distinction between real science and the religiously-inspired belief in supernatural explanations for natural phenomena—including the origin and history of life. Why does the resistance to evolution persist in this modern day and age? The great contribution of “Measuring the Evolution Controversy” is the rich content of data and analysis that asks detailed questions about the social, economic and political backgrounds of those who tend to reject evolution versus those who accept evolution as science. The authors deftly analyze their data drawn from institutions of higher learning in the United States and particularly New England—which stands as a microcosm of the rest of the country, and indeed elsewhere in the world. It is their scientific approach to these issues which makes this book stand out as a uniquely original contribution.” Dr. Niles Eldredge, Curator Emeritus of Paleontology at The American Museum of Natural History, New York. — “Pro-science activists and educators constantly bemoan the resistance to the teaching of evolution in the United States. All of us have anecdotes about encounters with the public, parents and students who are misinformed by their churches, Religious-Right groups, and creationist organizations. Paz-y-Miño-C and Espinosa present hard data that support the anecdotal evidence. They also show that although anti-evolutionism typically begins with religion, it is a multi-faceted problem that intersects with political and cultural ideologies. Gathered through careful research over a period of years, their data will enable scientists and defenders of science education to comprehend the roots of the evolution controversy and counteract resistance to evolution more strategically and effectively.” Dr. Barbara Forrest, Co-author with Paul R. Gross of Creationism’s Trojan Horse: The Wedge of Intelligent Design (2007), and expert witness for plaintiffs, Kitzmiller et al. v. Dover Area School District (2005).

Journal Book Covers Incompatibility Science Religion - VERTICAL

Click on image to enlarge

Book-Chapter: Paz-y-Miño-C., G. & Espinosa A. 2014a. The Incompatibility Hypothesis: Evolution vs. Supernatural Causation. Pp. 3-16. [PDF] In G. Trueba (Ed.) Why Does Evolution Matter? The Importance of Understanding Evolution. Cambridge Scholars Publishing, Newcastle, United Kingdom. ISBN (10): 1-4438-6518-4, ISBN (13): 978-1-4438-6518-0.

Scientific Article: Paz-y-Miño-C, G. & Espinosa A. 2014b. Acceptance of Evolution by America’s Educators of Prospective Teachers: the disturbing reality of evolution illiteracy at colleges and universities. New England Science Public: Series Evolution Vol. 2, No. 1. [PDF] The complete 92-page study includes 23 figures, statistics, 34 maps, 12 tables, and a companion slide show ‘Image Resources’ for science journalists, researchers and educators. The supplementary materials include 15s figures and 25s tables. This article has been featured in the Richard Dawkins Foundation Newsletter and website. RDF has also posted a note in its Facebook page.

Book-Chapter: Paz-y-Miño-C., G. & Espinosa A. 2013a. The Everlasting Conflict Evolution-and-Science versus Religiosity. pp. 73-97 [PDF]. In G. Simpson & S. Payne (eds) Religion and Ethics NOVA Publishers, New York. Download OPEN ACCESS at NOVA.

Scientific Article: Paz-y-Miño-C., G. & Espinosa A. 2013b. Galapagos III world evolution summit: why evolution matters. Evolution: Education and Outreach, 6:28. [PDF]. Open Access.

Scientific Article: Paz-y-Miño-C, G. & Espinosa A. 2013c. Attitudes toward evolution at New England colleges and universities, United States. New England Science Public: Series Evolution 1: 1-32. [PDF]. Read commentaries in Happy Birthday Charles Darwin – The Boston Globe and Basic Knowledge of Darwin’s Theory Lost in Some Classes – The Boston Globe Metro. The Standard Times of New Bedford published the note Evolution Misunderstood By Students, Faculty.

Scientific Article: Paz-y-Miño-C, G. & Espinosa, A. 2012a. Introduction: Why People Do Not Accept Evolution: Using Protistan Diversity to Promote Evolution Literacy. Journal of Eukaryotic Microbiology 59:101-104. [PDF].

Public Talks, Interviews, and Discussions where The Incompatibility Hypothesis is addressed:

Interview by the Richard Dawkins Foundation for Reason and Science (April 1, 2014) where both the book Evolution Stands Faith Up: Reflections on Evolution’s Wars, and the Incompatibility Hypothesis is discussed.

Disproof Atheism Society, Boston University (February 2014).

Atheists Alliance of America 2013, National Convention in Boston (watch and/or DOWNLOAD VIDEO from the AAA website).

Atheists Alliance of America 2013 (watch video in YouTube posted on September 2, 2013).

 

Other Scientific Publications Related to Acceptance of Evolution in the US and the World:

Paz-y-Miño-C, G. & Espinosa A. 2012b. Educators of prospective teachers hesitate to embrace evolution due to deficient understanding of science/evolution and high religiosity. Evolution: Education and Outreach 5:139-162. [PDF]. Follow a discussion on this study in The Chronicle of Higher Education.

Paz-y-Miño-C, G., Espinosa A. & Bai, C. 2011a. The Jackprot Simulation couples mutation rate with natural selection to illustrate how protein evolution is not random. Evolution: Education and Outreach 4:502-514 [PDF] Visit The Jackprot Simulation website to access computer program and tutorials.

Paz-y-Miño-C, G. & Espinosa A. 2011b. On the theory of evolution versus the concept of evolution: three observations. Evolution: Education and Outreach 4:308–312 [PDF].

Paz-y-Miño-C, G. & Espinosa A. 2011c. New England faculty and college students differ in their views about evolution, creationism, intelligent design, and religiosity. Evolution: Education and Outreach 4:323–342 [PDF].

Paz-y-Miño-C, G. & Espinosa, A. 2010. Integrating horizontal gene transfer and common descent to depict evolution and contrast it with “common design.” J. Eukaryotic Microbiology 57: 11-18 [PDF].

Paz-y-Miño-C, G. & Espinosa, A. 2009a. Acceptance of evolution increases with student academic level: a comparison between a secular and a religious college. Evolution: Education & Outreach 2:655–675 [PDF].

Paz-y-Miño-C, G. & A. Espinosa. 2009b. Assessment of biology majors’ versus non-majors’ views on evolution, creationism and intelligent design. Evolution Education and Outreach 2: 75-83 [PDF].

Related Readings:

Book: Paz-y-Miño-C., G. 2013. Evolution Stands Faith Up: Reflections on Evolution’s Wars. NOVA Publishers, New York.

Popular media article: Paz-y-Miño-C, G. & Espinosa A. 2012c. Atheists’ knowledge about science and evolution. Secular World 8(1): 33-36 [PDF].

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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.comAmazon UK.

Paz-y-Mino-C_Book_Cover_Evolution_Stands_Faith_Up_JPEG“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.

EvoLiteracy News 05 08 2015

Happy Friday everyone! Today’s EvoLiteracy News include: First, a behavioral study suggesting that blue whales might lack the innate behavioral repertoire to avoid collisions with cargo ships; after all, ships are relatively new, strange objects in the oceans, in contrast to the millions-of-years of whale evolutionary history in pristine environments. Second, a very important analysis on why scientist should avoid using bar-graphs to report data and, instead, go for more compelling alternatives  for data depiction in scientific journals. And third, a super simple, yet powerful video on how to interpret population pyramids. Enjoy! — GPC.

Blue whales have limited behavioral responses for avoiding collision with large ships. Published in Endangered Species Research.

Why do blue whales not avoid collisions with cargo ships by simply swimming away or deep diving when danger approaches? It seems like the whales lack the behavioral repertoire to interpret the ships as danger; after all, cargo ships are new, foreign items in the whales’ natural environment; whales have evolved for millions of years without unnatural disturbances in the oceans. A new study by McKenna et al. (total five coauthors) brings some light into this problem, but clear-cut, definite answers are still needed.

Blue Whale illustration by Soul Pix

Blue Whale – Illustration by Soul Pix

McKenna et al. summarize the research as follows: “Collisions between ships and whales are reported throughout the world’s oceans. For some endangered whale populations, ship strikes are a major threat to survival and recovery. Factors known to affect the incidence and severity of collisions include spatial co-occurrence of ships and whales, hydrodynamic forces around ships, and ship speed. Less understood and likely key to understanding differences in interactions between whales and ships is whale behavior in the presence of ships. In commercial shipping lanes off southern California, [the authors] simultaneously recorded blue whale behavior and commercial ship movement. A total of 20 ship passages with 9 individual whales were observed at distances ranging from 60 to 3600 m. [The researchers] documented a dive response (i.e. shallow dive during surface period) of blue whales in the path of oncoming ships in 55% of the ship passages, but found no evidence for lateral avoidance. Descent rate, duration, and maximum depth of the observed response dives were similar to whale behavior immediately after suction-cup tag deployments. These behavioral data were combined with ship hydrodynamic forces to evaluate the maximum ship speed that would allow a whale time to avoid an oncoming ship. [The authors’] analysis suggests that the ability of blue whales to avoid ships is limited to relatively slow descents, with no horizontal movements away from a ship. [The authors] posit that this constrained response repertoire would limit their ability to adjust their response behavior to different ship speeds. This is likely a factor in making blue whales, and perhaps other large whales, more vulnerable to ship strikes.” Open access to PDF of paper is available at ESR.

Should scientific journals request authors to change their practices for presenting continuous data in small sample size studies? An article in PLoS Biology recommends it.

This article is particularly important, it provides all of us with urgent advice on how to report statistical analyses (i.e. graphics of small samples) in our papers. Weissgerber et al. (total five authors) strongly recommend journal editors, authors and the scientific community to be more cautious when presenting results to readers, and here is why:

I will simplify the complexity of the Weissgerber et al. paper (although it is very friendly written) by addressing only what is substantial and eliminating the technicalities. However, readers might need to explore the content below with quality attention.

Let’s start by summarizing the authors’ abstract: “Figures in scientific publications are critically important because they often show the data supporting key findings… [As] scientists, we urgently need to change our practices for presenting continuous data in small sample size studies. Papers rarely [include] scatterplots, box plots, and histograms that allow readers to critically evaluate continuous data. Most papers [present] continuous data in bar and line graphs. This is problematic, as many different data distributions can lead to the same bar or line graph. The full data may suggest different conclusions from the summary statistics. [The authors] recommend training investigators in data presentation, encouraging a more complete presentation of data, and changing journal editorial policies…

Weissgerber et al. (PLoS Biology 2015) examined 700 studies published in reputable physiology journals. They “focused on physiology because physiologists perform a wide range of studies, including human studies, animal studies, and in vitro laboratory experiments.” The authors found that 86% of the studies reported statistical analyses in bar graphs, which can be misleading, particularly when small samples are being measured. They explain this in three main figures. Below, I summarize the Weissgerber et al.’s images and text, plus include explanations in color to facilitate the interpretation of the material (remember that the original article can be downloaded from PLoS Biology).

First: fundamentally different data sets could lead authors to report the results [and statistics] in bar graphs and draw from them unwarranted conclusions.
Figure ONE PLoS Biol 2015

Adapted from Weissgerber et al. (PLoS Biology 2015). Click on image to enlarge.

Many different datasets can lead to the same bar graph, as depicted in the example of Panel A (above), a common practice in 86% of the scientific papers examined by Weissgerber et al. (PLoS Biology 2015). For instance, Panel A depicts two seemingly different groups, the black bar on the left is lower than the white bar on the right. Is this difference true and for the reasons we think?

The visualization of the full data (as depicted in Panels B, C, D and E) may suggest different conclusions as cautioned by Weissgerber et al. (PLoS Biology 2015).

Panel B: look how the data-point distributions in both groups appear symmetric. Although the data suggest a small difference between these groups, there is substantial overlap between groups (the position of many of the dots on the left clearly overlaps with the position of the dots on the right).

Panel C, the apparent difference between groups is driven by a single outlier.

Panel D suggests a possible bimodal distribution of the data points. Additional data are needed to confirm that the distribution is indeed bimodal and to determine whether this effect is explained by a covariate.

Panel E, the smaller range of values in group two (right) may simply be due to the fact that there are only a few observations (four data points). Additional data for group two would be needed to determine whether the groups are actually different.

Second: A common assumption in bar graphs is that the reported groups are not only different, but also independent. And that might not always be the case.
Figure TWO PLoS Biol 2015

Adapted from Weissgerber et al. (PLoS Biology 2015). Click on image to enlarge.

Additional problems can emerge when using bar graphs to show paired data, as explained by Weissgerber et al. (PLoS Biology 2015):

The bar graph on Panel A (mean ± SE, where SE is Standard Error) suggests that the groups (black and white) are independent and provides no information about whether changes are consistent across individuals.

The scatterplots shown in the Panels B, C and D demonstrate that the data are paired, associated and not independent, as follows:

Panel B, data point values for every subject on the left group are higher on the right group (a one to one correspondence, they are closely associated).

Panel C, there are NO consistent differences between the two conditions (i.e. the data points, or “subjects,” on the left group behave erratically in respect to their counterparts on the right group: some lines go up, others go down, others are roughly horizontal, which indicates no clear pattern, nor close association between the groups).

Panel D suggests that there may be distinct subgroups of “responders” and “nonresponders.”

Third: Scatter plots are better alternatives to reporting data than bar graphs, particularly of small samples. And, using Standard Deviation lines, instead of Standard Errors, might be more informative to readers.
Figure THREE PLoS Biol 2015 bar vs scatter diagrams

Adapted from Weissgerber et al. (PLoS Biology 2015). Click on image to enlarge.

Bar graphs and scatter plots convey very different information, as Weissgerber et al. (PLoS Biology 2015) explain:

Bar graphs discourage the reader from critically evaluating the statistical tests conducted in the analyses and the authors’ own interpretation of the data.

Panel A presents data in bar graphs showing mean values (the height of the bars) ± SE (Standard Errors, or the “T” shaped lines on top of the bars). Panel A suggests that the second group (white bar) has higher values than the remaining groups. But this might not be necessarily true because the Standard Errors measure only “the accuracy of the mean.” However, see what happens in Panel B (below).

Panel B presents data in bar graphs showing mean values ± SD (Standard Deviations, or the “longer T shaped lines” [in respect to those of Panel A] on top of the bars). Note that Panel B reveals that there is considerable overlap between groups (i.e. the horizontal projections of the “T” shaped lines overlap with one another). This is because Standard Deviations measure “the variation in the samples,” rather than the accuracy of the mean as in the case of the Standard Errors.

Thus, showing SE (Panel A) rather than SD (Panel B) magnifies the apparent visual differences between groups, and this is exacerbated by the fact that SE obscures any effect of unequal sample size.

Yet, Weissgerber et al. (PLoS Biology 2015) indicate that the scatter plot (Panel C) –a better alternative to A or B– clearly shows that the sample sizes are small in all groups, plus group one has a much larger variance than the other groups, and there is an outlier in group three. These problems are not apparent in the bar graphs shown in Panels A or B.

The complete article, supplementary materials, and companion Excel file to assist readers conduct similar analyses can be downloaded from PLoS Biology.

Video:

My video/animation of the day comes, again, from TED-Ed Originals on “Population Pyramids: Powerful Predictors of the Future.” I use this animation to explain to students the relevance of understanding basic data on population demography. The producers explain: “Population statistics… can help predict a country’s [demographic] future (and give important clues about the past). [A] population pyramid [can help] policymakers and social scientists make sense of [demographic] statistics by, [as discussed in the animation, analyzing different types of pyramids].”

EvoLiteracy News 05 04 2015

Today, my picks for EvoLiteracy News include: First, the 2014-2015 report on best college-cities released by the American Institute for Economic Research; different from other assessments, which are often student-satisfaction oriented, the AIER report concentrates on more serious metrics. Second, a review of the placement of sponges and comb jellies in phylogenetic reconstructions of all animals, with new ideas on how to improve our understanding of the evolution of “animal complexity.” Third, an overview of biodiversity extinction rates worldwide, which suggests a fast speed of species decline associated with climate change.  The video treat of the day comes from TEDEd and is about “Biodiversity” (ecosystems, species, genetics). Enjoy! — GPC.

Top College Cities in the US, AIER 2014-2015 Report.

Map AIER Report 2014 2015

The AIER College Destinations Index (click on image to enlarge)

The American Institute for Economic Research (AIER) has released its 2014-2015 College Destination Index, which ranks 75 college-/ university-cities (large, medium-/ small-size metropolitan areas, and small towns) in the United States, according to 4 categories and 12 criteria. The Top 15 Major Metropolitan Areas include Boston MA, Washington DC, San Francisco CA, New York NY and Baltimore MD (plus ten others). The Top 20 Mid-Size Metropolitan Areas: San Jose CA, Austin TX, Raleigh NC, Pittsburgh PA and Buffalo NY (plus fifteen others). The Top 20 Small Metropolitan Areas: Boulder CO, Durham NC, Ann Harbor MI, Madison WI and Gainesville FL (plus fifteen others). And the Top 20 College Towns: Ithaca NY, Ames IA, Corvallis OR, Iowa City IA and State College PA (plus fifteen others).

The categories and “per-category-within criteria” used to rank the cities and towns can be summarized as follows:

1st category Student Life, which includes the following criteria: student concentration, cost of housing, and city accessibility.

2nd category Economic Health, which includes: arts and leisure, international students, and innovation producers.

3rd category Culture: employment rate, entrepreneurial activity, and brain drain or gain.

4th category Opportunity: research and development per student, college educated, and earning potential.

The city list follows (click on image to enlarge). Major metropolitan areas (greater than 2.5 million residents), mid-size metro areas (1.0 to 2.5 million residents), small metro areas (250,000 to 1.0 million residents), and towns (under 250,000 residents):

AIER college cities in the US 2014 2015

Click on image to enlarge

The complete report is available at AIER.

The hidden biology of sponges and ctenophores (comb jellies), published in Trends in Ecology and Evolution.

Calcareous Sponges - Leidys Comb Jellies Images

Left, Calcareous Sponge (Everglades University). Right, Leidy’s Comb Jelly (National Aquarium)

This is a particularly important review by Casey Dunn, Sally Leys and Stephen Haddock, and here is why, as the authors state it “viewing all animals through a bilaterian lens distorts the view of animal evolution.” The authors explain:  “For more than a century, early animal evolution has been presented as a ladder, where ‘primitive’ living species are thought of as the ancestors of ‘complex’ living species… [T]his ladder-like perspective has led to considerable confusion, such as the frequent description of some living animals as ‘basal’, ‘living fossils’, or ancestors of other living animals, even though they are just as far from the base of the tree as other animals are…We cannot array animals from simple to complex, because there is no single axis of complexity. Organisms have a mix of simple and complex traits, but many are currently hidden to us…”

Sponges Comb Jellies TREE 2015

Dunn et al. state: “Strong ascertainment bias means that there are many aspects of nonbilaterian biology that we are not equipped to see: we call this ‘hidden biology’. This unseen hidden biology leads to a discrepancy between the traits organisms have (A) and the traits we see (B). One consequence is the underestimation of the complexity and diversity of nonbilaterian animals.”

Highlights from the journal include: “Animal evolution is often presented as a march toward complexity, with different living animal groups each representing grades of organization that arose through the progressive acquisition of complex traits. There are now many reasons to reject this classical hypothesis. Not only is it incompatible with recent phylogenetic analyses, but it is also an artifact of ‘hidden biology’, that is, blind spots to complex traits in non-model species. A new hypothesis of animal evolution, where many complex traits have been repeatedly gained and lost, is emerging. As [Dunn et al.] discuss [in the article], key details of this new model hinge on a better understanding of the Porifera and Ctenophora, which have each been hypothesized to be sister to all other animals, but are poorly studied and often misrepresented.”

The significance of the review is presented, by TREE, as follows:

  • Ctenophores or sponges are the sister group to all other animals.
  • Biases hide some complex traits in these animals and make them appear simpler than they are.
  • These biases supported the misconception that living animals represent grades of complexity.
  • It is critical to investigate the unique but hidden biology of ctenophores and sponges.
Sponges Comb Jellies Phylogenies TREE 2015

Hypotheses proposed for the phylogenetic relations between sponges, ctenophores, and other animals. (A) Porifera is the sister group to all other animals. Ctenophora and Cnidaria are sister groups, forming Coelenterata. (B) Porifera is the sister group to all other animals. Ctenophora and Bilateria are sister groups, forming Acrosomata, a relation recovered in some morphological analyses but no molecular analyses. (C) Ctenophora is the sister group to all other animals. Some analyses that recover this result also place Placozoa, Bilateria, and Cnidaria in a clade that has been called ‘Parahoxozoa’ (click on image to be redirected to TREE).

The complete study is available at TREE.

Accelerating extinction risk from climate change. South America, Australia and New Zealand at highest risk. Science Magazine.

Mark C. Urban has prepared a special report for Science, on species extinction rates associated with climate change, which he summarizes as follows: “Current predictions of extinction risks from climate change vary widely depending on the specific assumptions and geographic and taxonomic focus of each study. [The author] synthesized published studies in order to estimate a global mean extinction rate and determine which factors contribute the greatest uncertainty to climate change–induced extinction risks. Results suggest that extinction risks will accelerate with future global temperatures, threatening up to one in six species under current policies. Extinction risks were highest in South America, Australia, and New Zealand, and risks did not vary by taxonomic group. Realistic assumptions about extinction debt and dispersal capacity substantially increased extinction risks. We urgently need to adopt strategies that limit further climate change if we are to avoid an acceleration of global extinctions.”

According to the report, the predicted species extinction risks from climate change differed by region: “…the highest risks characterized South America, Australia, and New Zealand (14 to 23%), and the lowest risks characterized North America and Europe (5 to 6%).” The map below depicts, in color, the regional relative risk:

Extinction Risk as Function Climate Change - Science 05 01 2015

Predicted extinction risks from climate change (click on image to go to source)

The complete report is available, in full, at Science Magazine.

Video:

The video-treat of the day comes from TEDEdWhy Is Biodiversity So Important?” The narrative about this clip explains: “Our planet’s diverse, thriving ecosystems may seem like permanent fixtures, but they’re actually vulnerable to collapse. Jungles can become deserts, and reefs can become lifeless rocks. What makes one ecosystem strong and another weak in the face of change? Kim Preshoff details why the answer, to a large extent, is biodiversity.”

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

By Guillermo Paz-y-Miño-C PhD — © 2015

New England Science Public – An Initiative for the Public Understanding of Science – on Twitter @EvoLiteracy@gpazyminoResearchGateAcademia.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 NESCentNSF 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.

Jahar Tsarnaev RollingStone MagazineThe 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.

Even so, “Jahar” belongs more in jail than in the execution chamber. And, as a humanist, I plea for a life. — © 2015 by Evolution Literacy all rights reserved.

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 CollinsBoston 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

*  *  *  *  *      *  *  *  *  *     *  *  *  *  *

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

Paz-y-Mino-C_Book_Cover_Evolution_Stands_Faith_Up_JPEG“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.

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

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

Mountain Chickadee Image by Tringa Photography

Authors    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] 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.

Seismic Map of the US - USGS

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, VS30). 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.”

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 in color

Stegosaurus illustration by Karen Carr (click on image)

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

Male and Female Stegosaurus PLoS ONEAuthor 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 DNA Image from Shutterstock

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

 

EvoLiteracy News 03 28 2015

Science, the universal language…

Happy Saturday everyone, here are a few of my favorite news, videos and science links about topics of broad interest, enjoy!

Earth’s tectonic plates skitter about, from Science Magazine.

“…Geoscientists have unveiled a computer model that maps the details of [Earth’s crust] tectonic dance in 1-million-year increments—practically a frame-by-frame recap of geologic time. It shows that the [tectonic] plates speed up, slow down, and move around in unexpectedly short bursts of activity…” Read full story in Science Magazine and watch the amazing video below. “The animation portrays the motion of continents (grey, yellow, orange and red) and oceanic plates (blue) since Pangea breakup from 200 million years ago.”

 

Liftoff! US, Russia Launch Historic One-Year Space Mission.

US Russia One Year Mission to ISS“An unprecedented one-year mission to the International Space Station [began] Friday (March 27). NASA astronaut Scott Kelly and Russian cosmonaut Mikhail Kornienko [did] launch toward the orbiting lab aboard a Russian Soyuz capsule, at 3:42 p.m. EDT (1942 GMT), from Baikonur Cosmodrome in Kazakshtan.” According to NASA, “…a crewed Mars mission could take 500 days or more; learning more about the potential problems astronauts could experience during a long mission is important [for planning  future missions to the Red Planet]…” See The Yearlong Space Station Mission: Full Coverage.

Below, Mars One introduction film (plus many other related videos).

 

Dynamic evolutionary change in post-Paleozoic echinoids and the importance of scale when interpreting changes in rates of evolution PNAS.

C exquisitus by Simon Coppard The Natural History Museum LondonFrom the cover of the Proceedings of the National Academy of Sciences. Authors Melanie J. Hopkins and Andrew B. Smith provide “…an example of a 265 million-year-old marine invertebrate [sea urchin] clade where evolutionary rates show a net increase over time. This is punctuated by intervals of high rates of morphological evolution, coinciding with major shifts in lifestyle and the evolution of new subclades. The study demonstrates the dynamic nature of evolutionary change within major clades.” For complete study go to PNAS.

Debate over Kin Selection generates yet another response to the controversial 2010-Nature article authored by Martin A. Nowak, Corina E. Tarnita & Edward O. Wilson. The new critique was published in PLoS Biology.

Acanthognathus teledectus Photo April Nobile

Acanthognathus Photo April Nobile

The latest rebuttal to the Nowak et al. (2010) article is titled “Relatedness, Conflict, and the Evolution of Eusociality,” authored by X. Liao, S. Rong & D. C Queller. The researchers summarize their work [a theoretical mathematical model] as follows: “The evolution of sterile worker castes in social insects has fascinated biologists ever since Darwin; how can selection favor a trait that decreases reproductive fitness? W. D. Hamilton solved this dilemma in the 1960s with a theory showing that reproductive altruism could evolve if it increased the worker’s inclusive fitness, which included effects that it had on increasing the fitness of its relatives. This solution to a crucial evolutionary problem, sometimes called kin selection, was challenged in a recent paper (Nowak et al. 2010). The paper generated much controversy, but no one has contested its new theoretical model of the evolution of eusociality, which appeared to overturn much of what was previously thought to be true from kin selection theory. Here we [Liao et al. 2015] examine this model in greater depth, showing that its apparently novel conclusions are overgeneralized from narrow and often inappropriate assumptions. Instead, this modeling strategy yields results that confirm important insights from kin selection and inclusive fitness, such as the importance of relatedness and the existence of conflicts in social insect colonies.” For complete open access to article go to PLoS Biology.

Learn more about the kin selection debate in Op Piece “Dehumanizing Academia by Dismantling the Humanities,” including the crossfire between Richard Dawkins and Edward O. Wilson.

Cartoon

Stuck The Landing cartoon Mars Curiosity Rover

Antivaxxers and the Educated-Public-Herd Effect

By Guillermo Paz-y-Miño-C PhD — © 2015 with updates during 2016, 2017.

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

Antivaxxers will only Succumb to Educated Public

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

“…It is a risky bet… to attempt to replicate the antivaxxer-meme and infect the populous with the reckless idea that we should refuse, as a matter of self-determination and individual freedom principles, to ‘put unnatural substances [vaccines] in our bodies,’ or, worse, continue to link vaccinations to ‘mental retardation and autism in children,’ a fabricated story long ago debunked by science… [The] anti-science gang will only succumb to a robust ‘educated-public-herd effect.’”

Anti-vaccination views can spread quite infectiously in society, mimicking the contagious nature of pathogens. But a “culturally immune” community —here I mean aware of the fundamentals about how vaccines work— can remain forever-protected from, or, at least, resistant to antivaxxer-memes.

The_Selfish_Gene

The Selfish Gene 1st Edition (1976)

Not only good ideas, but also ill ones, like the opposition to inoculations, can self-replicate, mutate analogously to a gene, and disseminate in a population. Richard Dawkins coined the term “meme,” in The Selfish Gene (1976), to refer to such units of information/ideas sharing, although his examples were not about antivaxxers (people who nowadays battle against vaccines on pseudo-science grounds, religion, or consensus-ignorance —my emphasis) but rather illustrated how catchphrases, fashion or melodies emerged and settled in culture. Dawkins wrote: “we need a name for [this kind of] replicator, a noun that conveys the idea of a unit of cultural transmission, or a unit of imitation. ‘Mimeme’ comes from a suitable Greek root, but I want a monosyllable that sounds a bit like ‘gene.’ I hope my classicist friends will forgive me if I abbreviate mimeme to meme.”

The word meme itself passed around as a replicator among academics, it became highly scrutinized, as well as valued, and an entire field of study, memetics, was born in the 1980s. Sadly, by 2005, the Journal Memetics: Evolutionary Models of Information Transmission, the peer-reviewed forum for scholarly articles, published its last issue. JM became dormant more than extinct.

The metaphorical merit of the meme concept was both its major strength (for suggesting a didactic model to explain cultural information copying from one mind to another) and weakness (for not attaining consensus in the scientific community due to its subjectivity and the challenge to measure it). However, Dawkins and later “memeticists” (specialists in memetics) did manage to keep alive the meme debate for decades, and there is no indication that the meme hypothesis is irrelevant to modern science. After all, “cultural entities” are certainly hosted in brains, mimicked, subject to variation, competition for survival, and inheritance. Good, with-adaptive-value memes stick around, bad ones are prone to vanishing, but not without first instigating considerable damage.

Herd Immunity

Source: Illustration by Autumn Mariano

But, let us go back to antivaccination memes and their harmful makeup. As long as the number of vaccinated individuals in a population overwhelms the amount of unvaccinated, the “herd-immunity effect” will continue to protect those who have not yet developed defenses. The rule is mathematically simple: the probability of infection —and death— increases when the number of unvaccinated people augments. In fact, those lacking vaccine-induced immunity to smallpox, rubella, polio, pertussis, mumps, measles or diphtheria can “free-ride” in society only when the vast majority of the population has been vaccinated at an average rate of 83-88 percent, depending on the disease. That is perhaps all a nation needs to understand to get the shots!

But if the “public good” argument is no antidote for antivaxxer-poison, here I offer a single, yet historically gruesome example that illustrates why vaccinations have become required in many countries: smallpox, the sole predator of 300 to 500 million people during the 20th century, and possibly of 20 million North-, Central- and South-American natives after the Europeans’ arrived —from the Caribbean— in the 1520s.

Smallpox is caused by the variola virus, which transferred from wild or domesticated animals to Sub-Saharan humans, at least 3,000 years ago. Variola behaves like a “hit and run” pathogen, incessantly moving to the next target. Once it enters via inhalation the airway passages of the host’s lungs, it incubates for one or two weeks in lymphatic ganglia and disseminates to multiple organs. The patient becomes symptomatic when lacerations or blisters appear in the skin and endothelial membranes (inside the mouth, nose and throat), combined with fatigue, fever, forehead ache, overall muscle soreness and joint pain, nausea and vomiting. Ineffective immune response leads to death in 1-2 days. Smallpox is fatal in up to 30 percent of cases.

Smallpox Virus Images Evolution Literacy

Smallpox virus (click on image to be redirected to source:  gettyimages)

The key point is that when the virus runs out of “fresh prey,” it dies out, and this makes it vulnerable to vaccines. Via safe inoculations of laboratory-engineered-strains of the virus, scientists can “trick” the immune system to generate antibodies against variola. Relying on this procedure, smallpox was eradicated in the late 1970s. And by vaccinating most infants, in urban and rural areas worldwide, we all gradually built the herd-immunity effect on which the unvaccinated can freely —but unsafely— ride.

It is a risky bet, of course, to attempt to replicate the antivaxxer-meme and infect the populous with the reckless notion that we should refuse, as a matter of self-determination and individual freedom principles, to “put unnatural substances in our bodies,” or, worse, continue to link vaccinations to “mental retardation and autism in children,” a fabricated story long ago debunked by science (links to references provided below).

Lethal No-Injection Cartoon Evolution Literacy

Lethal Injection vs. Lethal Non-injection

Although non-adaptive memes are destined to disappear in the milieu of great-versus-wicked ideas, the human cost, in health and lives, during the path to eradicating the anti-vaccination movement, will be regrettably painful. Still new diseases will emerge in the future, old ones resurrect, while competent physicians try to manage them in crowded environments. But the anti-science gang will only succumb to a robust “educated-public-herd effect.” — © 2015 by EvoLiteracy, with updates during 2016 and 2017, all rights reserved.

Scientific paper on a 67-country survey on the state of vaccine confidence

The State of Vaccine Confidence 2016: Global Insights Through a 67-Country Survey, see also a commentary about this article in Science.

And on the same topic: The Vaccine Wars: Debunking myths, owning real risks, and courting doubters from Science.

Graphic generated by Science with data from the Centers for Disease Control and Prevention

Visual proof of why vaccines do more good than harm (Science)

Scientific papers rejecting the alleged association between childhood vaccines and autism, and between maternal immunization and autism (source PLoS)

Watch 4:34 min excellent video on “How We Conquered the Deadly Smallpox Virus”

 

Watch 8:47 min video “Just for Hits” by Richard Dawkins (2013)

 

And another video on “Should you get vaccinated?” by Piled Higher and Deeper PHD Comics 

national-average-vaccinations-usa

Above: Animation: Herd Immunity, How it Works

Above: Animation: Regional reduction in the unvaccinated population from 2000 to 2015

A - Measles Project TYCHO data for Health 2015

Measles vaccination and GDP 2014 The Economist - Evolution Literacy

B - Hepatitis-A Project TYCHO data for Health 2015

C - Mumps Project TYCHO data for Health 2015

D - Pertussis Project TYCHO data for Health 2015

E - Polio Project TYCHO data for Health 2015

F - Smallpox Project TYCHO data for Health 2015

G - Rubella Project TYCHO data for Health 2015

Additional Readings and Resources 

Memetics publications on the web.

Autism’s fight for facts: A voice for science. Convinced by the evidence that vaccines do not cause autism, Alison Singer started a research foundation that pledges to put science first. Nature 479, 28-30 ( 02 November 2011 ).

CDC AUTISM SPECTRUM DISORDER. Autism spectrum disorder (ASD) is a group of developmental disabilities that can cause significant social, communication and behavioral challenges. CDC is committed to continuing to provide essential data on ASD, search for factors that put children at risk for ASD and possible causes, and develop resources that help identify children with ASD as early as possible.

Learn about the latest Ebola research in Science Magazine.

Reduced vaccination and the risk of measles and other childhood infections post-Ebola, also in Science Magazine.

How the Anti-Vaxxers Are Winning – The New York Times

Watch how the measles outbreak spreads when kids get vaccinated – and when they don’t – The Guardian

The Next Pandemic? – The Economist

Autism and Vaccines

Source: The Scientific Facts About Autism and Vaccines nowsourcing.com

support-to-vaccinations-by-religious-group-and-ethnicity-us-pew-2016

Support to Vaccinations by Religious Group and Ethnicity United States – Pew 2016

Cartoons

Anti Vaccines Cartoons Evolution Literay

EvoLiteracy News 03 23 2015

Is Autumn the neglected season in climate change research? Researchers at Boston University and the University of Connecticut think so! (03 2015).

Autumn leaves“…This neglect occurs despite the importance of autumn events, including leaf senescence, fruit ripening, bird and insect migration, and induction of hibernation and diapause. Changes in autumn phenology alter the reproductive capacity of individuals, exacerbate invasions, allow pathogen amplification and higher disease-transmission rates, reshuffle natural enemy–prey dynamics, shift the ecological dynamics among interacting species, and affect the net productivity of ecosystems…” The review article was published in the March issue of Trends in Ecology & Evolution Vol. 30 (3).

Watch 2:48 min video “Climate change: Earth’s giant game of Tetris – Joss Fong:”

 

Coral-reef fish changes color to imitate other species and eat their progeny. Study just published in Current Biology (03 19 2015).

Colour-morphing reef fish Curr Biol 2015Researchers at the University of Cambridge have reported that “The dottyback changes its colour to match surrounding damselfish species, enabling it to counter the defences of its damselfish prey by disguising itself as a harmless part of their community, then swoop in to hunt their young… By changing colour to imitate local damselfish communities, dottybacks are able to overcome the predator avoidance behaviour in the juvenile fish they hunt.” Watch graphical abstract of research at Current Biology: Phenotypic Plasticity Confers Multiple Fitness Benefits to a Mimic.

Is the Human chin –its unique shape among the apes and other primates– an adaptation for chewing stress, speech, or a sexual ornament? Are chins spandrels —byproducts of selection operating elsewhere in the mandible or face? Are chins the product of genetic drift (some inbreeding among ancestral humans)? (03 17 2015).

Jaws Richard Kiel actor Bond Movies TWO

Richard Kiel in the role of “Jaws”

The Journal of Human Evolution has an article addressing theses questions. The findings can be summarized as follows: “Quantitative measures that capture the degree of chin expression were gathered from a sample of 123 primate taxa, and evolutionary rates associated with these measures were reconstructed in the primate phylogeny. The evolutionary rate associated with these measures was reconstructed to be far higher along the Homo tip (∼77 times greater than the primate background rate of evolution) than elsewhere in the primate phylogeny.” The results suggest that the human-chin morphology  is an exceptionally derived trait relative to other primates and a product of selection. — Note: the large chin in actor Richard Kiel was actually product of a syndrome called acromegaly.

Golden retrievers genetically predisposed to  cancer. Research has applications to understanding human cancer. From the cover of PLoS Genetics (02 02 2015).

Golden Retriver PLoS Genetics 2015PLoS Genetics summarizes Tonomura et al.’s work as follows: “Dogs are not only ‘man’s best friend’ for their loyalty, they are also the geneticist’s best friend. The artificial breed structure has created genetically isolated groups of dogs, with differential predisposition to diseases they share with us. This facilitates mapping of diseases relevant also to humans. Golden retrievers are predisposed to various cancers, including B-cell lymphoma and hemangiosarcoma. The genetic risk factors for these diseases in humans are still being elucidated. Surprisingly, golden retrievers have two nearby genetic loci with haplotypes predisposing to both diseases.” The complete article is available open access at PLoS Genetics.

Cartoon: Climate Change is a Hoax

Climate Change is a Hoax cartoon