Today: International Darwin Day 02 12 2016

EvoLiteracy News 02 12 2016

“Darwin Day… signifies the celebration of the achievements of reason, science, and the advancement of human knowledge. The igniting moments in human history when light was brought into our own origins, when understanding that ordinary apes, like Homo, were capable of the extraordinary, of discovering the truth and debunking obscurantism; yet we still struggle to make science the sole guiding star in our survival decisions, the reliable source of concern and joy, the toolkit to plan our departure from Earth –before our Sun in agonizing heat engulfs its nearest orbiting planets– and seek home somewhere else in the cosmos”Guillermo Paz-y-Miño-C

A few images and Evolution-Literacy links to celebrate International Darwin Day. — An update on our New England Science Public Series Evolution Volumes 1 and 2, including open access to the studies on acceptance of evolution in the United States. — Links to our Incompatibility Hypothesis papers (evolution versus supernatural causation). — A recount of a visit to the Down House (Darwin’s home). — And an article, from 2013, about the “history of Darwin Day” at the US Congress. Enjoy. – GPC

Here are some photos of Darwin’s statue at the British Museum of Natural History in London, taken back in 2010.

A - Darwin British Museum Nat Hist - Photo G-Paz-y-Mino-C 2010

Above: an overall view of Darwin’s statue (marble) at the British Museum of Natural History in London.

B - Darwin British Museum Nat Hist - Photo G-Paz-y-Mino-C 2010

Above: a close up of Darwin’s rostrum.

C - Darwin British Museum Nat Hist - Photo G-Paz-y-Mino-C 2010

Above: and another close up of this beautiful carving on marble.

E - Darwin British Museum Nat Hist - Photo G-Paz-y-Mino-C 2010

Above: the main hall at the British Museum of Natural History in London. Darwin’s statue is in the back, just at the end of the first level of the stairs.

F - British Museum Nat Hist - Photo G-Paz-y-Mino-C 2010

Above: the outdoors of the British Museum of Natural History in London.

Paz-y-Mino-C_Book_Cover_Evolution_Stands_Faith_Up_JPEGNOVA Publishers (New York) used one of these images for the cover of our book Evolution Stands Faith Up: Reflections on Evolution’s Wars (2013). “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. Find Evolution Stands Faith Up at NOVA: Soft Cover, Barnes & Noble, Amazon.comAmazon UK.

Update on NESP Series Evolution

The open access New England Science Public Series Evolution continues to be highly downloaded. Here are some updates:

NESP Series Evolution Vol 1 No 1 20131,670+ downloads of Volume 1, Number 1: Paz-y-Miño-C G & Espinosa A. 2013. Attitudes toward Evolution at New England Colleges and Universities, United States. New England Science Public: Series Evolution 1(1): 1-32 (ISSN: 2326-0971). The authors compile the most significant results of their conceptual and quantitative studies on the patterns of acceptance of evolution at New England colleges and universities, conducted between 2009 and 2012. They examine the views of New England Faculty and Educators of Prospective Teachers (higher-education faculty themselves, specialized in training future teachers) from 35 colleges and universities, as well as a representative sample of College Students from a Public, Private and two Religious institutions who were polled in three areas: the controversy over evolution versus creationism versus Intelligent Design; their understanding of how science and the evolutionary process work; and their personal convictions concerning the evolution and/or creation of humans in the context of their religiosity… Read MORE open access.

NESP Series Evolution Vol 2 No 1 2014430+ downloads of Volume 2, Number 1: Paz-y-Miño-C G & Espinosa A. 2014. Acceptance of Evolution by America’s Educators of Prospective Teachers. New England Science Public: Series Evolution 2(1): 1-92 (ISSN: 2326-0971). In NESP Series Evolution Vol 2 No 1, Paz-y-Miño-C and Espinosa use the conceptual framework of the Incompatibility Hypothesis (i.e. science/evolution and belief in supernatural causation are incompatible) to document the patterns of acceptance of evolution of 495 Educators of Prospective Teachers affiliated with 281 colleges and universities widely distributed in 4 regions, 9 divisions, and 50 states in the United States. These higher-education professionals (65% PhD-, 22% doctorate-holders) were polled in five areas: (i) their views about evolution, creationism and Intelligent Design, (ii) their understanding of how science and the evolutionary process work, (iii) their position about the hypothetical ‘harmony or compatibility’ between science/evolution and supernatural causation, (iv) their awareness of the age of the Earth, its moon, our solar system and the universe, and the application of the concept of evolution to the cosmos, and (v) their personal convictions concerning the evolution and/or creation of humans in the context of the educators’ religiosity… Read MORE open access.

The Incompatibility Hypothesis: evolution vs. supernatural causation

Incompatibility Hypothesis Paz-y-Mino-C Espinosa

“Like the oil vs. water experiment, evolution and supernatural causation don’t mix. Evolution raises to the surface.”

Supernatural causation (i.e. the belief in a Supreme Being, creator and sustainer of the universe, omnipresent, omnipotent, omniscient) is a cultural pollutant, incompatible with empirical reality. “Belief” disrupts, distorts, delays and/or stops (3Ds+S) the correct comprehension and acceptance of evidence. We have postulated that the controversy over evolution-and-science versus creationism is inherent to the incompatibility between scientific rationalism/empiricism and the belief in supernatural causation. This hypothesis (= incompatibility) helps us understand and explain the everlasting and fluctuating antagonism –in cycles, from moderate to intense opposition during human history– in the relationship between science/evolution and religion… Read MORE and access free PDFs of scientific articles, including  Evolution Controversy: A Phenomenon Prompted by the Incompatibility between Science and Religious Beliefs published in the International Journal of Science in Society (abstract below) [PDF].

Cover Int Journal Science Society Paz-y-Mino-C and Espinosa 2015Evolution Controversy – Science in Society: Paz-y-Miño-C G & Espinosa A. 2015. Evolution Controversy: A Phenomenon Prompted by the Incompatibility between Science and Religious Beliefs. Int. J. Sci. Soc. 7(2). ISSN 1836-6236. 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. First, 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. Second, change in evolution’s acceptance is a function of educational attainment, which explains the positive association between acceptance of evolution and level of education. And third, change in evolution’s acceptance is a function of religiosity, which explains the negative association between acceptance of evolution and level of religious beliefs… 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. Read MORE open access [PDF].

At the Down House: Darwin’s Home

Down House Side View from gardens“I visited the Down House, Darwin’s Home, in July 2010. Here are a few pictures I wanted to share in celebration of the International Darwin Day, February 12. Prior to visiting the Down House, which is located just a few miles South East of London, I went to Canterbury, Kent, to attend the International Society of Protistologists (ISoP) annual meeting, at the University of Kent. Coincidentally, back in 1991, as an undergraduate student, I obtained a Diploma in Endangered Species Management from the University of Kent, which offered such certification in partnership with the Jersey Wildlife Preservation Trust (nowadays Durrell Wildlife Conservation Trust)”… Read MORE.

Some History about Darwin Day at the US Congress

Paul Broun R Georgia on Evolution

Click on image to watch video. Paul Broun (R) “All that stuff I was taught about evolution… all that is lies straight from the pit of Hell”

“…Bill H.Res.41, itself, embodies the never-ending battle against irrationalism, the latter vividly present in the views of those who see evil in truth and menace in the realities discovered by science. Take, for example, last year’s remarks by congressman Paul Broun (R), from Georgia, a physician and member of the House of Representatives Committee on Science, Space and Technology (the very Committee to which the “Darwin Day bill” was referred), who declared: “God’s word is true. I’ve come to understand that. All that stuff I was taught about evolution and embryology and the big bang theory, all that is lies straight from the pit of Hell.”

And Mr. Broun went on, as documented in video watched worldwide: “It’s lies to try to keep me and all the folks who were taught that from understanding that they need a savior.” “You see, there are a lot of scientific data that I’ve found out as a scientist that actually show that this is really a young Earth.” “I don’t believe that the earth’s but about 9,000 years old.” “I believe it was created in six day as we know them.” “That’s what the Bible says.” Read MORE.

Related Stories

Darwin’s Skepticism about God

Evolution Wars Debunk II

Why the Notion that “The Theory of Evolution is Not an Explanation for the Origin of Life” is Wrong

Evolution Stands Faith Up – On Francis Collins’ and Karl Giberson’s “The Language of Science and Faith”

EvoLiteracy News 10 26 2015

Today in EvoLiteracy News: A recent study about the authenticity of the Shroud of Turin caught my attention for two reasons. First, it was published in Scientific Reports, a science-media outlet sponsored by Nature. Second, five authors believed to have tested two “hypotheses” when, in reality, they reconfirmed –indirectly– support for an old thesis (i.e. the Medieval origin of the shroud, 800 years ago) and speculated over a historicity-based idea (i.e. that the shroud originated in Jerusalem, 2000 years ago, and it was later transported to Turin). The study is an exemplar of conceptual error, and it can be used in scientific-methodology courses to educate our students on how to avoid making similar mistakes. – Guillermo Paz-y-Miño-C

Shroud of Turin, Poor Science, and the Persistence of a Myth

I will dedicate some length to examine this study (Uncovering the Sources of DNA Found on the Turin Shroud), which falls apart by itself when attempting to combine modern DNA analysis with a silly, pseudoscience project: to find scientific evidence to justify believing in a myth. The concerning part is that five authors, Barcaccia et al., were fortunate to publish the research (October 5, 2015) in Scientific Reports, a fairly known science-communication venue.

A - Shroud of Turin 2015

Negative of the Shroud of Turin printed as positive 1898

The team examined “two” hypotheses, one scientific, the other a historicity supposition. The scientific thesis –for which Carbon dating has provided unequivocal evidence since 1988/9— is that the Shroud of Turin is a fake, a fabrication of Jesus’ body’s imprint on ordinary linen traceable to the 13th and 14th centuries, specifically to 1260-1390 (C-dating is quite accurate). The historical supposition, in contrast, suggests that the shroud must have come from the years 30 or 33, of modern times, which makes it a 2000-year-old relict. The latter has no scientific sustain. But the authors build up –in a technical report format– the argument that their molecular analyses bring support to “both” hypotheses (Medieval origin and Jesus’ timeline). This is not the case. In fact, it is impossible to merge both proposals because the shroud is 800 years old, while the Jesus-person tale –if real– is three times older. Therefore, there is an irreconcilable mismatch in time between the two views.

Readers can judge the study for themselves (at this link), but I prefer to summarize the reality of its findings –while avoiding the authors’ convoluted logic– as follows:

First, Barcaccia et al. admit that the Carbon-dating piece of evidence –a crucial element in this case– demonstrates that the Shroud of Turin originates in Medieval times (statistical confidence 95 percent). That is, we are pretty sure that the linen does not come from 2000 years ago. The shroud is one third the age it is supposed to be under the historicity hypothesis. Therefore, everything else upon which the authors speculate in the study is irrelevant. The Barcaccia et al. conjectures, no matter how the investigators spin them, are inconsistent with the Carbon-dating clock: 800 years old.

Second, the shroud is contaminated with plant material (particularly pollen, which can be detected via chloroplast DNA analysis) belonging to plant species from, almost, all over the world (see figure below). Because the shroud’s linen is 800 years old, the contamination must have occurred during recent times.

C - Shroud of Turin 2015

Plant DNA species found on the Shroud of Turin. Schematic overview of the centers of origin of plant taxa identified in samples of the shroud. Image source Barcaccia et al. 2015.

Third, the linen of the shroud is also heavily contaminated with human DNA (detected via mitochondrial DNA profiling; see figure below), which belongs to multiple individuals, from multiple ethnic backgrounds and, therefore, from multiple geographic locations (Europe, West Asia, Northeastern Africa, Arabia, Middle-East, all the way down to India –not from the Americas). Again, because the shroud is 800 years old, human contact with it must have occurred during recent times.

D - Shroud of Turin 2015

Human mtDNA haplogroups found on the Shroud of Turin. Schematic overview of the current geographical distribution of human mtDNA haplogroups and sub-haplogroups identified in samples of the shroud. Image source Barcaccia et al. 2015 (click on it to enlarge).

Fourth, and this is not a trivial finding, although the authors report it as extraneous, the shroud is also contaminated with DNA from the bird Southern Grey Shrike (Lanius meridionalis), distributed in Southwest Europe, Northern Africa, the Near East, and Southwest Asia. And also with genetic traces of a marine Nemertine worm (Cerebratulus longiceps), from the Northern Pacific Ocean (species description from Alaskan samples, 1901). Once more, as it becomes crucial to remind the readers, because the shroud is 800 years old, bird- or marine worm-DNA must have contaminated the fabric during the past eight centuries.

Fifth, despite these findings, the authors bend over backwards, put aside the age of the shroud and free fall into speculating that if we –somehow– eliminate the noise of the overwhelming DNA contamination, we can “parallel” the genetic patterns of human DNA contamination with the historical path taken by the shroud’s carriers, allegedly from Jerusalem to Turin. A sort of “spatial” retracing of the shroud’s migration. That is, an attempt to find in the genetic markers –which in reality only inform us about the diverse geographic sources of the DNA contaminants– the evidence in support for the historicity hypothesis: Hh that the linen has traveled from Jerusalem to Turin, and via human hand-to-hand (with occasional bird or marine worm intervention) along an envisioned route. And this way of reasoning –by Barcaccia et al.– is so troubling, because it is a blunt Type One Error, a conceptual violation of scientific scrutiny. It picks and chooses what type of contaminant DNA is more informative than other (when all of them are, in principle, contaminants of a cloth one-third the age it is supposed to be), in order to fit the authors’ wish to force support for the historicity hypothesis. And this is done in plain sight of an 800-year young cloth or, in fact, a fake 2000-year-old-wanna-be relic.

“…To be authentic, the Shroud of Turin must be 2000 years old. It is not. Carbon dating places it only eight centuries ago, in Europe. And there is no evidence to link the shroud to Jerusalem, and to the years 30 or 33.”

Sixth, what Barcaccia et al. seem to have found, after cleaning some of the noise in the multiple genetic contaminations (i.e. by discarding some contaminants and keeping “informative” DNA sequences) is an artifact, a byproduct effect of the spatial source of the contamination, that gives the impression of a geographic pattern of migration of the shroud (from Sacred Land to Turin). In reality, it is a pattern of the source of the contamination (not a reflection of the origin of the shroud), consistent with the history of human-worshipers’ approaches to the linen, to touch it. This actually explains the apparent absence of human DNA contaminants from the Americas in contrast to the more-likely-contaminants to be found: the people living nearby the shroud, from the years 1200-1300s onwards. And this is a more parsimonious explanation to the Barcaccia et al.‘s speculations. The authors could have just rationalized over a 2×2 table (see figure below) when designing the tests for: Medieval-origin hypothesis (spatial and temporal evidence) and historicity hypothesis (spatial and temporal evidence). In other words: Medieval-origin hypothesis (Europe and 800 years) and historicity hypothesis (Jerusalem and 2000 years). It becomes obvious that the authors cannot combine, in any manner, one hypothesis with the other because the proposals do not match in time (the time dimension). Therefore, any spatial speculation of consistency, as Barcaccia et al. propose, is senseless. More so when the spatial argument for “possible parallelisms” between hypotheses relies on the capricious use of DNA-contaminants and the exclusion of the timeframe disparity (800 vs. 2000 years). Poor science, indeed.

E - Shroud of Turin 2015 Evolution Literacy

To be authentic, the Shroud of Turin must be 2000 years old. It is not. Carbon dating places it only eight centuries ago, in Europe. And there is no evidence to link the shroud to Jerusalem, and to the years 30 or 33. A: spatial evidence for the Medieval origin hypothesis vs. the Historicity hypothesis; European art techniques used to fake the shroud have been confirmed vs. the genetic contaminants used to speculate that the shroud may come from the Sacred Land. B: Temporal vs. spatial evidence; radio Carbon-dating places the shroud 800 years ago, which is inconsistent with the hypothetical Jerusalem origin. C: Temporal vs. spatial evidence; the hypothetical 2000-year-old age of the shroud is inconsistent with the Medieval European art techniques used to fake it 800 years ago. D: Temporal vs. temporal evidence; the 2000 years of age required for the hypothetical Jerusalem origin of the shroud is inconsistent with the actual 800 years of age determined by Carbon-dating. – GPC

CONCLUSION: Barcaccia et al. study is another, among many, in-text acknowledgments that the shroud of Turin is a Medieval fake, only 800 years young (C-dating) and not a 2000-year-old relic (as demanded it to be in any test of the historicity hypothesis). Reality occurs in a space-time context, yet the authors chose to put time aside to facilitate survival of the historicity tale. The shroud is heavily contaminated with plant, human, bird and marine worm DNA, a phenomenon enhanced exclusively during the past eight centuries, during which the linen has had increasing exposure to people –and their debris, including critters’ goo– from Europe and nearby locations (not to mention the rest of the world). The genetic spatio-temporal mapping presented by Barcaccia et al. reflects a pattern of contamination by humans of multiple ethnicities, consistent with convergent traveling, from diverse locations, in the direction to the object, the shroud, possibly to worship it. If anything, this paper documents the spatial distribution of human contamination of the linen from likely-geographic locations. It fails to provide any evidence in support of the historicity hypothesis (due to the time dimension incongruity), and it actually strengthens the notion that the shroud of Turin is a Medieval fake. The study by Barcaccia et al. is exemplar of how far poor judgment can go, and how belief in supernatural causation disrupts, distorts, delays or stops (the 3Ds + S cognitive effects of illusory thinking) the acceptance of scientific evidence before the very eyes of the investigators, and with their own data. – GPC

B - Shroud of Turin 2015

Negatives (left and right images) of the Shroud of Turin. The cloth is about 14 x 4 ft.

VIDEO: Click on image below to be redirected to NatGeo video Remaking The Shroud, in which techniques for faking it are discussed, and some modern-technology tests shown, including UV light and 3-D imaging.

F - Shroud of Turin 2015 Evolution Literacy NatGeo

EvoLiteracy News 10 23 2015

Today in EvoLiteracy News: Louder Vocalizations in Howler Monkeys Correlate with Small Testicles. The significance of this study is the simultaneous test of three hypotheses (vocal competition, environmental adaptation and size exaggeration) and the elegant documentation of an “evolutionary trade-off” in which vocalizations (rather than the usual morphological traits) are involved. Enjoy! – GPC

In 1871, Darwin suggested that the vocal organs of male Mycetes (Alouatta) –howler monkeys– have been sexually selected. What for? Darwin implied that, in sexually dimorphic species, females prefer and mate with males possessing conspicuous ornaments (e.g. large antlers, bright coloration, elaborate vocalizations), which convey information about fitness.

  • Darwin wrote: “…The vocal organs of the American Mycetes caraya [Alouatta caraya] are one-third larger in the male than in the female, and are wonderfully powerful. These monkeys in warm weather make the forests resound at morning and evening with their overwhelming voices. The males being the dreadful concert, and often continue it during many hours, the females sometimes joining in with their less powerful voices… Whether most of the foregoing monkeys have acquired their powerful voices in order to beat their rivals and charm the females, or whether the vocal organs have been strengthened and enlarged through the inherited effects of long-continued use without any particular good being thus gained, I will not pretend to say; but the former view, at least in the case of [another primate] the Hylobates agilis [the gibbon*], seems the most probable…” (The Descent of Man and Selection In Relation to Sex, 1871).
    • [*Darwin highlights that the gibbon (H. agilis) “…is remarkable from having the power of giving a complete and correct octave of musical notes, which we may reasonably suspect serves as a sexual charm…]

A new study published in Current Biology explains that hyoid bones (crucial for roars in Alouatta) are highly sexually dimorphic, vary among species and with greater sexual dimorphism in species with larger hyoids. The study examines a phenomenon called “evolutionary trade-off;” a situation in which the enhanced expression of one trait (hyoid bone) is directly associated with the diminished expression of another (size of testicles). The assumption is that both traits are costly for an organism to express and, therefore, the trade-off resides in allocating resources to only one of them, for optimization.

B- Howler Monkeys Curr Biol 2015Here is the story: All species of howler monkeys have a modified larynx with an enlarged hyoid bone, which works as a resonance chamber. Howls are energetically expensive to produce (link to video below). Now, what is the connection between the monkeys’ vocalizations and the size of their testicles? The study, authored by Dunn et al. (nine co-authors), explores three hypotheses: vocal competition (i.e. acoustic signals announce presence during defense of territories), environmental adaptation (i.e. hyoid bones are important for sound frequency adjustments in dense forests), and size exaggeration (i.e. voluminous hyoids work as enhancers of the acoustic impression of body size conveyed by roars).

F- Howler Monkeys Curr Biol 2015

RIGHT: Skeleton of a male Alouatta in which the hyoid bone is clearly visible –throat region. LEFT: two images of the hyoid bone showing its chamber-like structure (top) and smooth surface and elongated shape (bottom). The hyoid is very robust (made mostly of compact bone tissue).

Dunn et al. found support for the vocal competition and size exaggeration hypotheses, but not for the environmental adaptation. Here are some of the authors’ generalizations:

(1) males of various species, who live in larger groups of males, have smaller hyoid bones (panel A in figure below) and larger testicles (panel B), the latter an adaptation for sperm-sperm competition (the trade-off: because both roars and sperm production are expensive, only one trait is conspicuously expressed);

C- Howler Monkeys Curr Biol 2015

(2) males with large hyoid bones have smaller testicles (panel C in figure above; the trade-off again; these monkeys usually live in single-male-and-many-females groups);

(3) males with larger hyoid bones vocalize at low(er) frequencies (panel D in figure above; size exaggeration hypothesis); and

(4) all howler monkey species produce very low-frequency vocalizations in respect to their body mass and in contrast to other mammals or corresponding body mass (see figure below; also consistent with the size exaggeration hypothesis). – GPC

D- Howler Monkeys Curr Biol 2015

VIDEO: Take a look at the energetic movement of the thorax while this howler monkey vocalizes; the entire anatomy participates in the roaring. In the rainforest, howler monkeys’ vocalizations can heard from kilometers away.

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

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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.”