Another Blow Against Intelligent Design ID – Design Creationism

EvoLiteracy News 03 16 2016

The late Intelligent Design, or Design Creationism, continues to decompose. Indeed, pseudo-science has never been able to withstand the power of science. And the story below is quite compelling, not because scientists interested in studying the molecular sophistication of the bacterial flagellum had in mind to further debunk ID. In fact, the researchers (Beeby et al.) did not even mention Design Creationism in their work. But because their study, just published in PNAS, gives US, the people, the opportunity to extrapolate, once more, that there is not a hint of evidence in support to “irreducible complexity” in the anatomy or function of the bacterial flagellum. A reassurance that Design Creationism will forever be wrong. – Guillermo Paz-y-Miño-C

3D model bacterial propeller By Morgan Beeby Imperial College London

Three-dimensional models of bacterial propellers (rotors) in Vibrio (left) and Campylobacter (right). Images by Morgan Beeby Imperial College London (2016). Keep in mind that the rotors are made of proteins (read about it in Stepwise formation of the bacterial flagellar system, PNAS 2007).

Remember the bacterial flagellum? The pet-example of the late Intelligent Design movement? The alleged “case-study” of irreducible complexity? Well, there are more bad news for Design Creationism. A paper on the bacterial flagellum, recently published in the Proceedings of the National Academy of Sciences (PNAS), explores even further the motor (in reality, the flagellum’s rotor) diversity in two species of bacteria (Campylobacter and Vibrio, plus the study makes comparisons to a third species, Salmonella). Unfortunately, the article is not friendly written, and it can be difficult to understand; the science, however, is exquisite.

Before I summarize the study, watch this 22-sec video about the general structure of the bacterial flagellum. It is simple and will help you understand everything else below:

Here, I try to explain the paper by paraphrasing it: Beeby et al. (a total of six coauthors) have found evidence that “bacteria have tuned their swimming abilities [to their surrounding environments] by evolving structural adaptations to their flagellar motors [which are made of proteins], and that [have resulted] in altered torque generation.” [Note that torque is the twisting force that causes rotation of the flagellum]. In essence, “different bacteria show different swimming [styles], [plus different flagellar-motor anatomies], strikingly illustrated by [their] abilities to bore through viscous fluids (for example, the gastrointestinal mucus) in which other bacteria are [unable to swim].”

Bacterial motors with different torque By Morgan Beeby Imperial College London

There is plenty of evidence of gradually evolved differential complexity among flagellar-motors. Bacterial motors with different torque (Salmonella, Vibrio and Campylobacter). Images by Morgan Beeby Imperial College London (see article in PNAS 2016).

Although the authors say nothing about Intelligent Design in their study, for obvious reasons, i.e. who bothers to allude to a non-scientific proposal (ID) in a serious scientific paper (PNAS). We, the readers, however, can extrapolate from the Beeby et al.’s elegant study that there is NOT a hint of evidence in support to “irreducible complexity” in the form or function of the bacterial flagellum, as proposed by Design Creationists. But rather, there is plenty of evidence of gradually evolved differential complexity among flagellar-motors. This complexity is rooted in ancestry, from absence of the rotor in ancient forms of bacteria, to presence and diversity of rotors in more recent forms of bacteria. That is, “gradual change with modification” (or classical Darwinian evolution), exactly the opposite to the irreducibly-complex flagellum designed by a “Designer of Nature,” the imaginary force of causality invoked by Intelligent Designers. In conclusion, the science story about the bacterial flagellum is, by far, more exciting than the pseudo-science, creationist tale of ID. – Evolution Literacy

Related Story

Intelligent Design and Design Creationism Make it to PLoS ONE

Intelligent Design and Design Creationism Make it to PLoS ONE

EvoLiteracy News 03 03 2016

Breaking – PLoS ONE Retracts Paper by Liu M-J et al.

PLoS ONE retraction of paper

Click on image to be redirected to PLoS ONE decision.

Nature Calls it “Social Selection”

Nature calls it Social Selection

Click on image to be redirected to article in Nature.

The INDEPENDENT “Scientific Paper Sparks Controversy”

The Independent on PLoS ONE human hand Creator Intelligent Design

Click on image to be redirected to the Independent article.

Pocket Watch Hand Media ImagesThe paper by Liu M-J et al. (Biomechanical Characteristics of Hand Coordination in Grasping Activities of Daily Living) must be retracted from PLoS ONE, and its editor, Renzhi Han (Ohio State University Medical Center), dismissed from the journal for carelessness in processing the manuscript, to say the least. Here is why: the authors (apparent sympathizers of Intelligent Design) invoke the “Creator” in the Abstract, Introduction, Discussion, and also in the Comments section of the online version of their article, in which they respond to criticisms by the readers and editors at PLoS. And this is not an error of translation, nor a struggle in the authors’ attempt to explain, in English, the contrast between the evolutionary origin of the mechanic dexterity of the human hand and its alternative, unsupported hypothesis, “DESIGN CREATIONISM” responsible for it. No, the authors, with the blessings of the journal’s editor, insist that a Creator, or Designer, made the hand almost perfect. This is bad science and terrible editing by PLoS ONE. Below, I summarize the case and provide links to the journal and PDF. But keep in mind that PLoS ONE might retract the article, terminate the editor, and the information from the journal website might be removed. In any event, the paper by Liu M-J et al. must go from PLoS ONE to ZERO. – Guillermo Paz-y-Miño-C

The paper by Liu M-J et al. was received by PLoS ONE on October 28, 2015; accepted on December 14, 2015; and published on January 5, 2016. I missed it, but became aware of it by allusions to it in the social media (Retraction Watch alerted it on March 2, 2016).

Citation: Liu M-J, Xiong C-H, Xiong L, Huang X-L (2016) Biomechanical Characteristics of Hand Coordination in Grasping Activities of Daily Living. PLoS ONE 11(1): e0146193. doi:10.1371/journal.pone.0146193.

What is the paper about?

In the authors’ own words “…This study explores a method to identify the proper explanation for the hand architecture of muscular-articular connections from the analysis of behavioral result…”

Liu M-J et al. examine the biomechanics of the human hand; its dexterity and relationships between anatomy and function. The authors aim at conveying the message that any robotic attempt to mimic the ability of the human hand should pay close attention to its anatomy (and physiology), which, according to Liu M-J et al., would lead to best outcomes in robotic-engineering design. So far, so good. But what follows below is unacceptable, and for that reason the paper must be retracted and its editor, Renzhi Han (Ohio State University Medical Center), dismissed from PLoS ONE.

Tasks Performed by Human Hands Liu M-J et al PLoS ONE 2016

A hand wearing an instrumented glove demonstrates diverse types of dexterity (click on image to enlarge). Source Liu M-J et al. PLoS ONE 2016.

This is what the authors state in the ABSTRACT:

Hand coordination can allow humans to have dexterous control with many degrees of freedom to perform various tasks in daily living. An important contributing factor to this important ability is the complex biomechanical architecture of the human hand… It is not understood which biomechanical characteristics are responsible for hand coordination and what specific effect each biomechanical characteristic has. To explore this link, we first inspected the characteristics of hand coordination during daily tasks… from thirty right-handed subjects during a multitude of grasping tasks. Then, the functional link between biomechanical architecture and hand coordination was drawn by establishing the clear corresponding causality between the tendinous connective characteristics of the human hand and the coordinated characteristics during daily grasping activities. The explicit functional link indicates that the biomechanical characteristic of tendinous connective architecture between muscles and articulations is the proper design by the Creator to perform a multitude of daily tasks in a comfortable way. The clear link between the structure and the function of the human hand also suggests that the design of a multifunctional robotic hand should be able to better imitate such basic architecture.”

Thus, Liu M-J et al. invoked “design intervention” to account for complexity.

This is what the authors state in the INTRODUCTION:

The human hand is an amazing instrument that can perform a multitude of functions, such as the power grasp and precision grasp of a vast array of objects. The excellent behaviors of the human hand are enabled by a highly complex structure, with 19 articulations, 31 muscles and more than 25 degrees of freedom (DOF). While the abundant functions are favorable, this complex structure also raises a challenging problem of how the human body controls such a large number of mechanical DOFs with ease and an absence of effort…”

To help readers understand, we can simply call DOF “dexterity,” or the readiness and grace in physical activity, the skill and ease in using the hands.

Liu M-J et al. continue: “…Studies indicate that digits do not move alone in isolation of adjacent digits during functional activity, even when a specific movement requires an individual digit. On the contrary, the movements of multiple digits are correlated, and movement information of the human hand is redundant, so that only a small number of components account for most variances. The human hand adopts coordinated movements to reduce the number of independent DOFs and simplify the complexity of the control problem. Thus, hand coordination affords humans the ability to flexibly and comfortably control the complex structure to perform numerous tasks. Hand coordination should indicate the mystery of the Creator’s invention…”

Once again, Liu M-J et al. invoked a “Creator’s intervention” to account for complexity.

This is what the authors state in the DISCUSSION:

In closing the article, Liu M-J et al. reaffirm: “…the architecture is the biomechanical basis of the dexterous movement that provides the human hand with the amazing ability to perform a multitude of daily tasks in a comfortable way. In conclusion, our study can improve the understanding of the human hand and confirm that the mechanical architecture is the proper design by the Creator for dexterous performance of numerous functions following the evolutionary remodeling of the ancestral hand for millions of years. Moreover, functional explanations for the mechanical architecture of the muscular-articular connection of the human hand can also aid in developing multifunctional robotic hands by designing them with similar basic architecture.”

Now, this is what Liu M-J et al. and the Academic Editor, Renzhi Han, do not understand about alleged “design” in nature or “design creationism:”

The doctrine of Intelligent Design (ID), or Design Creationism, born in the 1980s, proposes that a Designer is responsible, ultimately, for the assemblage of complexity in biological systems; according to ID, evolution cannot explain holistically the origin of the natural world, nor the emergence of intricate molecular pathways essential to life, nor the immense phylogenetic differentiation of life, and instead ID proposes an intelligent agent as the ultimate cause of nature. In conceptually mistaken, type-I-error-based arguments to discredit evolution, ID has attributed randomness to molecular change, deleterious nature to single-gene mutations, insufficient geological time or population size for molecular improvements to occur, and invoked “design intervention” to account for complexity in molecular structures and biological processes. In 2005, ID was exposed in court (Dover, Pennsylvania, Kitzmiller et al. versus Dover School District et al. 2005) for violating the rules of science by “invoking and permitting supernatural causation” in matters of evolution, and for “failing to gain acceptance in the scientific community” (excerpt from Paz-y-Miño-C and Espinosa 2013, 2014).

And this is what Liu M-J et al. and the Academic Editor at PLoS have done: invoke and permit supernatural causation in matters of evolution.

Notification from PLOS Staff

Yesterday, March 2, 2016, the very journal PLoS ONE posted the following notification on its website (Comments section of article):

“… A number of readers have concerns about sentences in the article that make references to a ‘Creator’. The PLOS ONE editors apologize that this language was not addressed internally or by the Academic Editor during the evaluation of the manuscript. We are looking into the concerns raised about the article with priority and will take steps to correct the published record.”

But the reaction from PLOS just happened, after two months of the paper being on air. Look at this exchange between one of the readers of PLoS ONE and the first author of the paper, Mr. Liu M-J.

On February 15, 2016, Jason Friedman posted on the Comments section of PLoS ONE the following:

In the abstract (and similarly later in the paper) it is claimed: The explicit functional link indicates that the biomechanical characteristic of tendinous connective architecture between muscles and articulations is the proper design ‘by the Creator’ to perform a multitude of daily tasks in a comfortable way. I am interested to hear from the authors why one should come to this conclusion? I could not find any support for this claim in the article, and it seems out of place in this article…”

Mr. Liu M-J responded also on February 15, 2016:

Thanks for your comments. As we know, human hand is an amazing instrument that can perform a multitude of functions, such as the power grasp and precision grasp of a vast array of objects, with ease and an absence of effort. Although expended great attempts by scientists and engineers, there is no artificial hand matching the amazing capacity of human hand. The origins of human hand remain unclear. It is too miraculous to let us think that human hand is the masterwork of Creator and indicates the mystery of nature. The further discussion about the Creator is indeed out of place in our article…”

In addition, today, March 3, 2016, Mr. Liu M-J, posted this note at PLoS Comments:

We are sorry for drawing the debates about creationism. Our study has no relationship with creationism. English is not our native language. Our understanding of the word Creator was not actually as a native English speaker expected. Now we realized that we had misunderstood the word Creator. What we would like to express is that the biomechanical characteristic of tendious connective architecture between muscles and articulations is a proper design by the NATURE (result of evolution) to perform a multitude of daily grasping tasks. We will change the Creator to nature in the revised manuscript. We apologize for any troubles may have caused by this misunderstanding.”

A bit late, the analogy NATURE = Creator is not new among spiritualists (or even religions), the problem is that it was used in a scientific paper by professionals in a scientific field. And the Academic Editor at PLoS allowed it a complete ride up to publication. And that is the issue we are discussing. And the authors, and editor, must know that a “Creator” (unequivocally invoked three times in the paper and once in the Comments) has no place in Science.

What should PLOS and PLoS ONE do?

It is evident that neither the authors, nor the Academic Editor, understand how evolution via natural selection works. Worse, none is aware of the fallacies intrinsic to Intelligent Design, or Design Creationism. Here a common-knowledge principle applies “not knowing the law does not exempt anyone from having the law being applied to everyone.” What law? At least one and two bylaws: natural selection (which explains the origin and evolution of the human hand), plus the bylaws of publication of articles in scientific journals (i.e. substantiation by evidence, not by the whim of the authors or editors, and sound editorial process). [For accuracy, be aware that natural selection is not a “law,” I am using it here as an unavoidable mechanism that helps us explain much of the evolutionary processes; selection imposes restrictions on randomness and helps us dismiss, quite easily, the fallacy of “design creationism”]. What should be done now that we, the people, caught this “error” at PLoS, after two months since publication?

The allusions to the Creator or Designer by Liu M-J et al. are out of place, but they do invoke and permit supernatural causation in matters of evolution. Unfortunately, there is no evidence of a problem in translation, from the authors’ native language into English. In fact, the authors insist in the Abstract, Introduction, Discussion, and in the Comments section of their article that they do give credit, in a scientific publication, to the long-time debunked hypothesis of Intelligent Design, Design Creationism. The paper must be retracted from PLoS ONE, the Academic Editor, Renzhi Han (Ohio State University Medical Center), must be dismissed from PLOS, and the journal must assure the scientific community that the Public Library of Science (PLoS) will never, ever embrace design creationism in its publications. The paper by Liu M-J et al. must go from PLoS ONE to ZERO. — Evolution Literacy

On March 4, 2016, PLoS ONE officially retracted the paper:

Retraction by PLoS ONE 03 04 2016

Click on image to be redirected to PLoS ONE retraction announcement.

Suggested Reading

A Comprehensive Survey of Retracted Articles from the Scholarly Literature

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”

The Friendship Paradox vs. the Happiness Paradox

EvoLiteracy News 02 22 2016

Cartoon BizarroComics - EvoLiteracy 2016If you are on Twitter (or Facebook), you have probably asked yourself two questions: Am I less popular than my social-media friends? Am I less happy than them? These phenomena (i.e. cyber popularity or cyber happiness) are both real and perceptual.

A paper, by Bollen et al. (total four coauthors), which is available as manuscript (The Happiness Paradox: Your Friends Are Happier Than You), caught my attention. The authors provide evidence of complex associations between the “friendship paradox” and the “happiness paradox.” Enjoy. – Guillermo Paz-y-Miño-C

What is the Friendship Paradox? The perception that YOU are less popular than your friends (on average).

What is the Happiness Paradox? The perception that YOU are less happy than your friends (on average).

What is the issue (so what)? The friendship paradox has been documented in the scientific literature (see Suggested Readings below), but the happiness paradox has remained untested, without quantitative demonstration that it actually happens. Or that, if it does, it occurs in association –somehow– with the friendship paradox. The paper by Bollen et al. makes such connection.

To make it easier for our readers, I will summarize the Bollen et al. study in a digestible manner, although the authors themselves do a fine job explaining the theory, the data and the implications of the research to a specialized audience (see PDF of manuscript). But, for the non-scientists, my summary below might help.

The observations in nature (the social environment):

Online social networking is associated with elevated levels of loneliness, anxiety, displeasure, and dissatisfaction. For example, many times you are on Twitter (or Facebook, or alike social media), you experience an overall sensation that your average contacts (i.e. friends, people you follow, or your followers) have more friends or followers than you do, or are happier than you are.

When measured in number of friends-connections, most people tend to have fewer friends than their own friends do on average. Why? Watch the short video posted below (1 minute 36 seconds of your time) for a friendly introduction to the Friendship Paradox.

Now, let us examine numerically how the Friendship Paradox emerges from a simple example. Imagine a social network of four people, as depicted in the image below: Ana has 1 friend (Bill). Bill has 3 friends (Ana, Carla and Dan). Carla and Dan have 2 friends each (Bill, and each other).

Cartoon The Friendship Paradox - EvoLiteracy 2016

There are 8 friends in the network (1 + 3 + 2 + 2). Thus, on average, each person has 2 friends (8/4 = 2).

However, how many friends does each person’s friends have (i.e. how many friends of friends)? Ana is connected to +3 friends of friends, via Bill (who has 3 friends), a subtotal of 3 friends of friends. Bill is connect to 1 + 2 + 2 friends of friends (Ana has 1, Carla has 2, and Dan has 2), a sub total of 5 friends of friends. Carla is connected to 3 + 2 friends of friends (Bill has 3 and Dan has 2), a sub total of 5 friends of friends. And Dan is connected to 3 + 2 friends of friends (Bill has 3 and Carla has 2), a sub total of 5 friends of friends. Therefore, the grand total of friends of friends in the network is 18.

What is the average number of friends of friends? We obtain this number by dividing the total number of friends of friends in the network (=18) by the total number of friends in the network (=8), which gives us a value of 2.25. The Friendship Paradox becomes evident for Ana, Carla and Dan since their average number of friends in the network (=2.0) is lower than the average number of friends of friends in the network (=2.25). The phenomenon is particularly acute for Ana since she has a single friend (Bill) and, therefore, her friendship relations are clearly below both the average number of friends in the network (2.0) and the average number of friends of friends in the network (2.25).

This overall sampling bias effect (= the Friendship Paradox) results –in part– from Bill’s presence in the network. Bill has the most friends and is more often counted in the friends of friends tabulation, thus rising the average value (to 2.25).

The hypothesis

At least in part, Bollen et al. tested the hypothesis that the friendship and happiness paradoxes are predictable byproducts (effects) of universal social network connectivity patterns. And that associations between friendship and happiness also derived from such connectivity (note that the Friendship Paradox has been demonstrated numerous times, but Bollen et al. demonstrated it again with their sample to be able to link it to the Happiness Paradox, the central aspect of their paper).

The phenomena “friendship paradox” or “happiness paradox” result from the inherent structural bias in social networks that favor popular individuals (like Bill, above), who are, by definition, more likely to belong to someone’s social circle. For example, when individuals like you and I equate popularity of our cyber-friends with their cyber-prestige, and compare our own popularity to theirs, we tend to increase our levels of dissatisfaction with ourselves (i.e. we tend to enhance, in our minds, the effects of the friendship-paradox- or the happiness-paradox).

The predictions

Bollen et al. predicted that the effects of the friendship paradox will extend beyond popularity. If popular individuals tend to be happier, then their elevated happiness will become more prevalent as well. Thus, friendship-levels and happiness-levels (as per both paradoxes) should correlate, and this relationship should be measurable.

The authors also predicted that unhappiness will contribute more directly to the negative psycho-social effects of social networking, since it will affect how individuals assess their own subjective wellbeing (i.e. general happiness/unhappiness or life satisfaction/dissatisfaction relative to that of others).

The friendship paradox or the happiness paradox will generate predictable distributions of data, as shown in Fig. 1, below:

Figure 1 Friendship vs Happiness Paradoxes - EvoLiteracy 2016

Figure 1. Predictable distributions of data expected if the Friendship or Happiness paradoxes are supported by the data (redrawn and adapted from Bollen et al.).

The study

Bollen et al. examined 40,000 Twitter users connected by reciprocal friendship (i.e. people that follow each other).

Two distinctive groups were characterized, the Unhappy group and the Happy group, by applying a subjective assessment of their wellbeing (derived from the Twitter-users’ interactions with their cyber-neighbors), which ranged in a scale from -1.0 (unhappy) to +1.0 (happy).

As shown in Fig. 2, below, both the Unhappy and Happy groups experienced evident friendship-paradox effects (i.e. members of both groups did have, or thought that their friends had, more friends, on average, than themselves). Interestingly, the intensity of the friendship paradox was weaker in the Unhappy group (left) than in the Happy group (right).

Figure 2 Friendship vs Happiness Paradoxes - EvoLiteracy 2016

Figure 2. Friendship-paradox effects on the Unhappy (left) and Happy (right) groups. Note how the intensity of the friendship paradox was weaker in the Unhappy group than in the Happy group. The “clouds” of data correspond to point distributions of each of the 40,000 Twitter users in the study (modified from Bollen et al.).

In addition, as Fig. 3, below, suggests, both the Happy (top) and Unhappy (bottom) groups experienced clear happy-paradox effects. However, the intensity of the happiness paradox was stronger in the Unhappy group (see the very steep slope in the data point distribution, plus the amount of data points over the main line) than in the Happy group (see the not-so-steep slope in the data point distribution, plus the amount of data points over the main line). In essence, the majority of the sampled Twitter users were less happy (or more unhappy) than their friends on average. These findings support the idea that the Happiness Paradox is real.

Figure 3 Friendship vs Happiness Paradoxes - EvoLiteracy 2016

Figure 3. Scatter point distributions of an individual’s (exemplified by YOU) sense of happiness as function of his/her (exemplified by YOUR) friends’ average sense of happiness (modified from Bollen et al.).

Individual Happiness and average friends’ Happiness were more strongly related within the Unhappy group than within the Happy group (Fig. 3). Bollen et al. refer to the clustering of unhappy users with themselves, and happy users also with themselves, as being homophilic or assortative in their social networking (both are common terms in behavioral sciences).

Figure 4, below, corroborates the finding that Unhappy Twitter users had fewer friends, on average, than the Happy Twitter users had, on average.

Figure 4 Friendship vs Happiness Paradoxes - EvoLiteracy 2016

Figure 4. Unhappy Twitter users had fewer friends, on average, than the Happy Twitter users had, on average (modified from Bollen et al.).

Figure 5, below, corroborates the finding that the Happiness Paradox affected more the Unhappy Twitter users, on average, than the Happy Twitter users, on average.

Figure 5 Friendship vs Happiness Paradoxes - EvoLiteracy 2016

Figure 5. The Happiness Paradox affected more the Unhappy Twitter users, on average, than the Happy Twitter users, on average (modified from Bollen et al.).

Paradoxically, however, as shown in Fig. 6, below, there was a weak correlation between individual happiness and individual popularity for the Unhappy group (Pearson’s R = -0.047; range -0.08 to -0.013). For the Happy group, the correlation was more pronounced (Pearson’s R = 0.126; range 0.081 to 0.171).

Figure 6 Friendship vs Happiness Paradoxes - EvoLiteracy 2016

Figure 6. There was a weak correlation between individual happiness and individual popularity for the Unhappy group. For the Happy group, the correlation was more pronounced (modified from Bollen et al.).

The overall results suggest that unhappy Twitter users were more strongly affected by the lower happiness of their friends, possibly explaining why this group exhibited a stronger Happiness Paradox (Figs. 3 and 5) in the absence of a strong correlation between Happiness and Popularity (Fig. 6).

Warnings

Bollen et al. warn us that:

Observations of decreased happiness among social media users may result directly from a widespread inflated perception of the happiness of one’s friends.

Given the large role that social media (e.g. Twitter, Facebook) plays in the social lives of billions of individuals, the authors suggest that these environments may induce long-term changes in the public’s social behavior and may, over time, alter the very nature of social relations themselves. — EvoLiteracy.

Suggested Readings:

Why are your friends more popular than you?

Why your friends have more friends than you do?

Friends you can count on.

Your friends are more interesting than you.

Generalized friendship paradox in complex networks: The case of scientific collaboration.

World Visitors to EvoLiteracy

EvoLiteracy News 02 17 2016

World Visitors to EVOLUTION LITERACY – Readers from 103 countries visited EvoLiteracy during 2015. Three in every four readers were from the United States. About one in every five visitors were from Brazil, Canada, UK, Germany, India, Ecuador, France, Australia and Spain. And one in every ten cyberworms came from 93 other countries. EvoLiteracy is growing thanks to our world friends and followers. – Guillermo Paz-y-Miño-C.

UPDATE – a supplementary post to this one is available at EvoLiteray January 1, 2017.

World Visitors to Evolution Literacy 2015

There are 190+ countries in the world (member states of the United Nations). EvoLiteracy reaches half of them (52%). The image below includes flags of nations, which total 230+. We still need to reach as many nations as possible. Please share EvoLiteracy with others.

Flags of the World

Flags of 230+ nations in the world. Click on image to enlarge. Source Danilka’s Blog.

Top 25 Most Read Posts of 2015

Here are the most popular postings of 2015. I was glad to discover that the biology science videos made much of an impact, particularly among science educators. I also liked that three crucial postings about higher education (marked with an asterisk * below) were well received. To my surprise (and I thank the readers for liking it), the posting about Ecuador’s Academy of Science was ranked top 10. My personal favorite was Science Challenges Golden Age of Violin Making, and this is because I am fascinated with string instruments (classic guitars, ukuleles, charangos); I learned much while investigating the violin ancestry. But I cannot close without admitting how much pleasure gave me to see our readers liking Evolution Wars Debunk II (ranked 13th, a lucky number). Plus the most commented story was Shroud of Turin, Poor Science, and the Persistence of a Myth, which was reposted in various blogs and generated two weeks of discussions. Thanks to all for supporting EvoLiteracy. – GPC

EvoLiteracy – Biology and Science Videos

Photography – Wildlife – Fossils – Landscapes – Museums – Monuments – Cities

GPC Scientific Publications

Evolution Controversy and the Incompatibility of Science and Religion

5 GPC BioArt

EvoLiteracy News 10 26 2015 Shroud of Turin, Poor Science, and the Persistence of a Myth

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

2015 Nobel Prize in Chemistry Goes to Curiosity-Based Research

Antivaxxers and the Educated-Public-Herd Effect

10 Ecuador’s Academy of Sciences Earns International Recognition

11 Science Challenges Golden Age of Violin Making

12 The “Jackprot Simulation”

13 Evolution Wars: Debunk II

14 EvoLiteracy News 05 08 2015 Should scientific journals request authors to change their practices for presenting continuous data in small sample size studies?

15 The Incompatibility Hypothesis: Evolution vs Supernatural Causation

16 At The Down House: Darwin’s Home

17 The Art Of Nature: Sculptures Of Dinosaur Tracks and Traces

18 College Educated But Deeply In Debt For An Overpriced Degree *

19 New Book: Why does Evolution Matter? The Importance of Understanding Evolution

20 Imminent Collapse of Basic Science Under For-profit Model *

21 Dehumanizing Academia by Dismantling the Humanities *

22 EvoLiteracy News 03 19 2015 US Senator Ted Cruz Distorts NASA’s Mission Budget

23 Hiking among Trilobites, Ancient Whales and Dinosaurs

24 EvoLiteracy News 09 09 2015 Protisto-Biologists Flock to Seville for ECOP-ISOP Scientific Meeting

25 Reviews of Book Evolution Stands Faith Up – Reflections on Evolution’s War

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.

EvoLiteracy News 10 21 2015

Breaking News – New Species of Galapagos Tortoise is Identified

Sorry for the introductory drama. Today, my pick for EvoLiteracy News includes a study just published -hours ago- in PLoS ONE. A characterization of a distinctive lineage of Galapagos Giant Tortoises. The study is rich in data; below I summarize its major points. Enjoy! – GPC

C - New Sp Galapagos Tortoise Chelonoidis donfaustoi PLoS One 2015

The two populations of Galapagos tortoises in Santa Cruz Island apparently belong to separate species. Click on image to enlarge.

First, the discussion over the “correct genus” of the Galapagos tortoises has been vivid since 1914, with three justified proposals: Testudo (14 species: 1914), Testudo elephantopus (all subspecies, 1955), Geochelone (as genus, 1957) and Chelonoidis (as sub-genus of Geochelone, 1957). The latest proposal is that all sub-species (13 or 14), or valid biological species, should be placed within Chelonoidis (2006), as legitimate taxa (the problem with Geochelone is that it seems to be polyphyletic, a fancy word to imply “artificial” rather than a natural group, as Chelonoidis).

Second, historic classifications of tortoise varieties based on carapace shape are informative, but taxonomically unreliable (i.e. saddleback, dome, intermediate, and unknown).

Third, populations from different islands represent independent evolutionary lineages, geographically isolated, even within islands, and are distinguishable genetically (via nuclear microsatellites).

B - New Sp Galapagos Tortoise Chelonoidis donfaustoi PLoS One 2015

The skull of the holotype (i.e. the representative specimen) used for description of Chelonoidis sp. nov. from Cerro Fatal, Santa Cruz. Click on image to enlarge.

Fourth, the new species is described for Santa Cruz Island. It belongs to a separate population (Chelonoidis donfaustoi sp. nov., from “Cerro Fatal,” estimated divergence 0.43 million years ago), genetically distinctive and only 20 Km distant from Chelonoidis porteri (from “Reserva,” estimated divergence 1.74 million years ago).

Fifth, the new species C. donfaustoi is genetically identifiable (via nuclear microsatellite and mitochondrial DNA), which suggests reproductive isolation.

Sixth, the new species has only 250 surviving individuals, which makes it one of the rarest, possibly one of the most endangered lineages of extant Galapagos tortoises.

CONCLUSION: The paper by Poulakakis et al. (total 12 authors), which was published today in PLoS ONE, is interesting and well documented. Keep in mind, however, that populations naturally –and not unusually– move, drift over time, colonize environments, become isolated, and gradually diversify (i.e. the foundation of species radiation). In this respect, the study adds specificity to our previous understanding of the Galapagos tortoises’ population genetics. It gives us additional hints about island connectivity during the  geologic past of the archipelago; for example, if we look closely into the mtDNA (mitochondrial) haplotype phylogeny of the extant and extinct tortoises, including museum specimens (below), the newly described “species” (C. donfaustoi) branches as sister taxa of the San Cristobal Island tortoise C. chathamensis, today a separate island, but likely connected to Santa Cruz in the past. Hopefully, the study by Poulakakis et al. generates support to conservation efforts (funding) of these magnificent giant tortoises. – GPC

D - New Sp Galapagos Tortoise Chelonoidis donfaustoi PLoS One 2015

Tree constructed from data including mitochondrial DNA haplotypes sampled from extant and extinct species, plus museum specimens of Galapagos tortoises. Click on image to enlarge.

F - New Sp Galapagos Tortoise Chelonoidis donfaustoi PLoS One 2015

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.

EvoLiteracy News 10 06 2015

I just returned from Chicago after attending the VII International Conference on Science in Society (October 1-2, 2015), an annual event organized by Common Ground (publishers) at the University Center Chicago. The program included theme presentations, workshop sessions, colloquium, poster session and garden conversation. About 70 scholars attended, from 20 countries.

Common Ground is the publisher of the International Journal of Science in Society. We published a paper in it a few months ago (Evolution Controversy: A Phenomenon Prompted by the Incompatibility Between Science and Religious Beliefs), which served as the theme for our presentation/workshop.

Each of three parallel workshop sessions was attended by about 20 people. I enjoyed our session (The Values of Science) very much, perhaps precisely due to the size of the meeting, the diversity of scholars participating (i.e. sociologists, chemists, anthropologists, philosophers, physicists, biologists, educators, media specialists), and the interdisciplinary format of the discussions.

At the meeting, we were informed that The Science in Society Community, including the conference and the journal, had joined with their sister community Interdisciplinary Social Sciences. –  GPC

The entire program is available here. Our workshop session included:

The Values of Science

Anti-scientism and Its Impact on the Relationship between Science and Religion: The Role of Science in a Postmodern Society. Dr. Mohamed Almisbkawy, Department of Philosophy, British University in Egypt, Fayoum University, Cairo, Egypt. Overview: The clash between classic science and religion was due to the similarly in their internal structures. Science has overcome this nature of scientific system by shifting from scientism to anti-scientism.

Evolution Controversy: A Phenomenon Prompted by the Incompatibility between Science and Religious Beliefs. Dr. Guillermo Paz-y-Miño-C, New England Center for the Public Understanding of Science and New England Science Public, Roger Williams University, Bristol, USA. Dr. Avelina Espinosa, New England Center for the Public Understanding of Science and New England Science Public, Roger Williams University, Bristol, USA. Overview: This paper explores the evolution controversy under three predictions of the incompatibility hypothesis.

Chicago Sci Soc Presentation - G-Paz-y-Mino-C Oct 1 2015

Some of the images used in our presentation at the VII International Conference on Science in Society, Chicago, October 1-2, 2015. We discussed in detail the Incompatibility Hypothesis.

Formally Trained Science Communicators: A Solution to the Unreasonable Expectations Placed on Lay People and Professional Scientists. Dr. Teresa Branch-Smith, Department of Philosophy, University of Waterloo, Waterloo, Canada. Jay Michaud, Department of Philosophy, University of Waterloo, Waterloo, Canada. Overview: We need to formally train science communicators to facilitate the transmission of knowledge from scientists to people because it requires expertise that neither group should be expected to acquire independently.

Chicago Science in Society Oct 1-2 2015

Our hostesses and organizers of the VII International Conference on Science in Society at The University Center Chicago, October 1-2, 2015.

 

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Suggested Reading:

Just Published: Evolution Controversy and the Incompatibility of Science and Religion

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

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.

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 image (left) to go to the journal website to download the PDF.

A media-friendly summary can be read HERE.