Posted on EvoLiteracy News, Recommended Books, Scientific Literacy

A Synthesis of the Galápagos

Our latest book has been released (BOOK’s WEBSITE).

Here is the publisher’s description:

“…There are hundreds of books and thousands of scientific articles about the Galápagos. This volume is distinctive. The authors, Guillermo Paz-y-Miño-C and Avelina Espinosa, synthesize, integrate, and conceptualize the most recent evolutionary-biology research being conducted in the archipelago’s terrestrial and aquatic environments; the conflicts resulting from human interactions with nature, including local population growth and tourism practices in the context of short- and long-term conservation efforts; and make predictions about the destiny of the Galápagos’ unique biodiversity and landscapes under various scenarios of climate-change impacts, urbanization trends, diversification of tourism, and conservation investments. Offering over 260 figures and diagrams, this work will appeal to a broad audience, including professors in academia, college instructors, postdoctoral fellows, graduate students, and research undergraduates. Another target audience is study-abroad and international field-trip instructors and their students who travel to the Galápagos year-round. Science writers and policymakers will find in this book useful information to discuss and debate about imminent environmental threats to afflict the Galápagos as a consequence of human population growth, tourism practices, and climate change…”

Chapter One  Cacti on Rocky Grounds and Forests in the Highlands’ Mist (59 pp)

Chapter Two  Crowded Shores, Murky Waters, and the Open Sea (84 pp)

Chapter Three  Endemism, Rareness, and Endemic Creatures of the Isles (60 pp)

Chapter Four  Microbes and Viruses, Always Present (94 pp)

Chapter Five  Homo the Settler (34 pp)

Chapter Six  Homo the Explorer, the Sightseer (32 pp)

Chapter Seven  Homo the Caretaker (61 pp)

Chapter Eight  Earth’s Wounds: Their Impact on the Fragile Islands (73 pp)

Chapter Nine The Destiny of an Archipelago (42 pp)

Chapter Ten Berlanga, Darwin, Melville, and Galápagos During World War II (3 pp)

For book’s website click HERE.

Posted on Uncategorized

Microbial Detection of Kin and Kind

ISTE & WILEY have just published The Explosion of Life Forms: Living Beings and Morphology (2021)

We (Guillermo PAZ-Y-MIÑO-C and Avelina ESPINOSA) authored Chapter 6: The Many Shapes of Microbial Detection of Kin and Kind. The book was edited by our colleagues Georges Chapouthier, Emeritus Director of Research at the French National Centre for Scientific Research, and Marie-Christine Maurel, Professor at Sorbonne University and a researcher at the Institut de Systématique, Évolution, Biodiversité laboratory at the National Museum of Natural History.

Below are the publisher’s description and list of chapters in the book, as well as the abstract of our chapter:

“One of the essential characteristics of living beings is the explosion of variety in their forms that is intrinsically linked to the diversity of the environments they have adapted to. This book, the result of collaboration between international specialists, analyzes the multiplicity of these morphologies. It explores the origin of forms, their role in defining living things, and the relationship between form and function. It exposes the role of genes and epigenetics and examines the forms of bacteria, protists and plants. The Explosion of Life Forms also studies the memory of animals and their sensory processes, the forms of robots (built in the image of living things), and medical technologies aimed at restoring damaged living forms. Finally, this work questions a common principle of construction in the diversity of forms, as well as the idea of an abandonment of the form, a possible hidden defect of some modern philosophies.”

Chapter 1. Possible Traces and Clues of Early Life Forms by Marie-Christine MAUREL

Chapter 2. The Nature of Life by Andreas LOSCH

Chapter 3. From Form to Function by Jean-Pierre GASC

Chapter 4. On Growth and Form: Context and Purpose by Jean-Pierre GASC

Chapter 5. The Emergence of Form in the History of Epigenetics by Jonathan B. WEITZMAN

Chapter 6. The Many Shapes of Microbial Detection of Kin and Kind by Guillermo PAZ-Y-MIÑO-C and Avelina ESPINOSA – Bacteria, archaea and protists are anatomically/functionally equipped to detect close genetic relatives, as well as distantly related conspecifics. In this chapter, the authors discuss the adaptive value of a microbe’s ability to discriminate/recognize kin from non-kin. Because the theoretical framework of this field was initially developed for animals – and some plants, they first explain its foundations and later examine unicells’ examples. Emphasis is on “shapes” and genetics. The authors highlight the relevance of kin detection for altruistic cooperation (including among pathogens) or for the identification of “cheater cells” (the beneficiaries of others’ selfless acts, but that do not contribute to the collective well-being), and for the formation of temporary or permanent cell alliances, which are informative for understanding the evolutionary origins of multicellularity.

Chapter 7. Development and Evolution of Plant Forms 101 Florian JABBOUR and Guilhem MANSION

Chapter 8. Forms of Memory by Robert JAFFARD

Chapter 9. The Construction of Sensory Universes by Dalila BOVET

Chapter 10. Emotional and Social Forms of Robots by Laurence DEVILLERS

Chapter 11. When Medical Technology Mimics Living Forms by Didier FASS

Chapter 12. From Living to Thinking: Mosaic Architecture by Georges CHAPOUTHIER

Chapter 13. Converging Technologies or Paradoxes of Power by Jean-Michel BESNIER

Posted on Blog Master Posting, Research Articles

Anti-amebic effects of Chinese rhubarb, what?

“Because current amebiasis drugs are toxic to patients, generate resistance in the pathogen, or can potentially induce cancer, alternative anti-amebic compounds need to be discovered and tested to treat and manage amebiasis. Our study suggests that anthraquinones might be such alternative compounds.”

Our latest publication on amebas is now available open access (links below). Although our research program focuses on taxa, clone and kin discrimination/recognition in unicellular eukaryotes (protists), occasionally we conduct experiments on applied, related topics. Readers might find this post specialized, which is true; we will continue posting about broad(er) themes for all audiences. For now, try to follow the abstract of the scientific article and a simple figure that explains the experiments:

Entamoeba histolytica infects 50 million people worldwide and causes 55 thousand fatalities every year. Current anti-amebic drugs (e.g. paromomycin) work either at the level of the intestinal lumen (where trophozoites proliferate via cell divisions) or on the invasive trophozoites that have penetrated the gut or colonized internal organs (e.g. metronidazole). Some of these drugs are highly toxic to patients, have generated trophozoite resistance, or caused mutations and cancer in laboratory animals. Thus, alternative anti-amebic compounds need to be identified to minimize the side effects (on patients) or resistance (by amebas) to current treatments. The literature suggests that anthraquinones (chemicals found in medicinal plants) have antibacterial, antiparasitic, anti-inflammatory and antioxidant properties. Here we provide experimental evidence that Chinese rhubarb (Rheum palmatum) leaves’ extract (rich in the anthraquinone rhein) inhibits E. histolytica trophozoite growth in vitro. In addition, from a set of ten isolated/synthetic anthraquinones (which we suspected to have anti-amebic properties), four analogs (rhein; AHHDAC = 1-amino-4-hydroxy-9, 10-dioxo-9, 10-dihydro-anthracene-2-carboxylic acid; unisol blue AS; and sennoside B) efficiently inhibited amebic growth at EIC50 concentrations comparable to metronidazole. The mechanism of action of these compounds still needs to be determined, although anthraquinones might enhance the production of toxic oxygen metabolites as it has been suggested for various protists (e.g. Leishmania, Plasmodium, Trypanosoma). Our research is the first to explore anti-amebic effects of Chinese rhubarb leaves’ extract and isolated/synthetic anthraquinones on pathogenic Entamoeba.

Above (click on image to enlarge) – Experimental design: tests with Chinese rhubarb (Rheum palmatum) extract (“rhein extract”) or with isolated/synthetic anthraquinones. Top: Extract obtained from Chinese rhubarb leaves was added to suspensions of Entamoeba histolytica trophozoites and incubated for 24h or 48 h at 37 °C; likewise, metronidazole (20 μM), TYI-S-33 media or TYI-S-33 media + DMSO (dimethyl sulfoxide) were added to separate suspensions (both controls); each series was done in triplicate (x3, total 24 wells). Bottom: From commercially available isolated/synthetic anthraquinones (rationale in Methods), four analogs (rhein; AHDDAC = 1-amino-4-hydroxy-9, 10-dioxo-9, 10-dihydro-anthracene-2-carboxylic acid; unisol blue AS; or sennoside B) were added (concentrations 60 μM or 120 μM) to the suspensions of trophozoites and incubated for 24h or 48 h at 37 °C; metronidazole, TYI-S-33 media or TYI-S-33 media + DMSO were separately added as in above; each series was done in triplicate (x3, total 84 wells).

The open access files are available at Helion, PDF, and NCBI PubMed.

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Posted on Blog Master Posting, Book Reviews

Another review of “Kin Recognition in Protists and Other Microbes”

Daniel Haeusser, Associate Blogger at Small Things Considered, has written a two-book review in which ours is included (rationale below). The purpose of Small Things Considered is to “share appreciation for the width and depth of the microbial activities on this planet.”

“…These two books provide insights into the biological concept of ‘kin’ from different perspectives, with different audiences in mind. Both are superb at accomplishing the goals and style they set forth. Whether you think of kin with a warm feeling of camaraderie, or with a wariness toward a threat that might take advantage of your connection, these books on biological kinship are each worth checking out…”

“A Little More Than Kin, Less Than Kind” is the title of Daniel’s assessment. The first volume, “Kin: How We Came to Know Our Microbe Relatives” (Harvard University Press, 2017), was written by John L. Ingraham. Readers can find the full text of the review here. Briefly, Daniel writes “Kin explores the history of our understanding about how life is genetically connected, and how studying microbes in particular led to a radically new image of the Tree of Life. In “Kin Recognition in Protists and Other Microbes: Genetics, Evolution, Behavior and Health” (Cambridge Scholars, 2018) Guillermo Paz-y-Miño-C and Avelina Espinosa review the latest research on the ability of cells to differentiate self from non-self, and to cooperate in a community while excluding selfish, or cheating, behavior.” ‒ “These two books provide insights into the biological concept of ‘kin’ from different perspectives, with different audiences in mind. Both are superb at accomplishing the goals and style they set forth. Whether you think of kin with a warm feeling of camaraderie, or with a wariness toward a threat that might take advantage of your connection, these books on biological kinship are each worth checking out.”

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Related Readings

New Review of Kin Recognition in Protists and Other Microbes

Other Reviews of Kin Recognition in Protists and Other Microbes

Book Website

Link to Book at publisher Cambridge Scholars

Posted on Articles Evolution Literacy, Recommended Books, Science Historic Locations, Science Traveling

Rome, 2800 years of history – Great location for a scientific meeting

By Guillermo Paz-y-Miño C and Avelina Espinosa

We just visited Rome for the second time. Our first journey was back in 2010 when we traveled to Sicily, Rome, Florence and Pompeii before heading to the UK. But the last encounter with this imposing capital was, finally, what we always wanted: extensive, no rush and with enough opportunities to explore everything possible during three weeks in a 2800-year-old settlement.

As readers of EvoLiteracy know, we do not take vacations, but we explore Earth as much as we can within our academic schedules to attend scientific meetings. We never engage into “checklist traveling” (adding names of locations briefly visited) but rather dedicate quality time to experience –and learn about– each destination in detail. Time, however, is always a constraint.

Our primary reason for going to Rome was the ECOP-ISoP 2019 gathering or the “VIII European Congress of Protistology – International Society of Protistologists Joint Meeting” (July 28 to August 2). Avelina is Program Committee Chair of ISoP and oversees the academic planning and organization of the conference(s), including symposia and special events; local organizers materialize each meeting via specific committees. PDFs of the program (talks, poster sessions) can be downloaded from this LINK.

We attend the ISoP meetings yearly and have reported about them before: Vancouver (2018),  Prague (2017), Moscow (2016) and Seville (2015). Previous conferences have taken place in Banff (2014), Oslo (2012), Berlin (2011) and Kent-Canterbury (2010), which we have attended as well (no postings of those years, but see photography and science traveling during the past 15 years).

This time, the package of the ECOP-ISoP 2019 meeting included a flyer describing our book “Kin Recognition in Protists and Other Microbes: Genetics, Evolution, Behavior and Health” (2018), together with endorsements by Joan E. Strassmann (Washington University in St. Louis), Virginia P. Edgcomb (Woods Hole Oceanographic Institution) and Joachim G. Frommen (University of Bern). Additional info about the book can be obtained from the publisher Cambridge Scholars.

Nowadays, we are getting used to presenting posters; they bring back memories of our student years when poster presentations were the main format available to us. Fun though. Here is what we shared at ECOP-ISoP 2019 (click on image for higher resolution). Note at the bottom that we highlight two of our cover-journal articles (2012 and 2019), and the book “Kin Recognition in Protists and Other Microbes: Genetics, Evolution, Behavior and Health”.

While exploring Rome, we walked 417,024 steps, equivalent to 209 km or 130 miles (about 10 km or 6.2 mi a day); we took 8,879 photos, of which 154 (1.7%) were shared on social media (Facebook and Twitter). Between the two of us, we lost 10 pounds, despite eating pizza daily. – Here are the most important locations (dots) at which we stopped to do something other than walking.

Below is a graphic account of our experience, before and after the ECOP-ISoP meeting. The images (more than 100) follow a chronological order of the sites visited. No doubt Rome is a great location for a scientific meeting, enjoy:

Above: the Saint Peter’s Basilica in the Vatican, as seen from the Angel’s Castle.

Above: a closer look B&W of the Saint Peter’s Basilica.

Above: colors at the Saint Peter’s Basilica in the Vatican [secular camera].

Above: colors inside the Saint Peter’s Basilica, Vatican [secular camera].

Above: the main pulpit at the Saint Peter’s Basilica, Vatican [secular camera].

Above: colors inside the Saint Peter’s Basilica, Vatican [secular camera].

Above: the Pantheon [secular camera].

Above: Fontana di Trevi, the 5th most visited place in Rome after the Colosseum, Saint Peter’s Basilica, Pantheon and Vatican Museums.

Above: Piazza Venezia… day

Above: Piazza Venezia… night.

Above: Fontana dell’Adriatico, Piazza Venezia.

Above: the imposing monument to Vittorio Emanuele II, Piazza Venezia.

Above: another take of the imposing monument to Vittorio Emanuele II, Piazza Venezia.

Above: up close, Piazza Venezia.

Above: the Castel Sant’Angel.

Above: Michael de Archangel at the Castel Sant’Angelo (on top of the castle).

Above: another take of Michael de Archangel at the Castel Sant’Angelo (inside the castle).

Above: the Sant’Angelo Bridge as seen from the Castel Sant’Angelo.

Above: pigeon photobombing at the Castel Sant’Angelo in Rome. Look at the St. Peter’s Basilica in the background.

Above: through an opening, shots at the Vatican (this is what we wanted to show in the previous image before the pigeon photobombed it).

Above: impossible to not know what it is.

Above: ROME, monumental… beyond monumental.

Above: ROME, monumental… beyond monumental.

Above: ROME, monumental… beyond monumental.

Above: when PROTISTS meet ancient ROME. Kin Recognition in Protists and Other Microbes (2018) made it to the Foro Romano…

Above: Colosseum from within…

Above: ROME, monumental…

Above: just outside the Colosseum – Image One of Two – taken at the right place and time.

Above: just outside the Colosseum – Image Two of Two – taken at the right place and time; for this one, we went back to the Colosseum a few days later and looked for the exact spot to take the picture (different angle, of course).

Above: ROME, monumental…

Above: ROME, monumental…

Above: Measuring the Evolution Controversy (our 2016 book) at the Vatican…

Above: ROME, monumental…

Above: ROME, bellissima…

Above: ROME, bellissima…

Above: at the Palatine.

Above: …and the last one of the Colosseum (for this particular day).

Above: ROME, bellissima.

Above: QUESTIONS IN ROME (at the ECOP-ISoP 2019 meeting) – colleagues asked us a few questions about “Kin Recognition in Protists and Other Microbes” – (1) Are there alternative ways to order the book (meaning to make the purchase affordable)? The best option is to order it directly from the publisher. Another option is to ask your university library to purchase the book and have it at your campus. – (2) Is the book suitable for high schools? Short answer yes. Long answer, as we state in the book “offering over 200 figures and diagrams, this [book] will appeal to a broad audience, including researchers in academia [our first target audience: scientists], postdoctoral fellows, graduate students and research undergraduates. Science writers and college educators will also find it informative and practical for teaching”. We know of two high school teachers that have gotten the book for their own use as reference for lectures. – (3) Do we sign copies of the book? Yes, if you are at ECOP-ISoP- Rome-2019, approach us with your copy and we will sign it.

Above: theistic evolutionists have a crush on this guy…

Above: water clock…

Above: there is symmetry in this image, and for a reason.

Above: Roma, bellissima… Ponte Fabricio.

Above: just outside the Pantheon.

Above: the Pantheon.

Above: Head of Saint Giovanni Battista at Santa Maria degli Angeli.

Above: Basilica Papale Santa Maria Maggliori, even more spectacular than the Saint Peter’s Basilica.

Above: Galileo Galilei by Tsung Dao Lee, Basilica di Santa Maria degli Angeli.

Above: …and the outdoors of the Basilica Papale Santa Maria Maggliori, ROME… today’s walk [secular camera].

Above: we went back to the Basilica Papale Santa Maria Maggliori for a few B&W and color shots – This monument rivals the Saint Peter’s Basilica in the Vatican.

Above: we went back to the Basilica Papale Santa Maria Maggliori for a few B&W and color shots – This monument rivals the Saint Peter’s Basilica in the Vatican.

Above: we went back to the Basilica Papale Santa Maria Maggliori for a few B&W and color shots – This monument rivals the Saint Peter’s Basilica in the Vatican.

Above: ScooteRome…

Above: spectacular Rome, Terme di Caracalla…

Above: Terme di Caracalla…

Above: Terme di Caracalla…

Above: Terme di Caracalla…

Above: Rome, ancient…

Above: Rome, ancient…

Above: …and another basilica in ROME (impossible to miss them in every block) – Basilica di Santa Maria in Trastevere, another competitor in beauty [secular camera].

Above: National Museum of the Venetian Palace.

Above: Giordano Bruno at the Campo Dei Fiori (where he was burned in 1600 for heresy).

Above: at Piazza Navona.

Above: mirror showing “the heavens” [figuratively, of course] at the Gesὺ Church in Rome [secular camera].

Above: Giordano Bruno… ROME, today’s walk – “…On February 8, 1600, when the death sentence was formally read to him, he addressed his judges, saying: ‘Perhaps your fear in passing judgment on me is greater than mine in receiving it.’ Not long after, he was taken to the Campo de’ Fiori, his tongue in a gag, and burned alive…

Above: the SHHH paradox – “SHHH”… they tell you on loud speakers at the Vatican museums. The SHHH itself is louder than the noise made by hundreds of people visiting the exhibits. The SHHH is to show respect at the temples and for the deities that are always deaf.

Above: only Rome looks like this…

Above: we got great tickets to Noche Española with Plácido Domingo (row 13, center).

Above: Rodin at the Vatican…

Above: Egypt at the Vatican Museums…

Above: sarcophagus of Imhotep at the Vatican Museums…

Above: we found this Roman cat roaming around ancient Rome. It soon decided to pause, self-groom and sleep…

Above: woman on scooter and Rome…

Above: THOTH [Egypt 1300 – 1250 BC], a baboon, Vatican Museums.

Above: detail of oil on wood by Filippo Balbi 1855 at the spectacular Terme di Diocieziano.

Above: One of the “Colossal Animal Heads of the Michelangelo’s Cloister”.

Above: Socrates at Palazzo Massimo alle Terme.

Above: we visited the Bioparco di Roma (the ZOO) and took some images. The zoo is quite good for education, with great signs and posted info about what is in the enclosures; a particular emphasis on animal behavior is evident in the posting (i.e. tips about what the animals do and what it means).

Above: under a fig tree…

Above: pygmy hippo.

Above: close up with a primate-cousin.

Above: reticulated giraffe…

Above: the story of Rome as told at the Bioparco di Roma (the Zoo) next to the wolves enclosure…

Above: a few more shots of reticulated giraffes at the Bioparco di Roma… Trilogy.

Above: a few more shots of reticulated giraffes (mom and offspring) at the Bioparco di Roma.

Above: and one more shots of reticulated giraffes at the Bioparco di Roma.

Above: a few more shots of reticulated giraffes at the Bioparco di Roma.

Above: Lowland Amazon tapirs nose-pointing at something [feeding time], Bioparco di Roma

Above: TAPIR TRIO – top: tongues in – bottom: tongues out… Bioparco di Roma…

Above: chimps feeding…

Above: this is what captivity can do to apes.

Above: an empire collapsed, then gravity took everything else down.

Above: the famous Loba Capitolina at the Capitolini.

Above: Marcus Aurelius at the Museum Capitolini.

Above: Bernini’s Medusa, Museum Capitolini.

Above: …and a fantastic mosaic made of marble… Museum Capitolini.

Above: it does rival any other best museum in the world… the Palazzo Doria Pamphilj.

Above: Hercules at the Palazzo Doria Pamphilj.

Above: same spot, same time…

Above: the spectacular Palazzo Doria Pamphilj.

Above: another take of Centaur at the spectacular Palazzo Doria Pamphilj.

Above: and yet another take of Centaur at the spectacular Palazzo Doria Pamphilj.

Above: Basilica di San Giovanni in Laterano.

Above: main door, Basilica di San Giovanni in Laterano.

Above: inside details of Basilica di San Giovanni in Laterano.

Above: From Egypt to Rome…

Above: Jacob Wrestling With The Angel [Giacobbe e l’Angelo by Stefano Maderno] – Palazzo Doria Pamphilj.

Above: Lion (well, half of a lion) Gallerie Nazionale D’Arte Antica.

Above: BEE – ROME… Gallerie Nazionale D’Arte Antica.

Above: Monumento Celebrativo del “Bicentenario dei Carabinieri”. Imposing, we tried to give it a winter touch (Rome was 100-F-hot on that day).

Above: splendor of Latona e i figli by Domenico Pieratti (1600s) Gallerie Nazionale D’Arte Antica.

Above: Piazza della Repubblica.

Above: CLAUDIO… Emperor of Rome [Museo dell’Ara Pacis].

Above: Museo dell’Ara Pacis.

Above: shot of the Colosseum at dusk.

Above: “TRUMP supporters or Celtics fans”? – That was the question when purchasing the tickets to the Catacombs of San Sebastian (located Southeast of Rome’s downtown); apparently, a joke to anyone requesting info in American-English. We offered a simple answer “we are atheists stopping by.” – This is the original of Bernini’s 1679 The Salvator Mundi (restored 2006), spectacular work on marble, his last sculpture at age 82.

Above: The last shots of Rome – Palazzo della Consulta.

Above: FONTANA di TREVI – despite the thousands of people around, we elbowed ourselves a spot and took some shots of the Fontana, the 5th most popular site in Rome… arrivederci.

Above: BOSTON – back home and to conspiracy inferences that “the plane was not landing due to an arbitrary decision [by the Italian pilot] to take us somewhere else.” – In fact, as the pilot explained and it was obvious to see from the windows, there were very low clouds at ground level allowing visibility to only 1,000 feet (about 300 meters), unsafe for landing. We made it about an hour later, after flying in loops (identical in shape to the Circus Maximus in Rome) to make up time. The human mind is so prone to believing on anything but facts; and yes, it only takes one adamant passenger to trigger the rumor. ‒ EvoLiteracy © 2019

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Posted on Articles Evolution Literacy, Blog Master Posting, EvoLiteracy News, Excerpts from scientific articles, Research Articles

Clone Discrimination/Recognition in Entamoeba Featured on Cover of Scientific Journal

By Avelina Espinosa & Guillermo Paz-y-Miño-C

Our latest review on clone-clone discrimination/recognition in Entamoeba species has been featured on the cover of the Journal of Eukaryotic Microbiology (JEUK-MIC, Volume 66, Issue 2, March-April 2019). This is the second time our work has made it to the cover of JEUK-MIC (the first time was back in 2012, coincidentally in the March-April Volume 59, Issue 2). Below are the links to the 2019 article, as well as the abstract and caption to the cover image.

Discrimination Experiments In Entamoeba and Evidence from other Protists Suggest Pathogenic Amebas Cooperate with Kin to Colonize Hosts and Deter Rivals. 2019. Avelina Espinosa & Guillermo Paz-y-Miño-C. Journal of Eukaryotic Microbiology 66(2): 354–368.

Entamoeba histolytica is one of the least understood protists in terms of taxa-, clone- and kin-discrimination/recognition ability. Yet, the capacity to tell apart same or self (clone/kin) from different or non-self (non-clone/non-kin) has long been demonstrated in pathogenic eukaryotes like Trypanosoma and Plasmodium, free-living social amebas (Dictyostelium, Polysphondylium), budding yeast (Saccharomyces), and in numerous bacteria and archaea (prokaryotes). Kin discrimination/recognition is explained under inclusive fitness theory; that is, the reproductive advantage that genetically closely related organisms (kin) can gain by cooperating preferably with one another (rather than with distantly related or unrelated individuals), minimizing antagonism and competition with kin, and excluding genetic strangers (or cheaters = non-cooperators that benefit from others’ investments in altruistic cooperation). In this review, we rely on the outcomes of in vitro pairwise discrimination/recognition encounters between seven Entamoeba lineages to discuss the biological significance of taxa-, clone- and kin-discrimination/recognition in a range of generalist and specialist species (close or distantly related phylogenetically). We then focus our discussion on the importance of these laboratory observations for E. histolytica‘s life cycle, host infestation, and implications of these features of the amebas’ natural history for human health (including mitigation of amebiasis).

About the Cover (above): Population bottlenecks (PB) in the life cycle of Entamoeba histolytica. (1) Upon host’s ingestion of contaminated food and water, ameba-cysts (dormant stage of the organism) will face the enzymatic milieu of the oral cavity (the mouth environment can be highly variable in temperature, concentration and mix of chemicals originated from diverse foods and the host’s own microbiota); (2) once reaching the stomach, the cysts will be exposed to high acidity, an inducer of severe ameba-cysts-population crashes; (3) cysts arrival at the small intestine, a more favorable environment for excystation; (4) not all amebas released during excystation will survive (simply due to intrinsic differential survival); (5) the colonization of the mucous layer on the small-intestine endothelium (nutrient-rich) will induce fast ameba clonal proliferation, but the successful population expansion will depend on variable conditions inside the host and be limited by the presence of different clone competitors (priority effects, see text); (5a) a potential trophozoite invasion of the colon in the large intestine (if it occurs) will be countered by the host’s immune responses (i.e. endothelium guarded by white-blood cells) and also by other ameba clones already established in the colon; (5b) in the uncommon cases of systemic infection, the liver, lungs and other organs (rarely the brain) can be colonized by amebas, which form abscesses, but abscess formation involves high mortality (both caused by host immunity and amebas’ own programmed cell death, PCD, imposed by abscess development); (from 5 to 6) prior to being eliminated from the body, the amebas must encyst, but not all cells will successfully form cysts; (7) and (8) cysts released into the external environment will face additional population crashes, although not directly associated with the fate of the host. To overcome the challenges of population demise (PBs) and stochastic opportunities to recover inside the host, amebas will need to associate and cooperate with clone members (kin); single amebas will not survive and associations or cooperation with genetic strangers will be maladaptive (prone to cheating). Dotted line indicates cases of direct elimination of cysts from the small intestine. ‒ EvoLiteracy © 2019

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Related Articles

Kin Recognition in Protists and Other Microbes: Genetics, Evolution, Behavior and Health

Symposium Kin-Discrimination in Protists just featured on JEUK

Kin Recognition or Kin Discrimination in Single-Celled Organisms – Protists

 

Posted on Articles Evolution Literacy, Book Reviews, Commentary, Recommended Books

New Review of “Kin Recognition in Protists and Other Microbes”

By Guillermo Paz-y-Miño-C

Joachim “Jo” G. Frommen, a behavioral ecologist at the University of Bern, has written a review of our book “Kin Recognition in Protists and Other Microbes: Genetics, Evolution, Behavior and Health.” The article came out (as early view) in the Journal of Eukaryotic Microbiology (JEUK-MIC). Before sharing details of Jo’s take on our work, here is an excerpt that captures his overall opinion:

“This a highly timely and interesting book. People not being too familiar with microbiology will find it a fascinating and inspiring introduction into kin recognition in non-animal systems, which thereby challenges our thinking of underlying cognitive processes such as learning. Students of evolutionary biology will find it highly useful to read, for example, about the advent of multicellularity and sociality, leading to major transitions in evolution. Researchers in microbiology will appreciate a comprehensive summary of the field, with some additional dives into methodological details. Teachers will take advantage of the more than 120 detailed figures showing experimental setups, results and schematic diagrams, as well as of the great appendix linking to recent media resources that can be downloaded and included in lectures… This is a great book, which I can highly recommend.”

Well, first, thanks to Jo for a sharp and generous assessment. Avelina Espinosa (my coauthor) and I were quite pleased to see that Jo grasped the book precisely in the way we wrote it, plus the intention with which we put it together. We spent much time conceptualizing the chapters, their order and content, the illustrations and terminology boxes, the recapitulations of previous sections prior to “diving” deeper into more complex themes, and the didactic summaries at the end of each major subject.

Jo further summarizes the book as follows:

“…Chapter one (Kin recognition: Synopsis and the advent of protists models) sets the stage for the following chapters by explaining the most important terms and concepts of the kin recognition literature. It further highlights the importance of kin recognition in animals and introduces protists as promising model organisms. Chapter two (The genetics of kin recognition: from many cells to single cells) explains the genetic mechanisms of kin recognition (e.g. green beard effects) using red fire ants (Solenopsis invicta) and social ameba (Dictyostelium discoideum) as examples. Chapter three (Can protists learn phenotypic cues to discriminate kin?) introduces learning as possible nongenetic kin recognition mechanisms. While this chapter is intentionally rather speculative, it is highly inspiring at the same time when thinking about definitions of terms like learning or memory. Chapter four (Entamoeba clone-recognition experiments: morphometrics, aggregative behavior, and cell-signaling characterization) introduces one of the authors’ own study systems, and how it might help us understanding clone recognition. Although the book focuses mainly on kin recognition in protists, the authors devote almost 100 pages of chapter five (The prokaryote´s tale) to show the impact of relatedness on the evolution, ecology and pathogenicity of prokaryotes. By doing so, they largely increase the breadth and information content of the book and open it to a wider audience…”

Indeed, Jo got it just right. We purposely dedicated a comprehensive chapter to kin discrimination/recognition in bacteria (most case studies) and Archaea (a few case studies). In fact, there is so much excellent research in prokaryotes that a book dedicated entirely to them should be compiled (not by us, but by somebody else).

Jo continues:

[click to enlarge]

“…Chapter six (Protists´ clonality, kinship and pathogenicity) illuminates the gregarious and social behaviors of pathogenic protists like Plasmodium or Trypanosoma. In chapter seven (Micro-biogeography: kinship and social/spatial structure) the authors focus on the local and global distributions of various protist species, with a special focus on Becking’s Everything is Everywhere hypothesis. Chapter eight (Multicellular aggregations: from single cells to many cells) highlights the importance of understanding the multifarious levels of protists’ social organization and cooperation, when aiming to understand the evolution of multicellularity more generally, which is considered as one of the Major Transitions in Evolution. The short ninth chapter (Conclusions and future directions) eventually provides a brief summary of the book and suggests promising future research avenues for the study of kin recognition in protists…”

Yes, we do suggest in the book some directions in which the field of kin discrimination/recognition could venture in the immediate and longer-term future, particularly now that unicellular organisms have been incorporated into research programs worldwide. We state, for example, that “…despite the academic progress made during the past two decades, the field of kin recognition in protists and other microbes is just getting started. For the immediate future, we predict a significant increase in studies on the genetics, evolution, behavior and health aspects of the cell-to-cell molecular mechanisms of communication, cooperation, facultative or permanent multicellular aggregations, as well as mathematical modeling on high-complexity organismal systems, and their interactions, for which microbes will generate the data central to the simulations.”

Jo makes a fair observation:

“…As a grain of salt, I would have loved to see some more terminological strictness at some occasions. The field of kin recognition is full of semantic debates, often leading to confusion whenever researchers from different backgrounds come together. The same is also true for the concept of learning. Defining clear terms before opening the discussion would have been helpful to the reader, even if not everybody may agree on the definition itself. The authors acknowledge this mess of concepts and try to avoid the debate by using very broad definitions, which I agree are inclusive, but may be too broad to be useful at the same time. However, these are very minor shortcomings that reflect current debates in the field and do not diminish the scientific and scholarly value of this great book, which I can highly recommend.”

Yes, as we noted in the book “…the field of kin recognition, has no consensus on definitions or proposed mechanisms, likely due to the vast diversity and complexity of life histories across organisms, and also because researchers use terminology depending on circumstances or preference…” We deliberately avoided the discussion of terms and the way they have been used by specialists in the field, a debate that goes back decades, and a topic that might require a separate review for comprehensive coverage. Terminology guides us and is central to scientific inquiry; but it can, occasionally, drag us back and prevent us from making progress, or even accepting the obvious, like “learning abilities” in microbes, which continue to be skeptically honored by scholars due to the customary deference for “high-cognition learning in humans” versus the “learning-like mechanisms” in other organisms. Research with microbes suggests that learning is ubiquitous in nature and that “unicells” sense stimuli coming from the environment, selectively react to chemosignals excreted by themselves or others, store information about such signals and retrieve it when needed (although, in our book we linked “potential learning” primarily to protists’ recognition/discrimination of close genetic relatives, kin).

In sum, Avelina and I thank Jo Frommen for his attentive and positive review of “Kin Recognition in Protists and Other Microbes: Genetics, Evolution, Behavior and Health.” ‒ EvoLiteracy © 2019

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Related Readings

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Posted on Science Traveling

Exploring beautiful New Zealand

“New Zealand deserves many visits to be fully explored; its beauty and richness of landscape seem endless. The intensity of colors like the deep blue of the sky or the fresh green of the vegetation can only be experienced in the flesh, no other way is possible.”

By Guillermo Paz-y-Miño-C

In our quest to explore islands, Avelina and I visited New Zealand during the first three weeks of January, 2019. We are compiling information about biodiversity, human development, and the future of island environments in response to global phenomena, e.g. population growth or climate change. So far, we have been to New Zealand, Hawai’i, the Galapagos, Jamaica and Sicily. Here are the images of our latest journey to the North Island of New Zealand (in no particular order). Enjoy the ride…

Above: the emblematic Pukeko… Western Springs Lakeside Park, Auckland

Above: the three kiwi species (diorama) at the Otorohanga Kiwi House (Native Bird Park) – We did get to see kiwis in captivity (night enclosure, no photos allowed – good)

Above: sheep – At the town of Tirau, New Zealand – “The Corrugated -Iron Capital of the World”

Above: we found this Tuatara (endemic to New Zealand) on the ground at the Otorohanga Kiwi House facilities. – We could not get closer than 3-m (9-ft) to take the photos; it was dark and with vegetation around (blocking our view). We managed to find an opening from which to take some shots

Above: imposing vegetation… and the Tasman Sea

Above: Kiwis crossing… be alert – via Waipoua

Above: exploration summary – 4300 km of driving (2670 mi) in the North Island; 309,550 walking steps while visiting Auckland (i.e. according to our wrist-portable step-counter), nearby and distant cities/towns, their museums and monuments, national parks and protected areas (in other words, about 155 km or 96 mi by foot)!

Above: Sometimes, this is all you need…

Above: …well, you also need this

Above: some good field guides

Above: Boston – Los Angeles (the first 6 hours)

Above: LA to Auckland (13 hours) – middle of the Pacific, through the polarized window of our “modern” plane. We could see the Sun outside (it looked like the moon), but it was “night” inside. Then, quickly, but gently, the “sunrise” effect was controlled from the cockpit to give us the illusion of arriving during the early morning

Above: again, driving on the right / wrong side

Above: antique Honda, well kept

Above: the first colors of New Zealand; the Whenuakite Kiwi Sanctuary – [btw these are the real colors]

Above: Trail at the Kauri-Tree forest in Waipoua

Above: the Albert Park Band Rotunda in Auckland

Above: at the Albert Park, downtown Auckland

Above: at the Albert Park, downtown Auckland

Above: Albion Printing Press from 1863, General Library, University of Auckland

Above: Alligator hiding “behind” duckweed…

Above: And another take of alligator hiding “behind” duckweed…

Above: a take of the beautiful “island of green” in the middle of the Auckland downtown; a vegetation patch with six old, very old imposing trees and their branches; each creature looks like a giant octopus..

Above: anti-earthquake building (hopefully), downtown Auckland

Above: we visited the spectacular Aranui Cave in Waitomo, about two hours South of Auckland. We also entered the Glowworm Caves, which were spectacular as well, but no photos were allowed in there (good policy). In any event, here is a series of seven images taken in the Aranui Cave (where photos were allowed), choose your favorite.

Above: at the spectacular Aranui Cave in Waitomo

Above: at the spectacular Aranui Cave in Waitomo

Above: at the spectacular Aranui Cave in Waitomo

Above: at the spectacular Aranui Cave in Waitomo

Above: at the spectacular Aranui Cave in Waitomo

Above:  this is a CLOSE UP, these stalactites are about 2-3 inches each, others a bit larger.

Above: corner view of the Auckland Art Gallery

Above: the main hall, Auckland Art Gallery

Above: Auckland from the summit of Mount Victoria

Above: Auckland, as seen from the Sky Tower

Above: Auckland… the moon, almost full

Above: B&W moments

Above: Auckland, New Zealand

Above: some time for a panoramic of the Auckland Museum [its actual name is Auckland War Memorial Museum, but the exhibits are not restricted to war or related memories; in fact, the most impressive aspect of the museum is its collection of Maori and Pacific artifacts, spectacular]

Above: Australasian gannet… one of thousands in a five-patch colony. Tasman Sea

Above: Australasian gannet, a bit mad

Above: Australasian gannet after attempting to approach its nest and mate, but too windy… another approach was necessary – Tasman Sea

Above: Quiet bamboo walk at the Chinese Garden, Hamilton Gardens

Above: Before the Rain… Wairoa River

Above: at the Albert Park, downtown Auckland

Above: We managed to get 11 different postcards with illustrations (antiques) depicting the birds of the Tongariro National Park

Above: Black Swan in B&W, Western Springs Lakeside Park, Auckland

Above: an elegant Black Swan at the Western Springs Lakeside Park, Auckland

Above: we found these black swans at Lake Taupō… male and female. They had five offspring with them, almost adult size; the parents were ready to defend them (i.e. charge) if anybody got too close…

Above: close up (color) of the Sky Tower in Auckland

Above: a view of the Bream Head [little peninsula in the back] from nearby Ruakaka, Highway 1 North; about an hour and a half from Auckland – BTW natural colors; the NZ sky is that blue and the landscape that green. – NZ is beautiful

Above: this was not our transportation – “The Dome” – Dome Forest Conservation Area

Above: this was our transportation — every time we rent a car, they give us a bright color one. This time was red. Last time (in Vancouver), a bright blue large truck almost impossible to park. In any event, can you spot the rooster and the hen? There are somewhere in the photo. Highway 1 North, an hour away from Auckland

Above: North Island, New Zealand… sheep skins inside (???)

Above: the youthful looking campus of the University of Auckland

Above: Chinese Pagoda at the Hamilton Gardens

Above: How many? – Australasian gannets, a huge colony. Tasman sea

Above: The colors of New Zealand, North Island, nearby Te Rerenga [btw these are the real colors]

Above: “Dogs [that roam] Kill Our Kiwi”

Above: How do I look, asked the gosling. Zoom in to see the gloom. Western Springs Lakeside Park, Auckland

Above: an overused dynosphere, Sky Tower, Auckland

Above: the Auckland Art Gallery

Above: we found this imposing feral rooster nearby Warkworth. We drove North and reached Waitangi, about 230 km / 143 mi (x2) from Auckland

Above: feral roosters (chickens) are quite common in all New Zealand

Above: some “large birds”, Auckland Zoo

Above: we got ourselves these beautiful field-notes-books and a portable guide of NZ birds and mammals illustrated by Lloyd Esler. What makes the latter special is the sketchy, yet accurate depiction of the species

Above: Hamilton Gardens, in the city of Hamilton

Above: Colony of Australasian gannets on top… one is taking off. Tasman Sea

Above: Australasian gannets flying over the Tasman Sea

Above: the General Library, University of Auckland

Above: inside the General Library, University of Auckland

Above: Zero Tolerance… posted at the entrance to the General Library, University of Auckland

Above: muddy giant tortoise, Auckland Zoo

Above: another muddy giant tortoise, Auckland Zoo

Above: The day ended at a breezy Rotorua Lake

Above: Warm afternoon… Tongariro National Park, North Island

Above: Hamadryas feeding and grooming together… Auckland Zoo

Above: the “harbor building” in Auckland is quite nice, but the street on front of it was under renovation and made it difficult to take a good shot

Above: at the Albert Park, downtown Auckland

Above: Hinana, Auckland Museum

Above: Hotunui, ceremonial, saturation of beauty… Maori and Pacific Island cultures… Auckland Museum

Above: Immense landscape, Tasman Sea

Above: Indian Char Bagh, Hamilton Gardens

Above: The Italian Renaissance Garden at the Hamilton Gardens

Above: Juvenile Hamadryas, Auckland Zoo

Above: Kakapo and Pukeko, street painting, Auckland

Above: Katherine Mansfield’s Coronoa typewriter, with the text of “The Garden Party” – Waikato Museum. – The typewriter is quite small, about 30-cm / 12-in wide (front view); very well preserved

Above: Kauri tree, 7-m diameter, Waipoua Forest – we drove 460 km (286 mi) to the Waipoua Kauri Forest, Northwest part of the North Island. It took us four hours (one way) from Auckland to get to the site. Our purpose was to see the gigantic Kauri trees (in the genus Agathis). We did find them. Impressive, enormous (the largest diameter 6-m / 18 ft), majestic

Above: Kauri Tree (smaller), Waipoua Forest

Above: Kauri trees, the “Four Sisters,” Waipoua Forest

Above: Another take of Kauri trees, the “Four Sisters,” Waipoua Forest

Above: Kawakawa, North Island

Above: Kiwi, Auckland Museum

Above: Kiwi Cross, Mount Raupehu, Tongariro

 

Above: we visited the town of Otorohanga (2:30 hours South of Auckland), searching for Kiwis; this is what we found

Above: Lake Taupo, Tongariro National Park

Above: Male Hamadryas, Auckland Zoo

Above: At the Mansfield Garden, Hamilton Gardens – antique and antique colors

Above: Maori Warriors’ Canoes; the one on the left is for 100 people – Waitangi Treaty Grounds & Museum

Above: Maori carving, Rotorua Gyser Museum

Above: Maori statue, Auckland Museum

Above: Maori statue, Auckland Museum

Above: this Masked Lapwing was simply hanging around at the Otorohanga Kiwi House, looking for free meals

Above: Modern Auckland; one of its metro stations (Britomart). Lots of colors

Above: we spotted this “New Zealand Christmas Tree” (quite common btw). It belongs to the genus Metrosideros. – Can you spot the bees? How many?

Above: a giant mirror, “Light Weight O” by Catherine Griffiths (2018), reflecting O’Connell Street in Auckland

Above: Moss, Waipoua Kauri Forest

Above: a center-view of the Mount Eden crater, Auckland

Above: a side-view of the Mount Eden crater, Auckland

Above: Mount Ngauruhoe Tongariro National Park

Above: Mount Raupehu, Tongariro National Park

Above: mud pool at the moment of boiling; spot the drop – Te Puia

Above: Nga Pou or Rangitihi, Auckland Museum – the Maori Court Central is impressive; the collection of artifacts, spectacular

Above: Nyala eating with style, Auckland Zoo

Above: After trying to photograph the Tuatara (image at the beginning of post) under challenging conditions, we felt the presence of the New Zealand Pigeon from above. It was a wet-yet-semi solid sensation; honorable, since it came from an endemic bird, unique to the Continent of Zelandia. The Pigeon is the size of a hen, imagine the rest

Above: this flat image looks like a painting, but it is not. It corresponds to the endemic and endangered New Zealand Pigeon (quite big, up to 20 in / 50 cm). We found it at the Otorohanga Kiwi House

Above: a cute boat at Opua North Island

 

Above: another panoramic of the Auckland Museum [its actual name is Auckland War Memorial Museum, but the exhibits are not restricted to war or related memories; in fact, the most impressive aspect of the museum is its collection of Maori and Pacific artifacts, spectacular]

Above: We found these pheasants (M/F) foraging nearby the town of Taupō, North Island, New Zealand [introduced species, of course] – suboptimal to get a shot; they were moving; coming in and out of the bushes; close, but not together to get a single photo; alert, but mostly ignoring us; the male did his usual singing and wing flapping… nature continued

Above: The Pōhutu geyser in Te Puia, New Zealand – It erupts about 30-m (once-twice per hour)

Above: another view of Pohutu geyser, Te Puia

Above:  Pukeko series, Western Springs Lakeside Park, Auckland

Above: Pukeko posing – Pukeko series, Western Springs Lakeside Park, Auckland

Above: …and another Pukeko – Pukeko series, Western Springs Lakeside Park, Auckland

Above: Purple Flower Tree, Waikato

Above: Quiet, pretending to not be seen – Western Springs Lakeside Park, Auckland

Above: Rhino and Nyala at the Auckland Zoo

Above:  Richard Owen and Moa skeleton at the Auckland Museum

Above: Sauropod and Theropod dinosaurs at the Auckland Museum

Above: “Rock Drop” by Judy Millard at the Auckland Art Gallery. Immense, yet beautiful. – The AAG is a world class building with a large collection of paintings and sculptures, particularly modern art, Kiwi style

Above: The colorful Rotorua Museum

Above: Sky Tower, downtown Auckland

Above: downtown / harbor Auckland

Above: more of the downtown, Auckland, 10 PM

Above: Southern Black-backed Gull, Auckland harbor

Above: Summit of Mount Victoria, Auckland

Above: it took us five days to find the right restaurant, Tanpopo Ramen, downtown Auckland – complex flavors in simple noodle soups, mixed with vegetables, some pork, seaweeds, ginger, soy sauce, and even corn. Finally, after some intense searching

Above: the iconic Clock Tower at the University of Auckland

Above: “take two” of the iconic Clock Tower at the University of Auckland

Above: “the insights” of the Clock Tower at the University of Auckland – a fantastic piece of architecture (finished in the 1920s); beautiful inside, with many corners and turns, stairs, arcs, pillars; symmetry and color

Above: close up of the top, Clock Tower at the University of Auckland

Above: even closer up of the top, Clock Tower at the University of Auckland

Above: The Cloud, downtown Auckland

Above: The Essence of a Tree – found at the Albert Park in downtown Auckland

Above: The Huia, male (left) and female (right). Now extinct, the bird was common in the North Island of New Zealand. There are some unconfirmed reports of its existence. – We found this beautiful art (about 3×5 meters; 9×15 ft) in the streets of Auckland

Above: The Spitfire TE456 cf 1948, Auckland Museum

Above: biologists will appreciate… Nearby the town of Maramarua

Above: Three muddy Giant Tortoises, Auckland Zoo

Above: Tivaevae manu, tataura, quilt – Cook Islands, Auckland Museum

Above: Jesus – At the town of Tirau, New Zealand – “The Corrugated -Iron Capital of the World”

Above: at the Town of Tirau, Pig

Above: Trail to the Kauri-Tree forest in Waipoua

Above: a detail in B&W at Mount Victoria, Auckland

Above: a “black bird”, Turdus merula, Mount Eden, Auckland

Above: at Waikawau, when we just reached 4000 km of driving in the North Island of New Zealand

Above: Waikino Bridge & Village

Above: the beautiful Wāitukei sculpture in Rotorua

Above: WWI Monument, Thames

Above: “Whol Why Wurld” (2017) by Jess Johnson & Simon Ward, Auckland Art Gallery – Quite modern, attractive, plus the computer animations were so pleasant to watch. Soft music created a micro-atmosphere of calmness

Above: a shiny young Hamadryas… Auckland Zoo. Primates always remind us that wild animals belong in the wild

Above: White Rhino, the end

Above: last day of the journey — Our trilogy in the Continent of Zelandia; the Tasman Sea as seen from the North Island of New Zealand – one of our last images… time to fly North, back home

Above: Back in Boston… 4-F or ‒15-C… It took us 40-min to defrost the car

New Zealand deserves many visits to be fully explored; its beauty and richness of landscape seem endless. The intensity of colors like the deep blue of the sky or the fresh green of the vegetation can only be experienced in the flesh, no other way is possible. — EvoLiteracy © 2019.

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Posted on Articles Evolution Literacy, EvoLiteracy News, Research Articles, Scientific Literacy

The most outrageous act by scientists in 2018

“Remember the saying ‘when they go low, we go high’? Well, they did go low, as low as you can imagine. And I will try to go high, as much as ‘their low’ allows me. — The tale starts with a cartoonish illustration of a baboon, labeled ‘figure 1.’ Next to the baboon’s rump appears a sketch of its feces or ‘the sample.’ — Someone posted online a video zooming in and revealing the details of ‘the sample.’ The face of Donald J. Trump had been purposely inserted into the sketch. — Outrageous acts by scientists cannot simply vanish.”

By Guillermo Paz-y-Miño-C

Remember the saying “when they go low, we go high”? Well, they did go low, as low as you can imagine. And I will try to go high, as much as “their low” allows me.

The tale starts with a 1.5-inch cartoonish illustration of a baboon, labeled “figure 1,” in the journal Scientific Reports, a branch of the prestigious Nature. Next to the baboon’s rump appears a 1/4-of-an-inch sketch of its feces. From here on, I will refer to it as “the sample.” The purpose of the publication was to document a new technique for DNA extraction from baboons’ excretions and, potentially, from any other animal. The breakthrough was significant, it allowed scientists to exclude unwanted DNA (exogenous) that the organism had eliminated after digesting multiple food items (each with its own DNA), and focus the analysis on a single DNA, in this case the baboon’s (host DNA).

The study was released January 31, 2018. But it took until early December to gain media notoriety. Why? Someone posted online a video zooming in and revealing the details of “the sample.” A minimum of 800-percent magnification was needed to spot the meme, and only a 3000-close-up exposed it fully. The face of Donald J. Trump had been purposely inserted into the sketch.

Although a youthful celebration surged on Facebook/Twitter, scientists condemned the deed (regardless of their opposition to the White House’s current stance on science). But it was not clear who was responsible. The authors? An illustrator? At what point during the editorial process ―which included resubmissions of the work― was the image modified to depict the face of Trump?

I commented on the journal’s website, at the end of the article: “Author(s) and/or the person who did the illustration deceived the editorial or article-production process by introducing a concealed message irrelevant to the research; he/she/they misused the purpose of the Scientific Reports platform, i.e. to communicate best science to the scientific community.”

On December 14, 2018, the journal posted: “The editors have become aware of unusual aspects to the ‘Extract fecal DNA’ illustration in figure 1. We are investigating, and appropriate editorial action will be taken once the matter is resolved.”

Rejections by scholars continued on the Scientific Reports’ interface; here, I abridge some. Scooter wrote “Any credibility these ‘researchers’ may have enjoyed was instantly nullified by their juvenile attempt at making a political statement. What are you people, like 10-years-old?” Anil added: “Dear authors, if you consider you have exercised your ‘freedom of expression’, you are wrong. What you did has absolutely nothing to do with the science you reported. Freedom is ‘whatever I want to do within a sphere of accountability and responsibility'”. And Ron stated: “So you thought it would be cute to add the President’s face to [the] monkey [sample]. Congratulations, because now that’s how this study will be known and not for its content. It also validates the idea that academia is biased and scientific research is being politicized.”

By December 19, 2018, Scientific Reports concluded: “In the original version of this article, there were unusual aspects to the ‘Extract fecal DNA’ illustration in figure 1. These features have been removed.”

Shocking as it might seem to readers, the journal had limited options. Retracting the paper, something suggested on social media, would have been difficult to justify. The science about “single DNA extraction from a mixed-DNA source” was sound. Plus, nowhere else in the article additional dirt was found. In the long run, the journal, and perhaps other periodicals, will have to adjust their guidelines and alert contributors that serious actions shall follow if hidden messages are smuggled into the scientific reporting.

As for the authors, Kenneth L. Chiou and Christina M. Bergey, it remains a mystery what individual roles they played on the prank; Scientific Reports did not offer an explanation. Chiou and Bergey claim affiliation with the Department of Anthropology, Washington University St. Louis; Department of Psychology, University of Washington Seattle; Department of Anthropology, New York University; Consortium in Evolutionary Primatology, New York; and Department of Anthropology, Pennsylvania State University. Will these institutions simply rebuke Chiou or Bergey?

After the storm and end-of-the-year calmness, will the authors worry about good standing with their sponsors: the National Science Foundation (federal funding), Leakey Foundation, Wenner-Gren Foundation, National Geographic Society and NYU University Research Challenge Fund (including the National Institutes of Health, which supports the Genome Technology Center at NYU)? Will the sponsors penalize the authors beyond the glare?

Outrageous acts by scientists cannot simply vanish. The baboon’s DNA tale belongs in history and in our long-term memories. — EvoLiteracy © 2019.

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Posted on Articles Evolution Literacy, Commentary, EvoLiteracy News, Scientific Literacy, Video

Nobel Prize in economics goes to climate and innovation – What?

“Despite these brilliant minds, conceptual modeling and empirical research subsequently published by thousands of economists enthused by Nordhaus’ and Romer’s legacies, the global environmental crisis has worsen. The planet’s warming, pollution of the land, air and oceans, and biodiversity loss are ubiquitous in origin. Yet, the markets or innovation technologies have failed to stop the ecocide, or even minimize it. Climate science has been called a hoax and regulations pro nature protection are being ignored or dismantled.”

By Guillermo Paz-y-Miño-C

This year’s Nobel Prize in economics has been awarded to American professors William D. Nordhaus (Yale University) and Paul M. Romer (New York University Stern School of Business) for the integration of “climate change” and “technological innovations” into long-run macroeconomic analyses, respectively.

The Royal Swedish Academy of Sciences, which has granted the “Sveriges Riksbank Prize in Economic Sciences” —the official name— since 1969, highlights that Nordhaus and Romer developed the methods to understand a problem of global relevance: how the economy interacts with nature (exemplified by climate change) and with human knowledge (the ideas and innovations generated to solve problems).

It has long been known to scholars that nature imposes limitations on the economy. At the same time, innovation or “ideas” determine how societies undertake challenges. In the 1990s, Nordhaus introduced the factor “climate” into economic projections. He came up with “DICE,” a Dynamic Integrated Model of Climate and the Economy (watch VIDEO) in which three subcomponents interacted: traditional economic growth theory (markets that produce goods using capital and labor, with natural resources as energy inputs), the carbon cycle (particularly carbon dioxide emissions to the atmosphere derived from burning fossil fuels), and climate (the damage to nature resulting from the accumulation of greenhouse gases).

Separately, and during the 1980s, Romer had observed that technological development correlated with economic prosperity. He asked simple, yet fundamental questions: Where did ideas for new technologies come from? What kind of a product was an idea? Romer proposed that ideas by inventors, engineers or scientists emerged “endogenously” in the marketplace via “rivalry and excludability.” For example, access to inventions like a computer software, a secret soft drink recipe or a coded satellite TV-broadcast could be restricted by encryption (the software or satellite signal) or patent laws (the ownership of the soda formula). For Romer, rivalry and excludability of ideas were central to growth because the latter depended on innovation.

Neither Nordhaus nor Romer offered definitive answers to the challenges of extracting resources from nature with low environmental impact or generating the right amount of knowledge —innovation technologies— to manage such resources to generate sustained and sustainable long-term affluence. In fact, the Committee for the Prize in Economic Sciences noted that the recognition to the researchers was for addressing difficult questions about the economy and providing the conceptual and numerical tools to studying and modeling them.

Nonetheless, based on Nordhaus’ work, corrective measures were suggested to carbon and greenhouse-gases emissions, including carbon taxes on countries. A tactic also rooted in a 1920s notion —in England— that polluters should pay for the damage they caused to society by their polluting practices. A more modern assumption derived from Nordhaus’ research has been that if carbon emissions are limited by law and a high price is set to carbon pollution (by global emissions trading systems), then, minimization of pollution is possible.

Romer’s modeling, on the other hand, later showed that different from the economic growth driven by the accumulation of physical capital (the traditional view), prosperity motivated primarily by the accumulation of ideas did not inevitably experience decreasing returns. He alerted that although unregulated markets will produce technological change, they will tend to underprovide research and development (R&D) and the very goods that R&D could create. To secure global long-run growth, Romer suggested that governments ought to intervene via regulations (patents) and subsidies and incentives to innovation (research). The laws should limit —in time and space— the monopoly rights to goods and balance them with encouragement to creativity.

Despite these brilliant minds, conceptual modeling and empirical research subsequently published by thousands of economists enthused by Nordhaus’ and Romer’s legacies (1980s onwards), the global environmental crisis has worsen (see IPCC October 7, 2018, report). The planet’s warming, pollution of the land, air and oceans, and biodiversity loss are ubiquitous in origin. Yet, the markets or innovation technologies have failed to stop the ecocide, or even minimize it. Climate science has been called a hoax and regulations pro nature protection are being ignored or dismantled in various countries (see reports on the United States A and B).

One would expect that a Nobel Prize granted to our scientists might reignite public commitment to honor academic work and support it; or realize that wealth and prosperity will vanish without competitive research. But there is a campaign out there to delegitimize science, and it is growing strong in respect to climate. — EvoLiteracy © 2018.

This op-piece appeared in The Standard Times (South Coast Today), see HERE.

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Related Articles

Nobel Prize for the economics of innovation and climate change stirs controversy – Science Magazine October 8, 2018

Economists who changed thinking on climate change win Nobel Prize – Nature Magazine October 8, 2018

Key climate panel, citing impending crisis, urges crash effort to reduce emissions – Science Magazine October 8, 2018

Intergovernmental Panel on Climate Change (IPCC) Special Report on 1.5ºC: Responding to climate change is far more like a marathon than a sprint – Real Climate October 7, 2018