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

 

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

Other Reviews of Kin Recognition in Protists and Other Microbes

Book Website

Link to Book at publisher Cambridge Scholars

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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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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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

Vancouver: The Urban Experience

“…We dedicated quality time to explore Vancouver, its intriguing urban environments. The city is impressive, modern, diverse, busy, with plenty spots to stop by and simply look at. We carried with us a ‘step counter,’ a wrist-watch-like device that told us the number of steps walked daily: a grand total of 234,190 steps during two weeks, about  117 km or 73 miles…”

By Guillermo Paz-y-Miño-C

I finally had the time to upload some images from our visit to Vancouver at the end of July and beginning of August, 2018. My collaborator, Avelina Espinosa, and I attended the 5th joint meeting of the Phycological Society of America and the International Society of Protistologists (the latter, ISoP, the society to which we belong). The meeting took place at The University of British Columbia. Here are the PDFs of the full program and abstracts of the presentations (200 talks, 100 posters).

In the past, I have posted photographic/academic reports of similar ISoP meetings in 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).

The ISoP meetings are medium in size (in the hundreds of attendees) and broad in scope. They gather scientists from all over the world, specialists on: systematics of unicellular eukaryotes (= protists), diversity and biogeography of these organisms, functional ecology (particularly aquatic environments), impacts of climate change on microbial communities, the origins of cell organelles and their physiology and metabolic pathways (e.g. chloroplasts, mitochondria), among other topics. Some  are evolutionary biologists working on the genetics, behavior or health aspects of protists. A few study the origins and evolution of multicellularity, for which microbes are good models.

We presented a poster (below) at the meeting (Kin Recognition in Protists and other Microbes: A Synthesis), which summarized the content of both our latest book on protists and a review article just published in the Journal of Eukaryotic Microbiology. Here is the poster’s abstract: “KRP-and-OM is the first scientific compilation dedicated entirely to the genetics, evolution and behavior of cells capable of discriminating/recognizing taxa (other species), clones (other cell lines) or kin (as per gradual genetic proximity). It covers the advent of microbial models in the field of kin recognition; the polymorphisms of green-beard genes in social amebas, yeast and soil bacteria; the potential that unicells have to learn phenotypic cues for recognition; the role of clonality and kinship in pathogenicity (dysentery, malaria, sleeping sickness and Chagas); the social/spatial structure of microbes and their biogeography; and the relevance of unicells’ cooperation, sociality and cheating for our understanding of the origins of multicellularity. With 200+ figures, KRP-and-OM (the book) is conceptualized for a broad audience, including researchers in academia, post doctoral fellows, graduate students and research undergraduates.”

Click on the image below to enlarge the e-version of the poster [click again to see it in real size]:

Before and after the conference, we dedicated quality time to explore Vancouver, its intriguing urban environments. The city is impressive, modern, diverse, busy, with plenty spots to stop by and simply look at. We carried with us a “step counter,” a wrist-watch-like device that told us the number of steps walked daily (grand total 234,190). From it we estimated the distance traveled by foot during the two weeks spent in situ (117 km or 73 miles). The photographic report follows below. If interested click on the images for higher resolution; click twice if you want to see them real size.

The urban experience

We walked 234,190 steps (about  117 km or 73 miles) during 14 days (8.5 km/day or 5.3 miles/day); drove only 652 km or 405 miles (not much in comparison to other trips); and took 1,808 photos (a bit short this time); 82 of the images (4.5%) were shared on social media (Facebook and Twitter). In summary, we had an “urban experience” (walk/drive) with some wilderness and nearby sightseeing. Marutama, in the Westend of Vancouver, was the best restaurant for Ra-Men (specially Tan-Men).

The images © below follow a chronological order of our trip, well, as much as possible. Enjoy.

Above: always needed, maps, more so in Vancouver, a large city with intricate traffic.

Above: Montreal; we flew from Boston to Montreal, transited for an hour and continued to Vancouver.

Above: “Closer to Mars,” figuratively, of course. On our way to Vancouver.

Above: at our hotel; we actually stayed, for the duration of the meeting, at the University of British Columbia’ residence for visitors (UBC Conferences and Accommodation, West Coast Suites). Quite impressive, well kept, comfortable and elegant, with a nice kitchen, better than the expensive hotel we later moved into (downtown) for the rest of the visit.

Above: Masmasa’lano, Multiversity Galleries, at the Museum of Anthropology, University of British Columbia (UBC).

Above: Buddha, Multiversity Galleries, at the Museum of Anthropology, UBC.

Above:  A close up of Buddha, Multiversity Galleries, at the Museum of Anthropology, UBC.

Above: Carved on wood at the Welcome Plaza, House PostMuseum of Anthropology, UBC.

Above: Carnival Mask, Multiversity Galleries, Museum of Anthropology, UBC.

Above: Haida Bear by Bill Reid, Great Hall, Museum of Anthropology, UBC.

Above: Haida Bear by Bill Reid, Great Hall, Museum of Anthropology, UBC.

Above: More wood carving, House Post, Great Hall, Museum of Anthropology, UBC.

Above: Outdoors of the Museum of Anthropology, image taken from the grounds, UBC.

Above: Raven Discovering Humankind in a Clamshell, The Bill Reid Rotunda, Museum of Anthropology, UBC.

Above: Carving at the temporary exhibit Culture at the CentreMuseum of Anthropology, UBC

Above: Moon Gate Tunnel at the UBC Botanical Garden.

Above: Tree Walk at the UBC Botanical Garden.

Above: Wild flowers at the UBC Botanical Garden.

Above: Leaves and Mosses at the Nitobe Garden, UBC campus.

Above: Log Bridge at the Nitobe Garden, UBC campus.

Above: Memorial to Professor Nitobe at his Garden, UBC campus.

Above: Pacific Bell and Bell Tower at the Asian Studies outdoors, UBC campus.

Above: Trees and Shrubs spot at the Nitobe Garden, UBC campus.

Above: Water Lilies and Duckweeds at the Nitobe Garden, UBC campus.

Above: Water Lilies and Duckweeds (B&W) at the Nitobe Garden, UBC campus.

Above: Kids playing at the Spanish Banks Beach Park.

Above: The Friendship Bench at the UBC campus.

Above: It’s A Mystery by John Nutter at the UBC campus.

Above: Blue Whale at the Beaty Biodiversity Museum, UBC campus.

Above: Centre for Business Ethics at the UBC campus.

Above: “I Want It All I Want It Now” at the main library, UBC campus.

Above: Quantum Matter Institute at the UBC ccampus.

Above: Urgent Care Centre at the UBC campus (examine this photo carefully).

Above: Fees apply to all at the Urgent Care Centre, UBC campus.

Above: “The Nest” at the UBC campus.

Above: Victory Through Honour Pole by Ellen Neel, at the UBC campus.

Above: Danbo Restaurant in downtown Vancouver.

Above: Danbo Restaurant in downtown Vancouver.

Above: Blue Buildings and Blue Sky, downtown Vancouver.

Above: The Burrard St. Bridge in downtown Vancouver.

Above: The Burrard St. Bridge in downtown Vancouver.

Above: Is this scientifically true? Granville Public Market, Granville Island.

Above: At the Granville Public Market, Granville Island.

Above: “Three Berries” (well, sort of) at the Granville Public Market, Granville Island, Vancouver.

Above: At the Granville Public Market, Granville Island, Vancouver.

Above: Downtown Vancouver.

Above: Light-Shed, Vancouver Harbour.

Above: Vancouver Harbour.

Above: Sky Jump at the Whistler Olympic Park (located Northwest of Vancouver).

Above: Our rented truck at the Whistler Olympic Park.

Above: Pre-entrance to the Vancouver Public Library.

Above: Pre-entrance to the Vancouver Public Library.

Above: The iconic Steam Clock in downtown Vancouver.

Above: Marutama Ra-Men, the best in town; there are two locations in Vancouver.

Above: Ra-Men being made at Marutama in downtown Vancouver.

Above: Tan-Men Mild at Marutama Ra-Men.

Above: Plain rice at Marutama Ra-Men.

Above: Kakuni Pork Belly at Marutama Ra-Men.

Above: The Sun Yat-Sen Classical Chinese Garden in downtown Vancouver.

Above: Trees Falling at the Sun Yat-Sen Classical Chinese Garden, downtown Vancouver.

Above: The Details of a City, downtown Vancouver.

Above: The Lions Gate Bridge, downtown Vancouver.

Above: At the Vancouver Aquarium.

Above: Chrysaora fuscescens at the Vancouver Aquarium.

Above: More of The Harbour.

Above: A-Maze-Ing Laughter by Yue Minjun, downtown Vancouver.

Above: Space Centre & Museum of Vancouver.

Above: And a close up of the Space Centre & Museum of Vancouver.

Above: Vancouver Art Gallery, in the downtown.

Above: “A Rushing Sea of Undergrowth” by Emily Carr 1935, Vancouver Art Gallery.

Above: “Ayumi” by Corey Bulpitt at the Vancouver Art Gallery.

Above: Buckminster Fuller‘s Geodesic Dome at the Vancouver Art Gallery.

Above: “Peter” by Corey Bulpitt at the Vancouver Art Gallery.

Above: “Tarah” by Corey Bulpitt at the Vancouver Art Gallery.

Above: The famous Morgan Guitars exhibited at the Vancouver Airport.

Above: “Meeting is Over”…

Above: Rain and Propeller, Vancouver Airport.

Above: Sunlight and Propeller, light bends, closer to Boston.

— EvoLiteracy © 2018.

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When it comes to weedkiller and cancer, the answer is complex

“Why did New Scientist, ‘the world’s most-read weekly popular science and technology magazine,’ as described on its website, decide to departure from covering ‘international news from a rational, analytical standpoint rooted in the scientific method’ and inject extra doubt into the glyphosate debate? I am referring to the directional ‘probably not’ when swiftly-answering its own query ‘does weedkiller cause cancer?'”

By Guillermo Paz-y-Miño-C

“Does weedkiller cause cancer? Probably not.” These engagement-bite question and answer, as they are known in social media circles when postings lure followers to quick-comment about a topic, were used by New Scientist on Facebook right after a jury in San Francisco concluded that the giant agrochemical and biotech Monsanto must pay $289 million in damages to Dewayne Johnson, who has cancer of the immune system (lymphoma), a condition he and his attorneys claim was caused by exposure to glyphosate-based herbicides commercialized by Monsanto from 1974 to 2000.

The jury’s decision went viral. A 46-year-old school groundskeeper was dying, a world known corporation was being blamed for it, and the state of California offered the perfect stage for litigation. The German Pharmaceutical group Bayer, which back in June, 2018, formalized its engulfing of Monsanto for $60-plus billion, went into frantic damage control, and for a reason. About four thousand other plaintiffs await their day in court. Hundreds of millions, if not billions, of dollars in potential damage awards could be in dispute, more so if Monsanto-Bayer fail in their appeal to the California decision.

But, why did New Scientist, “the world’s most-read weekly popular science and technology magazine,” as described on its website, decide to departure from covering “international news from a rational, analytical standpoint rooted in the scientific method” and inject extra doubt into the glyphosate debate? I am referring to the directional “probably not” when swiftly-answering its own query “does weedkiller cause cancer?”

As the reader might imagine, the New Scientist’s position caused turmoil among academics and science educators, whose mentors and themselves have relied, since 1956, on the London-based enterprise to get their weekly news. For researchers, New Scientist is a classic, like The New York Times or BBC are for journalists.

The concerns in many of the five hundred comments that New Scientist’s Facebook followers wrote were: why did New Scientist appear to align with Monsanto-Bayer, rather than simply apply the scientific method to communicate the facts about glyphosate to the public? Based on the available research, why did New Scientist take the path of “probably not,” rather than an objective “there are some studies suggesting an association between glyphosate and cancer, and others arriving at inconclusive results”? Moreover, why did New Scientist explicitly state in the heading to its post that “there is no evidence that the weedkiller glyphosate causes cancer”? The latter is false; it implies that the studies that have found such indication should be arbitrarily ignored. And that is not how science works.

Some commentators on the New Scientist post added links to the scientific literature and prestigious journals in which associations between glyphosate exposure and cancer had been reported in laboratory animals and limitedly in humans. Others defended Monsanto-Bayer and listed the publications by researchers affiliated with the multi-company Glyphosate Task Force. But the vast majority questioned, not Monsanto-Bayer, but New Scientist for relying on its outreach platform to seed generalized distrust on any probable link between glyphosate and cancer.

The New Scientist’s captions appeared as large texts on a micro-video with images of Mr. Johnson, containers with Round-up (one of the herbicide’s market names), crop fields being labored, activists “impersonating death” and opposing the weedkiller, small airplanes spraying glyphosate, quotes that the International Agency for Research on Cancer (IARC) “considers glyphosate probably carcinogenic” to laboratory animals when exposed in high doses (in direct contradiction to the very New Scientist headings), but that other “studies in humans have found no evidence of a link,” and that “other agencies have concluded there is no increased risk of cancer” due to contact with glyphosate. Yet, the take-home message in the clip was: glyphosate does not or “probably does not” cause cancer (see also companion article “There is no evidence that the weedkiller glyphosate causes cancer…”).

From a rational, analytical standpoint, rigorous scientists would hardly take the “probably not” path. Here is why. It is not a scientific answer. When investigators find evidence, even if limited but of statistical rigor in a controlled study, they state categorically that such evidence exists under the parameters of the research. When no evidence is found, or the numerical sustain is weak, the studies are never declared “probably not” (a “leading-the-mind” hint), but rather inconclusive; and that is Science 101.

Skepticism is what drives science and researchers. As for the question “does weedkiller cause cancer?” Well, there is increasing evidence that it does in laboratory animals and, apparently, in humans, as well as there are historical, inconclusive or unsubstantiated findings (see review articles from 2016, 2017). But then, there is the legal fight between citizens, their attorneys, and a multi-billion corporate colossal. The answer is complex, but it is not “probably not.” — EvoLiteracy © 2018.

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