“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).
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.
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).
“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.”
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?
“…Belief is powerful, it disrupts, distorts, delays or stops the comprehension and acceptance of scientific evidence. Scientists call this phenomenon the ‘3Ds+S’ cognitive effects of illusory thinking. Now, the best tonic against its infectious sequels was discovered long ago; it consisted, still does, on proper healthcare education for all. And, in contrast to misleading and unwarranted ‘paramedicine,’ the side effects of widespread science education will always be cheaper, plus save, for sure, some lives…”
By Guillermo Paz-y-Miño-C
Cancer hides or thrives in our bodies. Someone we know, close or distant, is destined to die because of it. And although therapies continue to improve thanks to scientific advances, diverse cancers persist and it might take decades, if ever, to fully manage them.
In the United States, breast, prostate, lung and colorectal cancer are the most prevalent, and chemotherapy, radiotherapy, surgery, and/or hormone therapy the usual treatments. Yet, more than half of the patients with cancer opt for “complementary medicine” to improve, as they believe, their quality of life and survival.
But, do herbs and botanicals, vitamin and mineral supplements, probiotics, traditional medicines, homeopathy, naturopathy, acupuncture, chiropractic or osteopathic manipulation, massage, prayer, reflexology, energy medicine, or special diets have an actual impact on prolonging cancer patients’ lives? The short answer seems to be no.
Physicians from the Yale School of Medicine have just published the study “Complementary Medicine, Refusal of Conventional Cancer Therapy, and Survival Among Patients with Curable Cancers” in the Journal of the American Medical Association (JAMA). From a data set of 1.9 million individuals, gathered between 2004 and 2013 and stored in the National Cancer Database, the researchers extracted a representative sample of cancer patients whom opted for complementary medicine (CM) versus those exposed to conventional cancer treatment (CCT).
The study was straightforward. It aimed at identifying and comparing survival rates between CM and CCT groups.
Patients exposed to complementary medicine had a greater risk of death than those under conventional cancer treatment. In fact, only 82 percent of the CM patients versus 87 percent of the CCT patients survived during a 5-year monitoring lapse since they were first diagnosed with the condition. The trend was noticeable in women suffering breast cancer, with only 85 percent of the CM patients versus 90 percent of the conventionally-treated patients surviving since diagnosis (also during a 5-year follow up).
According to Skyler Johnson, Henry Park and Cary Gross, authors of the study and fellows at the Department of Therapeutic Radiology, as well as the Cancer Outcomes, Public Policy, and Effectiveness Research Center at Yale, the general risk of death associated with complementary medicine was primarily linked to the patients’ refusal to receive: surgery (7 versus 0.1 percent refusal between the CM versus CCT groups, respectively), chemotherapy (34 versus 3 percent), radiotherapy (53 versus 2 percent), and/or hormone therapy (34 versus 3 percent).
Quite interestingly, patients in the complementary medicine group were more likely to be young, women, have breast or colorectal cancer, belong to high socio-economic cohorts, have private medical insurance, high-school education, and reside in the Intermountain West or Pacific West of the United States (where alternative-medicine schools are common, protected by state legislation).
In essence, the Yale study concluded that if patients went for unconventional cures to fight cancer, rather than scientific medicine, they had higher risk to die and do it earlier. Complementary medicine did not help.
As David Gorski, member of the Department of Surgery at Wayne State University School of Medicine and the Department of Oncology at the Barbara Ann Karmanos Cancer Institute (both in Michigan), already alerted back in 2014 when compiling a comprehensive review for the journal Nature “the vast majority of ‘integrative’ [complementary oncology] treatments [were] supported by little, if any, scientific evidence.” He pointed out, with concern and irony, “therein lies a key problem with integrative oncology. The less ‘alternative’ the intervention, the more it resembles conventional oncology; the more ‘alternative’ the intervention, the more it resembles the quackery from which integrative oncologists rightly distance themselves.”
Why do patients opt for unscientific methods to battle cancer? There are multiple reasons, and only one of them has to do with “hope,” trust on a possibility (the “alternative cure”) beyond the “conventional scientific wisdom,” one that might work and, if not, at least, it won’t hurt. There is always a friend or a relative that recommend “holistic cures” to somebody they love. But the Yale study demonstrates that such paths can indeed be harmful: remember that they were associated with higher risk of dying and doing it earlier among patients choosing “complementary practices.”
“Just believing in self- or collective-greatness will not materialize into competitive performance… For us, it will be impractical and blindfolding to insist on national self-flattering. But, if there is anything we do better than anybody else is to blindfold ourselves.”
By Guillermo Paz-y-Miño-C.
Overconfident? Self enhanced? Smarter than average? Yes.
Such widespread public opinions about relative intelligence were first reported in the United States in 1965. Yet, as a team of researchers puts it in a replication study just published in the academic journal Public Library of Science (PLoS), “American’s self-flattering beliefs about intelligence are alive and well several decades after their discovery.”
When asked to assess the statement “I am more intelligent than the average person,” via phone or online polling, 65 percent of responders either agreed or strongly agreed with the premise.
The pollsters, Patrick Heck, Daniel Simons and Christopher Chabris, affiliated with the Autism & Developmental Medicine Institute in Pennsylvania, the Department of Psychology at the University of Illinois-Champaign, and the Institute for Advance Study in Toulouse-France, respectively, interviewed 2,800 adults in the 50 states of the country, and analyzed their responses as per sex, age, race/ethnicity, and educational attainment.
More men (about 70 percent) than women (about 60 percent) considered themselves smarter than average, a trend comparable to the adults younger than 44 years of age (also 70 percent were confident in their intellect) versus those older than 44 years (60 percent). In terms of race/ethnicity, about 65 percent of both “whites” and “non-whites” agreed with the notion “I am more intelligent than average,” with the peculiar feature that up to 71 percent of “non-whites,” who responded to the survey online (rather than by phone and were likely skillful computer users), mostly or strongly concurred with the statement.
Interestingly, responders with college or post-graduate degrees underestimated themselves, with 70+ percent thinking they were above average intelligence; note that the pollsters expected 80+ percent of the highly educated to think that way according to their usual cohort performance in IQ-tests. Those with “no college” or “some college” education, by contrast, surpassed the expected 47 percent confidence score on self-brain-ranking, with 55-62 percent of them believing (themselves) to be smarter than the mean.
“…both the naturally talented as much as the taught-to-reason-average-individual can perform better in ‘the real world’ if provided with educational tools to excel…”
Overconfidence is not necessarily bad. It can actually boost performance, encourage bold, creative thinking and help persist on innovative projects even though they might have been initially dismissed by others (for an evolutionary take see Nature). The “smarter than average effect,” as it is known among psychology scholars, is apparently ubiquitous across cultures (particularly in the West; but see an alternative perspective here), although the trends in the United States are not directly applicable elsewhere.
There is no doubt that education brings self confidence to people, but there is also innate differential talent among individuals, which can be developed even further with proper mentoring and schooling. Take youth math ability, for example, the most reliable predictor of later-in-life career success (go to scientific article): all significant aspects of modern societal development, which are bound to science and technology, depend on quantitative, rational thinking to solving problems and innovating progress. And both the naturally talented as much as the taught-to-reason-average-individual can perform better in “the real world” if provided with educational tools to excel. Thus, “above average performance” — in respect to the past — can be continuously built in anyone and, by doing so, raise the bar for all.
Paradoxically, at some point, perhaps at a crucial one in history (now!), just believing in self- or collective-greatness (as celebrities often claim “as long as you believe, anything is possible,” which is always followed by tens of thousands of “likes” and “shares” in social media) will not materialize into competitive performance; at least not when so many countries out there are committed to, via meaningful actions in elementary-, high-school- or higher-education, lead the future.
“…Academics ‘are trapped; compelled to participate in activities they find distasteful,’ including the intricate world of scientific publications, which involves a range of journal publishers, editors, book producers, open-access periodicals, for-profit series, online-journals and other venues to disseminate research; plus, of course, individuals —charming, powerful or both— that free ride at the expense of others’ work…”
In an article just published in PLoS ONE, December 2017, Eric A. Fong and Allen W. Wilhite, researchers at the University of Alabama in Huntsville, document three practices in academia: (1) the inclusion of “honorary authors” in scientific publications (i.e. the addition of individuals to manuscripts as authors, even though they have contributed little, if anything, to the actual research), (2) coercive citations (i.e. when editors direct authors to add citations to articles from the editors’ journals ‒arguably to boost the journal’s citation index), and (3) padding (i.e. when authors add superfluous citations to a paper in an attempt to increase its chance for publication). Fong and Wilhite surveyed 12,000 scholars from 18 disciplines (i.e. health-care, engineering, science, social sciences and business) at diverse universities in the United States.
The specific fields of specialization of the interviewed researchers were: medicine, nursing, biology, chemistry, computer science, mathematics, physics, engineering, ecology, accounting, economics, finance, marketing, management, information systems, sociology, psychology, and political science. The Fong and Wilhite’s study is comprehensive and I suggest the reader to look at the original publication for details. In the figure below, I simply share the statistical trends that summarize the research. I have adapted an image from the PLoS ONE article (open access journal) to make it more appealing to a non-specialized audience.
In the image, note the following: (1) Adding honorary authors to manuscripts was common practice among 1 in every 3 of the surveyed scholars; it reached +40% in the health-care professions. (2) About 1 in every 5 scholars added such authors to a grant proposal; and, again, about 40% was typical in the health-care professions. (3) Coercive citations were common in +5% of the scholars in science, and beyond 20-25% in engineering and business. (4) The practice of padding a scientific article with irrelevant citations was common among, at least, 1 in every 5 authors, and particularly evident among those in science and engineering (around 30%), and +45-50% in business and the social sciences. Finally, (5) padding in grant proposals was common in +10-20% of all disciplines, and up to ≈40% in business.
The responders to the survey acknowledged that the main reason for adding honorary authors in their manuscripts was the relationship of director/authority of the honorary author in respect to the “real authors” of the paper (+20% of the responders thought that way); others included as co-authors their mentors, colleagues, individuals-for-reciprocity-reasons, for their reputation, or for funding. However, 60% of all responders added honorary authors to their grant proposals simply due to the latter’s “reputation,” and, thus, to increase the chances of getting the projects funded.
Interestingly, between ≈60% and +90% of all responders disapproved of the coercive citation practice across disciplines. But keep in mind that, despite the quantitative approach to the study, the responses were also based on perception, i.e. the researchers’ insight about honorary authors, coercive citations or padding in scientific publications and grant proposals.
Fong and Wilhite concluded that:
“…there is a significant level of deception in authorship and citation in academic research and while it would be naïve to suppose that academics are above such scheming to enhance their position, the results suggest otherwise. The overwhelming consensus is that such behavior is inappropriate, but its practice is common. It seems that academics are trapped; compelled to participate in activities they find distasteful…”
“…misattribution, spans the academic universe. While there are different levels of abuse across disciplines, we found evidence of honorary authorship, coercive citation, and padded citation in every discipline we sampled. We also suggest that a useful construct to approach misattribution is to assume individual scholars make deliberate decisions to cheat after weighing the costs and benefits of that action. We cannot claim that our construct is universally true because other explanations may be possible, nor do we claim it explains all misattribution behavior because other factors can play a role. However, the systematic pattern of superfluous authors, coerced citations, and padded references documented here is consistent with scholars who [are] making deliberate decisions to cheat after evaluating the costs and benefits of their behavior…”
To close: In my (our) own experience, I (we) have never included honorary authors in my (our) publications, or have never been an honorary author of a paper. But some colleagues have asked me (us), more than once, why have I (we) included such and such person in that or that paper, assuming that that individual did not deserved it. My (our) rationale has always been that if a substantial aspect of a manuscript had not been possible to be completed, unless that person had contributed directly or indirectly to the research, that individual ought to be acknowledged as co-author. This includes the very conceptual transformation of a manuscript due to crucial feedback, interpretation of results, and substantial modification of the scope with which an article was put together. — In cases like that, I have expected my name to be included as co-author, but that has happened sporadically (more during the times I was a postdoc and contributed with conceptual, methodological, analytical and copy-editing feedback to graduate students’ dissertations). In various occasions, I have requested to not be included in manuscripts as a co-author; this practice is not unusual among researchers.
In terms of coercive citations, I have never been asked by a journal editor to cite an irrelevant paper with the purpose of contributing to boosting the journal’s citation index (which, by the way, would require hundreds of authors to be simultaneously coerced to cite multiple articles to have a statistical influence on the journal’s performance), although I have been suggested by journal editors to take a look at some studies (published in other journals), of which I was not aware, and that I actually found very helpful to come across, and decided to discuss and cite them in a paper. However, and this is a big “however,” peer-reviewers have attempted to coerce us (Avelina Espinosa and I), more than once, to cite their papers (or their close collaborators’), or papers of their liking, in our studies. In many cases, such papers were irrelevant, or we disagreed fundamentally with them to even give them a citation in our manuscripts. On one occasion, a well known individual in a field insisted that we should cite non-scientific books in our work, and did so with assertive authority (plus specifically stated where in our text we had to acknowledge the merits of the organization with which the individual was affiliated ‒sounds surreal, right?), an issue we later resolved with the journal editor, who agreed with us and considered the suggestion to be imprudent. So, yes, coercive predators do exist and attempt to exert power at will… if you let them. But journal editors are very experienced, for the most part, and tend to not allow such approaches to peer-reviewing.
On grants, we have never included potential honorary recipients to increase our chances of getting funded. But, when attending a national-funders meeting in Washington DC, a few years ago, we were advised to add a specific anchor-individual to our team, otherwise “we will continue to be seen as outsiders” (verbatim) in that specific community of peer-reviewers. Of course, we declined to include that person in our proposals (three of which were not funded by the agency), although we did complete the research and publish the papers (N = 14) that we projected in the proposals to be the outcomes of the projects. Not only that, we were fortunate to publish an academic best-seller-2017-book summarizing all the research and with no strings attached to any honorary contributor.
“…MTEC now available at university libraries in the United States, Canada, Germany, Hong Kong, Israel and Scotland…”
Measuring The Evolution Controversy is now available at university libraries in the United States, Canada, Germany, Hong Kong, Israel and Scotland, either as hard copy, e-book or both. Some data bases locate the book in Australia, South America and Asia, but the library-catalogue entries are difficult to confirm. I will continue to update this post as new libraries join the list. If your institution has the book and is not listed below, please let me know (write a comment at the end or contact me via email). The book can be ordered from Cambridge Scholars. — GPC
“The great contribution of ‘Measuring the Evolution Controversy’ is the rich content of data and analysis that asks detailed questions about the social, economic and political backgrounds of those who tend to reject evolution vs. those who accept evolution as science. Paz-y-Miño-C and Espinosa deftly analyze their data drawn from institutions of higher learning in the United States and particularly New England —which stands as a microcosm of the rest of the country, and indeed elsewhere in the world. It is their scientific approach to these issues which makes this book stand out as a uniquely original contribution.” —Niles Eldredge, PhD, Curator Emeritus of Paleontology at The American Museum of Natural History, New York.
“Pro-science activists and educators constantly bemoan the resistance to the teaching of evolution in the United States. All of us have anecdotes about encounters with the public, parents and students who are misinformed by their churches, Religious-Right groups, and creationist organizations. Paz-y-Miño-C and Espinosa present hard data that support the anecdotal evidence. They also show that although anti-evolutionism typically begins with religion, it is a multi-faceted problem that intersects with political and cultural ideologies. Gathered through careful research over a period of years, their data will enable scientists and defenders of science education to comprehend the roots of the evolution controversy and counteract resistance to evolution more strategically and effectively.” — Barbara Forrest, PhD, co-author with Paul R. Gross of Creationism’s Trojan Horse: The Wedge of Intelligent Design (2007), and expert witness for plaintiffs, Kitzmiller et al. v. Dover Area School District (2005).
“The sweet spot of this collection of essays is the interface of science, history and literacy. Paz-y-Miño-C is, in essence, a champion of rationalism and a passionate defender of literacy standards. His essays deftly weave hard survey data and memorable turns of phrase with evocative imagery… While the essays in this collection are vast in coverage —from climate change to energy policy, stem cell research, vaccinations and, especially, evolution— a clear underlying theme emerges: [the author’s] goal is no less than to counter, through the lens of history and the majesty of rationalism, social forces that sanction ignorance, celebrate denial and… continue to diminish our global status in the fields of science and technology.” Jeff Podos, PhD, Professor of Biology, University of Massachusetts Amherst, USA.
“Paz-y-Miño-C is a firm believer in evolutionary processes. He would like to see decisions made on the basis of facts, not unsupported opinion. He abhors and fears irrational thinking, especially ‘the views of those who see evil in truth and menace in the realities discovered by science.’ He marvels at the intricacy and diversity of life, and how it came about through natural selection… and is clearly frustrated by the unwillingness of so many to see the beauty and majesty in this view of the world and all that it explains.” – Jan A. Pechenik, PhD, Professor of Biology, Tufts University, USA, author of The Readable Darwin: The Origin of Species, as Edited for Modern Readers.
“…Colleges and universities must lead freedom of speech, nurture the battlefield of ideas, pursue world-competitive standards, deter grade inflation (a historical, pervasive companion of conflict resolution), stand for science and reason, teach the realities of the cosmos and evolution without spiritual justifications, and be the safe spaces where the trigger warning ‘no ignorance allowed’ is respected…” – GPC
[click on subtitle to be redirected to The Standard Times]
“There’s been a trend around the country of trying to get colleges to disinvite speakers with a different point of view, or disrupt a politician’s rally. Don’t do that, no matter how ridiculous or offensive you might find the things that come out of their mouths. Let them talk. If you don’t, you just make them a victim, and then they can avoid accountability.”
“That doesn’t mean you shouldn’t challenge them. Have the confidence to challenge them, the confidence in the rightness of your position. But listen. Engage. If the other side has a point, learn from them. If they’re wrong, rebut them. Teach them. Beat them on the battlefield of ideas.”
These were President Obama’s remarks at the Howard University commencement ceremony, back in May 2016. He highlighted a nowadays generalized concern in academia: that millennials (the generation born between the 1980s and early 2000s) have grown intolerant of any view contrary to their deepest, yet maturing convictions, a phenomenon documented by Gallup in its latest report “Free Expression On Campus.”
Although “college students believe First Amendment rights remain strong” in the United States, they also hold conflicting views about “shuttering free speech and impeding a free press under certain circumstances.” For instance, even though 81 percent of college students think that freedom of the press is very secure or secure in the country, and 73 percent think likewise about freedom of speech, one in every five college students (22 percent) believe that “to create a positive learning environment for all, it is more important for colleges to prohibit certain speech or expression of viewpoints that are offensive or biased, than to create an open learning environment where students are exposed to all types of speech and viewpoints —even offensive or biased.”
“…boycott actions against free speech may be rooted in capricious interpretations of First Amendment rights by students active and verbal at their institutions…”
But, what is offensive or biased rhetoric? Slurs and language that intentionally seek to hurt or offend (69 percent of students think so), or the wearing of costumes that stereotype racial or ethnic groups (63 percent believe that), or political views that may upset or offend (27 percent of students think colleges should limit such speech). The Gallup data, therefore, implies that boycott actions against free speech may be rooted in capricious interpretations of First Amendment rights by students active and verbal at their institutions.
Should the media cover protests held at colleges and universities? One in every four students (28 percent, mean of men + women) opposes reporters’ coverage of demonstrations in campus. This view is noticeable among women (37 percent) and African Americans (32 percent). Gallup calls this overall occurrence “support of free press rights in the abstract” (or “in principle”) but not in practice. Protesters believe the press will be unfair in its reporting (49 percent say this), they assert to have the right to be left alone (48 percent), and want to tell their own version of the story on the internet and social media (44 percent). In fact, 86 percent of the polled students prefer the social media for allowing them more control over the story.
Why has intolerance of free speech become ubiquitous? Only tentative answers exist to this question. Greg Lukianoff and Jonathan Haidt, authors of “The Coddling of the American Mind,” have taken a psychological path to explain how “in the name of emotional well-being, college students are increasingly demanding protection from words and ideas they don’t like.” The ultimate aim, Lukianoff and Haidt state, “is to turn campuses into ‘safe spaces’ where young adults are shielded from words and ideas that make some uncomfortable. This movement seeks to punish anyone who interferes with that aim, even accidentally.”
“…Emotional reasoning, distorted thinking, magnification of events, and catastrophizing incidents seem to be central to the individual and collective minds of those who perceive offense in daily experiences…”
The “impulse” is called “vindictive protectiveness” and, as described by Lukianoff and Haidt, “it is creating a culture in which everyone must think twice before speaking up, lest they face charges of insensitivity, aggression, or worse.” Emotional reasoning, distorted thinking, magnification of events, and catastrophizing incidents seem to be central to the individual and collective minds of those who perceive offense in daily experiences. Thus, via negative filtering, groups develop a culture which focuses almost exclusively on the unconstructive, and this allows for simpleminded demonization.
“…The challenge is to identify objectively what is intellectually or psychologically damaging and what is mild…”
Universities must be the safe spaces where the trigger warning “no ignorance allowed” is respected – GETTY IMAGES
“The great contribution of ‘Measuring the Evolution Controversy’ is the rich content of data and analysis that asks detailed questions about the social, economic and political backgrounds of those who tend to reject evolution vs. those who accept evolution as science. Paz-y-Miño-C and Espinosa deftly analyze their data drawn from institutions of higher learning in the United States and particularly New England —which stands as a microcosm of the rest of the country, and indeed elsewhere in the world. It is their scientific approach to these issues which makes this book stand out as a uniquely original contribution.” —Niles Eldredge, PhD, Curator Emeritus of Paleontology at The American Museum of Natural History, New York.
“Pro-science activists and educators constantly bemoan the resistance to the teaching of evolution in the United States. All of us have anecdotes about encounters with the public, parents and students who are misinformed by their churches, Religious-Right groups, and creationist organizations. Paz-y-Miño-C and Espinosa present hard data that support the anecdotal evidence. They also show that although anti-evolutionism typically begins with religion, it is a multi-faceted problem that intersects with political and cultural ideologies. Gathered through careful research over a period of years, their data will enable scientists and defenders of science education to comprehend the roots of the evolution controversy and counteract resistance to evolution more strategically and effectively.” — Barbara Forrest, PhD, co-author with Paul R. Gross of Creationism’s Trojan Horse: The Wedge of Intelligent Design (2007), and expert witness for plaintiffs, Kitzmiller et al. v. Dover Area School District (2005).
“The sweet spot of this collection of essays is the interface of science, history and literacy. Paz-y-Miño-C is, in essence, a champion of rationalism and a passionate defender of literacy standards. His essays deftly weave hard survey data and memorable turns of phrase with evocative imagery… While the essays in this collection are vast in coverage —from climate change to energy policy, stem cell research, vaccinations and, especially, evolution— a clear underlying theme emerges: [the author’s] goal is no less than to counter, through the lens of history and the majesty of rationalism, social forces that sanction ignorance, celebrate denial and… continue to diminish our global status in the fields of science and technology.” Jeff Podos, PhD, Professor of Biology, University of Massachusetts Amherst, USA.
“Paz-y-Miño-C is a firm believer in evolutionary processes. He would like to see decisions made on the basis of facts, not unsupported opinion. He abhors and fears irrational thinking, especially ‘the views of those who see evil in truth and menace in the realities discovered by science.’ He marvels at the intricacy and diversity of life, and how it came about through natural selection… and is clearly frustrated by the unwillingness of so many to see the beauty and majesty in this view of the world and all that it explains.” – Jan A. Pechenik, PhD, Professor of Biology, Tufts University, USA, author of The Readable Darwin: The Origin of Species, as Edited for Modern Readers.
This morning, I learned from Avelina Espinosa that our symposium articles on Kin-Discrimination in Protists have been featured on the latest issue of the Journal of Eukaryotic Microbiology (May-June 2016). I posted a report about this topic a few weeks ago, when the papers became available online as “early view.” Here are page updates about these publications and a view of the journal cover (i.e. several developmental stages of the social amoeba Dictyostelium discoideum; photo by Usman Bashir):
To remind the readers, these articles summarize outcomes of the symposium “Evidence of Taxa-, Clone-, and Kin-discrimination in Protists: Ecological and Evolutionary Implications,” which took place at the VII European Congress of Protistology, organized last summer in partnership with the International Society of Protistologists (ECOP-ISOP 2015), and hosted by the University of Seville, Spain.
The complete report about the three articles is available at Kin Recognition or Kin Discrimination in Single-Celled Organisms – Protists, which appeared on April 4, 2016, and was featured at EvoLiteracy. As suggested in that report, readers might also benefit from exploring the initial paper that inspired the organization of the ECOP-ISOP 2015 symposium:
Can single-celled organisms distinguish between same (self or clone) and different (diverse clones)? Can they tell apart kin from non-kin? Can they “learn” to discriminate or recognize members of their own versus others’ cellular lineages? Answers to these questions are provided in three articles (first, second, and third) just published (early view) in the Journal of Eukaryotic Microbiology. The studies summarize outcomes of the symposium “Evidence of Taxa-, Clone-, and Kin-discrimination in Protists: Ecological and Evolutionary Implications,” which took place at the VII European Congress of Protistology, organized last summer in partnership with the International Society of Protistologists (ECOP-ISOP 2015), and hosted by the University of Seville, Spain. I participated at this Symposium and co-authored two of the trilogy papers. But my purpose here is to bring attention to the topic “kin discrimination” or “kin recognition” in unicellular organisms, an area of research that has made much progress in the past fifteen years. There are some technicalities in the text below, but I ask the readers to make an effort and try to understand the broad themes, while being patient with the details. Enjoy! – Guillermo Paz-y-Miño-C.
The unicellular eukaryote Entamoeba invadens (a protist) colored with Green or Red markers. When the Green and Red cells fully aggregate in mixed assemblages, they look yellow under the microscope, an indication that the amebas are able to distinguish members of the same clone, without being affected by the coloration. When grown in the laboratory with non-clone members, the amebas only aggregate with same-clone cells, an indication of preference to group with themselves. Photo courtesy of A. Espinosa 2016.
Readers unfamiliar with “protistan” biology might benefit from grasping some terminology (i.e. protist, prokaryote, eukaryote, clone, multicellularity, kin recognition/discrimination), which I explain next by answering simple questions. For those trained in biology, it might be fine to skip the first five subtitles, below, and move on directly to “From multicellular to unicellular: a round trip:”
What is a protist?
Remember that some organisms are made of single cells. Yes, the entire organism is a cell. For example, bacteria (like the E. coli that lives in the human gut) or amebas, which are also microscopic and can be found in a pond. However, one of the main differences between a bacteria and an ameba is that the former has no nucleus, in contrast to the latter that has it. For that reason, bacteria are called prokaryotes (pro = “before” or “prior to” or, in this case, no nucleus) and amebas are called eukaryotes (eu = “well” or “good” or, in this case, with nucleus). However, many other organisms have nucleated cells (and are, therefore, eukaryotes), like a frog, an orchid, a chimpanzee, a maple tree, or a Blue Whale. The term “protist” applies to unicellular eukaryotes, while the amphibian, the plant, or the aquatic mammal are called multicellular eukaryotes, since their bodies are made of billions of nucleated cells.
Now, the term “protist” is tricky because it includes extremely diverse organisms (which earliest ancestors likely emerged two billion years ago), and over the years scientists have realized that many exceptions exist of organisms that, although are not always unicellular in their life cycles, they are (or should be considered) protists. One of them is the social ameba (or amoeba), Dictyostelium, which forms multicellular assemblages (moving “slugs;” watch video) during its life stages, and also lives in nature as a single-celled, free ranging ameba. To learn more about the ambiguities intrinsic to the term “protist,” and for more examples, go here.
What is a clone?
Because unicellular organisms reproduce, in many cases, via simple cell divisions, the resulting progeny is often identical to the parental cell. A single ameba, for example, can give origin to 2 identical daughter cells, which, in turn, can generate 4 cells (i.e. 2, 4, 8… see cartoon on the right). The resulting thousands, or millions, of cells are “clones” (identical copies of each other). Now, during so many cell divisions, mutations that change the sequence of DNA can –and do– occur, making the descendant cells gradually different from the parental ones. Over time, maybe hundreds of years, a cell line could change enough to become a different clone. Moreover, after thousands or millions of years, different species of amebas can emerge, each distinctive from one another and from the species that gave them origin in the past, a phenomenon known as speciation.
What is multicellularity?
Volvox (a green-algae protist) forms large sphere-colonies made of hundreds, or thousands, of individual cells (see daughter colonies inside). Click on image for source.
Perhaps a more didactic question here is ‘where do multicellular organisms (i.e. frogs, orchids, chimps, maple trees, blue whales) come from’? A first, quick answer is that all multicellular organisms known today originated –at some point– in ancient assemblages of unicellular ancestors (traceable to billions of years ago). However, a more cautious answer is that we have a fragmentary understanding about how primitive single-celled eukaryotes took the path (here I mean driven by natural selection) toward permanent associations in immense cellular cooperatives, which we now call multicellular organisms (note that scientists consider the advent of multicellularity a “major evolutionary transition” in the history of Earth). And that is why studying modern protists, like gregarious amebas (in the genus Entamoeba), or facultative social amebas (i.e. not always social, but in response to environmental circumstances), like Dictyostelium, can give us hints about how multicellularity originated. This particular topic is discussed in the three articles published in JEUKMIC (first, second, and third), and to which I refer in this post. But before I get into that, take a look at the image of Volvox (inset). The organism Volvox is a green-algae protist, which forms large sphere-colonies made of hundreds, or thousands, of individual cells. Inside these spheres, daughter colonies develop and, when they mature, the parental spheres bursts and the descendant colonies are released into the aquatic environment, where they continue to grow and proliferate. Today’s multicellular aggregations of protists, like Entamoeba, Dictyostelium or Volvox, give us clues about how multicellularity might have originated in ancient Earth. Moreover, they are good model-systems to study kin recognition or kin discrimination (which include an organism’s skills for grouping and cooperating with the right partners, and behaving altruistically toward them) in the context of the origin and evolution of multicellularity.
What is kin recognition or kin discrimination?
“The ‘field of kin recognition’… has no consensus on definitions or proposed mechanisms, possibly due to the vast diversity of life histories across organisms and their phylogenetic complexities…”
NASA’s twin astronauts Scott, left, and Mark Kelly. Photo: Tony Cenicola. In humans, identical twins are the only natural “clones;” their genetic relatedness is equal to 100% (represented by r = 1.0). However, the rest of us are related to our siblings only by 50%, or r = 0.5. Our relatedness with our parents is the same, r = 0.5. Can the reader tell why? If so, here is a question: what would be your genetic relatedness with an uncle/aunt, or with a grand parent, or with a second cousin?
This topic can be a bit confusing. However, in one of the articles (the first one listed below), the authors explain why: “…The ‘field of kin recognition’… has no consensus on definitions or proposed mechanisms, possibly due to the vast diversity of life histories across organisms and their phylogenetic complexities (here, phylogeny means ancestry, somewhat analogous to genealogy, not of your own family, but rather of distinctive species or kinds of organisms grouped in distinctive categories). [The authors] refer to “recognition” as an organism’s ability to identify kin [family members] versus non-kin [members of another family]; in addition, [the authors] use the term “discrimination” as the capacity to distinguish one clone from another. Because [the authors] discuss instances of taxa- [taxa = in this particular case means species], clone-, and kin-discrimination/recognition in single-celled organisms capable of both discriminating between same and different, and discriminating/recognizing among clones of distinctive [degree of genetic relatedness, like, for example, values of r less than 1.0], [the authors] use these terms together…”
Why is it relevant to study kin recognition or kin discrimination in single-celled organisms?
To answer this question, I will borrow, again, text from the first article: “…Multicellularity is a major evolutionary transition in which single-celled organisms switched from living individually to permanent assemblages. It is possible that multicellularity originated —more than once— in clonality, via a gradual aggregation of closely related cells, capable of recognizing one another by means of chemical cues, and which lived consistently in intimate proximity and benefited from specialized division of labor (i.e. distinctive tissues and organs with given functions). Such specialization included the full allocation of soma-reproduction [soma = the entire body of an organism] to a small population of cells within the soma, the gametes [i.e. ovules, sperm]… Protists are central to the reevaluation of the theoretical framework and concepts in the field of kin recognition, and to research about the origins and evolution of multicellularity...”
From multicellular to unicellular: a roundtrip
The first article (by Paz-y-Miño-C and Espinosa) is a concise review on “Kin Discrimination in Protists: From Many Cells to Single Cells and Backwards.” In it, the authors summarize the current understanding of the genetics of kin discrimination/recognition in unicellular Eukaryotes, and they do it historically by going back in time, to Darwin and his Origin of Species (1859; Darwin speculated* that selection may be applied to the family; kin discrimination/recognition rely on kin-selection theory), and the influential 1960s, when the modern field of kin recognition was, arguably, born. Here is a simplified version of the first article’s abstract:
“During four decades (1960s to 1990s), the conceptualization and experimental design of studies in kin recognition relied on work with multicellular eukaryotes, particularly invertebrates and vertebrates, and some plants. This pioneering research had an animal behavior approach. During the 2000s, work on taxa-, clone- and kin-discrimination and recognition in protists produced genetic and molecular evidence that unicellular organisms could distinguish between same (self or clone) and different (diverse clones), as well as among conspecifics of close or distant genetic relatedness (Table 1, below). Here we discuss some of the research on the genetics of kin discrimination/recognition and highlight the scientific progress made by switching emphasis from investigating multicellular to unicellular systems (and backwards). We document how studies with protists are helping us to understand the microscopic, cellular origins and evolution of the mechanisms of kin discrimination/recognition and their significance for the advent of multicellularity...”
[Click on Table 1, below, to enlarge]
Readers might find the following excerpts from this article quite intriguing, e.g. “learning” in unicellular organisms (is that possible?):
“…In 1899, H. S. Jennings wrote: ‘Paramecium… an animal that learns nothing, that exercises no choice in any respect, that is attracted by nothing and repelled by nothing, that reacts entirely without reference to the position of external objects, that has but one reaction [movement –watch video below] for the most varied stimuli… can hardly be said to have made the first step in the evolution of mind, and we are not compelled to assume consciousness or intelligence in any form to explain its activities.”
Above: movement behavior in Paramecium. This video is 13-min long and shows various types of Paramecium. If you watch it for a couple of minutes, it shall give you an idea about how these ciliateslook like and move.
“Except for mind, consciousness and intelligence, which are not prerequisites for kin discrimination or recognition (both can also operate in a reflex manner: stimulus-response), Jennings was mistaken about his entire characterization of Paramecium. Since the early 1900s, sensitization, trial-and-error learning, and classical or operant conditioning (relevant attributes among some of the multicellular eukaryotes that learn to recognize kin) have been documented in Paramecium; [including] micro-tube-escape swimming behavior via discrimination learning (1910s), habituation to approach baited and un-baited targets using bacteria as food-reinforcer (1950s), and swim-approach behavior toward mild-electrically-charged fields in learning discrimination tasks using positive and punishment reinforcements (2000s).”
And the authors add: “…But, to our knowledge, there is no direct, experimental evidence that protists can rely specifically on sensitization (i.e. the enhancement of a response to an incremental exposure to a stimulus, for example, the differential frequency exposure to kin versus non-kin during a life cycle), trial-and-error learning (i.e. repeated attempts to solve a task until success, for example, attempts to behave altruistically toward kin, and the benefits it entails, versus the costs of maladaptive altruism toward non-kin), or classical or operant conditioning to discriminate between kin and non-kin (i.e. learning to associate a behavioral or chemical cue with the advantages/disadvantages of aggregating, cooperating or reproducing with conspecifics of [diverse degree of relatedness]). All these topics, remain open areas of investigation and experimentation with protists since, like Paramecium, they possess basic sensory perception capabilities, which could have been co-opted [= adapted] during evolution to function in kin discrimination/recognition…”
Social amebas (or facultative social)
The second article (by Strassmann) is a another review, in this case on “Kin Discrimination in Dictyostelium Social Amoebae.” In it, the author recounts her research program on various species of social amebas, including Polysphondylium violaceum, D. purpureum and D. giganteum. Here is a simplified version of the abstract:
“Evolved cooperation is stable only when the benefactor is compensated, either directly or through its relatives. Social amoebae cooperate by forming a mobile multicellular body in which about 20% of participants ultimately dies to form a stalk [watch video below]. This benefits the remaining individuals that become hardy spores at the top of the stalk, together making up [a] fruiting body. In studied species [of social ameba] with stalked migration, P. violaceum, D. purpureum, and D. giganteum, sorting based on clone identity occurs in laboratory mixes, maintaining high relatedness within the fruiting bodies. D. discoideum has unstalked migration where cell fate is not fixed until the slug forms a fruiting body. Laboratory mixes show some degree of both spatial and genotype-based sorting, yet most laboratory fruiting bodies remain chimeric. However, wild fruiting bodies are made up mostly of clonemates. A genetic mechanism for sorting is likely to be cell adhesion genes tgrB1 and tgrC1, which bind to each other. [These genes] are highly variable, as expected for a kin discrimination gene. It is a puzzle that these genes do not cause stronger discrimination between mixed wild clones, but laboratory conditions or strong sorting early in the social stage diminished by later slug fusion could be explanations.”
Above: the amazing videos of social behavior in amebas, by John Bonner, Professor of Biology at Princeton University. He obtained the images as an undergraduate student. This is a 2-min video of historical value, watch it to the end (it turns spectacular).
Schematic phylogeny based on ssrRNA sequences of the Entamoeba clones discussed in the Espinosa et al. article. Free-living: E. moshkovskii Laredo; commensal E. terrapinae and E. dispar; and parasitic E. invadens IP-1, E. invadens VK-1:NS, E. moshkovskii Snake and E. histolytica HM-1:IMSS.
“Studies on clone- and kin-discrimination in protists have proliferated during the past decade. We report clone-recognition experiments in seven Entamoeba [varieties] (E. invadens IP-1, E. invadens VK-1:NS, E. terrapinae, E. moshkovskii Laredo, E. moshkovskii Snake, E. histolytica and E. dispar). First, we characterized morphometrically each clone (length, width, and cell-surface area) and documented how they differed statistically from one another (as per single-variable or canonical-discriminant analyses). Second, we demonstrated that amebas themselves could discriminate self (clone) from different (themselves versus other clones). In mix-cell-line cultures between closely-related (E. invadens IP-1 versus E. invadens VK-1:NS) or distant-phylogenetic clones (E. terrapinae versus E. moshkovskii Laredo), amebas consistently aggregated with same-clone members. Third, we identified six putative cell-signals secreted by the amebas and which known functions in Entamoeba spp. included: cell proliferation, cell adhesion, cell movement, and stress-induced encystation. To our knowledge, this is the first multi-clone characterization of Entamoeba spp. morphometrics, aggregative behavior, and cell-signaling secretion in the context of clone-recognition. Protists allow us to study cell-cell recognition from ecological and evolutionary perspectives. Modern protistan lineages can be central to studies about the origins and evolution of multicellularity.”
Conclusion
Again, I would like to quote the first article: “…because protists are among the most ancient organisms on Earth, belong to multiple taxonomic groups and occupy all environments, they can be central to reexamining traditional hypotheses in the field of kin recognition, reformulating concepts, and generating new knowledge [to our current understanding of the origins and evolution of multicellularity].” – GPC – Evolution Literacy.
You can contact Guillermo Paz-y-Miño-C via email at guillermo.pazyminoc@gmail.com
Protists are among the most ancient organisms on Earth; they belong to multiple taxonomic groups and occupy all environments. Studies with protists can be central to generating new knowledge to our current understanding of the origins and evolution of multicellularity.
* Darwin (1859) speculated about the “puzzle of the sterile social insects,” in which female workers at a nest dedicate their lives to the persistence of the colony (structured around a large progeny), via assisting a fertile queen to reproduce with the available males. Darwin suggested that, in such cases of apparent sacrifice —by the workers— for the good of all, “selection may be applied to the family.” But, in the late 1800s, he could not offer a detailed mechanistic explanation for the latter. Fisher (1930) and Haldane (1932, 1955) wrestled with the genetics and mathematics of altruism and the anecdotic expression “I would lay down my life for two brothers or eight cousins” became legacy of their work. Hamilton (1964) and Maynard-Smith (1964) further reasoned that the ability to discriminate between close and distant genetic relatives could be directly linked to survival and reproductive success, and, ultimately, to kin selection (Maynard-Smith 1964, 1977). — For references, go to source.
Evolution Literacy 
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