THE BOAT’S STILL A ROCKIN’Ideas championed by Lynn Margulis inform the current revolution in science and medicine, particularly, the importance of microbes and the radical interdependency of life. However, it is unlikely that Margulis will ever receive the credit she deserves or be fully acknowledged within the general scientific community for her contributions to the new, more holistic understanding of the history of life on Earth.

No matter how insightful or prescient Lynn Margulis’s science and vision may have been, the caricature made of her by so many of the big names in neo-Darwinian evolutionary biology over her 50-year career as controversial, crazy or just plain wrong robbed her of the kind of recognition those same big names will enjoy for generations. Unlike symbiosis, which has escaped the marginalia of biology texts, Lynn Margulis is still largely unknown by the public and she continues to be diminished and disappeared by those who were so certain she was wrong. Their names may be remembered, but their certainties have crumbled.Near the end of her life, Lynn was asked if she ever got tired of being called controversial, she remarked, “Idon’tconsidermyideascontroversial.Iconsiderthemright.”This wasn’t arrogance. She was answering the question from her point of view. Always open-minded, she was willing to be proven wrong, but until there was good, solid, and convincing evidence

contrary to her ideas—not simply consensus or authority—she would rely on her own knowledge, observations, and gift for synthesis, rather than received wisdom. TEN YEARS AGOThis newsletter looks back over the past decade to glimpse just a few of the ways in which Lynn’s ideas have “rocked the boat.” The voyage has not been smooth sailing. Crests and troughs are both noted.

Margulis at Puffers Pond where her ashes were spread in late 2011.

In 2008, the International Human Microbiome Consortium (IHMC) was established to enable researchers to begin to characterize the relationship of the human microbiome in the maintenance of health. Lynn Margulis, whose name is synonymous with both the microcosmos and symbiosis, could easily be called the godmother of microbiomes. THE HIV/AIDS “CONTROVERSY”During the same year, a small meeting, Spirochaete Co-evolution in the Proterozoic Eon: Ecology, symbiosis, and pathogenesis (an excursion into environmental immunology) was organized by Professor Dr. Wolfgang E. Krumbein and Lynn Margulis. The gathered scientists, medical researchers, historians and physicians endorsed the following statement.

“Powerful new techniques of microbiology, including molecular ecology and evolution inspire us to urge reinvestigation of the natural history of mammalian, tick-borne, and venereal transmission of spirochetes in relation to impairment of the human immune system.”

The meeting also resulted in the publication of the 2009 position paper, Spirochete round bodies - Syphilis, Lyme disease & AIDS: Resurgence of “the great imitator”?. That paper tops the list of downloads (300+) every month through the www.envevo.org website. Round bodies are a pleomorphic form that typically helical-shaped spirochete bacteria can assume in response to negative environmental conditions, such as the presence of antibiotics. To this day, the Infectious Disease Society of America (ISDA), the National Institutes of Health (NIH), the Centers for Disease Control (CDC), and many researchers and clinicians maintain that spirochete round bodies are not viable and that a short course of antibiotics cures spirochetoses, such as Lyme disease and syphilis. Evidence presented at the 2008 meeting disputed these positions and pointed to the failure of screening tests to adequately

diagnose active spirochetoses. The evidence for spirochete pleomorphy, the viability

John Scythes and Wolfgang E. Krumbien at the Berlin meeting on spirochetes.

Lynn Margulis (upper left) presents at the small “round bodies” meeting in Berlin, Germany 2008

of round bodies, the ineffectiveness of antibiotics and the failure of screening tests has only mounted in the years since the meeting on Spirochaete Co-evolution in the Proterozoic Eon. ROUND SPIROCHETESA year before the meeting, Spirochaeta coccoides sp. nov. had been described in the literature. These spirochetes lack the characteristic helical form and periplasmic flagella of spiral forms altogether. This discovery “indicatedthat‘nonspiralspirochetes’aremorewidespreadinnature” than had been previously thought. In 2012, further analysis revealed that Sprirochaeta bacteria had a unique cell wall and a chimeric genome with “massive” horizontal gene transfers from Clostridia.

MISPLACED CONCRETENESSAs a gifted synthesizer of knowledge from multiple disciplines, Lynn Margulis was able to see that the neo-Darwinist orthodoxy rested on unquestioned assumptions, rules with little evidence, inappropriate tree models, and the wielding of Occam’s broom to sweep away inconvenient anomalies and contrary evidence. Margulis was keenly aware that most of the attacks on her science were based in the trained incapacities and uncritical acceptance of neo-Darwinist gene-determinism. Her detractors made arguments from consensus, authority, Whiteheadian misplaced concreteness, and molecular correlations

misinterpreted as causation. Neo-Darwinist reductionism did not recognize what Denis Noble has called biological relativity. It is good to keep in mind that hundreds of thousands of peer-reviewed papers were published over 70 years that accepted or assumed the certainty of the Modern Synthesis. In spite of all that ink, the Modern Synthesis has now been shown to be woefully incomplete and largely wrong. Certainty is the stuff of religious fundamentalists, not scientists.SHOW US THE MONEY“Itisdif;iculttogetamantounderstandsomething,whenhissalarydependsonhisnotunderstandingit.”―Upton SinclairMargulis often quipped that cancer kept more people alive than it killed. This bit of black humor was a comment on the enormous investment made in cancer research. She also opined that the quality of research was in inverse proportion to its proximity to human health. Recent revelations about the inability to reproduce the results of numerous published studies lends credence to her skepticism. According to JAMA, cancer and HIV/AIDS receive disproportionately large amounts of funding relative to the costs they impose on society. Is it moral to take far more than a fair share of funding and shortchange other research that would save lives?

Galina Dubinina (Institute of Microbiology of the Russian Academy of Sciences, Moscow) presents on spirochetes at the 2008 small meeting in Berlin..

NOT BUYING INMargulis was conservatively skeptical of the uncritical acceptance of a new pathogen, labeled the Human Immuno-deficiency Virus (HIV). To her, such a name was an exercise in circular logic, especially in the absence of even one definitive peer-reviewed paper that empirically demonstrated convincing isolation and identification of the virus, and explained how the virus caused the collapse of the immune system. It is the destruction of the human immune

system that results in the syndrome called Acquired Immune Deficiency. A syndrome is not a disease. Rather, it is a coherent and varying set of symptoms observed. People with compromised immune systems die from a variety of opportunistic

infections and cancers. These infections and cancers were previously seen in cases of syphilis. Individuals at high risk of AIDS are also at high risk of syphilis. A history of syphilis is also one of the best indicators that an individual will test positive for HIV. In the late 1970s, an epidemic of syphilis was going underground. Clinicians had noticed that the signs of primary syphilis infection were often absent, perhaps due to the overuse of antibiotics. Where did that burgeoning epidemic go in the 1980s? The mnemonic, PARESIS, is used to describe symptoms seen in AIDS, but it originated to describe the symptoms of syphilis. The letters stand for P = Personality changesA = AffectR = Reflexes (hyperreflexia) E = Eye (Argyll Robertson Pupil – aka “Prostitute’s Pupil”) S = Sensorium – hallucinations, delusions I = Intellect decreased – memory, orientation, judgement S = SpeechLynn Margulis was unable to judge the evidence for HIV.. She said so. She was not a virologist. But as a scientist, she questioned how a cause could be announced absent peer-reviewed empirical evidence and reproducible studies. She wondered how a virus that mutated so quickly that it escaped vaccines could be identified. Her reasonable and scientific questions were answered with threats that she would lose her funding! She had experienced this kind of attack before: her work on symbiosis had been called “shit” and her NASA funding cut by neo-Darwinists.There are many, many peer-reviewed HIV papers. However, when those who lack the ability to judge the evidence for HIV, like a social psychologist, are nonetheless

Syphilis skulls on display in the Hunterian Museum in London, UK.

convinced to a certainty by the quantity of papers (many of which begin by accepting the HIV/AIDS hypothesis) their opinion is based on a circular argument and a logical fallacy (consensus). Opinions are like assholes. Everyone has one.Remember the mountain of peer-reviewed papers that were based in the assumptions and assertions of the Modern Synthesis. These accepted that random mutation was the exclusive answer to how organisms evolve. In the Homage to Darwin debate, Lynn called out this kind of thinking which she described as “test-itis”―only on tests did you find one right answer. In nature singular answers are rarely the case. During the Homage debate, the part of the human genome named “junk DNA” was discussed. A name was enough for some, like Richard Dawkins, to accept that it was “a fossil”. It did nothing and thus did not merit further investigation. Lynn Margulis countered that a name is not a substitute for understanding—it was as unscientific as saying, “God did it”—it was not a scientific answer. We now know that most of the DNA-formerly-known-as-junk plays other roles in how the genome is used by the cell. NAME CALLINGThe editors of Wikipedia’s Lynn Margulis page state, “The [2009 round bodies] paperdidnotquestiontheexistenceofHIVorAIDS,northatHIVcausesAIDS,butsuggestedthatsyphiliscouldhavebeenaco-factorinthespreadofAIDS.” Inexplicably the Wikipedia editors follow this statement with a direct contradiction of what they have just stated as fact and their own rules for using only “reliable, published secondary sources”. They include ad hominem attacks by Seth Kalichman, a “social psychologist who studies behavioral and social aspects of AIDS” and Jerry Coyne, an unrepentant neo-Darwinist with a history of fallacious attacks on Lynn Margulis and others from his disreputable Why Evolution is True blog. Wikipedia’s editors defend these attacks by ignoring the fact that neither of these people has any understanding or pertinent expertise in either spirochetoses or the etiology of AIDS.

A NEW INQUISITIONScience encourages skepticism, demands that attempts be made to falsify hypotheses, and requires keeping an open-mind to contrary evidence and alternative explanations. In suggesting a co-factor in the etiology of AIDS, Margulis was in the company of many notable

scientists, including Luc Montagnier, Nobel Prize Judging of a witch from Monty Python and the Holy Grail.

recipient for his co-discovery of the HIV virus. Contradicting himself, Seth Kalichman has also stated, “Ithinkthereremaindoctorsinthe;ieldwhosayHIVisnecessarybutinsuf;icienttocauseAIDS.Itiscertainlyapointworthyofdebateamongphysiciansandscientists.Idonotthinkthisisproblematic.” True believers in the certainty of the HIV/AIDS hypothesis, such as Seth Kalichman, are engaged in an indiscriminate campaign, a version of McCarthyism, that smears, blacklists, and seeks to ruin anyone who dares to question or even report on challenges to the HIV/AIDS hypothesis. Even Luc Montagnier has been attacked for straying from the one true faith. Certainty requires that the reputations of the most distinguished dissenters be destroyed, and that the most promising other avenues of research be assiduously ignored rather than investigated. When someone as scientifically ill-equipped to judge the facts as Seth Kalichman wraps himself in morality and is deciding who is “good” and who is “evil” in medical research, life science, and in science reporting something is seriously wrong.PREACHING TO THE FUNDED Many proponents of the HIV/AIDS hypothesis claim that any and all connections between syphilis and AIDS have been thoroughly investigated, have produced no evidence of a link, and thus have been forever proven untrue. However, these same advocates assume that spirochete round bodies are not viable, that antibiotics cure spirochetoses, and they accept that the standard screening tests for syphilis and Lyme are reliable. These assertions reveal a unquestioning bias. Such a bias flies in the face of ongoing research that continues to show that round bodies are viable, round bodies are refractory to antibiotics, and that the standard tests for syphilis return an unacceptably high percentage of false negatives. Ditto for Lyme disease.

THE WAKE OF THE MODERN SYNTHESISFrom 2008 through 2009, Lynn was the George Eastman Visiting Professor and Fellow of Balliol College, Oxford University. The Linnean Society of London, awarded her the Darwin-Wallace Medal in 2009, the same year as the now famous Homage to Darwin Debate on Evolution.2010 was the year NASA celebrated 50 years of astrobiology. Seeking Signs of Life:

A Symposium Celebrating the 50th Anniversary of NASA's Exobiology Program with its keynote addresses by James Lovelock and Lynn Margulis. Drs. Lovelock

and Margulis were among the program’s earliest Principal Investigators. NASA supported Margulis’s work on symbiogenesis, and Lovelock and Margulis’s work on

Sir Crispin Tickell, Lynn Margulis, and Martin Brasier at the Linnean Society of London on the occasion of her Darwin-Wallace medal.

the Gaia hypothesis that contributed to current understanding of how life and Earth have co-evolved.2011 saw the publication of James Shapiro’s influential book, Evolution: A View from the 21st Century. Shapiro’s message was that DNA alone does nothing, and that many non-Darwinian and non-random processes are at work in evolution.In 2012, A Symbiotic View of Life: We Have Never Been Individuals recognized that biological individuality does not exist.In 2013, Animals in a bacterial world, a new Imperative for the life sciences pointed out what had been obvious to Lynn Margulis: eukaryotes evolved in a bacterial world, bacteria are the building blocks of eukaryotes, eukaryotes are communities made up of chimeric cells and persistent and necessary bacterial symbionts. There is no individuality. Life is radically interdependent.LIMITS OF GROWTH

Toby Tyrrell published On Gaia: A Critical Investigation of the Relationship Between Life and Earth in 2013. His strongest argument against Gaia was “nitrogen starvation”. He reasoned that for Gaia to be correct, enough nitrogen should be fixed for all life. After all, the atmosphere is predominantly unfixed nitrogen gas. But even with enough fixed nitrogen to go around, organisms would still die. Tyrrell missed the fact that natural selection, an elimination process, is a necessary part of the Earth system. The Earth cannot support the prodigious reproduction of even a single species. If nitrogen starvation did not eliminate some offspring, they would perish from one of the other limits on biotic potential: lack of energy, water, gas, other matter, space, or the density of other organisms. Tyrrell is a professor of Earth system science at the University of Southampton, but his book lacks any

Poster for Seeking Signs of Life

serious “systems thinking”. Tyrrell also attempted to remove all mention of Gaia on Wikipedia’s Earth system science (ESS) page. The fact that ESS came out of Lovelock and Margulis’s work at NASA on the Gaia hypothesis did not seem to matter to Tyrrell. NAUGHTY NEOLOGISM 2014 saw the publication of John Archibald’s One Plus One Equals One: Symbiosis and the evolution of complex life. The book’s title is taken without attribution from Lynn Margulis’s “math of biology”, a foreshadowing of how she fares in Archibald’s take on the story of endosymbiosis. Archibald gushes over Thomas Cavalier-Smith who he portrays as one of the foremost experts on protozoa and “endosymbiosis”. This may strike some as strange when Cavalier-Smith claims, ”Mutationisthegreatestinnovatorbyfar.Evenlateralgenetransferislessinnovativeandlessfrequentthanwidelysupposed.”

Margulis, actually “wrote the book” on Kingdom Protoctista, The Handbook of Protoctista. Lynn’s place as a taxonomist, expert on eukaryotic microbes, and the modern champion of symbiosis isn’t easy to erase. Archibald makes the mistake of accepting Thomas Cavalier-Smith’s 1985 attempt to radically redefine symbiogenesis as synonymous with endosymbiotic gene transfer (EGT). This “moving the goal posts” is intellectually dishonest. Scientific terms have definitions that cannot be changed on a whim. Cavalier-Smith has a history of

throwing various taxonomic schemes and neologisms into science in the hopes that something will stick. Symbiogenesis has been defined for over a century as a process in nature that begins with symbiosis and may eventually lead to EGT. Symbiogenesis is potent and ubiquitous in nature, not something ancient and rare as Cavalier-Smith would like to have it. Cavalier-Smith and John Archibald make the mistake of thinking of dynamic processes as static things. This misconception of nature was highlighted by John Dupré in his presentation, The ontology of

Konstantin Mereschkowski defined the term symbiogenesis in 1905. Image supplied by Edouard Kolchinsky.

One of dozens of slides Lynn Margulis used to illustrate her “math of biology” 1+1=1; as in one sperm and one egg equals one fertilized egg.

evolutionary process, at the 2016 joint Royal Society and British Academy meeting, New Trends in Evolutionary Biology: Biological, Philosophical and Social Science Perspectives. HISTORY AS HERESY 2014 saw the publication of Questioning the HIV-AIDS hypothesis: 30 years of dissent by Patricia Goodson. It should come as no surprise that Goodson’s objective and dispassionate history was attacked by Seth Kalichman. This resulted in a statement by the publisher, Frontiers in Public Health, that reclassified Goodson’s review as “opinion”. Kalichman states that the HIV/AIDS hypothesis can no longer be questioned or debated. He claims that Goodson’s history is “a primer on AIDS denialism”. Shoot the historian. NOT LEARNING FROM MISTAKESAll dissent from the Modern Synthesis was similarly characterized as pseudoscience, ridiculed and attacked. Margulis was a target of those attacks throughout her 50-year career. Margulis was accused of being anti-Darwinian or on the side of the Creationists. It is important that we learn from such gross assaults on the scientific endeavor. Otherwise we risk falling victim to the “temptation of certainty”, like Jerry Coyne and Seth Kalichman, who uncritically accept consensus and authority, attack anyone who believes in scientific inquiry, and dismiss all contrary explanations and evidence without consideration or investigation.

EARLY SIGNS OF FASCISMVictoria N. Alexander, a biosemiotician who focuses on the role of chance in biology, offers her 2012 essay on Lynn Margulis, Evolutionary “Naturalism,” Chance and Conspiracy, which explores why Margulis eschewed groupthink and relied on her own empiricism. Written originally for Dorion Sagan's collection, Lynn Margulis: The Life and Legacy of a Scientific Rebel, it did not make it into the book. Nonetheless it is a thought-provoking read. Here is just a snippet to whet your appetite.“Inthelastfewyearsofherlife,Margulissupportedtwo

verycontroversialhypotheses:theroleofthesyphilisspirocheteinthespreadofAIDSandthecontrolleddemolitionofthethreehigh-risetowersonSeptember11th.Sheiswidely

criticized(ifnotread/understood)forboth.Botharehighlypoliticallychargedissues,sothistime,inadditiontobeingwronglylumpedinwithIDadvocates,shehasbeenlabeled“extremist,”“truther,”“denialist,”andotherreactionarytagsappliedtoanyonenotingtheearlysignsoffascism.”-V.N.Alexander

2015 The Invention of Nature: Alexander von Humboldt’s New World by Andrea Wulf. A best-selling biography of the greatest scientist of the early 19th century, another of Lynn Margulis’s illustrious predecessors.“AlexandervonHumboldtmayhavebeenthepreeminentscientistofhisera,secondinfameonlytoNapoleon,butoutsidehisnativeGermanyhisreputationhasfaded.Wulfdoesmuchtoreviveourappreciationofthisecologicalvisionarythroughherlively,impressivelyresearchedaccountofhistravelsandexploits,remindingusofthelastingin;luenceofhisprimaryinsight:thattheEarthisasingle,interconnectedorganism,onethatcanbecatastrophicallydamagedbyourowndestructiveactions.”

—TheNewYorkTimesBookReview,Top10BooksoftheYear

2016 Why Gaia is not a God of Totality by Bruno Latour. Here is a snippet that deals with Toby Tyrrell’s On Gaia.

“...thereexistbookswhicharesoclearheadedbutsouncomprehendingoftheirownsubjectmatter,sonicelyobdurateintheirthinking,thattheyrender,intheend,agreatserviceinclarifyingissuesbymissingthepointsorelentlessly.That’sthecasewithTyrrell’sattempt.Ihaverarelyreadsuchan“uncriticalinvestigation”ofanyscienti;ictheory.”

Ed Yong published I Contain Multitudes: The Microbes Within Us and a Grander View of Life in 2016. Yong, a science reporter, has put out a very Margulisian book. It’s hard not to think that Yong has read Lynn’s books or watched Scott Gilbert talk about extending her ideas. Then, in the midst of this wonderful discussion of symbiosis, comes this odd moment when Yong warns his readers not to make the mistake of thinking that symbiosis is not Darwinian, because it is. Obviously, someone has gotten to Yong. Yong does his best to explain what he means by this. He reminds us that because bacteria evolve as described by Darwin that anything that follows must also be Darwinian. This is utter nonsense, which is a shame because Yong has gotten so much right. In On the Origin of Species, Darwin never mentions bacteria or protozoa or “animalcules”. Darwin lived in the two Kingdom taxonomy, Animals and Plants. His discussion was of the gradual process of descent

Alexander von Humboldt

with modification acted upon by naturals selection. Unlike the neo-Darwinians, Darwin left the door open to other possibilities. But Darwinism and neo-Darwinism model evolution as a bifurcating tree, organisms reproduce via coupled sex/reproduction, and inheritance is vertical (Darwin) or strictly vertical via sex (neo-Darwinian). None of this is true for the vast majority of biota over the vast majority of evolutionary time. Unlike Darwinian gradual descent with modification, or neo-Darwinian gradual accumulation of random beneficial mutations to genes and sexual recombination, the speed of both bacterial reproduction via binary fission and the recombination of bacterial DNA via bacterial sex are both orders of magnitude faster and greater than contemplated by Darwin or the Modern Synthesis. Darwin does not describe and neo-Darwinism does not allow saltational evolution by symbiogenesis or horizontal gene/genome acquisition. It is a very long stretch to describe the radical interdependency of life that microbiomes exemplify as Darwinian or neo-Darwinian.2017 is the year that Denis Noble published Dance to the Tune of Life: Biological Relativity. Noble gives the invasion of biology by physics a dope slap. He is not the first to speak of levels of organization in organisms, but he recognizes that what has been forgotten already has a name given it by physicists. He also discusses how organisms under stress harness stochasticity in order to rapidly run rapid successive experiments on specific sites within their genome (natural genetic engineering) to find successful strategies for survival.

AN INORDINATE SYMBIOSIS byMichaelF.DolanDolanMicroscopicalObservatoryBelchertown,MA01007USAmdolan.ecsn@outlook.com

Atthe84thNobelSymposiumin1992LynnMargulisandJoelE.Cohencontributedapaperthathypothesizedthediversityofbeetles(Coleoptera)couldhavebeengeneratedbyaseriesofmicrobialsymbioses. Theywrote,“Wepredictthatbetween20and22physiologicallydistinctivemicroorganisms(primarilybacteriaandfungi)areregularlyassociatedwithcoleopterans.Genomiccombinatoricsmayexplainwhy,asJ.B.S.Haldaneobserved,“GodhasexpressedsuchaninordinatefondnessforHismost[lamboyantmorphotypes:Hismillionsofspeciesofbeetles.”

Michael Dolan and Lynn in the Margulis Lab

AsIreportedinmychapterinDorionSagan’sbook,LynnMargulis:TheLifeandLegacyofaScienti;icRebel,LynnconfessedtomethatStephenJayGouldberatedherforsuchspeculation. “Whatisthis,theKabbalah?Whatisthis,numerology?”Gouldsaidinexasperation.AsIexplainedinthechapter,Gouldhadlittleappreciationformicrobialsymbioses. IwaspleasedthentoseeapaperbyHisashiAnbutsuandcolleaguesintheOctober17,2017issueoftheProceedingsoftheNationalAcademyofSciences,USAinwhichtheyreporthowtheweevilsymbiontNardonellaiscrucialforbeetles’developmentofsclerotizedbodies,consideredacrucialdevelopmentinbeetleevolution,thatallowedthemtoproliferateandspeciateacrosstheEarth.

Theyreport,“Notably,theonlymetabolicpathwayretainedintheNardonellagenomeswasthetyrosinesynthesispathway,identifyingtyrosineprovisioningasNardonella’ssolebiologicalrole.Weevilsarearmoredwithhardcuticle,tyrosineistheprincipalprecursorforcuticleformation,andexperimentalsuppressionofNardonellaresultedinemergenceofreddishandsoftweevilswithlowtyrosinetiter,con[irmingtheimportanceofNardonella-mediatedtyrosineproductionforhost’scuticleformationandhardening.”

Althoughsheranintotroublelaterinhercareeroverspeculationontheevolutionofinsects,Lynnappearstohavebeenonthemarkinpredictingacrucialroleforsymbiontsinbeetleevolution.2018 Hummingbird Films premieres the film Symbiotic Earth: How Lynn Margulis Rocked the Boat and Started a Scientific Revolution internationally to great acclaim.FROM LEEWENHOEK TO PRAKASH AND CYBULSKI

From the website“TheirinspirationfortheFoldscopecamefrom;ieldvisitsaroundtheworldwheretheycontinuallyencounteredbulky,brokenmicroscopes,oralackofmicroscopesentirely.Originallyinspiredbytheideaofacheap;ielddiagnostics,andwithsupportfromaGatesGrant,theprojectblossomedintotheinventionoftheFoldscope,afoldablemicroscopemademostlyof

paper,withacostofgoodslessthanoneU.S.dollar.”

John Feldman goes over the storyboard for Symbiotic Earth with Aaron Rubinstein of the UMass Libraries to help clear content for the film.