Editing Lynn Margulis (section)

==Career==
In 1966 she moved to [[Boston University]], where she taught biology for twenty-two years. She was initially an Adjunct Assistant Professor, then was appointed to Assistant Professor in 1967. She was promoted to Associate Professor in 1971, to full Professor in 1977, and to University Professor in 1986. In 1988 she was appointed Distinguished Professor of Botany at the [[University of Massachusetts Amherst|University of Massachusetts at Amherst]]. She was Distinguished Professor of Biology in 1993. In 1997 she transferred to the Department of Geosciences at UMass Amherst to become Distinguished Professor of Geosciences "with great delight",<ref name="Yount-2003">{{cite book |last1=Yount |first1=Lisa |title=A to Z of biologists |year=2003 |publisher=Facts on File |location=New York, NY |isbn=978-1-4381-0917-6 |page=198 |url=https://books.google.com/books?id=pOdHrsTZ-RYC}}</ref> the post which she held until her death.<ref name=haskett>{{cite encyclopedia |last1=Haskett |first1=Dorothy Regan |title=Lynn Petra Alexander Sagan Margulis (1938–2011) |url=http://embryo.asu.edu/pages/lynn-petra-alexander-sagan-margulis-1938-2011 |encyclopedia=The Embryo Project Encyclopedia |publisher=Arizona Board of Regents, Arizona State University |access-date=December 18, 2014}}</ref>

===Endosymbiosis theory===
{{Main|Symbiogenesis}}
[[File:Glaucocystis sp.jpg|thumb|The [[chloroplast]]s of [[glaucophyte]]s like this ''[[Glaucocystis]]'' have a [[peptidoglycan]] layer, evidence of their [[endosymbiotic theory|endosymbiotic]] origin from [[cyanobacteria]].<ref>{{cite journal |journal=[[American Journal of Botany]] |year=2004 |volume=91 |issue=10 |pages=1481–1493 |title=Diversity and evolutionary history of plastids and their hosts |first=Patrick J. |last=Keeling |doi=10.3732/ajb.91.10.1481 |pmid=21652304|doi-access=free }}</ref>]]

In 1966, as a young faculty member at [[Boston University]], Margulis wrote a theoretical paper titled "On the Origin of Mitosing Cells".<ref>{{cite journal |last1=Sagan |first1=Lynn |title=On the origin of mitosing cells |journal=Journal of Theoretical Biology |year=1967 |volume=14 |issue=3 |pages=225–274 |doi=10.1016/0022-5193(67)90079-3 |pmid=11541392|bibcode=1967JThBi..14..225S }}</ref> The paper, however, was "rejected by about fifteen scientific journals," she recalled.<ref name=BrockmanInterview>Margulis, Lynn, [http://www.edge.org/documents/ThirdCulture/n-Ch.7.html Gaia Is a Tough Bitch] {{Webarchive|url=https://web.archive.org/web/20171122013320/https://www.edge.org/documents/ThirdCulture/n-Ch.7.html |date=November 22, 2017 }}. Chapter&nbsp;7 in The Third Culture: Beyond the Scientific Revolution by John Brockman (Simon & Schuster, 1995)</ref> It was finally accepted by ''[[Journal of Theoretical Biology]]'' and is considered today a landmark in modern [[endosymbiotic theory]]. Weathering constant criticism of her ideas for decades, Margulis was famous for her tenacity in pushing her theory forward, despite the opposition she faced at the time.<ref name="Lake-2011"/> The descent of mitochondria from bacteria and of chloroplasts from cyanobacteria was experimentally demonstrated in 1978 by [[Murder of Robert Schwartz#Background|Robert Schwartz]] and [[Margaret Dayhoff]].<ref>{{cite journal |last1=Schwartz |first1=R. |last2=Dayhoff |first2=M. |title=Origins of prokaryotes, eukaryotes, mitochondria, and chloroplasts |journal=Science |year=1978 |volume=199 |issue=4327 |pages=395–403 |doi=10.1126/science.202030 |pmid=202030 |bibcode=1978Sci...199..395S}}</ref> This formed the first experimental evidence for the symbiogenesis theory.<ref name="Lake-2011"/> The endosymbiosis theory of organogenesis became widely accepted in the early 1980s, after the genetic material of [[mitochondria]] and [[chloroplast]]s had been found to be significantly different from that of the symbiont's [[nuclear DNA]].<ref>{{cite encyclopedia |first=Nicholas W. |last=Gillham |title=Chloroplasts and Mitochondria |encyclopedia=Encyclopedia of Genetics |editor-first=Eric C.R. |editor-last=Reeve |url=https://books.google.com/books?id=PuCYAgAAQBAJ&pg=PA721 |date=January 14, 2014 |publisher=Routledge |isbn=978-1-134-26350-9 |pages=721–735}}</ref>

In 1995, English evolutionary biologist [[Richard Dawkins]] had this to say about Lynn Margulis and her work:
<blockquote>I greatly admire Lynn Margulis's sheer courage and stamina in sticking by the endosymbiosis theory, and carrying it through from being an unorthodoxy to an orthodoxy. I'm referring to the theory that the eukaryotic cell is a symbiotic union of primitive prokaryotic cells. This is one of the great achievements of twentieth-century evolutionary biology, and I greatly admire her for it.<ref name=BrockmanInterview/></blockquote>

===Symbiosis as evolutionary force===
{{main|Symbiosis}}
{{See also|Horizontal gene transfer}}

Margulis opposed competition-oriented views of evolution, stressing the importance of symbiotic or cooperative relationships between species.<ref name="Mann-1991">{{cite journal |last1=Mann |first1=C |title=Lynn Margulis: Science's unruly Earth mother |journal=Science |year=1991 |volume=252 |issue=5004 |pages=378–381 |doi=10.1126/science.252.5004.378 |bibcode=1991Sci...252..378M |pmid=17740930}}</ref>

She later formulated a theory that proposed symbiotic relationships between organisms of different phyla, or kingdoms, as the driving force of [[evolution]], and explained [[genetic variation]] as occurring mainly through transfer of nuclear information between [[bacteria|bacterial cells]] or [[virus]]es and [[eukaryotic cell]]s.<ref name="Mann-1991"/> Her organelle genesis ideas are now widely accepted, but the proposal that symbiotic relationships explain most genetic variation is still something of a fringe idea.<ref name="Mann-1991"/>

Margulis also held a negative view of certain interpretations of [[Neo-Darwinism]] that she felt were excessively focused on competition between organisms, as she believed that history will ultimately judge them as comprising "a minor twentieth-century religious sect within the sprawling religious persuasion of Anglo-Saxon Biology."<ref name="Mann-1991"/>
She wrote that proponents of the standard theory "wallow in their zoological, capitalistic, competitive, cost-benefit interpretation of Darwin – having mistaken him ... Neo-Darwinism, which insists on [the slow accrual of mutations by gene-level natural selection], is in a complete funk."<ref name="Mann-1991"/>

===Gaia hypothesis===
{{Further|Gaia hypothesis}}
Margulis initially sought out the advice of [[James Lovelock]] for her own research: she explained that, "In the early seventies, I was trying to align bacteria by their metabolic pathways. I noticed that all kinds of bacteria produced gases. Oxygen, hydrogen sulfide, carbon dioxide, nitrogen, ammonia—more than thirty different gases are given off by the bacteria whose evolutionary history I was keen to reconstruct. Why did every scientist I asked believe that atmospheric oxygen was a biological product but the other atmospheric gases—nitrogen, methane, sulfur, and so on—were not? 'Go talk to Lovelock,' at least four different scientists suggested. Lovelock believed that the gases in the atmosphere were biological."<ref name=BrockmanInterview/>

Margulis met with Lovelock, who explained his Gaia hypothesis to her, and very soon they began an intense collaborative effort on the concept.<ref name=BrockmanInterview/> One of the earliest significant publications on Gaia was a 1974 paper co-authored by Lovelock and Margulis, which succinctly defined the hypothesis as follows: "The notion of the biosphere as an active adaptive control system able to maintain the Earth in homeostasis we are calling the 'Gaia hypothesis.'"<ref>{{Cite journal |last1=Lovelock |first1=J.E. |last2=Margulis |first2=L. |date=1974 |title=Atmospheric homeostasis by and for the biosphere: the gaia hypothesis |journal=Tellus A |volume=26 |issue=1–2 |pages=2–10 |doi=10.3402/tellusa.v26i1-2.9731 |doi-access=free |s2cid=129803613 |language=en |bibcode=1974Tell...26....2L }}</ref>

Like other early presentations of Lovelock's idea, the Lovelock-Margulis 1974 paper seemed to give living organisms complete agency in creating planetary self-regulation, whereas later, as the idea matured, this planetary-scale self-regulation was recognized as an [[Emergence|emergent]] property of the [[Earth system science|Earth system]], life and its physical environment taken together.<ref>{{cite book|last1=Lovelock|first1=James|title=The Ages of Gaia: A Biography of Our Living Earth|date=1988|publisher=W.W.Norton & Co|location=New York}}</ref> When climatologist Stephen Schneider convened the 1989 American Geophysical Union Chapman Conference around the issue of Gaia, the idea of "strong Gaia" and "weak Gaia" was introduced by James Kirchner, after which Margulis was sometimes associated with the idea of "weak Gaia", incorrectly (her essay "''Gaia is a Tough Bitch''" dates from 1995 – and it stated her own distinction from Lovelock as she saw it, which was primarily that she did not like the metaphor of Earth as a single organism, because, she said, "No organism eats its own waste").<ref name=BrockmanInterview/> In her 1998 book ''Symbiotic Planet'', Margulis explored the relationship between Gaia and her work on symbiosis.<ref>{{cite book |last1=Margulis |first1=Lynn |title=Symbiotic Planet |date=1998 |publisher=Basic Books |location=New York, NY}}</ref>

===Five kingdoms of life===
In 1969, life on earth was classified into [[five kingdoms]], as introduced by [[Robert Whittaker (ecologist)|Robert Whittaker]].<ref>{{Cite journal|last=Whittaker |first=R.H. |date=January 1969 |title=New concepts of kingdoms or organisms. Evolutionary relations are better represented by new classifications than by the traditional two kingdoms|journal=Science|volume=163 |issue=3863|pages=150–60 |pmid=5762760 |doi=10.1126/science.163.3863.150|bibcode = 1969Sci...163..150W |citeseerx=10.1.1.403.5430 }}</ref> Margulis became the most important supporter, as well as critic<ref>{{cite book|last1=Margulis|first1=Lynn |chapter=Five-Kingdom Classification and the Origin and Evolution of Cells |title=Evolutionary Biology |journal=BMC Evolutionary Biology |year=1974|volume=7|pages=45–78|doi=10.1007/978-1-4615-6944-2_2|pmid=17376230|pmc=1847511|isbn=978-1-4615-6946-6}}</ref> – while supporting parts, she was the first to recognize the limitations of Whittaker's classification of microbes.<ref>{{cite journal|last1=Margulis|first1=Lynn|title=Whittaker's Five Kingdoms of Organisms: Minor Revisions Suggested by Considerations of the Origin of Mitosis|journal=Evolution|year=1971|volume=25|issue=1|pages=242–245|jstor=2406516|doi=10.2307/2406516|pmid=28562945}}</ref> But later discoveries of new organisms, such as [[archaea]], and emergence of molecular taxonomy challenged the concept.<ref name="Hagen-2012">{{cite journal|last1=Hagen|first1=Joel B.|title=Five Kingdoms, More or Less: Robert Whittaker and the Broad Classification of Organisms|journal=BioScience|year=2012|volume=62|issue=1|pages=67–74|doi=10.1525/bio.2012.62.1.11|s2cid=86253586|doi-access=free}}</ref> By the mid-2000s, most scientists began to agree that there are more than five kingdoms.<ref>{{Cite journal|last1=Simpson|first1=Alastair G.B.|last2=Roger |first2=Andrew J.|year=2004 |title=The real 'kingdoms' of eukaryotes |journal=Current Biology |volume=14 |issue=17|pages=R693–6|name-list-style=amp |pmid=15341755 |doi=10.1016/j.cub.2004.08.038|s2cid=207051421|doi-access=free|bibcode=2004CBio...14.R693S }}</ref><ref>{{cite journal|last1=Adl|first1=SM|last2=Simpson|first2=AG|last3=Farmer|first3=MA|last4=Andersen|first4=RA|last5=Anderson|first5=OR|last6=Barta|first6=JR|last7=Bowser|first7=SS|last8=Brugerolle|first8=G|title=The new higher level classification of eukaryotes with emphasis on the taxonomy of protists.|journal=The Journal of Eukaryotic Microbiology|year=2005|volume=52|issue=5|pages=399–451|doi=10.1111/j.1550-7408.2005.00053.x|pmid=16248873|s2cid=8060916|display-authors=etal|doi-access=free|url=http://doc.rero.ch/record/14409/files/PAL_E1847.pdf}}</ref> Margulis became the most important defender of the five kingdom classification. She rejected the [[three-domain system]] introduced by [[Carl Woese]] in 1990, which gained wide acceptance. She introduced a modified classification by which all life forms, including the newly discovered, could be integrated into the classical five kingdoms. According to Margulis, the main problem, archaea, falls under the kingdom Prokaryotae alongside bacteria (in contrast to the three-domain system, which treats archaea as a higher taxon than kingdom, or the six-kingdom system, which holds that it is a separate kingdom).<ref name="Hagen-2012"/> Margulis' concept is given in detail in her book ''Five Kingdoms'', written with Karlene V. Schwartz.<ref>{{cite web|last1=Tao|first1=Amy|title=Lynn Margulis|url=https://www.britannica.com/EBchecked/topic/364780/Lynn-Margulis|website=Encyclopædia Britannica|access-date=December 18, 2014|date=October 22, 2013}}</ref> It has been suggested that it is mainly because of Margulis that the five-kingdom system survives.<ref name="Yount-2003"/>

=== Metamorphosis theory ===
In 2009, via a then-standard publication-process known as "communicated submission" (which bypassed traditional [[peer review]]), she was instrumental in getting the ''[[Proceedings of the National Academy of Sciences]]'' (''PNAS'') to publish a paper by [[Donald I. Williamson]] rejecting "the Darwinian assumption that larvae and their adults evolved from a single common ancestor."<ref name="Williamson-2009">{{cite journal|last1=Williamson|first1=D. I.|title=Caterpillars evolved from onychophorans by hybridogenesis|journal=Proceedings of the National Academy of Sciences|year=2009|volume=106|issue=47|pages=19901–19905|doi=10.1073/pnas.0908357106|pmid=19717430|pmc=2785264|bibcode=2009PNAS..10619901W|doi-access=free}}</ref><ref name="SciAm">[http://blogs.scientificamerican.com/observations/2009/10/29/controversial-caterpillar-evolution-study-formally-rebutted/ Controversial caterpillar-evolution study formally rebutted], ''[[Scientific American]] Online''</ref> Williamson's paper provoked immediate response from the [[scientific community]], including a countering paper in ''PNAS''.<ref name="Williamson-2009"/> Conrad Labandeira of the [[Smithsonian National Museum of Natural History]] said, "If I was reviewing [Williamson's paper] I would probably opt to reject it," he says, "but I'm not saying it's a bad thing that this is published. What it may do is broaden the discussion on how metamorphosis works and [...] [on] the origin of these very radical life cycles." But [[Duke University]] insect developmental biologist [[Fred Nijhout]] said that the paper was better suited for the "''National Enquirer'' than the National Academy."<ref>{{cite magazine|last=Borrell |first=Brendan |url=http://www.scientificamerican.com/article.cfm?id=national-academy-as-national-enquirer |title=National Academy as National Enquirer ? PNAS Publishes Theory That Caterpillars Originated from Interspecies Sex |magazine=Scientific American |access-date=November 23, 2011}}</ref> In September it was announced that ''PNAS'' would eliminate communicated submissions in July 2010. ''PNAS'' stated that the decision had nothing to do with the Williamson controversy.<ref name="SciAm" />

=== AIDS/HIV theory ===
In 2009 Margulis and seven others authored a position paper concerning research on the viability of round body forms of some spirochetes, "Syphilis, Lyme disease, & AIDS: Resurgence of 'the great imitator'?"<ref name="Margulis-2009">{{cite journal |url=http://www1.biogema.de/WEK/312-Margulis-final.pdf |title=Syphilis, Lyme disease & AIDS: Resurgence of "the great imitator"? |journal=Symbiosis |volume=47 |issue=1 |year=2009 |pages=51–58|doi=10.1007/BF03179970 |last1=Margulis |first1=Lynn |last2=Maniotis |first2=Andrew |last3=MacAllister |first3=James |last4=Scythes |first4=John |last5=Brorson |first5=Oystein |last6=Hall |first6=John |last7=Krumbein |first7=Wolfgang E. |last8=Chapman |first8=Michael J. |s2cid=25177964 }}</ref> which states that, "Detailed research that correlates life histories of symbiotic [[spirochete]]s to changes in the immune system of associated vertebrates is sorely needed", and urging the "reinvestigation of the natural history of mammalian, [[tick]]-borne, and venereal transmission of spirochetes in relation to impairment of the human immune system". The paper went on to suggest "that the possible direct causal involvement of spirochetes and their round bodies to symptoms of immune deficiency be carefully and vigorously investigated".<ref name="Margulis-2009"/>

In a ''[[Discover Magazine]]'' interview, Margulis explained her reason for interest in the topic of the 2009 "AIDS" paper: "I'm interested in spirochetes only because of our ancestry. I'm not interested in the diseases", and stated that she had called them "symbionts" because both the spirochete which causes syphilis (''[[Treponema]]'') and the spirochete which causes Lyme disease (''[[Borrelia]]'') only retain about 20% of the genes they would need to live freely, outside of their human hosts.<ref name="Teresi-2011"/>

However, in the ''Discover Magazine'' interview Margulis said that "the set of symptoms, or syndrome, presented by syphilitics overlaps completely with another syndrome: AIDS", and also noted that [[Kary Mullis]]{{efn|[[Kary Mullis]] won the 1993 [[Nobel Prize]] for the [[polymerase chain reaction]], and was known for his unconventional scientific views.}} said that "he went looking for a reference substantiating that HIV causes AIDS and discovered, 'There is no such document' ".<ref name="Teresi-2011"/>

This provoked a widespread supposition that Margulis had been an "[[AIDS denialist]]". Jerry Coyne reacted on his ''Why Evolution is True'' blog against his interpretation that Margulis believed "that AIDS is really syphilis, not viral in origin at all."<ref>{{cite web |author=Jerry Coyne |website=Why Evolution is True |url=https://whyevolutionistrue.wordpress.com/2011/04/12/lynn-margulis-disses-evolution-in-discover-magazine-embarrasses-both-herself-and-the-field/ |date=April 12, 2011 |title=Lynn Margulis disses evolution in Discover Magazine – Embarrasses both herself and the field}}</ref> [[Seth Kalichman]], a social psychologist who studies behavioral and social aspects of AIDS, cited her [Margulis] 2009 paper as an example of AIDS denialism "flourishing",<ref>{{Cite journal |last1=Kalichman |first1=S. C. |last2=Eaton |first2=L. |last3=Cherry |first3=C. |doi=10.1007/s10865-010-9275-7 |title="There is no Proof that HIV Causes AIDS": AIDS denialism beliefs among people living with HIV/AIDS |journal=Journal of Behavioral Medicine |volume=33 |issue=6 |pages=432–440 |year=2010 |pmid=20571892 |pmc=3015095}}</ref> and asserted that her [Margulis] "endorsement of HIV/AIDS denialism defies understanding".<ref>{{cite book |author=Seth C. Kalichman |title=Denying AIDS: Conspiracy Theories, Pseudoscience, and Human Tragedy |author-link=Seth Kalichman |url=https://books.google.com/books?id=_mtDBCDwxugC&pg=PA181 |date=January 16, 2009 |publisher=Springer Science & Business Media |isbn=978-0-387-79476-1 |pages=181–82}}</ref>