“Oneoftheproblemsofthewayinwhichtwentieth-centurybiologywasfrequentlypresentedtothepublicwastomistakethemetaphorsofupanddown—andmanyothermetaphors—forreality.Thishasalsobeenaproblemforscientiststhemselves,sincemanyweretakeninbytheirownrhetoric,andmanystillare.Theresulthasbeenabiologicalscienceversionoftheillusionthatthereisacentreoftheuniverse.InbiologythisillusorycentreisoftensupposedtobeDNAmolecules,astherepositoryofgenes.WhendiscoveringthestructureofDNA,FrancisCrickfamouslyannouncedtohisdrinkingcompanionsinaCambridgetavernthathehaddiscoveredthe'secretoflife'.ThedirectorofhisInstitute,MaxPerutz,wasrathermorecarefulthanCrickwhenhesaidthatDNAwasthe'scoreoflife'.Thatismorecorrectsinceamusicalscoredoesnothinguntilitisplayed.DNAdoesnothinguntilactivatedtodoso.”“Theillusionhasbecomesostrongthatmanypeoplethinkweknowexactlywhatageneisandhowgenescontrolthebody.Thosearealsoillusions.Recentexperimentalworkinbiologicalsciencehasdeconstructedtheideaofagene,andanimportantmessageofthisbookisthatithastherebydethronedthegeneasauniquelyprivilegedlevelofcausation.Aswewillsee,genes,deMinedasDNAsequences,areindeedessential,butnotinthewayinwhichtheyareoftenportrayed.Theyarepassive,notactive,causes.”—DenisNoblefromDancetotheTuneofLife:BiologicalRelativity

Biological Relativity

Cover of Denis Noble’s new book on the 21st-century integrative approach to evolution that recognizes biological relativity.

THE LIGHT OF EVOLUTION IS BIOLOGICAL RELATIVITYMany people think that evolution is a theory. Lynn Margulis defined evolution as simply change over time. If you asked a random sample of 100 people if they believe that things change over time, I would guess that most of the time 100 out of 100 would agree. Theories of evolution, on the other hand, are formal educated guesses about how organisms change over time if you’re a neo-Darwinist or how the biosphere changes over time if you’re a systems thinker. The Modern Synthesis is based in 19th-century animal/plant taxonomy and the fossil record beginning with the Cambrian explosion. Its big question is still how do new species originate. Very little of life on Earth, perhaps 1%, is animal or plant. Bacteria which make up the vast majority of the biota don’t fit neatly into whatever species means. Life is likely 3800 million years old while animals are maybe 700 million years old and, plants around 475 million years old. Any evolutionary theory so conceived has limited application to life on Earth. Denis Noble makes the case in Dance to the Tune of Life: Biological Relativity that the Modern Synthesis, while undoubtedly productive for a time, is a misconception of reality that has reached the limits of its explanatory power. The problems are fundamental. No amount of cosmetic surgery is going correct them. Progress in processes that are not neo-Darwinian cannot be credited to the explanatory power of the Modern Synthesis. It is insufficient to do so. Most of these “new trends” are not new nor are they trends. They have been known and studied quite apart from neo-Darwinism for a long time. Symbiosis and symbiogenesis, for example, have been investigated for over a century while being dismissed and discouraged by proponents of the Modern Synthesis. Awareness or mentions of these processes by neo-Darwinists fall far short of serious investigation. It is true that these processes have been bolstered or confirmed by evidence from molecular biology, but that evidence generally contradicted the view of the Modern Synthesis. The Modern Synthesis is no longer synonymous with evolutionary biology, molecular biology, or any of the multiple disciplines currently contributing to our understanding of evolution. Denis Noble advocates for a new and integrative systems approach that encourages and sheds light on the

sweeping array of questions and investigations that are now moving evolutionary biology forward. ENVIRONMENTAL EVOLUTION AND EUKARYOSIS

The questions that drove Lynn Margulis were how did the origin and evolution of life change Earth and how did a changing Earth lead bacteria, the building blocks of life, to evolve into eukaryotic cells. Unlike the Modern Synthesis, these questions were contextual. They probed Earth systems through all of geologic time. Margulis understood, as does Denis Noble, that the cell is the basic unit of life. This recognition of context or relativity explains why Margulis was 50 years ahead of her time in her vision of evolution. Martin Brasier, the late Oxford paleontologist, defined science not as the revelation of underlying simplicity, laws or ideals, but as “auniquesystemforthemeasurementofdoubt.” This is a helpful conception because it explains why science must be skeptical, but also measured in its skepticism. It avoids the temptation of certainty and leaves the

mind open to surprise. Science measures. It compares tests to controls. Experiments and analyses are designed to minimize bias and expose logical fallacies. Results must be reproducible. Science questions unquestioned assumptions. Its theories must be predictive. It does not ignore anomalies, but acknowledges and investigates them. It recognizes that science-based knowledge is approximation, corrigible and that context is required. Noble takes the measure of the doubt in the 20th-century reductive approach compared to the 21st-century integrative approach in Dance to the Tune of Life: Biological Relativity lecture. His book is a must-read. THE ROYAL SOCIETY MEETINGBilled as New trends in evolutionary biology: biological, philosophical and social science perspectives, the meeting consisted of 20 talks, 2 round table panel discussions and about a third of the time was reserved for audience questions and participation. As previously mentioned, most of the “new

Lynn Margulis caricatured as “Science’s Unruly Earth Mother” - Science 19 Apr 1991: Vol. 252, Issue 5004, pp. 378-381

trends” were processes long dismissed by the Modern Synthesis. Over the past decades, anomalous evidence has confirmed these processes. However, they are not neo-Darwinian because they are biologically and biochemically mediated by cells, they generate major genome changes affecting many characters, they can be rapid, and occur before being tested by natural selection. One example is symbiogenesis, which made its way into the margins of biology texts, but continues to be characterized as a rare event that happened long ago. Now, through the of magic of we-have-long-known-about-this, symbiogenesis is claimed to be part and parcel of the Modern Synthesis. DESPERATELY SEEKING SYNONYMITYWhen John Feldman sneak previewed his documentary, Symbiotic Earth: How Lynn Margulis Rocked the Boat and Caused a Scientific Revolution, in Barcelona recently, the question arose, “Where is this revolution or paradigm shift?” Biology students and young researchers have accepted symbiogenesis and these other processes as neo-Darwinian. There is nothing surprising about this because these students and younger biologists associate the Modern Synthesis and neo-Darwinism with evolutionary biology. But association can be very different from an informed and contextual understanding.WHAT IS A NEO-DARWINIST?Early in her course, Environmental Evolution: the Origin and Effect of Life on Earth, Lynn Margulis would to ask graduate students and seniors in biology the question: “What is an animal?” If she had asked, “How many of you know what an animal is?” every hand in the class—regardless of major—would have gone up. It would be easy to mistake those raised hands for understanding. However, Lynn Margulis did not ask a question whose answer provided no clarity. She asked for a definition. The assumption that you know what an animal is because you are familiar with a number of animals is not the same as understanding the criteria for that classification. I sat through a decade of those classes. I don’t recall even one biology student being able to successfully state what classifies an organism as an animal. I would submit that many biology students, young scientists, and even older biologists consider themselves neo-Darwinists or think that their research falls under the Modern Synthesis because that is a common association they make. However, it is a kind of suspension of disbelief because they ignore the Modern Synthesis. If you assume all these processes are neo-Darwinian, then

it would be hard to recognize them as revolutionary. This is the piecemeal acceptance of revolutionary evidence, without the systems context to illuminate the inadequacy of the Modern Synthesis. It is also why no definition of the Modern Synthesis was offered at the Royal Society meeting!If you want the definition of the Modern Synthesis, take a look at how Neil deGrasse Tyson explains evolution in the 2014 remake of Carl Sagan’s Cosmos series. Tyson, an astrophysicist, is unaware that he is mis-informed, as are most in science, academia, government, literature, the arts, and the public by this outmoded theory of evolution. There is also the current HBO series West World where the character of Dr. Robert Ford (played by Anthony Hopkins) explains to his assistant Bernard (played by Jeffrey Wright) that “evolutionforgedallofsentientlifeonthisplanetusingonlyonetool,themistake.” The Modern Synthesis toolbox holds only one tool: the mistake, the blind random mutation. The organism is acted upon by the environmental elimination process: natural selection. No mention of new trends.

Let’s not forget that Darwin himself had a better selection of tools in his On the Origin of Species toolbox. Now we are presented with a toolbox that holds many tools. Some vintage ones, such as symbiogenesis. And long recognized ones, such as horizontal gene transfer, that couldn’t be swept under the

rug. But wait there’s more: interspecific hybridization, whole genome duplications, the movement of mobile genetic elements (natural genetic

HBO’s current 2016 series West World tells viewers that evolution used only one tool to forge all life on Earth: the mistake

Neil deGrasse Tyson presents the Modern Synthesis sans trends in the 2014 series, Cosmos: A Spacetime Odyssey.

engineering), plasticity, and niche construction. Magicallly, we are told that all these fit in the The Selfish Gene toolbox. What ever happened to that little toolbox that only held one tool, the mistake? MEETINGS WILL CONTINUE UNTIL MORALE IMPROVESPerry Marshall, a participating audience member, has written what I consider to be a very accurate description of the Royal Society meeting. So I will not spend time on an overview in this newsletter. I would note that I have seen many reports of the Royal Society meeting and some of the reporting is really bad, in particular, the article by Carl Zimmer in Quanta magazine. The interaction of Denis Noble and David Shukar is either intentionally misrepresented or Zimmer failed to grasp what Noble had just spent his entire presentation explaining. Zimmer would have his readers believe that Shukar’s declaration that natural selection can be rapid and not involve the environment was a gotcha moment. The idea that natural selection occurs without the environment or competition makes no sense from a neo-Darwinist point of view! What is natural selection? Its competition plus environment, Stupid. The crux of the exchange was what followed. And here I must borrow Perry Marshall’s reconstruction:

“ShukertriedtointerruptbutNobleheldhisground:

‘No,YOUneedtolisten.Iusedtothinkexactlylikeyou.Iembracedthereductionistmindsetforyears.WhenIgotoutofschoolIwasacard-carryingreductionist.Reductionismispowerfulandit’suseful.Iamnotdissingit.Manytimesweneedit.Butitisnotthewholestory.’

Nobledescribedhowbacterialregulatorynetworksrebuiltthosegenesinfourdaysbyhyper-mutating,activelysearchingforasolutionthatwouldgivethemtailsandenablethemtoNindfood.

‘Naturalselectiondidnotachievethat.Naturalgeneticengineeringdid.’”

I wish I could transcribe exactly what was said to shine a light on Zimmer’s heavy-Window at the Royal Society with the motto

“NULLIUS IN VERBA”

handed spin, but sadly the audio files of the meeting posted on the Royal Society site currently do not include the Q&A that followed presentations. The Royal Society has advised me that they are seeking the permission of all participants and will post the audio of all who had no objections to their comments during the Q&A being distributed sometime after January 16, 2017.NULLIUS VERBA John Hands has reported on the meeting in the BBC online Science Focus. During the first Round Table audience discussion, Hands introduced himself as the author of Cosmosapiens: Human Evolution from the Origin of the Universe and made the following comments.“It’sappropriatethatthismeetingisbeingheldattheRoyalSociety,whosemotto,wewereremindedyesterday,is“Nulliusinverba”:Acceptnothingonauthority.

Thecurrentparadigminevolutionarybiology,NeoDarwinism,alsocalledtheModernEvolutionarySynthesis,hasbeentheauthorityforsome65years.Itis,ofcourse,amathematicalmodelbasedonseveralunquestionedassumptions,whoseproofwasgivenby1940sgametheoryborrowedfromeconomics.

Whatwehaveheardoverthelast2daysisempiricalevidencethatnewspeciesariserapidly,fromsuchmechanismsassymbiogenesis,horizontalDNAtransfer,hybridisation,wholegenomeduplication,interactivesystemsproducingnovelemergentproperties,andothermechanismsdescribedinPart2ofmybook.

Thesemechanismscontradictthefundamentaltenetsofneo-Darwinism,namely:1. randomgenemutationsprovidephenotypicalcharacteristicsenablingsuccessfulDarwiniancompetition;

2. theserandomgenemutationsspreadthroughapopulation’sgenepoolbysexualreproduction;

3. Darwiniangradualismleadstothegenetictransformationofpopulationsofindividualspeciesmembersovertensofthousandsofgenerations;

4. informationNlowsone-wayfromagenetoaproteininacell.

Notonewhitofempiricalevidenceshowsthatnewspeciesarisefromtheneo-Darwinianmechanism.Tothecontrary,Darwiniancompetitioncausesnottheevolutionofspeciesbutthedestructionofspecies.Itiscollaboration

initsvariousformsthatcausesbiologicalevolution.HenceI’msurprisedbycallsforextendingtheneo-DarwinianEvolutionarySynthesis.Youcan’textendsomethingthatisbroken.

Surelywhatisneedednow,after65years,isusingtheempiricalevidencetodevelopanewparadigmforbiologicalevolution.”

The panel to which Hands made this comment included Douglas Futuyma (Fū-tū-mă) from Stony Brook University who had made the case for the Modern Synthesis on the first day of the meeting, Do we really need to extend the MS? In his presentation he had maintained that “...wemustrecognisethatthecoreprinciples,thecoreprinciplesoftheevolutionarysynthesis,arestrongandarewell-supported,okay?”

Obviously, it wasn’t okay with Hands or many others in the audience. A pause stretched in anticipation of a rigorous defence for those core principles. Here was the golden opportunity to give this upstart a good thrashing with the bludgeon of that strong and supporting evidence. But there was no such defence. Futuyma sat mum, okay?JURASSIC SNARKFutuyma had begun his talk, “IthinkI’mexpectedtorepresentthe,theJurassicviewofevolution.[asmatteringofchuckles]SoIwilldomybesttoliveuptothatexpectation.” Having made this attempt to cast himself as someone open-minded, who didn’t take himself too seriously, he nonetheless wasted no time living up to that expectation by adopting a snide and dismissive attitude that relied on a series of assertions, judgments and assumptions that conflated nearly all evolutionary discovery and knowledge regardless of history as being “...partandparcelofthinkingbypracticingevolutionarybiologistswhostill,inacertainway,retainthegeneralframeworkoftheModernSynthesisintheirthinking,buthaveactivelyappliedandextendedittoavastvarietyofnewphenomena.” (my emphasis) What you might ask is that certain way?

”A major accomplishment”—Professor James Shapiro, author of Evolution: A View from the 21st-Century.

Futuyma went on, “Whentransposableelementswerediscovered,forexample,itwasveryfewyearsbeforetherewerepopulationgeneticmodelsoftheirbehaviorandconsequencesfornaturalpopulations.”

The 30 years lost from the career of the discoverer of transposition, the brilliant cytogeneticist Barbara McClintock, counted as “veryfew” to Futuyma. He had no doubt that a great deal of “theeffortwearetalkingabouthere...willbeseenasakindofglossonwhatwealreadyknow.” What we already know and what is actively applied in evolutionary research in many cases has little or nothing to do with the Modern Synthesis. As University of Edinburgh Professor of Developmental Biology, Jonathan Bard, commented to

Richard Dawkins during the 2009 Homage to Darwin debate, “It’sjustnotterriblyhelpfultotakethegene’seyeview.It’snotsomuchthatit’swrong,butitisn’tmuchuse,becauseselectiondoesn’tactonthegene.Itactsonphenotypes[farmore]complicated.Weknowoneofthemostdistressingexperimentsanybodycandoistoknockoutageneandseethatithasnotevenasubtlephenotypiceffect.” As a student of Lynn Margulis and Gaia theory, I found Futuyma’s discussion of niche construction revealed the disconnected view reductionists have of nature. Futuyma stressed that within an ecological niche or habitat what is relevant to one species of organism can be “utterlyirrelevant” to other species within that space. He stated that this was obvious to those who developed the Modern Synthesis. At the tea break, I asked him how he thought it was possible within a finite biosphere for there to be this kind of absolute isolation? He had no idea what I was talking about. I mentioned that dust from the Sahara fertilises the Amazon rainforest—perhaps that was too biogeological. He said that I must be talking mysticism. There is nothing mystical about the radical interdependence of life on Earth. For example, there have been dramatic changes in both animal behavior and the patterns of vegetation in the western United States due to the reintroduction of wolves. Only when you mistake the inanimate pieces of your model of nature for the phenomenon itself can you adopt this kind of delusion of separateness.

1983 Nobel laureate, McClintock at her lab microscope in 1947. It is acknow-ledged that she left science in 1953 due to neo-Darwinist ridicule of her research.

Futuyma’s talk is worth listening to, but not because there is much substance. He sets up an expectation of a defence, but delivers a masterful mix of rhetoric, various logical fallacies and assertions without proof that sounds convincing. He presents the doubts, limitations, and omissions of the theory as if they were evidence for it. He strategically replaces “neo-Darwinism” or “Modern Synthesis” with “evolutionary biology”, but they are not synonymous. Evolutionary biology includes all these non-Modern Synthetic processes while the Modern Synthesis cannot by definition.DEVELOPMENTAL BIOLOGY FILMS - A RESOURCE FOR OPEN EDUCATIONUMass-Amherst is making the series of 70 NSF science films rescued by Lynn Margulis, available to OpenStax, a nonprofit based at Rice University. OpenStax’s mission is to improve student access to educa-tional materials. They publish open licensed college textbooks and their library now has more than 25 books for college and AP courses used by hundreds of thousands of students. The Developemental Biology Films will become an audiovisual resource for students studying OpenStax biology.

DEEP TIME SMART PHONE APPIn the tradition of Lois Brynes’s Walk Through Time and the The Trail of Time along the South Rim of the Grand Canyon, Deep Time Walk unfolds Earth history over 4.6km with each meter = one million years.“TheDeepTimeWalkAppisaground-breakingnewproject,whichenablesanyone,anywheretoexperienceawalkingaudiohistoryofthelivingEarth.Wehaveassembledabroadandexperiencedteamtoproduceit.ThescientiNicscriptisbasedonup-to-dateknowledgegatheredbyrenownedecologistDrStephanHarding,fromSchumacherCollegewhohasledthewalksince2007.Theaward-winningplaywrightPeterOswaldiswritingthepoeticscriptandtherichacousticsoundscapesarebeingdesignedbysoundengineerJoLangton.TheproductionwillbedirectedbyJeremyMortimer.”—deeptimewalk.org

A scientist and a fool are your companions on a walk through 4600 million years of Earth history

MICROBES DIDN’T INVADE US, THEY INVENTED US Contributor Ann Cox sent in this link to Student Science article on How Ancient Microbes “Invented” Metabolism featuring 2016 MacArthur Fellow Dianne Newman who states “Microbes are metabolically far more sophisticated than we are.”

For those interested in the details of the “highest” (in relation to the biosphere) life forms on Earth, Paul Falkowski’s 2015 book, Life’s Engines: How Microbes Made Earth Habitable provides the details. Quoting the publisher:“Foralmostfourbillionyears,microbeshadtheprimordialoceansalltothemselves.ThestewardsofEarth,theseorganismstransformedthechemistryofourplanettomakeithabitableforplants,animals,andus.Life'sEnginestakesreadersdeepintothemicroscopicworldtoexplorehowthesemarvelouscreaturesmadelifeonEarthpossible—andhowhumanlifetodaywouldceasetoexistwithoutthem.

PaulFalkowskilooks‘underthehood’ofmicrobestoNindtheenginesoflife,theactualworkingpartsthatdothebiochemicalheavy

liftingforeverylivingorganismonEarth.Withinsightandhumor,heexplainshowtheseminiatureenginesarebuilt—andhowtheyhavebeenappropriatedbyandassembledlikeLegosetswithineverycreaturethatwalks,swims,orNlies.Falkowskishowshowevolutionworkstomaintainthiscoremachineryoflife,andhowweandotheranimalsareveritableconglomerationsofmicrobes.

Avibrantlyentertainingbookaboutthemicrobesthatsupportourveryexistence,Life'sEngineswillinspirewonderabouttheseelegantlycomplexnanomachinesthathavedrivenlifesinceitsorigin.”

SEASTARS AREN’T FISH Ann Cox also wrote, “Starfish larvae have always fascinated me.  I guess this is one reason why.  Cilia—too many to count! “VideoshowsthebeautifulandefNicientmechanismthattinystarNishlarvaeusetoswim,feedandgrow.”

What is it about biologists that they continue to use terms that are misleading, archaic or confusing? Starfish are not fish. They should be called by their modern correct name, seastars.

Blue-green algae aren’t algae. The proper terminology is cyanobacteria. Algae are protists or protoctists, not protozoa or protophyta. There is no gut flora in your gut, but there are microbiota. Why call the eukaryotic motility organelle a flagellum? It bears no resemblance to a flagellum of a bacterium. The only reason for calling different things by a single term is to confuse people. So here is a quiz about flagellum.1. How many proteins are there in a bacterial flagellum compared to a eukaryotic flagellum?2. What size is the cross section of a bacterial flagellum compared to a eukaryotic flagellum?3. What moves the bacterial flagellum compared to a eukaryotic flagellum?4. What is the motion of the bacterial flagellum compared to a eukaryotic

flagellum?A PAIR OF NOBLESOne of the pleasures of the Royal Society meeting on New Trends in Evolution was meeting and talking to Denis Noble’s brother, Ray. If you’d like to hear both Nobles discussing Biological Relativity you can on Ray Noble’s Thin Edge podcast Dialogue with Denis Noble.