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The Philosophy of Biology Mechanisms in Molecular Biology Tudor M. Baetu Downloaded from https://www.cambridge.org/core. IP address: 27.106.64.254, on 18 Mar 2020 at 06:40:15, subject toI tShSeN C 2a5m15b-r1id1g26e (Coonrleine) terms of use, available at https://www.cambridge.org/core/terms. https://doi.org/10.1017/9781108592925 ISSN 2515-1118 (print) Downloaded from https://www.cambridge.org/core. IP address: 27.106.64.254, on 18 Mar 2020 at 06:40:15, subject to the Cambridge Core terms of use, available at https://www.cambridge.org/core/terms. https://doi.org/10.1017/9781108592925 ElementsinthePhilosophyofBiology editedby GrantRamsey KULeuven MichaelRuse FloridaStateUniversity MECHANISMS IN MOLECULAR BIOLOGY Tudor M. Baetu Université du Québec à Trois-Rivières Downloaded from https://www.cambridge.org/core. IP address: 27.106.64.254, on 18 Mar 2020 at 06:40:15, subject to the Cambridge Core terms of use, available at https://www.cambridge.org/core/terms. https://doi.org/10.1017/9781108592925 UniversityPrintingHouse,CambridgeCB28BS,UnitedKingdom OneLibertyPlaza,20thFloor,NewYork,NY10006,USA 477WilliamstownRoad,PortMelbourne,VIC3207,Australia 314–321,3rdFloor,Plot3,SplendorForum,JasolaDistrictCentre, NewDelhi–110025,India 79AnsonRoad,#06–04/06,Singapore079906 CambridgeUniversityPressispartoftheUniversityofCambridge. ItfurtherstheUniversity’smissionbydisseminatingknowledgeinthepursuitof education,learning,andresearchatthehighestinternationallevelsofexcellence. www.cambridge.org Informationonthistitle:www.cambridge.org/9781108742306 DOI:10.1017/9781108592925 ©TudorM.Baetu2019 Thispublicationisincopyright.Subjecttostatutoryexception andtotheprovisionsofrelevantcollectivelicensingagreements, noreproductionofanypartmaytakeplacewithoutthewritten permissionofCambridgeUniversityPress. 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IP address: 27.106.64.254, on 18 Mar 2020 at 06:40:15, subject to the Cambridge Core terms of use, available at https://www.cambridge.org/core/terms. https://doi.org/10.1017/9781108592925 Mechanisms in Molecular Biology ElementsinthePhilosophyofBiology DOI:10.1017/9781108592925 Firstpublishedonline:September2019 TudorM.Baetu UniversitéduQuébecàTrois-Rivières Authorforcorrespondence:TudorM.Baetu,[email protected] Abstract:Thenewmechanisticphilosophyisdividedintotwolargely disconnectedprojects.Onedealswithametaphysicalinquiryintohow mechanismsrelatetoissuessuchascausation,capacities,andlevelsof organization,whiletheotherdealswithepistemicissuesrelatedtothe discoveryofmechanismsandtheintelligibilityofmechanistic representations.TudorM.Baetuexploresandexplainstheseprojects, andshowshowthegapbetweenthemcanbebridged.Hisproposed accountiscompatiblebothwiththeassumptionsandpracticesof experimentaldesigninbiologicalresearch,andwithscientifically acceptedinterpretationsofexperimentalresults. Keywords:mechanism,newmechanisticphilosophy,biology,philosophyof science,philosophyofbiology ©TudorM.Baetu2019 ISBNs:9781108742306(PB),9781108592925(OC) ISSNs:2515-1126(online),2515-1118(print) Downloaded from https://www.cambridge.org/core. IP address: 27.106.64.254, on 18 Mar 2020 at 06:40:15, subject to the Cambridge Core terms of use, available at https://www.cambridge.org/core/terms. https://doi.org/10.1017/9781108592925 Contents 1 MechanismsandTheirDiscovery 1 2 WhatIsaPhenomenon? 7 3 HowDoMechanismsandPhenomenaRelatetoOne Another? 22 4 WhatIsthePhysicalNatureofBiologicalMechanisms? 39 ARecapitulationandSomeClarifications 62 References 66 Downloaded from https://www.cambridge.org/core. IP address: 27.106.64.254, on 18 Mar 2020 at 06:40:15, subject to the Cambridge Core terms of use, available at https://www.cambridge.org/core/terms. https://doi.org/10.1017/9781108592925 MechanismsinMolecularBiology 1 1MechanismsandTheirDiscovery 1.1MechanismsandMechanisticExplanations Manyexplanationsinbiologytellushowphenomenaareproducedasaresult ofchangesandinteractionsamongthevariouspartsofaphysicalsystem.Such systems of parts changing over time are commonly known as ‘mechanisms’, whilethemore-or-lessdetaileddescriptionsofthesesystemsandtheseriesof changestheyundergoarereferredtoas‘mechanisticexplanations’. Ifthereaderisleftwonderingwhataphenomenonisandhowamechanism explains it, a concrete example may help. Biologists take reproducible sequencesofevents,wherebyexposureofabiologicalsystemtoastimulusis consistentlyfollowedbyasimilarkindofresponse,tobephenomenainneedof anexplanation(Figure1).Takesunburns,forexample.Prolongedexposureto ultravioletradiationconsistentlyresultsinapronouncedrednessandswelling of the skin. Since this sequence of events can be consistently reproduced in humans and many other animals, it is unlikely to be just a coincidence. It is somethingthatdemandsanexplanation. Sunburns belong to a family of related phenomena of great clinical impor- tance known as inflammatory responses. These responses are triggered by a wide variety of harmful stimuli, including radiation, tissue damage, patho- gens,andantigens,andtypicallyconsistoffivedirectlyobservablesymptoms: erythema (redness), edema (swelling), pain, heat, and loss of function (e.g., immobility).Inmostcases,inflammatoryresponsesshutdownafterthethreat has been eliminated or the harmful stimulation has subsided, which is highly desirablesince aprolongedorchronicinflammatoryresponsehasdetrimental consequencesfortheorganism. Much research in immunology and medicine has been devoted to finding out how – that is, by means of which mechanisms – inflammatory responses are produced. Since my goal is simply to give the reader an idea of what a mechanisticexplanationmaylooklike,Iwillfocusononeofthebetterunder- stoodmechanismsinvolvingatypeofwhitebloodcellsknownasT-cells.By theendofthe1980s,ithadbeenestablishedthat,whenanorganismisexposed toharmfulstimuli,T-cellsbeginsecretingavarietyofmoleculesnecessaryfor mountinginflammatoryresponses.Thus,onekeyresearchquestionwastofind outhowT-cellsareactivated.ThemolecularunderpinningsofT-cellactivation turned out to revolve around a couple of regulatory DNA-binding proteins, oneofwhichisthetranscriptionalfactornuclearfactorκB,orNF-κBinshort (Sun et al. 1993). In resting T-cells, NF-κB is trapped in the cytoplasm by a protein known as inhibitor of NF-κB, or IκB. When cells are exposed to harmful stimuli (Figure 2A), however, a chain of protein–protein interactions Downloaded from https://www.cambridge.org/core. IP address: 27.106.64.254, on 18 Mar 2020 at 06:40:15, subject to the Cambridge Core terms of use, available at https://www.cambridge.org/core/terms. https://doi.org/10.1017/9781108592925 2 ElementsinthePhilosophyofBiology Figure1Inflammatoryresponsesasphenomenatobeexplained leadstothedissociationofinactiveIκB/NF-κBcomplexes(B).NF-κBisfreed (C)andcannowmovetothenucleus,whereitbindsspecificDNAsequences andenhancestheexpressionofanumberofgenes,manyinvolvedinimmune responses(D).Thisresultsinavarietyofnewproteinsbeingmanufacturedin the cell, such as the cyclooxygenase-2 (COX-2) enzyme, which catalyzes the synthesis of prostaglandins. Once secreted in the bloodstream, prostaglandins promote vasodilation, which is responsible for erythema and edema (redness and swelling of the skin); sensitize spinal neurons to pain; and act on the thermoregulatorycenterofthehypothalamustoproducefever(E). We can now form a general idea about how inflammatory responses are initiated when organisms are exposed to harmful stimuli. What is missing is an explanation of how the responses shut down. It was eventually discovered thatNF-κBalsoenhancestheproductionofitsowninhibitor,IκB.Thenewly synthesized IκB binds NF-κB, trapping it back in the cytoplasm (F). ProstaglandinstoocurbNF-κBactivitybyinterferingwiththesignalingpath- wayleadingtothedegradationoftheinhibitoryproteinIκB(G).Thus,following stimulation, T-cells are initially activated, resulting in an inflammatory response, then are automatically turned off by means of a negative feedback loop molecular mechanism, which performs a function analogous to that of acommonthermostat. The above explanation is in many respects incomplete. For instance, it is not specified how prostaglandins cause the symptoms of inflammation. Quantitative-dynamic details are also missing. The explanation doesn’t say anything about the duration of the inflammatory response or whether cyclical inflammatory responses are generated in response to persistent stimulation. Finally,somefamiliaritywithchemistryistacitlyassumed,suchasthenotion thatprotein–proteinandprotein–DNAinteractionsareweakerformsofbinding incomparisontothecovalentbondsholdingmoleculestogether.Nevertheless, despiteassumed,abstracted,andunknowndetails,theabovenarrativeandthe accompanying diagram should help the reader imagine how inflammatory responses are produced as a result of a sequence of changes and interactions involvingvariouscellularandmolecularcomponentsofanorganism. Downloaded from https://www.cambridge.org/core. IP address: 27.106.64.254, on 18 Mar 2020 at 06:40:15, subject to the Cambridge Core terms of use, available at https://www.cambridge.org/core/terms. https://doi.org/10.1017/9781108592925 MechanismsinMolecularBiology 3 Figure2AsimplifiedrepresentationoftheNF-κBmechanismanditsrolein regulatinginflammatoryresponses 1.2TheDiscoveryofBiologicalMechanisms Theelucidationofbiologicalmechanismsoftenbeginswiththeformulationof hypotheses sketching out possible mechanisms.1 For instance, experimental results indicating that protein synthesis inhibitors block T-cell activation led someresearcherstohypothesizethatinflammatoryresponsesrelyonamechan- ism of genome expression regulation. Initial speculative work is followed by whatLindleyDarden(2006b,Ch.4)describesasagradualfillinginofmissing mechanisticdetails.Thisusuallyrequiresasignificantamountofexperimental research. Inafirststep,asystemresponsibleforproducingthephenomenonofinterest, orwhatWilliamBechtelandRobertRichardson(2010,Ch.3)callthe‘locusof control’, is identified. In practice, this amounts to the characterization of an experimentalsetupinthecontextofwhichaphenomenoncanbeconsistently reproduced. Forinstance, the experimental setupused to elucidate theNF-κB regulatory mechanism consisted mainly of a cell model of T-cell activation. Normal T-cells extracted from the blood of a healthy donor or precancerous (‘immortalized’)T-celllinesweregrowninanartificialmediumandstimulated 1 PeterMachamer,LindleyDarden,andCarlCraver(2000,18)defineamechanismsketchas“an abstractionforwhichbottomoutentitiesandactivitiescannot(yet)besuppliedorwhichcontains gapsinitsstages.Theproductivecontinuityfromonestagetothenexthasmissingpieces,black boxes,whichwedonotyetknowhowtofillin.Asketchthusservestoindicatewhatfurtherwork needstobedoneinordertohaveamechanismschema.”Incontrast,amoredetailedmechanism schema,suchastheonedepictedinFigure2,isa“truncatedabstractdescriptionofamechanism thatcanbefilledwithdescriptionsofknowncomponentpartsandactivities...Wheninstantiated, mechanism schemata yield mechanistic explanations of the phenomenon that the mechanism produces”(2000,15,17). Downloaded from https://www.cambridge.org/core. IP address: 27.106.64.254, on 18 Mar 2020 at 06:40:15, subject to the Cambridge Core terms of use, available at https://www.cambridge.org/core/terms. https://doi.org/10.1017/9781108592925 4 ElementsinthePhilosophyofBiology by the addition of a chemical inducer, such as lipopolysaccharides, a toxin releasedwhenthecellwallsofcertainbacteriaaredestroyed,andwhichcauses septicshockunderphysiologicalconditions. Inasecondstep,variablesdescribingtheexperimentalsetuparetargetedby experimentalinterventionsinthehopeofdemonstratingthatspecificchangesin theexperimentalsetupandthephysicalsystemsofwhichitiscomposedresult in changes in the phenomenon under investigation. For example, the IκB inhibitor was shown to be part of the regulatory mechanism of T-cell activity basedonexperimentalevidencedemonstratingthatmutationsinthesequence of IκB result in a prolonged activation of T-cells following stimulation. Carl Craver (2007, Chs. 2–3) gives an excellent analysis of the role that causal relevance plays in the identification of putative mechanistic components. In particular, he points out that causal relevance is demonstrated by means of controlled experiments, thus establishing a connection between the scientific practices involved in the elucidation of mechanisms and James Woodward’s (2003)interventionistaccountofcausation. Finally,amechanismmusteventuallybe‘recomposed’inordertoshowhow itgeneratesthephenomenon(Bechtel2011).Amechanism’srecompositioncan bephysical,forinstance,aninvitroreconstitution experiment,orconceptual, such asacomputer simulationorsimply a narrative ordiagramsuch asthose illustratedearlier.Onewayoranother,thegoalistodemonstratethatcompo- nentsorganized,acting,andhavingthepropertiesdescribedinthemechanistic explanationcanproduce,andideallyaresufficienttoproducethephenomenon underinvestigation. 1.3ExperimentalMethodologyFirst Inscientificpractice,hypothesisandexperimentation proceed intandem. The initial characterization of an experimental setup and the choice of variables targeted for intervention are motivated by existing hypotheses about the mechanism responsible for a phenomenon. Conversely, experimental results, suchastheabilityorfailuretoconsistentlyreproducethephenomenon,aswell as the fortuitous discovery of causally relevant factors, play a key role in the formulationofnewmechanistichypotheses. This Element, however, focuses almost entirely on experimental inquiry.2 Therearetworeasonsforthisunusualchoice.Thefirsthastodowiththefact thatmostphilosophersapproachexperimentalpracticefromtheperspectiveof 2 Perhapsaclarificationisneededhere.WhatImeanby‘experimental’or‘empiricalinquiry’is experimentalresearchinscience.Experimentalistsapproachhypotheticalexplanationswithan attitudeof‘suspendedbelief’untiladequatesupportingevidenceisproduced.Beingcautious, however,isnotthesameasbeingskeptical.Experimentalresearchisasustainedefforttoproduce Downloaded from https://www.cambridge.org/core. 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