Molecular Geometry of Body Pattern in Birds

170 Pages·2012·11.959 MB·English

by  Antonio Lima-de-Faria (auth.)

Molecular Geometry of Body Pattern in Birds
.
Antonio Lima-de-Faria
Molecular Geometry of Body
Pattern in Birds
Prof.Dr.A.Lima-de-Faria
LundUniversityDepartmentofCellandOrganismBiology
BiologyBuilding
So¨lvegatan35
SE-22362Lund
Sweden
Privateaddress:
Trumslagaregra¨nd10
SE-22639Lund
Sweden
ISBN978-3-642-25300-3 e-ISBN978-3-642-25301-0
DOI10.1007/978-3-642-25301-0
SpringerHeidelbergDordrechtLondonNewYork
LibraryofCongressControlNumber:2012931149
# Springer-VerlagBerlinHeidelberg2012
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Acknowledgments
TheRoyalPhysiographicSociety,Sweden,awardedtheauthoragranttocoverthecostsofthe
production of this work. These included the copyright fees requested by the Marketing
Department of Lynx Edicions, Barcelona, Spain. The dues were to cover the 200 figures
from the “Handbook of the Birds of the World’’ that were to be included in this work. This
grant was possible thanks to the unreserved and immediate decision of three colleagues:
the Permanent Secretary of the Royal Physiographic Society Professor Dr. Rolf Elofsson
(StructuralZoology),ProfessorDr.CharlotteErlanson-Albertsson(MolecularSignaling)and
Professor Dr. Bengt Olle Bengtsson (Genetics). The three supported the award before the
manuscriptwaswritten.
SpecialthanksareduetoDoctorJosepdelHoyo,Editorofthe“HandbookoftheBirdsof
theWorld,’’who,onthebasisofaletterofintent,recommendedanappreciablereductionof
thefeestobepayedtoLynxEdicions.Withouthisgenerousstandthisworkwouldnothave
beenpossible.
Last but not least, Med. Kand. Johan Essen-Mo¨ller is to be thanked for an unfailing
contribution in converting the manuscript into computer work which he carried out with the
utmostaccuracy.
v
.
Contents
1 Introduction ........................................................................... 1
1.1 TotheReader ..................................................................... 1
1.2 TwoCenturiesofOrnithology–AnImpressiveContributiontoScience ....... 1
1.3 ThePreparationofthePlatesCoveringSpecificBirdTraits .................... 2
2 TheMolecularDeterminationofaBird’sPattern ................................. 3
2.1 ASuccessionofMolecularEventsLeadstotheFormationofaBird ......... 3
2.2 PermanenceofCharactersinInheritanceandDevelopment ................... 3
2.3 NoAnimalisStructurallyorPhysiologicallyStatic–Programmed
CellDeath ....................................................................... 5
2.4 TheOriginofFeathersisaSourceofControversy–TheyEvolved
inDinosaursBeforeBirdsAppeared ............................................ 5
2.5 “FingersEvolvedtoPlaythePiano’’–TheIdeaofPurpose
inBiologicalThought ........................................................... 5
2.6 TheBiologicalPatternofBirdsisWrittenontheirFeathers ................... 5
2.7 FeatherGrowthandReplacementareHighlyOrdered ......................... 6
2.8 TheRegenerationofFeathersOccursPeriodicallyBeingDependent
onDayLengthandHormoneActivity .......................................... 6
2.9 HormonesControltheSize,ShapeandColourofFeathers .................... 6
2.10 TwoGenesareResponsibleforFeatherDevelopment ......................... 8
2.11 ProteinsandOtherMoleculesDecideHierarchicalOrder
inFeatherBranching ............................................................ 8
2.12 ChemistryandPhysicsofColours .............................................. 9
2.13 TheLocationofPigmentsinFeathersisGuidedbyProteins
andOtherMolecules ........................................................... 11
SourcesofFigures .................................................................... 12
3 TheOccurrenceofConspicuousFeathersatDifferentBodyLocations
andTheirGeneticInterdependence ............................................... 13
3.1 TwoLongFeathersEmergingfromtheTail .................................... 13
3.2 ABirdGetsitsBodyTraitWhetheritLikesitorNot–DNAFollows
itsOwnAtomicEvolution ....................................................... 16
3.3 TwoLongandShortFeathersProtrudingfromtheHead ....................... 18
3.4 TwoLongFeathersArisingfromtheWing ..................................... 21
3.5 ParticularFeathersWhichAppearinOtherBodyRegionsIndicating
aCommonMolecularEvent ..................................................... 21
3.6 FeatherNumbersWhichareMultiplesofTwoOccuronTailandHead ...... 21
3.7 TheOccurrenceofFixedNumbersinOtherAnimals .......................... 27
SourcesofFigures .................................................................... 28
vii
viii Contents
4 TheEvolutionoftheBirds ......................................................... 29
4.1 TheOriginofBirdsisDisputed–ArborealMonkeyswerenotAble
toDevelopWings ............................................................... 29
4.2 TheLongJourneythatLedtotheEstablishmentofChemicalPeriodicity .... 30
4.3 FromChemicaltoBiologicalPeriodicity ....................................... 30
4.4 ThePeriodicityofFlight ........................................................ 31
4.5 MolecularMechanismsthatmaybeResponsibleforPeriodicity
andtheEmergenceofCoherentStructures ..................................... 34
4.6 GeneticAnalysisDisclosesthattheSameGenesareInvolvedintheFlight
ofInsectsandBirds–TheImpossibleBecamePossible ....................... 35
4.7 TheDirectProductionofFlieswithFourWings ............................... 35
4.8 WingsinBirdsmayhaveAppeared“Ready-Made’’andAs“ASurprise’’
totheAnimal–BirdswithExtraWingsProducedintheLaboratory ......... 35
4.9 EvolutionwasnotKindtotheBirds–WingshavenoPrehensileFingers,
JawsLackTeethandthePenisisRare ......................................... 36
4.10 EvolutionCreatedSeriousLimitationsinBirds ................................ 36
4.11 ASenseofFrustrationorofAmputationmayhaveRemained
inaBird’sMind ................................................................. 36
4.12 TheConstantReplacementofTeethinVertebrates–“Actually
thereisMethodinthisSeemingMadness’’ ..................................... 39
4.13 MostBirdSpeciesLackaPenisButinFlatwormsthisOrgan
isHighlyDeveloped ............................................................. 40
SourcesofFigures ..................................................................... 41
5 TheBirdGenomeandtheMolecularDetermination
ofWings,LegsandBeaks .......................................................... 43
5.1 WhatisaGenome ............................................................... 43
5.2 TheUnityoftheChromosomeRemainsaQuestionMark ..................... 43
5.3 WhatwasRevealedbySequencingtheChickenGenome–
HumansandBirdsareGeneticallySimilar ..................................... 44
5.4 GenomeSequencingofaWildBirdDisclosesThatSongBehaviour
isDependentonRNAExpressionintheBrain ................................. 45
5.5 ComparisonofLargeandSmallChromosomesinBirds ....................... 45
5.6 HowtoObtainaBirdWithExtraWingsandLegs–GenesInteract
WithSpecificProteinsProducingNormalWingsandLegs .................... 45
5.7 WhetherWingsorLegsareFormedDependsontheChangeinPosition
ofaProtein ...................................................................... 47
5.8 GreatVariationinBeakMorphology–TheSameEvolutionarySolution
OccurredinDistantIslandsandalsoontheMainland ......................... 48
5.9 HowtoRecreateBeakEvolution–ProteinsShapetheBeaksofDucks
andFinches ...................................................................... 50
SourcesofFigures ..................................................................... 52
6 TheMentalAbilityofBirdsTakesManyForms ................................. 53
6.1 CognitionandtheUseofTools ................................................. 53
6.2 MigrationwasaHighlyInnovativeProcessthatDemandedNewSolutions .. 53
6.3 LandmasseshaveMovedAcrosstheEarth’sSurface .......................... 54
6.4 TheEmergenceofNewContinents,SeasandDeserts ......................... 55
6.5 BirdsareFacedwithChallenges–TheEarth’sMagneticFieldisUnder
ConstantChange ................................................................ 55
6.6 TheNightSky,withitsStars,TellstheBirdstheirLatitude–
TheStarCompass ............................................................... 55
Contents ix
6.7 ThePhysicalBasisoftheMagneticCompassandtheEvolutionofBird
Migration ....................................................................... 56
6.8 One-EyedSleepinDucksandBrainActivity ................................. 58
6.9 ActiveCooperationAmongBirdsLeadstoClassDistinction ................ 58
6.10 ToCopewithWaterRefractionBirdsareObligedtoMakeCorrections ..... 58
6.11 SongLearninginBirdsDependsontheConcentrationofaProtein
intheirBrainandtheActionofHormones .................................... 60
6.12 TheStarlingOwnedbyMozartWhistledtheThemeofhisConcerto ........ 60
SourcesofFigures .................................................................... 62
7 HowtoRedesigntheBodyPatternofanOrganism ............................. 63
7.1 ASophisticatedGeneticTechnologyOpenedtheWay ....................... 63
7.2 EarlyEvidenceonDrasticStructuralTransformations–FeetontheHead ... 63
7.3 TheHomeoboxGenes–FormationofIdenticalOrgansatDifferent
BodyLocations ................................................................. 63
7.4 GeneticistsTransformedCuriositiesintoValuableDevelopmentalKeys–
Eight-LeggedandFour-WingedFlieswereProduced ......................... 65
7.5 TheAntennatoLegTransformations .......................................... 65
7.6 EyesFormedonWings,LegsandAntennae–TheUnity
ofBodyConstruction ........................................................... 68
7.7 MouseGenesProduceEyesinFlies–TheImportanceofEyeGenes ........ 68
7.8 TheWingoftheFlyandtheHumanFingersareControlled
bytheSameProteins ........................................................... 68
7.9 FeatherDevelopmentisalsoControlledbyOneoftheseProteins ............ 69
7.10 MovingfromGeneConstructstoEmbryonicDevelopment–TheAvian
MolecularClock ................................................................ 69
7.11 TheFormationofStripesAlreadyintheEmbryo ............................. 70
7.12 TheSpacingofFeathersisDirectedbyaProtein ............................. 72
7.13 ChangeofGeneActionDuringDevelopment–ASingleGeneisImportant
butnotAlmightySinceanAntennacanRegenerateintoaLeg ............... 73
SourcesofFigures .................................................................... 74
8 TheMolecularGeometry .......................................................... 75
8.1 WhatisGeometry? ............................................................. 75
8.2 MathematiciansandPhysicistsKnowthatthereisnotOne,but
SeveralGeometries–EuclideanandNon-EuclideanGeometries ............. 75
8.3 MolecularGeometryisMultidimensional ..................................... 75
8.4 MolecularGeometryisDynamicandEphemeral–YetitPersists ............ 76
8.5 EveryBirdisaLessoninGeometry ........................................... 76
8.6 EmblematicBirdsandCrystalsdonotLie .................................... 77
8.7 TheUniquenessoftheAvianEye–ItSurpassestheHumanEye ............ 77
8.8 TheEye–AFocusoftheBird’sBody ........................................ 77
8.9 TheCircularityoftheEye ..................................................... 79
8.10 RingsAroundtheEyeExtendtotheWholeHead ............................ 79
8.11 HorizontalandVerticalStripesthatCrosstheEyeareAccompanied
byOtherswhichRunAboveandBelowit .................................... 79
8.12 TheCircularityoftheCrestanditsDivisionintoThreeDistinctSections ... 82
8.13 Single,DoubleandMultipleRingsAroundtheThroat,BreastandBelly .... 86
8.14 Throats,BreastsandBellieswithStripesFollowingtheHead-TailAxis ..... 86
8.15 TheWinghasaMoreComplexCircularity ................................... 87
8.16 TheBandsandConcentricSemicirclesoftheTail ............................ 94
8.17 Rump,LegsandBeakarealsoPartoftheBody’sGeometry ................. 94
x Contents
8.18 SurprisinglytheCircularityExtendstotheWholeBodyinSingleBirds ...... 99
8.19 TheBodyPatternofBirdsCondensedinaGeometricDisk ................. 101
8.20 TheGeometricDisk–LikeanyFigureofGeometry–Represents
aSimplificationofBiologicalReality ........................................ 105
8.21 WhatAbouttheIntermediateCases? ......................................... 105
SourcesofFigures ................................................................... 113
9 TheSymmetryofBirdsEmergesastheExpressionofanUninterrupted
AtomicOrder ...................................................................... 115
9.1 TheBirdshaveSpoken ......................................................... 115
9.2 TheAvianBilateralSymmetryanditsInternalAsymmetry ................... 115
9.3 NothingEssentiallyNewAroseattheBiologicalLevel ....................... 115
9.4 TheUninterruptedTransferofSymmetriesfromElementaryParticles
toHumans ....................................................................... 116
9.5 DNAKnowsNothingaboutSymmetriesanddidnotSeemtohavebeenAble
toCreateNovelOnes ........................................................... 118
9.6 MineralStructures,whichhavenoGenes,ProducetheSameOrderedPatterns
FoundinLivingOrganisms .................................................... 118
9.7 TheFinalPatternofaLivingOrganismAppearstoBeDependentonAtomic
ProcessesFarRemovedfromtheGeneticCode ............................... 118
9.8 PureSymmetriesareThoughttohaveonlyExistedintheVeryBeginning
oftheUniverse .................................................................. 121
SourcesofFigures ................................................................... 122
10 OrderisPresentatEveryLevelButisnotTotal ............................... 123
10.1 TheGeneticCodeandtheTranslationApparatushaveEvolved
inanOrderedWay ........................................................... 123
10.2 TheChromosomeMaintainsitsOriginalInformationbyaSeries
ofEfficientRepairMechanisms ............................................. 123
10.3 TheIntegrityofRNAisMaintainedbytheElimination
ofDefectiveMolecules ...................................................... 124
10.4 CorrectionandRepairofProteins ........................................... 124
10.5 HierarchicalDeterminationofMolecularTransitintheCell ............... 124
10.6 NuclearArchitectureRegulatesGeneExpression ........................... 126
10.7 CellDivisionandChromosomeMovementsareOrchestratedbyProteins . 126
10.8 TheUnexpectedRegularArrangementofChromosomesintheSperm .... 127
10.9 PreviouslyDespisedMicroRNAsandProteinsCoordinateEmbryonic
Morphogenesis ............................................................... 129
10.10 DirectedMutationsAdvantageoustotheOrganismarenoLonger
Disputed ...................................................................... 130
10.11 AdaptationinHigherOrganisms–OneoftheBlackBoxesofGenetics ... 131
10.12 OrderisNeverTotal–Yet“Errors’’areofParticularConfigurations
DeviatingonlySlightlyfromtheInitialCanalization ....................... 132
10.13 WithoutAtomicOrderAnyMolecularEdificewouldhaveCollapsed ..... 132
SourcesofFigures ................................................................... 133
11 ABird’sPlumageisaStageCurtainHidingaMolecularScenario–
AnOverview ....................................................................... 135
11.1 AClosingRemark ........................................................... 135
11.2 TheImpactofNovelTechnologiesonBirdStudies ........................ 135