1. MARK BOTIRIUS
Page 1 of 8
What is a species, and why is it important to know all of the stages in
the life history of an organism before studying its evolutionary
history?
Althoughitisnot immediatelyapparent,the answertothe question,“Whatisa species?”
doesnotreside inmerelythe scientificdefinitionof species. Rather,the real issue behindthis
questiondealswithknowledgeitself,andthe role categoriesplay inthe attainmentof knowledge.
Fundamentally,“species”isanattemptto categorize. Itis an attempttodraw a distinctionbetween
one objectversessome otherobject,andtorecognize those elementsthatare commonto a group
of objectswithinacategory. Thisisabsolutelynecessaryforthe attainmentof knowledge,andthe
attainmentof knowledge isthe fundamental purpose of science. Therefore,tounderstandwhata
speciesiswe mustnotbeginwith“species”,because“species” doesnotexistin thereal world. The
real worldispopulatedbyobjects. Anatom, a dog, a chair,a person…theseare all objects,oras I
like tocall them,“existents”. The perceptionof existentsalone,however,doesnotconstitute what
reasonable people considertobe knowledge,especiallyscientists. Inorderforknowledgetobegin,
humanbeingsmustnotonlyperceive anobjecttoexistinthe real world,he mustgrasp what it is. In
otherwords,he must forma concept. Perceptionandconceptionare notthe same thing. For
instance,while we canpointtoa dog inthe real world,because adog is an objectthatactually
exists,we cannotpointtothe conceptof “dogness”thatisthe meaning behindwhatitistobe a
dog. (Peikoff,1993, p. 112) Conceptsexistonlyinthe mindasa necessarytool forknowledgeand
meaning. Theyare not existents.
Conceptualizationisthe beginningof knowledgebecause conceptsare formedbythe
realizationthatthere isatruth that tiesa groupof individualperceptual objectstogetherasopposed
to those objectsthatdo notbelonginthe group. It isthe realizationthattohave white feathersisa
part of “swanness”,orwhatit meanstobe a swan. These truthsthat tie individualobjectstogether
become the core elementstohowwe categorize,define,discover,andgainknowledge aboutreality.
The problem,however,isthatthere isa seeminglyinfinite numberandvarietyof objectsin
existence andasa resultthere will alwaysbe some objectthatisneitherconceptuallyfundamentally
the same or fundamentallydifferentfromothersimilarobjects.Take,forexample,the conceptof a
table as beinganobjectwithfourlegsuponwhichthere isa flatlevel surface. Supposeone
encountersanobject where there isaflatlevel surface atthe same height,buthangingfromthe
ceilingfromchains. Isita table? (Peikoff,1993, p. 115)
I am pointingthisoutto emphasize thatthistype of difficultyisnotunique tothe species
concept. It is,rather,as much a part of knowledge asconceptualizationitself. If we truly
understandknowledge,thenwe will realize thatthisdoesnotinvalidate conceptualizationasthe
beginningof knowledge,rather,itstrengthensit,becausethisispreciselyhow conceptsare clarified,
or hownewconceptsare formed. Havingdiscussedthe differencebetweenexistents(objectsthat
actuallyexistinthe outside world) andconcepts(atruth,or truths thatis recognizedinthe mind
that tiesa groupof objectstogetheranddistinguishesthemfromotherobjectsand/orgroups) Iam
readyto define whataspeciesis.

2. MARK BOTIRIUS
Page 2 of 8
A speciesisman’sefforttoconceptualizeorganismsintodistinctcategoriesbasedon
observedtruths,orcharacteristics,thattie individual membersof the grouptogether,and
distinguishthemfromotherorganisms.
Justlike anyconcept,the speciesconceptalsorunsintosituationswhereorganismsare
neitheressentiallythe same oressentiallydifferentinsome definingcharacteristic. Onthe other
hand,unlike mostconcepts,thishascausedsome people todeclare thatthisrepresentssome
unique difficultywiththe speciesconceptitself. Idisagree,andif Ihave made my argument
reasonablywell thusfar,itshouldbe apparentthatthisexistswith allconcepts,thatit isnormal,
and isactuallya good characteristicthatfurthersourknowledge,notdiminishesit. Different
characteristicshave beenusedtogrouporganismsintospeciesandtheyhave all runintothis
difficulty. Forexample,the characteristicof morphology hasbeenused. Objectionstothis
characteristicinclude the factthatmale and femalesof the same speciesoftenexhibitdifferent
morphologiessuchasthe sexual dimorphismof the male andfemale goldfinchorthe tremendous
morphological variationsfoundindomesticdogs.Anotherobjectiontomorphologyisthatsome
organismsexhibitdifferentmorphologiesatdifferentstagesof theirlives(e.g.fungi),andyet
anotherobjectionisthatsimilarmorphologiescanarise frombothdivergentorconvergent
evolutionwhichinfluence speciationverydifferently.(Dr.RogersIMEClassLecture,2016)
Anothercharacteristicthathas beenusedtodesignate specieshasbeenagroupthatcan
reproduce witheachother,yetare reproductivelyisolatedfromothergroups. Like morphology,
there are also numerousobjectionsraised. The mostcommonobjectionisthatitisoftennot
possible todetermine whetherornottwo populationswouldbe able interbreedif theyhappento
Figure 1. Althoughmorphologywouldindicate that all ofthese dogs are a different species, most of theminfact
belongto the same sub-species. This figure is from Dr. Rogers’ class lecture.

3. MARK BOTIRIUS
Page 3 of 8
encountereachotherinthe future. Hybridizationfurthercomplicatesthe issue asinthe case of the
Little StripedWhiptailandthe TigerWhiptail. These twopopulationscansuccessfullybreed,
producingprogenythatare all female,thathave beendesignatedasNew MexicoWhiptails.
Moreover,notall organismsevenreproduce sexually,makingitsothat thischaracteristicdoesn’t
evenapplyinthe firstplace. Bacteriareproduce asexually(conjugationnotwithstanding),asdo
manyplants(bybudding,forexample). Manyorganismsproduce eggsthat can developintofully
functional adultswithoutbeingfertilized(parthenogenesis),andstill otherscanfertilizethemselves
(hermaphroditism). (Rogers,2017, pp.393-396)
The resultof all of these objectionstothe characteristicsusedtodesignateaspecieshas
beena clarificationof the speciesconceptitself. Itbecame obviousthatnosingle conceptwas
sufficienttounifyall of the borderlinecasesintoacomprehensiblesystem,andsoit became
necessaryto formulate newspeciesconceptstomeetthe challenge.The formulationof new
conceptsinresponse tonewinformationispreciselywhatitmeanstoadvance in knowledge.There
simplyisnoreasonfor usto force all populationsintoasingle speciesconceptwhenclearlynotall
populationsfitintoasingle system. Therefore,several speciesconceptshave arisentomeetthis
challenge. The three mostcommonare:
1. The biological speciesconceptwhichbasesaspeciesonwhetherornot populationscan
breedandare reproductivelyisolated.
2. The phylogeneticspeciesconceptwhichbasesspeciesonphylogeneticanalysis.
3. The evolutionaryspeciesconceptwhichbasesspeciesonlineage. (Futuyma,2013, p.461)
An additional factorthat
makesspeciesdeterminationbased
on morphological andsexual
characteristicsdifficultisthatmany
organismsexhibitremarkably
differentcharacteristicsduring
theirlifetimes. Theycanbe so
different,thatthe juvenile
organismcan bearno resemblance
to the adult. One of the most
obviousexampleswouldbe those
creaturesthat go through
metamorphosis,suchasinsectsof
the order Diptera(flies),and
Lepidoptera(butterfliesand
moths). Anotherexample is
pleomorphicfungi. A single
organismcan exhibitverydifferent
formsand reproductive strategies.
(Rogers,2017, p. 395) Consideralso
cnidarians. Althoughsome species
existsolelyaseitherapolyp(a
Figure 2. An example of a pleomorphic fungi. At various stages in its life
cycle it resembles different bacterial forms, yeast forms, and mycelial
forms, making it necessaryto knowthe entire life cycle of thisorganism
before determining its species. Thisis from Dr. Rogers’ class lecture.

4. MARK BOTIRIUS
Page 4 of 8
cylindrical sessileformwithtentaclesthatisattachedto a substrate) ora medusa(a free swimming
formthat resemblesajellyfish),some speciesexistasboth! Inthose speciesthatexistasboth
forms,the polypsproduce medusaasexually,butthe medusaare eithermale orfemale that
produce gametessexually. The resultingzygotesdevelopintoaplanktoniclarvawithciliathat
metamorphosisintoapolypthatattachesto a substratumto continue the cycle. Togetherthese
examplesillustrate whyit isimportanttoknow aboutthe life historyof anorganismbefore tryingto
determine itsspecies,whichisalsothe reasonwhywe needtostudyitslife historybeforestudying
itsevolutionaryhistory. If we misidentifythe organismthatcurrentlyexistsbecause we were
ignorantof its life history,howare we goingtoidentifyitsrelationshiptoorganismsthat
disappearedlongago? Before we canproperlyidentifyitsevolutionaryhistory,we mustbeginwith
a firmfoundation,andthatfoundationbeginswithasolidknowledgeof the existingorganisms’life
history.
Describe the developmental processes in a multicellular animal from
fertilization to the adult form.
As withalmostall biological processes,the processof developmentishighlycomplex. Itis
helpful,therefore,todiscussanimal developmental processesinfourstages:1.Fertilization,2.
Cleavage,3.Gastrulation,and4. Organogenesis.
Fertilization
The processof fertilizationbeginswhenthe eggispenetratedbythe sperm. Ingeneral,this
isnot an easyprocess,because animal eggshave aprotective coveringthatvariesdependingon
whatanimal speciesthe eggbelongsto. Forexample,insecteggs,suchas D melanogasterhave
chorion,while the eggsof mammalshave azona pellucida. Fortunately,mostspermhave
acrosomes. Acrosomesare organelleslocatedonthe headof the spermthat can digestthe
protective coveringof the eggs,enablingthe spermtogainentryintothe egg. Once the sperm
penetratesthe egg,the eggsof variousanimal speciesemployvariousstrategiestoprevent
polyspermy. Forexample,seaurchineggschange theirmembranepotential topreventmore than
one spermfromenteringthe egg,whereassome animal eggsreleaseenzymesthatdestroy
receptorsneededbythe spermforeggentry. Once inside the egg,the spermandeggnuclei unite,
and the eggis fertilized.
Cleavage
Cleavage isthe processbywhichthe eggbeginstodivide andthe exactprocessisdifferent
for eachspecies. Nonetheless,cleavagehasbeendividedintotwoverybroadcategorieswhichare
holoblasticcleavageandmeroblasticcleavage. Inholoblasticcleavage,the eggdividescompletelyas
it beginstoforma blastomere. This type of cleavage isfoundinanimalssuchasechinoderms(radial
cleavage),annelids,mollusks,flatworms(spiral cleavage) andfinallymammalsandnematodes
(rotational cleavage).Inmeroblasticcleavage,the blastomeredoesnotdividecompletely. Thistype
of cleavage isfoundinfish,reptiles,birds(discoidal cleavage) andinsects(syncytial cleavage).In
addition,differentspeciescanformdifferenttypesof blastomeres. Forexample,manyanimalsform
a hollowball of cellscalledablastula,whereasmanyinsectsformablastodermconsistingof alayer
of single cellsthatsurrounda yolkfilledinterior.

5. MARK BOTIRIUS
Page 5 of 8
In the case of D melanogaster,the morphologyof the flybeginswiththe developmentof
the syncytial blastoderm. Uponfertilization,the haploidnucleiof the twogametesfuse intoone
diploidnucleus,whichthenbeginstodivide. Afterapproximatelytendivisions,the nuclei are
transportedtothe blasterdermcortex bymicrotubuleswhere theycontinuetodivide forming
approximately4,000 nuclei alongthe periphery. Atone endof the egg,there isa concentrationof
bicoid mRNA,andat the otherendthere isa concentrationof nanos mRNA. These mRNAsbecame
concentratedatthe polesduringoogenesispriortofertilization. Thisarrangementsetsupthe
anterior/posterioraxisof the flywiththe Bicoidproteindeterminingthe anteriorpole,andthe
Nanosproteinthe posteriorpole. (Watson,2014, p. 754) Whenthe nuclei have completely
surroundedthe eggyolk,cell wallsformaroundthem, creatingacellularblastoderm. Althoughthe
mechanismisdifferent,the dorsal/ventral axis
of the flyisalsodeterminedbyaconcentration
gradientof twoproteins(GurkenandDorsal)
that wasestablishedinthe eggpriorto
fertilization. (Raven,Johnson,Mason,Losos,&
Singer,2011, p. 387)
Gastrulation
Gastrulationbeginswhenthe vegetal poleof
the blastulabeginstoinvaginate formingan
indentationcalledablastopore. The blastopore
deepens,eventuallyformingacavitycalledthe
archenteronwhile the hollow partof the
blastula,the blastocoel,eventuallyshrinks
altogether. Asusual,thisisa generalization,
and minorexceptionsexistacrossdifferent
species. Forinstance,figure threeshowsthe
formationof a yolkplugfillingthe blastopore,
whichhappensinfrogs,butnot inbirds,which
insteadformsomethingcalleda“primitive
streak”. With the formationof the archenteron
three germlayersdevelop. Theyare the
ectoderm,whicheventuallygivesrise tosuchstructuresas the epidermisandnervoussystem, the
mesoderm,whicheventuallydevelopsintothe structuresthatinclude the notochord,muscles,and
bone,andthe endoderm,whicheventuallydevelopsintostructuressuchasthe gut, lungs,andliver.
(RavenJ.M., 2011, p. 1113)
Organogenesis
Followingthe developmentof the three principal germlayersisorganogenesis. Of course,
the specificsof the developmentof organsare goingto vary dependingonthe morphologyof the
organism(forexample,inmammalsitbeginswiththe formationof the primitive notochordfromthe
mesodermandneural plate fromthe ectodermwhile ininsectsitbeginswithsegmentation)
howeverthere are some general principlesthatcanbe discussed. Ingeneral,the developmentof
organs andbodystructure is dependentonhow cellsdetermine theirfate. Inotherwords,how do
Figure 3. Depicted at the top is the formationof a
blastula, followed bygastrulationwhichresults inthe
disappearance of the blastocoel and the formationof
the archenteron. This is fromDr. Rogers’ classlecture.

6. MARK BOTIRIUS
Page 6 of 8
cellsdetermine if theywill formalungas opposedtoa bone? How dotheyknow to form a hand,as
opposedtoa leg? The answeristhat theydeterminethese thingseitherbysensingtheirlocationvia
cytoplasmicdeterminants(e.g.BicoidandNanos),bycommunicationwithneighboringcells(e.g.
“organizers”,suchas the SpemannOrganizerwhichisagroup of cellsthatsecretschemical signals
called“morphogens”tosurroundingcellsinfluencingtheirdevelopment) (RavenJ.M.,2011, p.
1122) or finallybythe directionof genes,suchasPair-rule andHox genes.
Recall thatthe initial axisof
the bodyplanwas determined
by concentrationgradientsof
cytoplasmicdeterminantssuch
as Bicosand Nanos. Figure 4 is
an excellentillustrationof the
cascade of eventsthatfollow
resultinginthe development of
an adultanimal. Followingthe
establishmentof axispolarity,
Gap genes(of which
Hunchback isa member) are
activatedthatdistinguishan
initial subdivisionof the
developingembryo. Next,Pair-
rule genesare activated
producingsevendistinctbands
indicatingthe beginningof
segmentationthatare followed
by the expressionof segment
polaritygenes. Finally,the
developmentof the embryofallsunderthe control of the Homeobox geneswhichthencontrol the
restof the flies’developmentintomaturity.
Extra Credit
Briefly outline the general contents of a bacterial genome. Discuss the
various categories and their functions in the cells.
The general contentsof a bacterial genome are depictedinthe followingfigure.
Figure 4. The elements that determine the development of organogenesisof
the fruit flybeginwith gradients of cytoplasmic determinants, followedby
the expressionof Gapgenes andSegment polaritygenes, culminatingwith
Hox genes. Thisis from Dr. Rogers’ class lecture.

7. MARK BOTIRIUS
Page 7 of 8
1. Transport and Binding.These are the proteinsthatare involvedinthe transportof materialsinto
and outof the cell. In orderfor E coli to survive inavarietyof environmental conditionsandutilizea
varietyof foodsources,itneedsalot of genestoproduce the requiredproteinsbecause,different
proteinsare neededtotransportdifferentfoodsources. Changingenvironmentalconditionssuchas
(differingpH) alsorequire differentproteins.
2. Energy metabolism.These are the proteinsforthe TCA cycle,the electrontransportchain,and
glycolysis.The proteinsthatenable all of the metabolicactivitiesof the cell are codedhere.
3. Proteinsecretion andmodification. Inorderforproteinstobe secretedtheyoftenhave tobe
modifiedwithsignal sequencesand,ortransportedtothe membrane bysignal recognitionparticles,
whichare themselvesproteins.
4. Aminoacidsynthesis. These are the genes foraminoacidsynthesisneededbythe cell to
manufacture the aminoacidsitneedstobuildproteins. Anexample isaminoacidsynthetasis.
5. Cell envelope. These are the proteinsneededbythe cell tobuilditscell wall (itismade of NAM
and NAGcross linkedbyproteins. Also,the cellmembraneof bacteriaisfull of membrane proteins
neededforvariousdutiesthatincludesignaling,andstructural support.
6. Transcription,transcriptionregulationfactors,transcriptionfactors. These are the proteinssuch
as RNA Polymerase LacI,andCAP(inthe case of the lac operon) thatare neededtoproduce the
mRNAsneededbythe cell.
7. DNA Replication. Codesforthe DNA polymerasespluseverythingelse neededtoassemble the
replicationmachinerytoinclude ligases,SSBshelicasesandsuch
8. Central intermediarymetabolism. These are the processesinthe cell thatare not involvedin
energymetabolism,butare necessaryforthe energyof the cell regardless. One example thatcomes
to mind,is gluconeogenesis.
Figure 5. The generalcontents of the E coli genome. Thisis from Dr. Rogers’ class lecture

8. MARK BOTIRIUS
Page 8 of 8
9. Toxinproduction/toxinresistance. These genescode forthe toxinsthatsome bacteriasecrete
that give themanadvantage overtheircompetitors,orenable themtodetoxifytoxinssecretedby
theircompetitorsagainstthem.
10. Translation. Genesthatcode for the proteinsthathelpholdribosomesintheircorrect
conformation,orevenelementslike aminoacetyl tRNA synthetasesthatare neededfortranslation.
11. Fattyacid/phospholipidmetabolism. Genesthatcode forthe anabolic andcatabolicreactions
neededbythe bacteriatobuildor breakdownfattyacidsandphospholipidsusedintheir
membranes.
12. Transposons,virussequences,ECEsandtransformation. Transposable elementsandvirus
sequencespickedbyinfectingphagesare includedinthiscategory. ECEsinclude plasmidsandgenes
neededfortransformationsuchasthose thatdirectthe bacteriato form a pilus,orconjugation
bridge.
13. Cofactors,prostheticgroups,andcarriers. These are moleculessuchNADHandFADH.
Prostheticgroupsthatbindtightlytoenzymes,suchasthe heme grouppresentincytochromes.
14. Chemotaxis. Bacterianeedthese tosense favorable andunfavorable environmentssotheycan
avoidtoxinsandfindfood. Chemotaxisisthe movementof bacteriainresponse tochemical signals
intheirenvironment.
References
Futuyma,D.J. (2013). Evolution (3rd ed.).Sunderland:SinauerAssociates.
Peikoff,L.(1993). Objectivism:The Philosophy of Ayn Rand. New York:PenguinGroup.
Raven,J. M. (2011). BIO202, Select MaterialfromBiology. Boston:McGraw-Hill CompaniesInc.
Raven,Johnson,Mason,Losos,& Singer.(2011). BIO201, Select MaterialfromBiology (9thed.).
Boston:McGraw-Hill CompaniesInc.
Rogers,S. O.(2017). Integrated MolecularEvolution (2nded.).BocaRaton: CRC Press.
Watson,e.a. (2014). Molecular Biology of the Gene (7th ed.).Boston:Pearson.