Lecture On Systematics - MIT OpenCourseWare
Learning objectives: Explore architecture/structure in economics and biology Explore selected structural representations in biology andeconomics and their possible wider utility. Appreciate the differences between dendograms andCladograms Understand the differentiation and similarity of structurearrived at by decomposition and by aggregation and thedifferent constraints that occur in economic and biologicalsystems. Examine some recent biological findings from animaldevelopment research and how this work links to evolvability Explore how the “New Science of Evo Devo” may relate toEngineering Systems.Professor C. Magee, 2006Page 1
Lecture Outline Some structural aspects of economics and relationships toprevious structural characterizations Abbreviated History of Systematics in Biology Some current thinking about biological systematics and recentindications of a new synthesis among molecular biology,evolutionary biology and systematics Biological Evolvability (and flexibility) Innovation and evolutionary thinkingProfessor C. Magee, 2006Page 2
Economics Structure Sub-division of the economy National boundaries Industry classifications (SIC and now NASIC) arehierarchical with 5 levels How are these industry classifications arrived at? Partially Input/output relationships: if two plants (locations)use similar inputs (suppliers) and have similar outputs(customers), they are classified together. This is similar tostudying community structure in a network with nodes beingplants and links being specific product flows Broader abstractions that gather similarities at a higher level:for example- agriculture and extractive industries,manufacturing and service Market similarities: Chapter from Mantegna and Stanley Companies are classified together according to howcorrelated their dynamic movement is over time. Metric isProfessor C. Magee, 2006Page 3
Dendograms From Similarity XCHVPGKOGEXONTXCHV0.60.4ULTRAMETRIC SPACESSource: An Introduction to Econophysics, R. Mantegna and E. Stanley, page 109, 2000Professor C. Magee, 2006Page 4Figure by MIT OCW.
Dendograms and Network CommunityStructure Dendograms from metrics allow one to see the strength ofrelationships that determine association of nodes Dendograms do not allow the communities to be seen as easily One must make horizontal slices at various levels ofsimilarity and see how many communities arise.Professor C. Magee, 2006Page 5
Dendograms From Similarity XCHVPGKOGEXONTXCHV0.60.4ULTRAMETRIC SPACESSource: An Introduction to Econophysics, R. Mantegna and E. Stanley, page 109, 2000Professor C. Magee, 2006Page 6Figure by MIT OCW.
Relationship between hierarchical clusteringand community structure analysisProfessor C. Magee, 2006Page 7
Dendograms and Network CommunityStructure Dendograms from metrics allow one to see the strength ofrelationships that determine association of nodes Dendograms do not allow the communities to be seen as easily One must make horizontal slices at various levels ofsimilarity and see how many communities arise. Community structure analysis arrives at the structure bydecomposition (removing links from a full network) whereashierarchical clustering (dendograms) is done by adding links inthe order of most similar to least similar (aggregation)Professor C. Magee, 2006Page 8
Professor C. Magee, 2006Page 9
Fraction of Vertices Classified Correctly10.80.60.4Shortest PathRandom Walk0.2002468Average Number of Inter-Community Edges per VertexProfessor C. Magee, 2006Page 10Figure by MIT OCW.
MB1.3AXPTAXONOMY OF A STOCK PORTFOLIOFigure by MIT OCW.After Mantegna and Stanley.Is the relatively low degree of correlation among DJI stocks “explainable”?Source: An Introduction to Econophysics, R. Mantegna and E. Stanley, page 110, 2000Professor C. Magee, 2006Page 11
Economics Structure Sub-division of the economy National boundaries Industry classifications (SIC and now NASIC) arehierarchical with 5 levels How are these industry classifications arrived at? Partially Input/output relationships Broader abstractions that gather similarities at a higher level:for example- agriculture and extractive industries,manufacturing and service Market similarities: Chapter from Mantegna and Stanley Sub-division of the field of study ( e.g. publications) Suggestions Professor C. Magee, 2006Page 12
Journal of Economic LiteratureClassification System (19 categories) General Economics andTeaching Schools of Economic Thoughtand Methodology Mathematical and QuantitativeMethods Microeconomics Macroeconomics andMonetary Economics International Economics Financial Economics Public Economics Health, Education and Welfare Labor and DemographicEconomics Law and Economics Industrial Organization Business Administration andBusiness Economics;Marketing; Accounting Economic History Economic Development,Technological Change, andGrowth Economic Systems Agricultural and NaturalResource Economics:Environmental and EcologicalEconomics Urban, Rural and RegionalEconomics Other Special TopicsProfessor C. Magee, 2006Page 13
Journal of Economic LiteratureClassification System (19 top categories) General Economics andTeaching Schools of Economic Thoughtand Methodology Mathematical and QuantitativeMethods Microeconomics Macroeconomics andMonetary Economics International Economics Financial Economics Public Economics Health, Education and Welfare Labor and DemographicEconomics Law and Economics Industrial Organization Business Administration andBusiness Economics;Marketing; Accounting Economic History Economic Development,Technological Change, andGrowth Economic Systems Agricultural and NaturalResource Economics:Environmental and EcologicalEconomics Urban, Rural and RegionalEconomics Other Special TopicsProfessor C. Magee, 2006Page 14
Journal of Economic LiteratureClassification System: Typical FinalSubstructure in which books and papersare the next level of detail L. Industrial Organization (one of 19 highest level categories) L9 – Industry Studies: Transportation and Utilities L90- General L91- Transportation: General L92- Railroads and Other Surface Transportation:Autos, Buses, Trucks and Water Carriers; Ports L93- Air Transportation L94- Electric Utilities L95- Gas Utilities; Pipelines; Water Utilities L96- Telecommunications L97-Utilities: General L98- Government Policy L99- OtherProfessor C. Magee, 2006Page 15
Economics Structure Sub-division of the economy National boundaries Industry classifications (SIC and now NASIC) arehierarchical with 5 levels How are these industry classifications arrived at? Partially Input/output relationships Broader abstractions that gather similarities at a higher level:for example- agriculture and extractive industries,manufacturing and service Market similarities: Chapter from Mantegna and Stanley Sub-division of the field of study ( e.g. publications) JEL Classification SystemDecomposition Approaches to Determining StructureProfessor C. Magee, 2006Page 16
Economics Structure Sub-division of the economy National boundaries Industry classifications (SIC and now NASIC) arehierarchical with 5 levels How are these industry classifications arrived at? Partially Input/output relationships Broader abstractions that gather similarities at a higher level:for example- agriculture and extractive industries,manufacturing and service Market similarities: Chapter from Mantegna and Stanley Sub-division of the field of study ( e.g. publications) JEL Classification SystemAggregation Approaches to Determining StructureProfessor C. Magee, 2006Page 17
Structure in Biology Sub-division of the field of study ( e.g. publications) No parallel found to JEL Classification SystemProfessor C. Magee, 2006Page 18
Categorical Topics from on-line BiologyText (19 given!) Evolution Animals General Science Behavior Genetics Biochemistry Immunology Cancer Microbiology Cell Biology Molecules Chemistry Physiology Diversity of Life Plant Biology DNA and RNA Viruses Ecology DevelopmentProfessor C. Magee, 2006Page 19
Structure in Biology Sub-division of the field of study ( e.g. publications) No parallel found to JEL Classification System Textbook topics are at best approximately homologous withthe activities in the field. Areas such as bioinformatics,mathematical modeling and observational techniquesreceive relatively more listings than for economics sowould probably appear on an equivalent to the JELClassification. Also, it is clear that systematics is an old andstill very active field not much covered in modernundergraduate textbooks. Paleontology is not part ofbiology but is essential to Biology Systematics. Sub-division (and aggregation) of the objects studied Extensive, historically dominant in field and still veryactiveProfessor C. Magee, 2006Page 20
Biological Classification History Aristotle (had lots of graduate students?) identified hundreds ofdiffering kinds of animals and plants based upon morphologyand function. John Ray: 1628-1705, [Cambridge UK] restarted biologicalclassification based on morphology and structural similarity. Linnaeus 1707-1778, [Swedish] is the most recognized biologicalclassifier. He introduced the idea of a unified hierarchical tree (7levels) and the “binomial” nomenclature for species and both ofthese still stand. However, the characteristics he used forclassification (sexual reproduction modes and organs) are now not asimportant as the ones used by Ray. Aggasiz, Paley, Sedgwick, Buckland (19th century): paleontology,embryology, ecology, and biogeography all became important inclassification through their work. Robert Whitaker in 1969 proposed 5 kingdoms whereas Linnaeusonly had 2 (plants and animals).Professor C. Magee, 2006Page 21
Lecture Outline Some structural aspects of economics and relationships toprevious structural characterizations Abbreviated History of Systematics in Biology Some current thinking about biological systematics and recentindications of a new synthesis among molecular biology,evolutionary biology and systematics Biological Evolvability (and flexibility) Innovation and evolutionary thinkingProfessor C. Magee, 2006Page 22
Biological Classification 5 Kingdoms: Plants, Animals, Fungi, Prokaryotes, Protists The 7 layer hierarchy continues: Phylum (for animals) and Divisions (for plants and Fungi) Class Order Family Genus Specie (named by genus Latinized specific) The bottom 2 layers and the top are fairly well specified butthe middle is a real muddle and extremely hard to makesensible in all 5 kingdoms. Darwin changed the way of thinking about the hierarchicaltree and thus an evolutionist framework with alternatives andtestability has emerged. The systematists (also cladists) arenow biology’s “high volume” classifiers with the kinds ofproblems discussed in the Gould reading for todayProfessor C. Magee, 2006Page 23
(Phylogenetic) Cladistics Cladistics is now accepted as the best method available forphylogenetic analysis, for it provides an explicit and testablehypothesis of organismal relationships.Three assumptions of cladistics Any group of organisms are related by descent from acommon ancestor. There is a bifurcating pattern of cladogenesis. Change in characteristics occurs in lineages over time.A Clade is a monophyletic taxon; a group of organismswhich includes the most recent common ancestor of all of itsmembers and all of the descendants of that most recentcommon ancestor. From the Greek word "klados", meaningbranch or twig.The basis for similarity is shared derived characteristicsamong the members of the cladeProfessor C. Magee, 2006Page 24
V. lacunateraVogesina aspera"Vogesina" gemellusPalpebrops donegalensis"Palpebrops" goeldiM. buddaeaMalvinella haugi"Malvinella" australisBouleiaParabouleiaP. pujraviiPlesiomalvinellabouleiAn Example CladogramFigure by MIT OCW. After Eldredge.An evolutionary tree or "cladogram," showing relationships among a group of Devoniantrilobites from the southern hemisphere. This diagram is typical of the thousands ofcladograms published every year by systematists studying the evolutionary relationshipsof fossil and recent organisms. In the majority of cases, it is possible to specify withconfidence which species are most closely related.Source: Darwin, Discovering the Tree of Life, Niles Eldredge, page 235, 2005Professor C. Magee, 2006Page 25
The cladistic pattern of great apes andhumansOrangutanHumanGorillaChimpFigure by MIT OCW. After Gould and Monnier.Source: Hen’s Teeth and Horse’s Toes, Stephen Jay Gould, page 357, 1983 (reprinted from Natural History, drawing by Joe Le Monnier)Professor C. Magee, 2006Page 26
Structure in Biology Sub-division of the field of study ( e.g. publications) No parallel found to JEL Classification System Textbook Topics list OK but biology would be much moredifficult to structure usefully than is economics as it ismuch larger and not as insular. Sub-division (and aggregation) of the objects studied Body plans, morphology, sexual reproduction modes andorgans Paleontology, embryology, ecology, and biogeography Evolutionary relationships and Molecular Biology(particularly in regard to switches and regulatory genes)are now the main drivers for ongoing new systematicsfindings.Professor C. Magee, 2006Page 27
Summary observations on Structure inBiology and Economics Uniformity of closeness by separate criteria is not the usualcase (Gould- nature is more interesting than this- and so istechnology or humanity’s creations) Pure decomposability of all dimensions is rare (works for purechemical elements but not for mixtures –alloys) Categorization/abstraction is highly useful but cannot beexpected to be perfect Statics are not enough, deeper understanding arises throughunderstanding changes over time. Deeper biological understanding is now particularly comingabout by combination of embryology (development) and longterm change (evolution) – “EVO-DEVO”Professor C. Magee, 2006Page 28
Developmental Biology (ClassicalEmbryology with Molecular Biology) One of the most rapidly developing areas of understanding forbiology May yield important insights relative to the “Evolvability” ofcomplex, large-scale engineering systems Some Observations from simple animals: Embryos possess “site maps” very early-cells learn wherethey are and what type of cell they will be in the full form. “Tool-kit genes” establish longitude, latitude and “mark thespot” of future appendages in the earliest embryo Genes that encode proteins are 1.5% of DNA butregulatory material make up another 3% This regulation is best thought of as a “switch”Professor C. Magee, 2006Page 29
The Role of Gene RegulatorySwitches in Development Individual switches are long sequences of DNA bound by alarge number and variety of proteins which can activate orsuppress gene transcription. Switches “compute” the input ofmultiple proteins and convert complex sets of inputs intosimpler 3D on/off patterns of gene expression. A single gene can be controlled by multiple switches so that asingle gene is used differently in many places (and times)during development. The makeup of every switch is different but they are composedof “reused” signature sequences of DNA that bind variousproteins in different ways. Simply varying the position of a few signature sequencesopens up a combinatorially large (cornucopia) number ofswitch varieties There has been good experimental confirmation of the actionof these switches (in flies) as “GPS integrators”.Professor C. Magee, 2006Page 30
The Role of Gene RegulatorySwitches in Development II Experimental work on flies has also shown that each stripe in a fly iscontrolled by its own unique switch. Thus, Turing’s “mathematicallybeautiful theory” of the organization of periodic patterns acrosswhole structures was not found but instead that the periodic patternsare the composite of numerous individual elements. The tool kit genes are used over and over in different contextsdifferently due to differing switches with spectacular diversity andexquisite geographic specificity. Hierarchies of genes and switches operate in development. Forexample, one switch at the level of the Hox gene which acts in eachbody segment and other switches that are recognized by HoxProteins that control how other genes are expressed in specificmodules. The forms of animals and body parts are not due to specific switchesbut“large sets of interconnected switches and proteins form ‘localcircuits’ that govern the development of complex structures.Animal architecture is a product of genetic regulatory networkarchitecture.” (from S. Carroll P 129 italics added)Professor C. Magee, 2006Page 31
An example fragment of the regulatory dActivators and repressors act on switches. Arrows are activation events, lines ending in flatdenote repression. Note the multiple tiers or hierarchy that enter into this regulation.GENETIC WIRING DIAGRAM OF REGULATORY LOGICFigure by MIT OCW. After Carroll.Source: Endless Forms Most Beautiful, Sean B. Carroll, page 129, 2005Professor C. Magee, 2006Page 32
The connection between devo and evo A paradox arose when it was discovered that the same or verysimilar tool kit genes were found in very disparate animalshow can the same genes be used to build such different(endless and beautiful) forms? A clue to resolving this came with the discovery of arrays ofswitches that enable individual tool kit genes to be used againand again in one animal in slightly or dramatically differentways in serially repeated structures. “Switches enable the same tool kit genes to be used differentlyin different animals.” (S. Carroll, EVO-DEVO, p131) The major evolutionary step was the Cambrian explosionbeginning about 540 million years ago –bilateralism and acornucopia of increasingly complex body types evolvedover the next 10-20 million yearsProfessor C. Magee, 2006Page 33
ProtostomesDeuterostomesFigure by MIT OCW. After Carroll.Source: Endless Forms Most Beautiful, Sean B.Carroll, page 142, 2005Professor C. Magee, 2006Page ia
The connection between devo and evo A paradox arose when it was discovered that the same or verysimilar tool kit genes were found in very disparate animalshow can the same genes be used to build such different(endless and beautiful) forms? A clue to resolving this came with the discovery of arrays ofswitches that enable individual tool kit genes to be used againand again in one animal in slightly or dramatically differentways in serially repeated structures. “Switches enable the same tool kit genes to be used differentlyin different animals.” (S. Carroll, EVO-DEVO, p131) The major evolutionary step was the Cambrian explosionbeginning about 540 million years ago –bilateralism and acornucopia of increasingly complex body types evolvedover the next 10-20 million years “The main story in the Cambrian is that of evolvingdifferent kinds and numbers of repeated body parts.” p. 159 EVO-DEVO message: all genes for this explosion presentfor 50 million or more years earlier. P. 159Professor C. Magee, 2006Page 35
The chordate evolutionary tree and theexpansion of Hox clusters in vertebrateevolutionOne HoxclusterHox clusterduplicationHox cluster orGenome duplicationsFigu
Classification. Also, it is clear that systematics is an old and still very active field not much covered in modern undergraduate textbooks. Paleontology is not part of biology but is essential to Biology Systematics. Sub-division (and aggregation) of the objects studied Extens
Introduction of Chemical Reaction Engineering Introduction about Chemical Engineering 0:31:15 0:31:09. Lecture 14 Lecture 15 Lecture 16 Lecture 17 Lecture 18 Lecture 19 Lecture 20 Lecture 21 Lecture 22 Lecture 23 Lecture 24 Lecture 25 Lecture 26 Lecture 27 Lecture 28 Lecture
systematics. In fact, pre-Darwinian systematics as ahistorical science provides an invaluable resource for understanding what it means that systematics is essentially historical. Systematics is an ideal subject for understanding historical scientific methodology precisely because we
systematics. The purpose of this chapter is to introduce the basics: what a plant is, what systematics is, and the reasons for studying plant systematics. PLANTS WHAT IS A PLANT? This question can be answered in either of two conceptual w
Apr 18, 2013 · systematics, integrating phylogenetic signal from the population up based on DNA and through time based on direct observation rather than inference. Molecular systematics in the 21st century For several years, molecular systematics has been the dominant phylogenetic paradigm [1]. By t
Lecture 1: A Beginner's Guide Lecture 2: Introduction to Programming Lecture 3: Introduction to C, structure of C programming Lecture 4: Elements of C Lecture 5: Variables, Statements, Expressions Lecture 6: Input-Output in C Lecture 7: Formatted Input-Output Lecture 8: Operators Lecture 9: Operators continued
Unlocking Knowledge, Empowering Minds About MIT OpenCourseWare › MIT OpenCourseWare Free and open educational resource (Syllabi, lecture notes, videos, psets, exams, Java applets ) No credit, degrees, or faculty access 1.5 - 2 million visitors/month (including 10,000 HS students) Publishing 1
systematics-1 Evolution and Biodiversity Laboratory Systematics and Taxonomy by Dana Krempels and Julian Lee Recent estimates of our planet's biological diversity suggest that the species number between 5 and 50 million, or even more. To effective
1550-1950, which she curated with Anne Sutherland Harris for the Los Angeles County Museum of Art; the show was accompanied by the catalogue of the same title co-authored by both scholars. Linda Nochlin has written numerous books and articles focusing attention on social and political issues revealed in the work of artists, both male and female, from the modernist period to the present day .
