Modeling Biotic Factors: Testing Understanding

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Modeling Biotic FactorsTesting Understanding
XKCO2L4XKCO24(NZ)(EXP(0.05TCC(NZ,NY,NX)-1.
5)) CO24CO2L(NZ,NY,NX) C4ACIDT0.0
DO 900 NB1,NBR(NZ,NY,NX) DO 800
K1,KLEAF(NB,NZ,NY,NX) C4ACID(K,NB)0.0
COMPL4(K,NB)0.0
IF(ARLF(K,NB,NZ,NY,NX).GT.1.0E-64)THEN
WSDN(K,NB)AMIN1(10.0,WSLF(K,NB,NZ,NY,NX)/
ARLF(K,NB,NZ,NY,NX)) VCDN4(K,NB)PEPC(NZ)
WSDN(K,NB) VCGRO4(K,NB)VCMX4(NZ)VCDN4(K,N
B) VGRO4(K,NB)VCGRO4(K,NB)(CO24
/(CO24XKCO2L4)) ETDN4(K,NB)CHL(NZ)WSDN(K
,NB) ETGRO4(K,NB)ETMX(NZ)ETDN4(K,NB)TFN1
CBXN4(K,NB)(CO24-COMPL4(K,NB))
/(ELEC(NZ,1)CO2410.5COMPL4(K,NB)) DO
700 LNC,1,-1 IF(ARLFL(L,K,NB,NZ,NY,NX).GT
.1.0E-64)THEN DO 600 N1,4
SURFX(N,L,K,NB,NZ,NY,NX)SURF(N,L,K,NB,NZ,NY,NX)
CF(NZ)FC34(NZ,1) DO 500
M1,4 IF(SURFX(N,L,K,NB,NZ,NY,NX).GT.0.
0)THEN IF(PAR(N,M,L,NZ,NY,NX).GT.0.0)T
HEN PARXQNTMPAR(N,M,L,NZ,NY,NX)
PARJPARXETGRO4(K,NB)
ETLF4(PARJ-SQRT(PARJ2-CURV4PARX
ETGRO4(K,NB)))/CURV2
EGRO4ETLF4CBXN4(K,NB)
VL4AMIN1(VGRO4(K,NB),EGRO4)
C4ACID(K,NB)C4ACID(K,NB)

• Talbot J. Brooks
• Asst. Research Professional
• ASU Dept. of Geography

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Overview and objectives

• Why do we model the biosphere?
• What approaches are available?
• What tools are available?
• What are the limitations?
• Daisy World A simple, but elegant approach to
  modeling
• Why is it so hard Modeling Photosynthesis
• An introduction to the processes
• Approaches an example
• Summation

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Why do we model biotics?

• To evaluate our understanding of the processes
  used within living organisms
• To evaluate our understanding of how living
  organisms interact with each other
• To understand how living organisms cope with
  their environments
• To understand how living organisms impact our
  climate/world

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Approaches

• Empirical
• Based primarily on cause-effect scenarios
• For example, given x number of heating degree
  days, a plant will grow by y amount
• Mechanistic
• Physics and math based
• Treat like a chemical reaction x number of
  reagents with y co-factors yields z product
• For example, x photon flux density hits y number
  of chlorophyll a molecules which are at a
  temperature of z.

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Different approaches serve different masters

• Empirical approach
• Tend to be easier to understand, therefore more
  widely used
• Relatively inexpensive to run
• Sometimes incorporated into more complex models
  - frequently done with climate modeling
• Examples
• How much to water you lawn reports
• Crop yield predictions used by financial groups

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Tools of the trade

• Empirical approach
• Programming languages
• Likely use VB, Visual C, Java
• Canned applications
• GIS (ESRIs Model Builder)
• AutoCAD
• Most applications/runs can be performed on a
  typical desktop computer
• Note that some of these approaches are static!

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Mechanistic tools

• Programming languages
• FORTRAN, C, Pascal, Cobal (business world), and
  some Unix scripting
• Does not use a canned applications
• Most applications/runs require large computer
  resources
• Models can be used in a dynamic fashion

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Mechanistic Approach

• Numerically intensive
• More likely to use scaling of processes with the
  model
• Expensive to run
• Often require a ton of input data to initialize
  the model
• Similar to Unix expert systems designed and
  used by experts environments are not user
  friendly
• Most frequently used for
• What if scenarios
• Theory validation
• Examples
• Sorkam and Ceres crop models
• Ecosys ecosystem growth model

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Limitations

• Empirical
• Accuracy often rapidly degrades with time
• Limited flexibility of application
• Fixed formats
• Mechanistic
• High overhead/cost
• Nerd factor
• Requires intensive validation for acceptance

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Daisyworld handout and demonstration

• http//www.acad.carleton.edu/ curricular/GEOL/Dave
  STELLA/ Daisyworld/daisyworld_model.htm
• http//www.gingerbooth.com/courseware/daisy.html

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Photosynthesis

• Introduction to fundamental processes
• An example
• Overview of diversity a few cool case studies
  that really screw things up

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Photosynthesis

• The process by which ALL carbon in living things
  is captured
• It is the capture of light energy and subsequent
  storage of that energy in biochemical form
• Stored biochemical energy is then used to make
  biomolecules (carbs, proteins, etc..)
• Generally follows the following equation
• 6 CO2 12H2O light? C6H12O6 6O26H2O
• Start counting the variables that go into
  modeling photosynthesis

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Anatomy of a leaf
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Photosynthesis requires energy!
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Actually runs in 2 major steps

• Light reactions light is used to generate a
  chemiosmotic gradient across a biomembrane.
  Gradient drive production of ATP, the energy
  storage molecule of all living things (kinda like
  a battery)
• Light independent reactions Energy stored in
  ATP is used to assimilate carbon into biomolecues

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The light reactions

• Chlorophyll is the primary light gathering
  pigment for most photosynthetic organisms.
• Carotenoids are protection pigments that prevent
  chlorophyll and the photosynthetic apparatus from
  being damaged.
• Both chlorophylls and carotenoids act in concert
  as antenna complexes.
• Solar energy, captured by many pigment molecules,
  flows to the reaction center, similar to rain
  drops collecting on a funnel.
• Through a complex set of electron transfers and
  chemical reactions, protons are released in the
  lumen.
• Chemiosmotic gradient dictates that the protons
  will flow towards the stroma and drive ATP
  synthesis.

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A few illustrations to help out
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(No Transcript)
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How photon capture works
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Its predictable Determining energetic
capacitance using fluorescence
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Chlorophyll activity for normal irradiance
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Light reactions take-home message

• The efficiency of photosynthesis, as described by
  reaction center activity, is directly dependant
  upon pigment concentration.
• The rate at which the process occurs is dependent
  not only upon light intensity, but the efficiency
  of all involved mechanisms and molecules
• Environmental stress, eg., limiting NPK and water
  will directly impact the formation of
  biomolecules used in the above and therefore
  reduce photosynthetic capacitance

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Light independent reactions

• Occur in the absence of light
• Require chemically stored energy generated from
  the light reactions
• Involve carbon fixation from bicarbonate (the
  available form in aquatic plants or as dissolved
  in the mesophyll in terrestrial plants)
• Generally occurs through 1 of 3 metabolic
  pathways
• C3
• C4
• Crassulacean Acid Metabolism (CAM)

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General pathway

• CO2 enters the leaf through the stomate
• CO2 equilibriates in the mesophyll as bicarbonate
• Bicarbonate is the form of carbon used by the C3
  and C4 PCR cycles!
• Temperature effects equilibrium of CO2 and
  bicarbonate

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C3 Photosynthetic Carbon Reduction (PCR) Cycle

• So named because the primary product is a
  3-carbon molecule called glyceraldehyde
  3-phosphate

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Significance of RuBisCO

• The primary carboxylating enzyme for C3 plants is
  Ribulose 1,5 bisphosphate carboxylase-oxygenase
  (RuBisCO)
• Rubisco can account for as much as 50 of
  soluble leaf protein - as such it is the most
  abundant protein in the world!
• The active binding site of this enzyme can be
  occupied by either CO2 or O2

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C4 Cycle uses carbon concentrating mechanism and
structural modification
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Kranz anatomy
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The geography of it all

• All photosynthetic types have been reported on
  every continent except Antarctica, in every
  ocean, and in freshwater
• Of the 275,000 species of vascular plants, 93
  are estimated to be C3 whereas 1, or about 2000
  species, are estimated to be C4 (the remaining 6
  are CAM)
• Land coverage for each subtype are remotely well
  documented, but indications are that speciation
  percentages are misleading
• Corn, sugarcane and sorghum are the major
  agronomic crops which use C4 photosynthesis.
• These crops may account for as much as 35-40 of
  cultivated land in North America (of which 40 of
  the land area is estimated to be cultivated). In
  other words, as much as 16 of North Americas
  land mass is occupied by C4 plants!

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The modelers woes

• Even if we can successfully model and scale
  processes from the biochemical to the landscape
  level, it is nearly impossible to capture the
  diversity
• Were we able to capture all of the diversity, no
  data exists by which we could validate the model
• Modeling living organisms requires an extensive
  background
• Computer science
• Biology
• Chemistry
• Physics
• Climatology/meteorology
• Mathematics

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C Determine photosynthetic type, implement C4
front end C in loops 900-gt500 or jump to C3 loops
2900-gt2500 C Loop structure is as follows C
900 branch level loop C 800 leaf level
loop C 700 layer level loop C 600
azimuth level loop C 500 inclination level
loop C 400 time step loop C
IF(ICTYP(NZ).EQ.4)THEN XKCO2L4XKCO24(NZ)(EXP
(0.05TCC(NZ,NY,NX)-1.5)) CO24CO2L(NZ,NY,NX)
C4ACIDT0.0 DO 900 NB1,NBR(NZ,NY,NX)
DO 800 K1,KLEAF(NB,NZ,NY,NX)
C4ACID(K,NB)0.0 COMPL4(K,NB)0.0
IF(ARLF(K,NB,NZ,NY,NX).GT.1.0E-64)THEN
WSDN(K,NB)AMIN1(10.0,WSLF(K,NB,NZ,NY,NX)/
ARLF(K,NB,NZ,NY,NX))
VCDN4(K,NB)PEPC(NZ)WSDN(K,NB)
VCGRO4(K,NB)VCMX4(NZ)VCDN4(K,NB)
VGRO4(K,NB)VCGRO4(K,NB)(CO24
/(CO24XKCO2L4)) ETDN4(K,NB)CHL(NZ)WSDN(K
,NB) ETGRO4(K,NB)ETMX(NZ)ETDN4(K,NB)TFN1
CBXN4(K,NB)(CO24-COMPL4(K,NB))
/(ELEC(NZ,1)CO2410.5COMPL4(K,NB)) DO
700 LNC,1,-1 IF(ARLFL(L,K,NB,NZ,NY,NX).GT
.1.0E-64)THEN DO 600 N1,4
SURFX(N,L,K,NB,NZ,NY,NX)SURF(N,L,K,NB,NZ,NY,NX)

CF(NZ)FC34(NZ,1) DO 500 M1,4
IF(SURFX(N,L,K,NB,NZ,NY,NX).GT.0.0)THEN
IF(PAR(N,M,L,NZ,NY,NX).GT.0.0)THEN
PARXQNTMPAR(N,M,L,NZ,NY,NX)
PARJPARXETGRO4(K,NB)
ETLF4(PARJ-SQRT(PARJ2-CURV4PARX
ETGRO4(K,NB)))/CURV2
EGRO4ETLF4CBXN4(K,NB)
VL4AMIN1(VGRO4(K,NB),EGRO4)
C4ACID(K,NB)C4ACID(K,NB)
VL4SURFX(N,L,K,NB,NZ,NY,NX)TAUS(L1,NY,NX)
C4ACIDTC4ACIDT
VL4SURFX(N,L,K,NB,NZ,NY,NX)TAUS(L1,NY,NX)
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World record holders are model killers!

• E. farinosa (brittlebush) highest recorded
  transpiration rate up to 10 gallons of water
  per day
• A. palmerii (pokeweed) highest known
  photosynthesis rate up to 304 grams of CO2 per
  square meter of leaf area per day (or about 3-4
  kg per plant)

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Geographic inspiration Encilia Farinosa
(brittlebush)

• During the winter, E. farinosa has relatively
  large green leaves.
• Photosynthesis occurs at is annual maximum rate.
• Leaf absorptance of total solar radiation is
  0.50
• Leaf surface is said to be glabrate.

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Trichomes!

• During the summer, leaves are small and have a
  gray appearance
• Trichomes, pictured at right, are three celled
  structure that shield the surface of the leaf.
• Total solar absorptance is 0.09

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Another cool example Yucca brevifolia (Joshua
Tree)
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Adapted to solar zenith angle
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A prickly final example Cholla
As some of us have had the misfortune of
experiencing, cholla are covered with needles
that reduce incident solar radiation by as much
as 60
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Conclusion

• How many variables did you come up with?
• Modeling is as much an art as a science
• Must learn when to employ which approach
• Must understand assumptions being made
• Must be creative
• Biotic factors greatly impact climate/weather
  modeling
• Carbon, nitrogen, and water cycles
• Albedo
• Surface energy balance