Constructing efficient ecosystems using optimization techniques

• US 20070043513A1
• Filed: 05/21/2004
• Published: 02/22/2007
• Est. Priority Date: 05/22/2003
• Status: Abandoned Application

• Current Assignee: Idaho Research Foundation, Inc.
• Original Assignee: Idaho Research Foundation, Inc.
• Inventors: Vandecasteele, Frederik
• Application Number:
  US10/557,859
• Publication Number:
  US 20070043513A1
• Time in Patent Office: Days
• US Class Current: 702/20
• CPC Class Codes: G06N 3/004 Artificial life, i.e. computing arrangements simulating life
• CPC Class Codes: G06N 3/126 Evolutionary algorithms, e.g. genetic algorithms or genetic programming
• CPC Class Codes: G06Q 10/04 Forecasting or optimisation specially adapted for administrative or management purposes, e.g. linear programming or "cutting stock problem" market predictions or forecasting for commercial activities G06Q30/0202

Abstract

A method for selecting groups of organisms to perform a predetermined function is disclosed. The method includes using the relative fitness of initial candidate groups of organisms for performing the function to select new groups of organisms that perform the function with greater efficiency than the initial candidate groups. In a working embodiment, a genetic algorithm and fitness testing of groups of organisms selected by the genetic algorithm are used to provide groups of organisms that can efficiently perform the predetermined function.

Claims

1. A method for selecting a group of organisms to perform a predetermined function, comprising:

measuring fitness values for performing the predetermined function for a first set of candidate groups of organisms;

deriving a second set of candidate groups of organisms from the first set using an optimization technique, the optimization technique using the fitness values of the groups in the first set to select the second set of groups;

measuring fitness values for performing the predetermined function for the groups in the second set; and

selecting a group of organisms from the second set of candidate groups of organisms to perform the predetermined function, wherein the group of organisms selected from the second set has a higher fitness value for performing the predetermined function than groups of organisms in the first set.

2. The method of claim 1, wherein the candidate groups of organisms also comprise amount and/or sequence of introduction information for the organisms in the group.

3. The method of claim 1, wherein the optimization technique comprises evolutionary computation.

4. The method of claim 3, wherein the evolutionary computation comprises a genetic algorithm, an evolution strategy, a genetic program, an evolutionary program, or an evolutionary algorithm.

5. The method of claim 4, wherein the evolutionary computation comprises a genetic algorithm.

6. The method of claim 1, wherein the first and second sets of candidate groups of organisms comprise microbial consortia.

7. The method of claim 1, wherein the first and second sets of candidate groups of organisms comprise groups of crop plants for intercropping.

8. The method of claim 1, wherein the predetermined function comprises an ecological function.

9. The method of claim 8, wherein the ecological function comprises increased or decreased diversity, biomass production, exploitation of available resources, stimulation of growth of other organisms, or inhibition of growth of other organisms.

10. The method of claim 1, wherein the predetermined function comprises an industrial function.

11. The method of claim 10, wherein the industrial function comprises energy production, a chemical reaction, bioremediation, biodegradation or waste recycling.

12. A method for selecting a consortium of microorganisms to perform a predetermined function, comprising:

generating an initial population of chromosomes, the chromosomes encoding groups of microorganisms selected from a panel of microorganisms;

determining fitness values for performing the function for the groups encoded by the chromosomes;

selecting chromosomes from the initial population in proportion to their fitness values;

exchanging pieces of the selected chromosomes and mutating the selected chromosomes to produce a second population of chromosomes;

determining fitness values for performing the function for the groups encoded by the chromosomes in the second population; and

selecting to perform the function a group encoded by a chromosome in the second population having a fitness value greater than one or more other groups encoded by chromosomes in the second population.

13. The method of claim 12, wherein the chromosomes further encode information on the relative amounts and/or sequence of introduction of the organisms encoded by the chromosomes.

14. The method of claim 12, wherein the function comprises biomass production, fermentation, biodegradation or bioremediation.

15. The method of claim 14, wherein the function comprises biomass production.

16. The method of claim 12, wherein the function comprises bioremediation.

17. The method of claim 16, wherein the function comprises bioremediation of an azo dye or pentachlorophenol.

18. A method for selecting a group of organisms to perform a predetermined function, comprising:

selecting an initial set of candidate groups of organisms, where the individual organisms in the groups of organisms in the set are selected from a panel of organisms;

selecting a second set of candidate groups of organisms for the purpose of performing the function using a genetic algorithm, the genetic algorithm using experimentally determined fitness values determined for the groups of organisms of the initial set to select the second set;

determining fitness values for the second set of candidate groups of organisms; and

selecting a group of organisms to perform the function from the second set of candidate groups of organisms.

19. The method of claim 18, wherein the panel or organisms comprises a panel of microorganisms.

20. The method of claim 18, wherein the groups of organisms are microbial consortia.

21. The method of claim 18, wherein the candidate groups further comprise amount and/or sequence of introduction information for the organisms in the candidate groups.