Gard model
Encyclopedia
The GARD model
In the context of abiogenesis
, the Lipid-world suggests assemblies of simple molecules, such as lipids, can store and propegate information, thus undergo evolution
.
These 'compositional assemblies' have been suggested to play a role in the origin of life (OOL
). The idea is the information being transferred throughout the generations is compositional information - the different types and quantities of molecules within an assembly. This is different from the information of an RNA
or DNA
, which is the specific sequence of bases in such molecule.
Thus, the model is viewed as an alternative or an ancestor to the RNA world hypothesis.
The composition vector of an assembly is written as:
.Where 
are the molecular counts of lipid type i within the assembly, and NG is how many different lipid types exist (repertiore size).
The change in the count of molecule type i is described by:
and 
are the basel forward (joining) and backward (leaving) rate constants, βij is a non-negative rate enhancement exerted by molecule type j within the assembly on type i from the environment, and ρ is the environmental concentration of each molecule type.
The assembly current size is
. The system is kept away from equlibrium by imposing a fission action once the assembly reaches a maximal size, Nmax, usually in the order of NG. This splitting action produces two progeny of same size, and one of which is grown again.
The model is subjected to a Monte Carlo algorithm
based simulations, using Gillespie algorithm
.
and collaborators have chosen GARD as an archtypal metabolism-first realization. They have introduced selection coefficient into the model, which increase or decrease the growth rate of assemblies, depanding on how similar or dis-similar they are to a given target. They found that the ranking of the assemblies are un-affected by the selection pressure, and concluded that GARD does not exhibit Darwinian evolution.
In the context of abiogenesis
Abiogenesis
Abiogenesis or biopoesis is the study of how biological life arises from inorganic matter through natural processes, and the method by which life on Earth arose...
, the Lipid-world suggests assemblies of simple molecules, such as lipids, can store and propegate information, thus undergo evolution
Evolution
Evolution is any change across successive generations in the heritable characteristics of biological populations. Evolutionary processes give rise to diversity at every level of biological organisation, including species, individual organisms and molecules such as DNA and proteins.Life on Earth...
.
These 'compositional assemblies' have been suggested to play a role in the origin of life (OOL
OOL
OOL may refer to:* Olivia O'Leary, Irish journalist, writer and current affairs presenter* Optimum Online, an Internet service provider in the United States* Gold Coast Airport in Gold Coast City, Queensland, Australia* Object-oriented language...
). The idea is the information being transferred throughout the generations is compositional information - the different types and quantities of molecules within an assembly. This is different from the information of an RNA
RNA
Ribonucleic acid , or RNA, is one of the three major macromolecules that are essential for all known forms of life....
or DNA
DNA
Deoxyribonucleic acid is a nucleic acid that contains the genetic instructions used in the development and functioning of all known living organisms . The DNA segments that carry this genetic information are called genes, but other DNA sequences have structural purposes, or are involved in...
, which is the specific sequence of bases in such molecule.
Thus, the model is viewed as an alternative or an ancestor to the RNA world hypothesis.
The GARD model
GARD is a general kinetic model for homeostatic-growth and fission of compositional-assemblies, with specific application towards lipids.The composition vector of an assembly is written as:
.Where are the molecular counts of lipid type i within the assembly, and NG is how many different lipid types exist (repertiore size).The change in the count of molecule type i is described by:
and are the basel forward (joining) and backward (leaving) rate constants, βij is a non-negative rate enhancement exerted by molecule type j within the assembly on type i from the environment, and ρ is the environmental concentration of each molecule type.The assembly current size is
. The system is kept away from equlibrium by imposing a fission action once the assembly reaches a maximal size, Nmax, usually in the order of NG. This splitting action produces two progeny of same size, and one of which is grown again.The model is subjected to a Monte Carlo algorithm
Monte Carlo algorithm
In computing, a Monte Carlo algorithm is a randomized algorithm whose running time is deterministic, but whose output may be incorrect with a certain probability....
based simulations, using Gillespie algorithm
Gillespie algorithm
In probability theory, the Gillespie algorithm generates a statistically correct trajectory of a stochastic equation. It was created by Joseph L...
.
Selection in GARD
In 2010, Eors SzathmaryEörs Szathmáry
Eörs Szathmáry is a Hungarian theoretical evolutionary biologist at the late Collegium Budapest Eörs Szathmáry (born 1959) is a Hungarian theoretical evolutionary biologist at the late Collegium Budapest Eörs Szathmáry (born 1959) is a Hungarian theoretical evolutionary biologist at the late...
and collaborators have chosen GARD as an archtypal metabolism-first realization. They have introduced selection coefficient into the model, which increase or decrease the growth rate of assemblies, depanding on how similar or dis-similar they are to a given target. They found that the ranking of the assemblies are un-affected by the selection pressure, and concluded that GARD does not exhibit Darwinian evolution.
External links
- Doron Lancet homepage at Weizmann Institute of ScienceWeizmann Institute of ScienceThe Weizmann Institute of Science , known as Machon Weizmann, is a university and research institute in Rehovot, Israel. It differs from other Israeli universities in that it offers only graduate and post-graduate studies in the sciences....
, who is the inventor of GARD. - Origin of life (OOL) at the Weizmann Institute.