TY - JOUR
T1 - Computing life
T2 - Add logos to biology and bios to physics
AU - Kolodkin, Alexey
AU - Simeonidis, Evangelos
AU - Westerhoff, Hans V.
N1 - Funding Information:
We thank the BBSRC , EPSRC (BBD0190791, BBC0082191, BBF0035281, BBF0035521, BBF0035521, BBF0035361, BBG5302251, SySMO), EU-FP7 (BioSim, NucSys, EC-MOAN), ZON-MW (91206069) and other funders for systems biology support ( http://www.systembiology.net/support ). HW and AK thank Fred Boogerd and Frank Bruggeman for fruitful discussions. AK and ES acknowledge funding from the Luxembourg BioTech Initiative.
PY - 2013/4
Y1 - 2013/4
N2 - This paper discusses the interrelations between physics and biology. Particularly, we analyse the approaches for reconstructing the emergent properties of physical or biological systems. We propose approaches to scale emergence according to the degree of state-dependency of the system's component properties. Since the component properties of biological systems are state-dependent to a high extent, biological emergence should be considered as very strong emergence - i.e. its reconstruction would require a lot of information about state-dependency of its component properties. However, due to its complexity and volume, this information cannot be handled in the naked human brain, or on the back of an envelope. To solve this problem, biological emergence can be reconstructed in silico based on experimentally determined rate laws and parameter values of the living cell.According to some rough calculations, the silicon human might comprise the mathematical descriptions of around 105 interactions. This is not a small number, but taking into account the exponentially increase of computational power, it should not prove to be our principal limitation. The bigger challenges will be located in different areas. For example they may be related to the observer effect - the limitation to measuring a system's component properties without affecting the system. Another obstacle may be hidden in the tradition of "shaving away" all " unnecessary" assumptions (the so-called Occam's razor) that, in fact, reflects the intention to model the system as simply as possible and thus to deem the emergence to be less strong than it possibly is. We argue here that that Occam's razor should be replaced with the law of completeness.
AB - This paper discusses the interrelations between physics and biology. Particularly, we analyse the approaches for reconstructing the emergent properties of physical or biological systems. We propose approaches to scale emergence according to the degree of state-dependency of the system's component properties. Since the component properties of biological systems are state-dependent to a high extent, biological emergence should be considered as very strong emergence - i.e. its reconstruction would require a lot of information about state-dependency of its component properties. However, due to its complexity and volume, this information cannot be handled in the naked human brain, or on the back of an envelope. To solve this problem, biological emergence can be reconstructed in silico based on experimentally determined rate laws and parameter values of the living cell.According to some rough calculations, the silicon human might comprise the mathematical descriptions of around 105 interactions. This is not a small number, but taking into account the exponentially increase of computational power, it should not prove to be our principal limitation. The bigger challenges will be located in different areas. For example they may be related to the observer effect - the limitation to measuring a system's component properties without affecting the system. Another obstacle may be hidden in the tradition of "shaving away" all " unnecessary" assumptions (the so-called Occam's razor) that, in fact, reflects the intention to model the system as simply as possible and thus to deem the emergence to be less strong than it possibly is. We argue here that that Occam's razor should be replaced with the law of completeness.
KW - Observer effect
KW - Occam's razor
KW - Silicon human
KW - Strong emergence
KW - Systems biology
UR - http://www.scopus.com/inward/record.url?scp=84878155897&partnerID=8YFLogxK
U2 - 10.1016/j.pbiomolbio.2012.10.003
DO - 10.1016/j.pbiomolbio.2012.10.003
M3 - Article
C2 - 23103359
AN - SCOPUS:84878155897
SN - 0079-6107
VL - 111
SP - 69
EP - 74
JO - Progress in Biophysics and Molecular Biology
JF - Progress in Biophysics and Molecular Biology
IS - 2-3
ER -