Metaphors in systems biology-A grid of super-computers
the human species is a grid of super-computers, each human individual is a super computer, each cell in a human body is a node of the super-computer, each individual molecule is a central processing unit (CPU), each protein type is a floating-point operation (or FLOP) within the CPU, each gene is a byte and each bit is a nucleotide.
Further based on a rough estimation they argue that systems biology at this level is unattainable with current technology. Basically they assumed that if there are 6×109 humans, with 1013 cells each, with 105 copies per protein type, with 3×105 protein types, 3×104genes, encoded by 104 nucleotides each, then a human species-level grid equivalent would correspond to 6×109 super-computers, 6×1022 nodes, 6×1027 CPUs, 1.8×1033 FLOPs, 5.4×1037 bytes and 5.4×1041 bits, which seems to be quite unrealistic. Forget about whole body simulation even whole cell simulation at this scale is not possible based on currently available computing infrastructure. Further they suggest that
The analogy is not entirely accurate, yet it forms a useful connection to the field of computer science and engineering. Without providing references or reviewing this subject, it is worth remembering that computer science has also been inspired by biology. Terms such as memory, virus, genetic algorithm abound. Our example discusses a naïve metaphor with a familiar face, namely computer systems and information storage. By taking a vague notion and transforming it to something amenable to estimation, it is evident that some of the aspirations of systems biology at this grand scale might simply be unattainable.
References:
OUZOUNIS, C., & MAZIERE, P. (2006). Maps, books and other metaphors for systems biology Biosystems, 85 (1), 6-10 DOI: 10.1016/j.biosystems.2006.02.007
8 Responses to “Metaphors in systems biology-A grid of super-computers”
Latest Tweets
-
Dear Entrepreneur, CXO of unknown start-up with uncertain business model, be grounded and humble. cheersFebruary 10, 2012 at 2:53 am -
Apache Giraph, a framework for large-scale graph processing on Hadoop, reaches 0.1 milestone http://t.co/ymaoSXtTFebruary 10, 2012 at 1:57 am
-
Got this today, nice collection of Studio Ghibali Songs. Yeee http://t.co/mtauzVI7February 10, 2012 at 1:46 am
It’s an interesting mental model — but what I’m astonished at is even within one cell (using the numbers you have above that translates into ~10^10 protein molecules), the number of variables is staggering. Even if each protein is one byte (which is ridiculous considering how much information is packed into the primary sequence, secondary/tertiary/quarternary structure, concentration, covalent modifications, etc), that is roughly ~10 Gb!
Hi Ben, I agree with you opinion that this model seems to be over simplification of complexity of biological system, also their calculation is not very accurate but it’s just a rough sketch to prove the fact that Multi-scale simulation of biological systems is tedious task due to lacking resources and funding , and not because our desire to do so.
Abhishek, I apologize if I wasn’t clear — I wasn’t criticizing the model at all. I am actually quite astonished that, just to deal with protein levels in a cell, you are dealing with 10 GB of information per “state” (let alone the massive scale of modeling the human species as a whole)
Sorry about that- I stuck in numbers, and missed the real massage. Indeed the numbers are huge so the challenges.
Metaphors in systems biology-A grid of super-computers: Using metaphors to explain complex scientific phenomenon.. http://tinyurl.com/lvhv42
Metaphors in systems biology-A grid of super-computers: Using metaphors to explain complex scientific phenomenon.. http://tinyurl.com/lvhv42
Metaphors in systems biology-A grid of super-computers http://tinyurl.com/lvhv42
Metaphors in systems biology-A grid of super-computers http://tinyurl.com/lvhv42