Bioengineers Simulate Human Metabolism

Some bioengineers at UCSD are building a model to simulate parts of human metabolism.

Bioengineering researchers at UC San Diego have painstakingly assembled a virtual human metabolic network that will give researchers a new way to hunt for better treatments for hundreds of human metabolic disorders, from diabetes to high levels of cholesterol in the blood. This first-of-its-kind metabolic network builds on the sequencing of the human genome and contains more than 3,300 known human biochemical transformations that have been documented during 50 years of research worldwide.

Note that these people are engineers, not scientists. They are treating the human body as just another complex system to engineer. They are using simulation just as engineers simulate airplanes, cars, and other systems designed by humans. Their simulations are a prelude to efforts to re-engineer the human body.

Simulations allow more rapid testing of much larger combinations of conditions. For human bodies simulations will allow testing of drugs and other treatments without need for the huge sums of money used in real human trials and also without the need to wait for lots of real wall clock time to go by. Plus, simulations can check out dangerous scenarios that would be far too risky to try with real humans.

An increasing portion of all biomedical research and development will take place in simulations. The cost of computing will continue to decline as the software becomes more complex and the data from real lab experiments feed in to make the models increasingly more realistic.

The simulation can predict the behavior of actual human cells.

In a report in the Proceedings of the National Academy of Sciences (PNAS) made available on the journal's website on Jan. 29, the UCSD researchers led by Bernhard Ø Palsson, a professor of bioengineering in the Jacobs School of Engineering, unveiled the BiGG (biochemically, genetically, and genomically structured) database as the end product of this phase of the research project. Each person's metabolism, which represents the conversion of food sources into energy and the assembly of molecules, is determined by genetics, environment, and nutrition. In a demonstration of the power and flexibility of the BiGG database, the UCSD researchers conducted 288 simulations, including the synthesis of testosterone and estrogen, as well as the metabolism of dietary fat. In every case, the behavior of the model matched the published performance of human cells in defined conditions.

This simulation is limited to known interactions and transformations done by cellular components. As more interactions become discovered and characterized these additional pieces of the puzzle can get added to existing simulations such as this one at UCSD. Fortunately, biochips which measure proteins and genes keep getting more powerful. For example, see my post Chip Measures Protein Binding Energies In Parallel