Biomedical Engineering Reference
In-Depth Information
The difference between the two approaches can be appreciated with parallel approaches in
archaeology. When a fossilized skeleton of a small animal is discovered, one approach to
reconstructing the physical structure of the animal and its lifestyle is to reason from first principles,
using the size, arrangement, thickness of the various bones, the size of the brain case, and other
physical indicators, such as the bowing of the long bones (which indicate the amount of musculature
present). Wear patterns on the teeth might suggest a diet rich in grains, and the presence of canines
may suggest the animal was omnivorous.
The second approach to assessing the fossil of the extinct animal is to compare the skeleton with
those of known animals. The leg and arm bones may approximate those of small modern monkey, for
example. The teeth may approximate those of a modern primate, with large, flat molars and
prominent canines. The relative size of the brain case, when compared to present-day monkeys,
might give an indication of the relative intelligence and social lifestyle of the extinct animal, based on
current primates.
Comparing fossilized skeletons of animals with those of modern animals is frequently practiced
because it's easy, rapid, and to the best of our knowledge, fairly accurate. Reasoning from first
principles is usually reserved for those cases where there is nothing resembling the newly discovered
fossil in the current fossil record. In many cases, the methods overlap and complement each other.
For example, first principles may be used to reconstruct the general body shape and stature of the
extinct animal, but give no indication of the skin or hair coloring. However, by extrapolating current
behavior and habitat knowledge of current species, a good guess can be made as to the composition
and color of the skin, fur, or feathers.
Similarly, in bioinformatics, ab initio and heuristic methods of determining protein structure are
commonly used in parallel or sequentially because of the accuracy limitations of either approach
when used alone. For example, hand editing is commonly applied to ab initio data to improve the
accuracy of the results. The primary methods used in the two basic approaches are reviewed here,
with an emphasis on the underlying modeling and simulation techniques involved in each method.
Ab Initio Methods
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