Re: "Algorithms" in Molecular Biology?

In general algorithms do not fit under the topic of math. You can see
this when mathematicians try to take a beginning algorithms course, and
think the equals sign means equality. In algorithms there is not
equality, there is however assignment. Take this X whatever it is, and
make it Y what ever that is. Of course you can make an algorithm which
through a series of steps entails the equality relationship or equality
class, but you can do so much more with algorithms. And also for
logicians will sometimes think that assignment is as implication, and
it is not either, however you can compose an algorithm which generates
the desired implication behaviours and tests for tautology or whatever.

I have a 1000 page book on algorithms, this book is used in most
computer science theory courses. I wish it had more Machine Learning,
which have more of the scientific algorithms, and a methodology to
determine which algorithms are better than others in terms of accuracy
and precision in addition to runtime complexity and computability. "An
Introduction to Algorithms", by cormen, leiserson and rivest. Defines
an algorithm thusly, "Informally, an algorithm is any will-defined
computational procedure that takes some value, or set of values, as
input and produces some value or set of values as output.

Furthermore they emphasize the relationship between inputs and outputs.
An application to biology is, that the cell is a black box, which
takes nutrients and produces wastes, at least one of the components of
living processes, as taught in my high school biology course.

I guess making a pizza, folding DNA or generateing proteins would fit
under that definition of an algorithm. Biological process take DNA
unfolded, through a sequence of parallel steps generate a folded DNA.


.

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