DNA compiler

In order to implement a DNA, RNA, protein and molecule compiler it seemed that understanding how LISP acts in great detail would be a good start. In order to study the course presented by MIT ( 6.001 Sussman ) , a ZIM wiki is created which references the lectures and concepts with links to the web, images, graphs, equations and notes. So that typing is a minimum, the shell script below was created to allow the temporary storage of the course videos for search. It is sometimes necessary to study in a non linear way and so the videos become a random access record until they have been completely reduced to concept notes and examples.

Many people have taken these same algorithmic concepts and incorporated them in other courses. The ideas presented there are especially applicable as the data RNA is also the function RNA in many circumstances. Though the entire biological system may be a design by successive approximation fit to a changing environment, the core elements are not ambiguous in their language. The proteome machinery is closer to a chaotic attractor and exhibits many of the evolutionary compromises in its action.

The overall process of using biological systems as effective computers, proceeds somewhat like the semiconductor industry. The first stage is to create the simplest element which can construct any other part of the system. In computers the hardware must be manufactured. Since the programming of DNA, RNA, protein systems can produce itself as an output, it provides a system which can be redesigned remotely as long as the raw materials and an energy source are present. It is the best fit for an exploratory craft. The advantages include the ability to recycle the system completely from an atomic level, complete flexibility of form and parallelism, self powering, ( usually ) non-toxic to life, and capable of autonomy.

The design need not incorporate those things that are so characteristic of life, like continuous motion. The design should be static in action without initiation and should consume no maintenance energy when not in use. Life constantly seeks advantage , however a constructed bio system has no such requirement as it will be recycled in any case and self design extension would be very much like implementing obfuscated code.

Since systems are considered to be isolated, they can be completely reduced to their molecular parts when a complete rewrite is necessary. The idea of contaminating a foreign planet with life is not a great risk as the designs would have no mechanism for self design. Life has self design mechanisms built in and so can become a risk because it is 3 billion year selected to survival and adaption.

#!/bin/bash
x=`cat index`

function show {
for i in `ls MIT*`
 do
 echo $i
done
}

cp /tmp/Flash* .

for i in `ls Flash*`
 do
  if [ $x -lt "10" ];then
   mv $i "MIT_6-001_Lecture0"$x".flv"
  else
   mv $i "MIT_6-001_Lecture"$x".flv"
  fi
done

x=$((x+1))
echo $x>index