2

2: What is a DNA-Molecule-Replication

Shaken formulation:

What is the DNA-Molecule-Replication ?

Answer

Process: a DNA-Molecule-Replication

Process Overview:

Definition:

A process by which a copy of a DNA molecule is made.
Alberts:ECB:G-6.

It is a kind of:

DNA-Replication

Its participants are:

object

Macromolecule
DNA-Molecule

instrument DNA-Polymerase-Replication-Enzyme

Process Details:

It is composed of the following subevents:

Replicon-Replication

Preconditions/postconditions:

preconditions the DNA-Polymerase-Replication-Enzyme mustn't be a Entity that plays a Instrument and that is broken
the following conditions will become false The result of the DNA-Molecule-Replication must be a Tangible-Entity.

Output actor fates:

Outputs:

result

DNA-Double-Strand
DNA-Molecule
DNA-Molecule

Question in KM

Template

What is <instance>?

Parameters

INSTANCE

INSTANCE

Code

	 
("p6: What is <instance>?

The answer is computed from the EXPLAIN function, which is the general
explanation function used in Shaken for objects and processes. It is
based on the use of Explanation Design Plans (EDPs). EDP structure the
way the infomation (based on slot values) is displayed to the
user. The leaves of this structure are VIEWS of the concept.

A view is a partial and specialized set of slot values of a particular
concept. These slot values are organized by accessors. Each
slot in the base KB is linked to a particular accessor, e.g. the slot
destination is linked to the accessor location.

The result of the explanation is displayed as a list. The
structure of the list follows the hierarchical structure of the
EDP."
 (defun answer-p6-data (instance expanded)
  (setq instance (intern instance :user))
  (let* ((explanation (rkf::list-explain 
		       `(("concept" . ,instance)
			 ("query-type" . ":explain-qn")
			 ("expanded" . ,expanded)
			 ))))
    `(,@explanation
      ("concept" . ,instance)
      ("query-type" . :explain-qn)
      (user::question-type user::p6)
      ("expanded" . ,expanded)))))


(defun list-explain (alist)
  (let* ((user::*show-comments* nil)
	 (*dictionary* nil)
	 (concept-name (util::alist-value alist "concept"))
	 (query-type-string (util::alist-value alist "query-type"))
	 (concept (coerce-concept (intern concept-name :user)))
	 (query-type (and query-type-string
			  (intern (read-from-string query-type-string) :keyword))))
    (if concept
	(let ((query-type (if (equal query-type :explain-qn)
			      (get-concept-query-type concept)
			    (or query-type
				(get-concept-query-type concept)))))
	  (list (cons "explanation" 
		      (list-edp (explain query-type concept alist) alist))
		(cons "question" (user::question-string query-type concept alist))
		(cons "dictionary" *dictionary*))))))

(defun explain (query-type concept alist)
  (when query-type
    (let* ((edp (select-edp query-type))
	   (explanation-plan (construct-node edp concept alist)))
      (apply-edp (get-node-type edp) edp explanation-plan)
      explanation-plan)))

Raw Answer

((values
  (<EDP>Process:  a DNA-Molecule-Replication
   (<EDP>Process Overview:
    (<EDP>Definition:
     (( A process by which a copy of a DNA molecule is made.)
      (Alberts:ECB:G-6.) ()))
    (<EDP>It is a kind of: (DNA-Replication))
    (<EDP>Its participants are:
     (<SLOT>object _Macromolecule990 _DNA-Molecule989)
     (<SLOT>instrument
      _DNA-Polymerase-Replication-Enzyme985)))
   (<EDP>Process Details:
    (<EDP>It is composed of the following subevents:
     (_Replicon-Replication984))
    (<EDP>Preconditions/postconditions:
     (<SLOT>preconditions
      <DEF>the DNA-Polymerase-Replication-Enzyme mustn't be a Entity that plays a Instrument  and that is broken)
     (<SLOT>the following conditions will become false
      <DEF>The result of the DNA-Molecule-Replication must be a Tangible-Entity.)))
   (<EDP>Output actor fates:
    (<EDP>Outputs:
     (<SLOT>result _DNA-Double-Strand988 _DNA-Molecule987
      _DNA-Molecule986)))))
 (concept . _dna-molecule-replication983)
 (query-type . explain-qn) (question-type p6) (expanded)
 (explanations
  ((_dna-molecule-replication983 instrument
    _dna-polymerase-replication-enzyme985
    ((a dna-polymerase-replication-enzyme
      (@ dna-replication instrument))))
   (_dna-molecule-replication983 object _macromolecule990
    ((a macromolecule with
      (instance-of
       ((possible-values polydeoxyribonucleotide
         dna-double-strand))))))
   (_dna-molecule-replication983 object _dna-molecule989
    ((a tangible-entity)
     (a dna-molecule (@ dna-molecule-replication object))))
   (_dna-molecule-replication983 subevent
    _replicon-replication984
    ((a replicon-replication
      (@ dna-molecule-replication subevent))))
   (_dna-molecule-replication983 result
    _dna-double-strand988
    ((a dna-double-strand with
      (has-part
       (((the polydeoxyribonucleotide has-part of
          (the dna-double-strand object of
           _dna-molecule-replication983))
         called the template strand)
        (a polydeoxyribonucleotide called
         daughter strand))))))
   (_dna-molecule-replication983 result _dna-molecule987
    ((a dna-molecule called DNA-Molecule-2 with
      (has-part
       (((the dna-strand has-part of
          (the dna-molecule object of
           _dna-molecule-replication983))
         called DNA-Strand-2
         (@ dna-molecule-replication result dna-molecule
          has-part))
        (a dna-strand called
         Daughter-Strand-Complementary-To-Strand-2 with
         (complement
          (((the dna-strand has-part of
             (the dna-molecule object of
              _dna-molecule-replication983))
            called DNA-Strand-2
            (@ dna-molecule-replication result dna-molecule
             has-part dna-strand complement))))
         (@ dna-molecule-replication result dna-molecule
          has-part))))
      (@ dna-molecule-replication result))))
   (_dna-molecule-replication983 result _dna-molecule986
    ((a tangible-entity)
     (a dna-molecule called DNA-Molecule-1 with
      (has-part
       (((the dna-strand has-part of
          (the dna-molecule object of
           _dna-molecule-replication983))
         called DNA-Strand-1
         (@ dna-molecule-replication result dna-molecule
          has-part))
        (a dna-strand called
         Daughter-Strand-Complementary-To-Strand-1 with
         (complement
          (((the dna-strand has-part of
             (the dna-molecule object of
              _dna-molecule-replication983))
            called DNA-Strand-1
            (@ dna-molecule-replication result dna-molecule
             has-part dna-strand complement))))
         (@ dna-molecule-replication result dna-molecule
          has-part))))
      (@ dna-molecule-replication result)))))))

Explanation

The DNA-Polymerase-Replication-Enzyme is instrument of the DNA-Molecule-Replication

KB rule (English):

The following rule was asserted for Concept DNA-Replication

The instrument of a DNA-Replication is: a DNA-Polymerase-Replication-Enzyme

Concept DNA-Molecule-Replication is a subconcept of concept DNA-Replication

KB rule (KM):
```
(every dna-replication has
 (instrument ((a dna-polymerase-replication-enzyme))))
```

The Macromolecule is object of the DNA-Molecule-Replication

KB rule (English):

The following rule was asserted for Concept

The object of a is: a Macromolecule with the following-properties:
- Its instance-of is possible-values Polydeoxyribonucleotide DNA-Double-Strand
Concept DNA-Molecule-Replication is a subconcept of concept

KB rule (KM):
```
(
 (a macromolecule with
  (instance-of
   ((possible-values polydeoxyribonucleotide
     dna-double-strand)))))
```

The DNA-Molecule is object of the DNA-Molecule-Replication

KB rule (English):

The following rule was asserted for Concept

The object of a is: a Tangible-Entity

Concept DNA-Molecule-Replication is a subconcept of concept

KB rule (KM):
```
( (a tangible-entity))
```
KB rule (English):

The following rule was asserted for Concept DNA-Molecule-Replication

The object of a DNA-Molecule-Replication is: a DNA-Molecule

KB rule (KM):
```
(every dna-molecule-replication has
 (object ((a dna-molecule))))
```

The Replicon-Replication is subevent of the DNA-Molecule-Replication

KB rule (English):

The following rule was asserted for Concept DNA-Molecule-Replication

The subevent of a DNA-Molecule-Replication is: a Replicon-Replication

KB rule (KM):
```
(every dna-molecule-replication has
 (subevent ((a replicon-replication))))
```

The DNA-Double-Strand is result of the DNA-Molecule-Replication

KB rule (English):

The following rule was asserted for Concept

The result of a is: a DNA-Double-Strand with the following-properties:
- Its parts are
  - the Polydeoxyribonucleotide part of the DNA-Double-Strand object of the DNA-Molecule-Replication called the template strand the Polydeoxyribonucleotide part of the DNA-Double-Strand object of the DNA-Molecule-Replication called the template strand
  - a Polydeoxyribonucleotide with the following-properties:
    - It is called daughter strand
    a Polydeoxyribonucleotide with the following-properties:
    - It is called daughter strand
Concept DNA-Molecule-Replication is a subconcept of concept

KB rule (KM):
```
(
 (a dna-double-strand with
  (has-part
   (((the polydeoxyribonucleotide has-part of
      (the dna-double-strand object of
       _dna-molecule-replication983))
     called the template strand)
    (a polydeoxyribonucleotide called daughter strand)))))
```

The DNA-Molecule is result of the DNA-Molecule-Replication

KB rule (English):

The following rule was asserted for Concept DNA-Molecule-Replication

The result of a DNA-Molecule-Replication is: a DNA-Molecule with the following-properties:
- It is called DNA-Molecule-2
- Its parts are
  - the DNA-Strand part of the DNA-Molecule object of the DNA-Molecule-Replication called dna-strand-2 the DNA-Strand part of the DNA-Molecule object of the DNA-Molecule-Replication called dna-strand-2
  - a DNA-Strand with the following-properties:
    - It is called Daughter-Strand-Complementary-To-Strand-2
    - Its complement is the DNA-Strand part of the DNA-Molecule object of the DNA-Molecule-Replication called dna-strand-2
    a DNA-Strand with the following-properties:
    - It is called Daughter-Strand-Complementary-To-Strand-2
    - Its complement is the DNA-Strand part of the DNA-Molecule object of the DNA-Molecule-Replication called dna-strand-2
KB rule (KM):
```
(every dna-molecule-replication has
 (result
  ((a dna-molecule called DNA-Molecule-2 with
    (has-part
     (((the dna-strand has-part of
        (the dna-molecule object of
         _dna-molecule-replication983))
       called DNA-Strand-2)
      (a dna-strand called
       Daughter-Strand-Complementary-To-Strand-2 with
       (complement
        (((the dna-strand has-part of
           (the dna-molecule object of
            _dna-molecule-replication983))
          called DNA-Strand-2))))))))))
```

The DNA-Molecule is result of the DNA-Molecule-Replication

KB rule (English):

The following rule was asserted for Concept

The result of a is: a Tangible-Entity

Concept DNA-Molecule-Replication is a subconcept of concept

KB rule (KM):
```
( (a tangible-entity))
```
KB rule (English):

The following rule was asserted for Concept DNA-Molecule-Replication

The result of a DNA-Molecule-Replication is: a DNA-Molecule with the following-properties:
- It is called DNA-Molecule-1
- Its parts are
  - the DNA-Strand part of the DNA-Molecule object of the DNA-Molecule-Replication called dna-strand-1 the DNA-Strand part of the DNA-Molecule object of the DNA-Molecule-Replication called dna-strand-1
  - a DNA-Strand with the following-properties:
    - It is called Daughter-Strand-Complementary-To-Strand-1
    - Its complement is the DNA-Strand part of the DNA-Molecule object of the DNA-Molecule-Replication called dna-strand-1
    a DNA-Strand with the following-properties:
    - It is called Daughter-Strand-Complementary-To-Strand-1
    - Its complement is the DNA-Strand part of the DNA-Molecule object of the DNA-Molecule-Replication called dna-strand-1
KB rule (KM):
```
(every dna-molecule-replication has
 (result
  ((a dna-molecule called DNA-Molecule-1 with
    (has-part
     (((the dna-strand has-part of
        (the dna-molecule object of
         _dna-molecule-replication983))
       called DNA-Strand-1)
      (a dna-strand called
       Daughter-Strand-Complementary-To-Strand-1 with
       (complement
        (((the dna-strand has-part of
           (the dna-molecule object of
            _dna-molecule-replication983))
          called DNA-Strand-1))))))))))
```

Terms

Terms		Definitions
the DNA-Double-Strand		An instance of DNA-Double-Strand
the DNA-Molecule-Replication		An instance of DNA-Molecule-Replication
the DNA-Molecule		An instance of DNA-Molecule
the DNA-Molecule		An instance of DNA-Molecule
the DNA-Molecule		An instance of DNA-Molecule
the DNA-Polymerase-Replication-Enzyme		An instance of DNA-Polymerase-Replication-Enzyme
the Macromolecule		An instance of Macromolecule
the Replicon-Replication		An instance of Replicon-Replication
DNA-Double-Strand		Two strands of DNA held together by hydrogen bonds. Examples: DNA double helix and replicon. Souther.
DNA-Molecule		Double-stranded polynucleotide formed from two separate chains of deoxyribonucleotide units; serves as the carrier of genetic information. Alberts:ECB:G-6
DNA-Molecule-Replication		A process by which a copy of a DNA molecule is made. Alberts:ECB:G-6.
DNA-Polymerase-Replication-Enzyme		Enzyme that catalyzes the synthesis of a DNA molecule on a DNA template from nucleoside triphosphate precursors. Alberts: ECB:G-16.
DNA-Replication		A process by which a copy of all or part of a DNA molecule or DNA strand is made. Includes the replication of the replicon subunits of DNA and repair of damaged strands. Souther.
DNA-Strand		One of two complementary anti-parallel chains that make up the DNA double helical molecule. Souther.
Entity		Things that are, such as Objects and Substances, as opposed to Things that happen.
Instrument		Things, such as tools, used by an Agent in some Event.
Macromolecule		Polymer molecule, such as a protein, nucleic acid, or polysaccharide, with a molecular mass greater than a few thousand daltons. Alberts:ECB:G-11
Polydeoxyribonucleotide		A molecular chain of deoxyribonucleotides chemically bonded by a series of phosphodiester linkages. Alberts:ECB:G-14.
Replicon-Replication		A process by which a copy of a replicon within a DNA molecule is made. Souther. see Mathews:BC:1160
Tangible-Entity		an Entity with physical extent
called		No Textual Definition
complement		an Entity has a complement another Entity.
has-part		the parts that comprise a whole.
instance-of		No Textual Definition
instrument		the entity that is used (by the agent if there is one) to perform an event.
object		the entity that is acted upon by an Event. The main passive participant in the Event.
plays		an Entity is playing the Role in an Event
result		the entity that comes into existence as a result of an action.
subevent		An event that is a step of another event, and occurs during it.