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Collating for real with CollateX

Okay, let's do some serious hands-on collation.

First of all we want to make sure that you have the latest version of CollateX. That's why we do…





In [ ]:



    


!pip install --pre --upgrade collatex

You don't need to do this every time, but make sure you do it regularly.

Next we need to tell Python that we will be needing the Python library that holds the code for CollateX…





In [2]:



    


from collatex import *

Now we're ready to make a collation object. We do this with the slightly hermetic line of code:

collation = Collation()

Here the small caps collation is the arbitrary named variable that refers to a copy (officially it is called an instance) of the CollateX collation engine. We simply tell the collation library to create a new instance by saying Collation().





In [3]:



    


collation = Collation()

Now we add some witnesses. Each witness gets a letter or name that will identify them, and for each we add the literal text of the witness to the collation object, like so…





In [4]:



    


collation.add_plain_witness( "A", "The quick brown fox jumped over the lazy dog.")
collation.add_plain_witness( "B", "The brown fox jumped over the dog." )
collation.add_plain_witness( "C", "The bad fox jumped over the lazy dog." )

And now we can let CollateX do its work of collating these witnesses and sit back for about 0.001 seconds. The result will be an alignment table, so we'll refer to the result with a variable named alignment_table.





In [5]:



    


alignment_table = collate(collation, layout='vertical', segmentation=False )

Well, that worked nicely it seems. But there's no printout, no visualization. That's okay, we can come up with a printout of the alignment table too:





In [6]:



    


print( alignment_table )



    


















    






+--------+--------+--------+
|   A    |   B    |   C    |
+--------+--------+--------+
|  The   |  The   |  The   |
+--------+--------+--------+
| quick  |   -    |  bad   |
+--------+--------+--------+
| brown  | brown  |   -    |
+--------+--------+--------+
|  fox   |  fox   |  fox   |
+--------+--------+--------+
| jumped | jumped | jumped |
+--------+--------+--------+
|  over  |  over  |  over  |
+--------+--------+--------+
|  the   |  the   |  the   |
+--------+--------+--------+
|  lazy  |   -    |  lazy  |
+--------+--------+--------+
|  dog   |  dog   |  dog   |
+--------+--------+--------+
|   .    |   .    |   .    |
+--------+--------+--------+

Usually you will want those segments that run parallel to be collected and displayed together. Since this is what most people seem to want, CollateX does that by default. We switched this option off in the example above for a moment because the result then shows you more clearly what the underlying primary structure is that CollateX returns. But for all practicle purposes you will probabably lose that segmentation=False option. So, let's get rid of that, and collate again…





In [7]:



    


alignment_table = collate(collation, layout='vertical' )



    











In [8]:



    


print( alignment_table )



    


















    






+---------------------+---------------------+---------------------+
|          A          |          B          |          C          |
+---------------------+---------------------+---------------------+
|         The         |         The         |         The         |
+---------------------+---------------------+---------------------+
|        quick        |          -          |         bad         |
+---------------------+---------------------+---------------------+
|        brown        |        brown        |          -          |
+---------------------+---------------------+---------------------+
| fox jumped over the | fox jumped over the | fox jumped over the |
+---------------------+---------------------+---------------------+
|         lazy        |          -          |         lazy        |
+---------------------+---------------------+---------------------+
|         dog.        |         dog.        |         dog.        |
+---------------------+---------------------+---------------------+

The aligment table visualization is CollateX's default way of rendering a collation result. There are various ways in which one can depict collated results of course. The output in alignment table form can be a good basis for further visualizations. CollateX can also format your collation as a variant graph. This is a visualization that lets you trace from left to right through a directed network, to follow which witness carries what readings.





In [10]:



    


graph = collate( collation, output="svg", segmentation=True )



    


















    








%3


0



2

The


0->2


A, B, C


1



3

quick


2->3


A


4

brown


2->4


B


12

bad


2->12


C


3->4


A


5

fox jumped over the


4->5


A, B


9

lazy


5->9


A, C


10

dog.


5->10


B


9->10


A, C


10->1


A, B, C


12->5


C

Okay, that's all good and nice, but that's just tiny fragments—we want decent chunks of text to collate! Well, we can do that too, although is requires a little more work. Specifically for reading in text files from the file system. If we didn't do it that way, we would have to key in all characters of each witness, and that's just a lot of unnecessary work if we have done those texts already in a file. The below code uses the open command to open each text file and appoint the contents to a variable with an appropriately chosen name.

The encoding="utf-8" bit is needed because you should always tell Python which encoding your data uses. This is probably the only place and time where you will use that encoding directive: when you open a (text) file.





In [11]:



    


collation = Collation()
witness_1859 = open( "./fixtures/Darwin/txt/darwin1859_par1.txt", encoding='utf-8' ).read()
witness_1860 = open( "./fixtures/Darwin/txt/darwin1860_par1.txt", encoding='utf-8' ).read()
witness_1861 = open( "./fixtures/Darwin/txt/darwin1861_par1.txt", encoding='utf-8' ).read()
witness_1866 = open( "./fixtures/Darwin/txt/darwin1866_par1.txt", encoding='utf-8' ).read()
witness_1869 = open( "./fixtures/Darwin/txt/darwin1869_par1.txt", encoding='utf-8' ).read()
witness_1872 = open( "./fixtures/Darwin/txt/darwin1872_par1.txt", encoding='utf-8' ).read()
collation.add_plain_witness( "1859", witness_1859 )
collation.add_plain_witness( "1860", witness_1860 )
collation.add_plain_witness( "1861", witness_1861 )
collation.add_plain_witness( "1866", witness_1866 )
collation.add_plain_witness( "1869", witness_1869 )
collation.add_plain_witness( "1872", witness_1872 )

Now let's check if these witnesses actually contain some text.





In [12]:



    


print( witness_1859 )



    


















    






WHEN we look to the individuals of the same variety or sub-variety of our older cultivated plants and animals, one of the first points which strikes us, is, that they generally differ much more from each other, than do the individuals of any one species or variety in a state of nature. When we reflect on the vast diversity of the plants and animals which have been cultivated, and which have varied during all ages under the most different climates and treatment, I think we are driven to conclude that this greater variability is simply due to our domestic productions having been raised under conditions of life not so uniform as, and somewhat different from, those to which the parent-species have been exposed under nature. There is, also, I think, some probability in the view propounded by Andrew Knight, that this variability may be partly connected with excess of food. It seems pretty clear that organic beings must be exposed during several generations to the new conditions of life to cause any appreciable amount of variation; and that when the organisation has once begun to vary, it generally continues to vary for many generations. No case is on record of a variable being ceasing to be variable under cultivation. Our oldest cultivated plants, such as wheat, still often yield new varieties: our oldest domesticated animals are still capable of rapid improvement or modification.


















In [13]:



    


print( witness_1860 )



    


















    






WHEN we look to the individuals of the same variety or sub-variety of our older cultivated plants and animals, one of the first points which strikes us, is, that they generally differ more from each other than do the individuals of any one species or variety in a state of nature. When we reflect on the vast diversity of the plants and animals which have been cultivated, and which have varied during all ages under the most different climates and treatment, I think we are driven to conclude that this great variability is simply due to our domestic productions having been raised under conditions of life not so uniform as, and somewhat different from, those to which the parent-species have been exposed under nature. There is also, I think, some probability in the view propounded by Andrew Knight, that this variability may be partly connected with excess of food. It seems pretty clear that organic beings must be exposed during several generations to the new conditions of life to cause any appreciable amount of variation; and that when the organisation has once begun to vary, it generally continues to vary for many generations. No case is on record of a variable being ceasing to be variable under cultivation. Our oldest cultivated plants, such as wheat, still often yield new varieties: our oldest domesticated animals are still capable of rapid improvement or modification.

And now let's collate those witnesses and let's put the result up as an HTML-formatted alignment table…





In [14]:



    


alignment_table = collate(collation, layout='vertical', output='html')



    


















    








    

        1859
        1860
        1861
        1866
        1869
        1872
    

    

        -
        -
        -
        Causes of
Variability.		
        Causes of
Variability.		
        Causes of
Variability.		
    

    

        WHEN we
        WHEN we
        WHEN we
        WHEN we
        WHEN we
        WHEN we
    

    

        look to
        look to
        look to
        look to
        compare
        compare
    

    

        the individuals of
the same variety or
sub- variety of our
older cultivated
plants and animals,
one of the first
points which strikes
us		
        the individuals of
the same variety or
sub- variety of our
older cultivated
plants and animals,
one of the first
points which strikes
us		
        the individuals of
the same variety or
sub- variety of our
older cultivated
plants and animals,
one of the first
points which strikes
us		
        the individuals of
the same variety or
sub- variety of our
older cultivated
plants and animals,
one of the first
points which strikes
us		
        the individuals of
the same variety or
sub- variety of our
older cultivated
plants and animals,
one of the first
points which strikes
us		
        the individuals of
the same variety or
sub- variety of our
older cultivated
plants and animals,
one of the first
points which strikes
us		
    

    

        ,
        ,
        ,
        ,
        -
        -
    

    

        is, that they
generally differ		
        is, that they
generally differ		
        is, that they
generally differ		
        is, that they
generally differ		
        is, that they
generally differ		
        is, that they
generally differ		
    

    

        much
        -
        -
        -
        -
        -
    

    

        more
        more
        more
        more
        -
        more
    

    

        from each other
        from each other
        from each other
        from each other
        from each other
        from each other
    

    

        ,
        -
        -
        -
        more
        -
    

    

        than do the
individuals of any
one species or
variety in a state
of nature.		
        than do the
individuals of any
one species or
variety in a state
of nature.		
        than do the
individuals of any
one species or
variety in a state
of nature.		
        than do the
individuals of any
one species or
variety in a state
of nature.		
        than do the
individuals of any
one species or
variety in a state
of nature.		
        than do the
individuals of any
one species or
variety in a state
of nature.		
    

    

        When
        When
        When
        When
        And if
        And if
    

    

        we reflect on the
vast diversity of
the plants and
animals which have
been cultivated, and
which have varied
during all ages
under the most
different climates
and treatment,		
        we reflect on the
vast diversity of
the plants and
animals which have
been cultivated, and
which have varied
during all ages
under the most
different climates
and treatment,		
        we reflect on the
vast diversity of
the plants and
animals which have
been cultivated, and
which have varied
during all ages
under the most
different climates
and treatment,		
        we reflect on the
vast diversity of
the plants and
animals which have
been cultivated, and
which have varied
during all ages
under the most
different climates
and treatment,		
        we reflect on the
vast diversity of
the plants and
animals which have
been cultivated, and
which have varied
during all ages
under the most
different climates
and treatment,		
        we reflect on the
vast diversity of
the plants and
animals which have
been cultivated, and
which have varied
during all ages
under the most
different climates
and treatment,		
    

    

        I think
        I think
        I think
        I think
        -
        -
    

    

        we are driven to
conclude that this		
        we are driven to
conclude that this		
        we are driven to
conclude that this		
        we are driven to
conclude that this		
        we are driven to
conclude that this		
        we are driven to
conclude that this		
    

    

        greater
        great
        great
        great
        great
        great
    

    

        variability is
        variability is
        variability is
        variability is
        variability is
        variability is
    

    

        simply
        simply
        simply
        simply
        -
        -
    

    

        due to our domestic
productions having
been raised under
conditions of life
not so uniform as,
and somewhat
different from,
those to which the
parent- species		
        due to our domestic
productions having
been raised under
conditions of life
not so uniform as,
and somewhat
different from,
those to which the
parent- species		
        due to our domestic
productions having
been raised under
conditions of life
not so uniform as,
and somewhat
different from,
those to which the
parent- species		
        due to our domestic
productions having
been raised under
conditions of life
not so uniform as,
and somewhat
different from,
those to which the
parent- species		
        due to our domestic
productions having
been raised under
conditions of life
not so uniform as,
and somewhat
different from,
those to which the
parent- species		
        due to our domestic
productions having
been raised under
conditions of life
not so uniform as,
and somewhat
different from,
those to which the
parent- species		
    

    

        have
        have
        have
        have
        had
        had
    

    

        been exposed under
nature. There is		
        been exposed under
nature. There is		
        been exposed under
nature. There is		
        been exposed under
nature. There is		
        been exposed under
nature. There is		
        been exposed under
nature. There is		
    

    

        ,
        -
        -
        -
        -
        ,
    

    

        also
        also
        also
        also
        also
        also
    

    

        , I think
        , I think
        , I think
        , I think
        , I think
        -
    

    

        , some probability
in the view
propounded by Andrew
Knight, that this
variability may be
partly connected
with excess of food.
It seems		
        , some probability
in the view
propounded by Andrew
Knight, that this
variability may be
partly connected
with excess of food.
It seems		
        , some probability
in the view
propounded by Andrew
Knight, that this
variability may be
partly connected
with excess of food.
It seems		
        , some probability
in the view
propounded by Andrew
Knight, that this
variability may be
partly connected
with excess of food.
It seems		
        , some probability
in the view
propounded by Andrew
Knight, that this
variability may be
partly connected
with excess of food.
It seems		
        , some probability
in the view
propounded by Andrew
Knight, that this
variability may be
partly connected
with excess of food.
It seems		
    

    

        pretty
        pretty
        pretty
        pretty
        -
        -
    

    

        clear that organic
beings must be
exposed during
several generations
to		
        clear that organic
beings must be
exposed during
several generations
to		
        clear that organic
beings must be
exposed during
several generations
to		
        clear that organic
beings must be
exposed during
several generations
to		
        clear that organic
beings must be
exposed during
several generations
to		
        clear that organic
beings must be
exposed during
several generations
to		
    

    

        the
        the
        the
        the
        -
        -
    

    

        new
        new
        new
        new
        new
        new
    

    

        conditions of life
        conditions of life
        conditions of life
        conditions of life
        conditions
        conditions
    

    

        to cause any
        to cause any
        to cause any
        to cause any
        to cause any
        to cause any
    

    

        appreciable
        appreciable
        appreciable
        appreciable
        appreciable
        great
    

    

        amount of variation;
and that		
        amount of variation;
and that		
        amount of variation;
and that		
        amount of variation;
and that		
        amount of variation;
and that		
        amount of variation;
and that		
    

    

        -
        -
        -
        ,
        ,
        ,
    

    

        when the
organisation has
once begun to vary,
it generally		
        when the
organisation has
once begun to vary,
it generally		
        when the
organisation has
once begun to vary,
it generally		
        when the
organisation has
once begun to vary,
it generally		
        when the
organisation has
once begun to vary,
it generally		
        when the
organisation has
once begun to vary,
it generally		
    

    

        continues
        continues
        continues
        continues
        con- tinues
        continues
    

    

        to vary
        to vary
        to vary
        to vary
        varying
        varying
    

    

        for many
generations. No case
is on record of a
variable		
        for many
generations. No case
is on record of a
variable		
        for many
generations. No case
is on record of a
variable		
        for many
generations. No case
is on record of a
variable		
        for many
generations. No case
is on record of a
variable		
        for many
generations. No case
is on record of a
variable		
    

    

        being
        being
        being
        being
        organism
        organism
    

    

        ceasing
        ceasing
        ceasing
        ceasing
        ceasing
        ceasing
    

    

        to be variable
        to be variable
        to be variable
        to be variable
        to vary
        to vary
    

    

        under cultivation.
Our oldest
cultivated plants,
such as wheat, still		
        under cultivation.
Our oldest
cultivated plants,
such as wheat, still		
        under cultivation.
Our oldest
cultivated plants,
such as wheat, still		
        under cultivation.
Our oldest
cultivated plants,
such as wheat, still		
        under cultivation.
Our oldest
cultivated plants,
such as wheat, still		
        under cultivation.
Our oldest
cultivated plants,
such as wheat, still		
    

    

        often
        often
        often
        often
        -
        -
    

    

        yield new varieties:
our oldest
domesticated animals
are still capable of
rapid improvement or
modification.		
        yield new varieties:
our oldest
domesticated animals
are still capable of
rapid improvement or
modification.		
        yield new varieties:
our oldest
domesticated animals
are still capable of
rapid improvement or
modification.		
        yield new varieties:
our oldest
domesticated animals
are still capable of
rapid improvement or
modification.		
        yield new varieties:
our oldest
domesticated animals
are still capable of
rapid improvement or
modification.		
        yield new varieties:
our oldest
domesticated animals
are still capable of
rapid improvement or
modification.

Hmm… but that's still a little hard to read. Wouldn't it be nice if we got a hint where the actual differences are? Sure, try…





In [15]:



    


alignment_table = collate(collation, layout='vertical', output='html2')



    


















    








 

  1859
  1860
  1861
  1866
  1869
  1872
 

 

  -
  -
  -
  Causes of
Variability.
  Causes of
Variability.
  Causes of
Variability.
 

 

  WHEN we
  WHEN we
  WHEN we
  WHEN we
  WHEN we
  WHEN we
 

 

  look to
  look to
  look to
  look to
  compare
  compare
 

 

  the individuals of
the same variety or
sub- variety of our
older cultivated
plants and animals,
one of the first
points which strikes
us
  the individuals of
the same variety or
sub- variety of our
older cultivated
plants and animals,
one of the first
points which strikes
us
  the individuals of
the same variety or
sub- variety of our
older cultivated
plants and animals,
one of the first
points which strikes
us
  the individuals of
the same variety or
sub- variety of our
older cultivated
plants and animals,
one of the first
points which strikes
us
  the individuals of
the same variety or
sub- variety of our
older cultivated
plants and animals,
one of the first
points which strikes
us
  the individuals of
the same variety or
sub- variety of our
older cultivated
plants and animals,
one of the first
points which strikes
us
 

 

  ,
  ,
  ,
  ,
  -
  -
 

 

  is, that they
generally differ
  is, that they
generally differ
  is, that they
generally differ
  is, that they
generally differ
  is, that they
generally differ
  is, that they
generally differ
 

 

  much
  -
  -
  -
  -
  -
 

 

  more
  more
  more
  more
  -
  more
 

 

  from each other
  from each other
  from each other
  from each other
  from each other
  from each other
 

 

  ,
  -
  -
  -
  more
  -
 

 

  than do the
individuals of any
one species or
variety in a state
of nature.
  than do the
individuals of any
one species or
variety in a state
of nature.
  than do the
individuals of any
one species or
variety in a state
of nature.
  than do the
individuals of any
one species or
variety in a state
of nature.
  than do the
individuals of any
one species or
variety in a state
of nature.
  than do the
individuals of any
one species or
variety in a state
of nature.
 

 

  When
  When
  When
  When
  And if
  And if
 

 

  we reflect on the
vast diversity of
the plants and
animals which have
been cultivated, and
which have varied
during all ages
under the most
different climates
and treatment,
  we reflect on the
vast diversity of
the plants and
animals which have
been cultivated, and
which have varied
during all ages
under the most
different climates
and treatment,
  we reflect on the
vast diversity of
the plants and
animals which have
been cultivated, and
which have varied
during all ages
under the most
different climates
and treatment,
  we reflect on the
vast diversity of
the plants and
animals which have
been cultivated, and
which have varied
during all ages
under the most
different climates
and treatment,
  we reflect on the
vast diversity of
the plants and
animals which have
been cultivated, and
which have varied
during all ages
under the most
different climates
and treatment,
  we reflect on the
vast diversity of
the plants and
animals which have
been cultivated, and
which have varied
during all ages
under the most
different climates
and treatment,
 

 

  I think
  I think
  I think
  I think
  -
  -
 

 

  we are driven to
conclude that this
  we are driven to
conclude that this
  we are driven to
conclude that this
  we are driven to
conclude that this
  we are driven to
conclude that this
  we are driven to
conclude that this
 

 

  greater
  great
  great
  great
  great
  great
 

 

  variability is
  variability is
  variability is
  variability is
  variability is
  variability is
 

 

  simply
  simply
  simply
  simply
  -
  -
 

 

  due to our domestic
productions having
been raised under
conditions of life
not so uniform as,
and somewhat
different from,
those to which the
parent- species
  due to our domestic
productions having
been raised under
conditions of life
not so uniform as,
and somewhat
different from,
those to which the
parent- species
  due to our domestic
productions having
been raised under
conditions of life
not so uniform as,
and somewhat
different from,
those to which the
parent- species
  due to our domestic
productions having
been raised under
conditions of life
not so uniform as,
and somewhat
different from,
those to which the
parent- species
  due to our domestic
productions having
been raised under
conditions of life
not so uniform as,
and somewhat
different from,
those to which the
parent- species
  due to our domestic
productions having
been raised under
conditions of life
not so uniform as,
and somewhat
different from,
those to which the
parent- species
 

 

  have
  have
  have
  have
  had
  had
 

 

  been exposed under
nature. There is
  been exposed under
nature. There is
  been exposed under
nature. There is
  been exposed under
nature. There is
  been exposed under
nature. There is
  been exposed under
nature. There is
 

 

  ,
  -
  -
  -
  -
  ,
 

 

  also
  also
  also
  also
  also
  also
 

 

  , I think
  , I think
  , I think
  , I think
  , I think
  -
 

 

  , some probability
in the view
propounded by Andrew
Knight, that this
variability may be
partly connected
with excess of food.
It seems
  , some probability
in the view
propounded by Andrew
Knight, that this
variability may be
partly connected
with excess of food.
It seems
  , some probability
in the view
propounded by Andrew
Knight, that this
variability may be
partly connected
with excess of food.
It seems
  , some probability
in the view
propounded by Andrew
Knight, that this
variability may be
partly connected
with excess of food.
It seems
  , some probability
in the view
propounded by Andrew
Knight, that this
variability may be
partly connected
with excess of food.
It seems
  , some probability
in the view
propounded by Andrew
Knight, that this
variability may be
partly connected
with excess of food.
It seems
 

 

  pretty
  pretty
  pretty
  pretty
  -
  -
 

 

  clear that organic
beings must be
exposed during
several generations
to
  clear that organic
beings must be
exposed during
several generations
to
  clear that organic
beings must be
exposed during
several generations
to
  clear that organic
beings must be
exposed during
several generations
to
  clear that organic
beings must be
exposed during
several generations
to
  clear that organic
beings must be
exposed during
several generations
to
 

 

  the
  the
  the
  the
  -
  -
 

 

  new
  new
  new
  new
  new
  new
 

 

  conditions of life
  conditions of life
  conditions of life
  conditions of life
  conditions
  conditions
 

 

  to cause any
  to cause any
  to cause any
  to cause any
  to cause any
  to cause any
 

 

  appreciable
  appreciable
  appreciable
  appreciable
  appreciable
  great
 

 

  amount of variation;
and that
  amount of variation;
and that
  amount of variation;
and that
  amount of variation;
and that
  amount of variation;
and that
  amount of variation;
and that
 

 

  -
  -
  -
  ,
  ,
  ,
 

 

  when the
organisation has
once begun to vary,
it generally
  when the
organisation has
once begun to vary,
it generally
  when the
organisation has
once begun to vary,
it generally
  when the
organisation has
once begun to vary,
it generally
  when the
organisation has
once begun to vary,
it generally
  when the
organisation has
once begun to vary,
it generally
 

 

  continues
  continues
  continues
  continues
  con- tinues
  continues
 

 

  to vary
  to vary
  to vary
  to vary
  varying
  varying
 

 

  for many
generations. No case
is on record of a
variable
  for many
generations. No case
is on record of a
variable
  for many
generations. No case
is on record of a
variable
  for many
generations. No case
is on record of a
variable
  for many
generations. No case
is on record of a
variable
  for many
generations. No case
is on record of a
variable
 

 

  being
  being
  being
  being
  organism
  organism
 

 

  ceasing
  ceasing
  ceasing
  ceasing
  ceasing
  ceasing
 

 

  to be variable
  to be variable
  to be variable
  to be variable
  to vary
  to vary
 

 

  under cultivation.
Our oldest
cultivated plants,
such as wheat, still
  under cultivation.
Our oldest
cultivated plants,
such as wheat, still
  under cultivation.
Our oldest
cultivated plants,
such as wheat, still
  under cultivation.
Our oldest
cultivated plants,
such as wheat, still
  under cultivation.
Our oldest
cultivated plants,
such as wheat, still
  under cultivation.
Our oldest
cultivated plants,
such as wheat, still
 

 

  often
  often
  often
  often
  -
  -
 

 

  yield new varieties:
our oldest
domesticated animals
are still capable of
rapid improvement or
modification.
  yield new varieties:
our oldest
domesticated animals
are still capable of
rapid improvement or
modification.
  yield new varieties:
our oldest
domesticated animals
are still capable of
rapid improvement or
modification.
  yield new varieties:
our oldest
domesticated animals
are still capable of
rapid improvement or
modification.
  yield new varieties:
our oldest
domesticated animals
are still capable of
rapid improvement or
modification.
  yield new varieties:
our oldest
domesticated animals
are still capable of
rapid improvement or
modification.

And finally, we can also generate the variant graph for this collation…





In [16]:



    


graph = collate( collation, output="svg" )



    


















    








%3


0



2

WHEN we


0->2


1859, 1860, 1861


263

Causes of Variability.


0->263


1866, 1869, 1872


1



4

look to


2->4


1859, 1860, 1861, 1866


268

compare


2->268


1869, 1872


6

the individuals of the same variety or sub- variety of our older cultivated plants and animals, one of the first points which strikes us


4->6


1859, 1860, 1861, 1866


32

,


6->32


1859, 1860, 1861, 1866


33

is, that they generally differ


6->33


1869, 1872


32->33


1859, 1860, 1861, 1866


39

much


33->39


1859


40

more


33->40


1860, 1861, 1866, 1872


41

from each other


33->41


1869


39->40


1859


40->41


1859, 1860, 1861, 1866, 1872


44

,


41->44


1859


45

than do the individuals of any one species or variety in a state of nature.


41->45


1860, 1861, 1866, 1872


269

more


41->269


1869


44->45


1859


61

When


45->61


1859, 1860, 1861, 1866


270

And if


45->270


1869, 1872


62

we reflect on the vast diversity of the plants and animals which have been cultivated, and which have varied during all ages under the most different climates and treatment,


61->62


1859, 1860, 1861, 1866


93

I think


62->93


1859, 1860, 1861, 1866


95

we are driven to conclude that this


62->95


1869, 1872


93->95


1859, 1860, 1861, 1866


102

greater


95->102


1859


262

great


95->262


1860, 1861, 1866, 1869, 1872


103

variability is


102->103


1859


105

simply


103->105


1859, 1860, 1861, 1866


106

due to our domestic productions having been raised under conditions of life not so uniform as, and somewhat different from, those to which the parent- species


103->106


1869, 1872


105->106


1859, 1860, 1861, 1866


135

have


106->135


1859, 1860, 1861, 1866


272

had


106->272


1869, 1872


136

been exposed under nature. There is


135->136


1859, 1860, 1861, 1866


143

,


136->143


1859, 1872


144

also


136->144


1860, 1861, 1866, 1869


143->144


1859, 1872


145

, I think


144->145


1859, 1860, 1861, 1866, 1869


148

, some probability in the view propounded by Andrew Knight, that this variability may be partly connected with excess of food. It seems


144->148


1872


145->148


1859, 1860, 1861, 1866, 1869


173

pretty


148->173


1859, 1860, 1861, 1866


174

clear that organic beings must be exposed during several generations to


148->174


1869, 1872


173->174


1859, 1860, 1861, 1866


185

the


174->185


1859, 1860, 1861, 1866


186

new


174->186


1869, 1872


185->186


1859, 1860, 1861, 1866


187

conditions of life


186->187


1859, 1860, 1861, 1866


273

conditions


186->273


1869, 1872


190

to cause any


187->190


1859, 1860, 1861, 1866


193

appreciable


190->193


1859, 1860, 1861, 1866, 1869


281

great


190->281


1872


194

amount of variation; and that


193->194


1859, 1860, 1861, 1866, 1869


200

when the organisation has once begun to vary, it generally


194->200


1859, 1860, 1861


267

,


194->267


1866, 1869, 1872


211

continues


200->211


1859, 1860, 1861, 1866, 1872


274

con- tinues


200->274


1869


212

to vary


211->212


1859, 1860, 1861, 1866


277

varying


211->277


1872


214

for many generations. No case is on record of a variable


212->214


1859, 1860, 1861, 1866


226

being


214->226


1859, 1860, 1861, 1866


278

organism


214->278


1869, 1872


227

ceasing


226->227


1859, 1860, 1861, 1866


228

to be variable


227->228


1859, 1860, 1861, 1866


279

to vary


227->279


1869, 1872


231

under cultivation. Our oldest cultivated plants, such as wheat, still


228->231


1859, 1860, 1861, 1866


244

often


231->244


1859, 1860, 1861, 1866


245

yield new varieties: our oldest domesticated animals are still capable of rapid improvement or modification.


231->245


1869, 1872


244->245


1859, 1860, 1861, 1866


245->1


1859, 1860, 1861, 1866, 1869, 1872


262->103


1860, 1861, 1866, 1869, 1872


263->2


1866, 1869, 1872


267->200


1866, 1869, 1872


268->6


1869, 1872


269->45


1869


270->62


1869, 1872


272->136


1869, 1872


273->190


1869, 1872


274->277


1869


277->214


1869, 1872


278->227


1869, 1872


279->231


1869, 1872


281->194


1872



















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