> "Natural selection and the concept of a protein space" has been d...
> Salisbury wrote in 1969 in "Natural Selection and the Complexity ...
While it is difficult to estimate the overall potential protein-spa...
Here is a great article that articulates the significance of 'Natur...
John Maynard Smith (1920-2004) was a British mathematical evolution...
© 1970 Nature Publishing Group
NATURE
VOL
225
FEBRUARY 7
1970
••
Fig. 2.
Cerebe
llar
cortex
of
the
same
rat
as
Fig.
1.
Unsta
in
ed
autoradio-
gram
of
a
cryostat
sectio
n.
M,
Molecular
layer;
P,
Purkinjc
cells
(non-
reacting);
G,
granular fayer;
\V,
white
n1atter.
Fig.
3.
Lumbar
spina
l
cord (a
nt
erior
horn)
of
a
rat,
45
min
after
a
si
ngle
injection
of
TSC-"C.
Rouin-fi
xed
and
embedded specimen,
counter-
stained
with
haematoxylin
and
eosin. i\fotoneuroncs
(l\I)
are
non-rea
ct-
ing; capsula
r
glial
cells (arrow)
and
astrocytes
in
the
grey
matter
(arrow
with
a
circle)
contain
numerous grains.
binding
by
non-reacting
structures
might
indicate
thos
e
ce
llular
elements
that
do
not
exert
GAD
activity.
Such
an
approac
h
is
actually
an
adaptation
of
the
principl
e
described
by
Ostrovsky
and
Barnard
5
•
Rats
weighing
160 g
were
inj
ected
intraperitoncally
with
5-20
mg
/
kg
thiosemicarbazide-
14
C (specific
activity
10
mCi/mmole,
obtained
from
the
Central
Isotope
Institute
,
Budapest).
Characteristic
convulsions
and
lethal
"jumps"
ap
peared
45-120
min
after
inje
c
tion.
The
animals
were
killed
by
decapitation
and
samples
of
tho
central
nervou
s
system
(brain,
medulla,
cerebellum,
spinal
cord)
as
well
as
o
th
er
tissues
were
eith
er
fixed
on
Bouin's
solution
and
prepared
for
autoradiography
in
the
usual
way
or
were
not
fixed
but
frozen
with
dry
ice,
cut
on
a
cryostat
and
applied
to
slides
pre-coated
with
Kodak
AR-10
stripping
film,
emu
lsion
side
up.
Th
e
exposure
time
was
3-8
weeks;
autoradiograms
were
develop
e
d
in
Kodak
autoradi
o-
g
raphic
d
eve
loper
and
some
were
countcrstained
with
ha
cmatoxy
lin
and
cosin.
Fig. I s
hows
a
coronal
section
of
the
brain
of
a
rat
given
two
intraperitoneal
injection
s
of
10
mg/kg
TSC-
14
C
,
with
an
interval
of
40
min
betw
een
them,
a
nd
then
killed
90
min
after
the
first
injection.
The
h
eaviest
r
eactio
n
is
confined
to
the
hippocampus
and
fascia
dentata
chiefly
in
the
layer
of
hippocampal
pyramids
(Fig.
1,
in
set);
silver
grains
are,
however,
not
found
in
the
nerve
cells
themselves
but
are
concentrated
in
the
surrounding
neuropil.
Activity
is
high
563
also
in
the
nucleus
hab
enu
l
aris
medialis.
There
is
a
moderate
reaction
in
the
cortex,
especially
in
the
vicinity
of
the
interhemispherical
fissure
.
Both
the
molecular
layer
and
the
granular
layer
of
the
ce
r
ebe
llum
contain
numerous
silver
grains
(Fig.
2).
The
localization
pattern
of
the
reaction
does
not,
however,
conform
to
any
of
the
neural
e
lem
en
ts
but
resembles
mor
e
closely
the
glial
structure.
The
reaction
is
slightly
stronger
around
Purkinje
cells,
which
are
themselves
devoid
of
any
r
eactio
n
both
in
pre-fixed
and
in
non-fixed
specimens.
On
the
other
hand,
in
deep
cerebellar
nuclei
(and
also
in
some
of
the
brain
stem
nuclei,
for
example
the
substantia
nigra
and
nucl
ei
ponti
s)
silver
grains
are
located
within
the
cyto
plasms
of
nerve
cells.
Weak
or
virtually
no
activity
can
be
seen
in
the
white
matter,
although
the
glial
cells
in
the
white
matter
react
if
high
er
doses
ofTSC
are
used
or
if
the
animals
are
killed
after
a
shorter
time
interval.
The
nerve
cells
in
the
spinal
cord
do
not
contain
silver
grains,
but
capsular
and
other
glial
cells
in
both
the
grey
and
white
matter
contain
numerous
grains
(Fig.
3).
According
to
Curtis
2
,
GABA
is
not
involved
in
spinal
inhibitory
mechanisms.
The
gross
distribution
of
s
ilv
er
grains
reduced
by
TSC-
14C
is
in
accord
with
the
distribution
of
GAD
and
GABA
anticipated
on
the
basis
of
earlier
biochemical
and
pharma-
cological
studies
(cerebellar
cortex
2
,
hippocampus•,
sub-
stantia
nigra
6
).
Wl>jle
the
concentration
of
silver
grains
in
n
erve
cells
(dentate
nucl
e
u
s,
substantia
nigra)
and
in
the
neuropil
surrounding
them
(hippocampus)
is
consistent
with
current
views,
it
is
striking
that
Purkinje
cells
do
not
exer
t
any
reaction.
Proteins
sensitive
to
TSC
are
undoubt-
ed
ly
more
widespread
than
GAD,
so
the
apparent
localiza-
tion
of
TSC
in
glial
cells
of
th
e
cere
be
liar
cortex
may
be
partly
due
to
binding
of
the
drug
to
other
B
6
-dependent
enzymes.
Th
e
possibility
cannot
be
excluded,
however,
that,
at
l
eas
t
in
this
area,
GABA
is
produced
by
glial
cells,
perhaps
in
order
to
be
taken
up
by
nerv
e
terminals
and/or
nerv
e
cells
in
a
second
step.
D
epa
rtment
of
Anatomy,
University
Medical
School,
Szeged,
Hungary.
BERTALAN
CsrLLIK
ELIZABETH
KNYIHAR
Received August
12;
revised Octob er
6,
1969.
1
Roberts,
E.,
in
Structure and
Function
of
Inhibitory
Mechanisms,
401
(Pergamon Press, Oxford,
1968).
'C
urtis
, D.
R.,
in
Structure
and Function
of
I
n
hibitory
Mechanisms,
420
(Pergamon
Press,
Oxford,
1968).
'Van
Gelder, N.
M.,
J
.
Neurochem.,
12
,
231,
239 (1965).
•
Killam, K.
F.,
Dasgupta,
S.
R.,
and
Killam,
E.
K.,
in
Inhibiti
on
in
the
Nervous
System and
Gam,na-Aminobutyric Acid,
302
(Pergamon
Pre
ss,
Oxford, 1960).
' Ostrovsky,
K.,
an
d
Barnard,
E.
A.,
Exp.
Cell Res.,
25, 456 (1961).
• Albers.
R.
W.,
in
Inhibitio"
in
the
Nervous
Sys
t
em
and Gamma-Amino-
butyric
Acid,
196 (P
erga
mon
Press, Oxford, 1960).
Natural
Selection
and
the
Concept
of
a
Protein
Space
SALISBURY
1
has
argued
that
there
is
an
apparent
con-
tradict
ion
between
two
fundamental
concepts
of
biology
-
the
belief
that
the
gene
is a
unique
sequence
of
nucleotid
es
whose
fun
ct
ion
it
is
to
det
e
rmine
the
sequence
of
amino-
acids
in
a
protein,
an
d
the
theory
of
ev
olution
by
natural
selection.
In
brief,
ho
calculated
that
the
numb
er
of
po
ssible
amino-acid
sequences
is
greater
by
many
orders
of
m
agnitude
than
the
number
of
proteins
which
could
have
existed
on
Earth
since
the
origin
of
life,
and
hence
that
functionally
effective
proteins
have
a
vanishingly
small
chance
of
arising
by
mutation.
Natural
selection
is
© 1970 Nature Publishing Group
564
therefore
ineffective
because
it
lacks
the
essential
raw
material--favourable
mutations.
I
should
like
to
look
at
the
problem
from
a
different
point
of
view.
I
shall
assume
that
mutations,
while
not
random
in
a
chemical
sense,
are
random
as
far
as
their
chances
of
improving
the
function
of
tho
corresponding
proteins
are
concerned.
I
shall
also
assume
that
evolution
has
occurred
either
by
the
natural
selection
of
favourable
mutations
or
by
the
chance
fixation
by
genetic
drift
of
selectively
neutral
mutations.
Tho
justification
for
making
these
assumptions
is
that
no
sensible
alternatives
have
been
suggested
and
that
no
evidence
exists
at
the
moment
to
invalidate
them.
If
these
assumptions
are
true,
what
can
we
say
about
tho
frequency
and
distribution
of
amino-
acid
sequences
which
are
functional,
either
as
enzymes
or
in
some
other
way
?
The
model
of
protein
evolution
I
want
to
discuss
is
best
understood
by
analogy
with
a
popular
word
game.
The
object
of
the
game
is
to
pass
from
one
word
to
another
of
the
same
length
by
changing
one
letter
at
a
time,
with
the
requirement
that
all
the
intermediate
words
are
meaningful
in
the
same
language.
Thus
WORD
can
be
converted
into
GENE
in
the
minimum
number
of
steps,
as
follows:
WORD
WORE
GORE
GONE
GENE
This
is
an
analogue
of
evolution,
in
which
the
words
represent
proteins;
the
letters
represent
amino-acids;
the
alteration
of
a
single
letter
corresponds
to
the
simplest
evolutionary
stop,
the
substitution
of
one
amino-acid
for
another;
and
the
requirement
of
meaning
corresponds
to
the
requirement
that
each
unit
step
in
evolution
should
be
from
one
functional
protein
to
another.
The
reason
for
the
last
requirement
is
as
follows:
suppose
that
a
protein
A B C D
...
exists,
and
that
a
protein
a b C D
...
would
be
favoured
by
selection
if
it
arose.
Suppose
further
that
the
intermediates
a B C D
...
and
A b C D
...
are
non-functional.
These
forms
would
arise
by
mutation,
but
would
usually
be
eliminated
by
selection
before a
second
mutation
could
occur.
Tho
double
step
from
a b C D
...
to
A B C D
would
thus
be
very
unlikely
to
occur.
Such
double
steps
with
unfavourable
inter-
mediates
may
occasionally
occur,
but
are
probably
too
rare
to
be
important
in
evolution.
This
is a
model
of
the
way
in
which
one
gene
may
change
into
another.
An
increase
in
the
number
of
different
genes
in
a
single
organism
presumably
occurs
by
the
duplication
of
an
already
existing
gene
foJiowed
by
divergence.
If
so,
it
remains
true
that
new
genes
arise
as
modifications
of
pre-existing
ones.
It
follows
that
if
evolution
by
natural
selection
is
to
occur,
functional
proteins
must
form
a
continuous
network
which
can
be
traversed
by
unit
mutational
steps
without
passing
through
nonfunctional
intermediates.
In
this
respect,
functional
proteins
resemble
four-letter
words
in
the
English
language,
rather
than
eight-lotter
words,
for
the
latter
form
a
series
of
small
isolated
islands
in
a
sea
of
nonsense
sequences.
Of
course,
this
is
not
to
deny
the
existence
of
isolated
island
proteins,
analogous
to
tho
four-letter
words
ALSO
and
ALTO.
It
is
easy
to
state
the
condition
which
must
be
satisfied
if
meaningful
proteins
are
to
form
a
network.
Let
X
be
a
meaningful
protein.
Let
N
be
the
number
of
proteins
which
can
be
derived
from
X
by
a
unit
mutational
step,
and
f
the
fraction
of
these
which
are
meaningful,
in
tho
sense
of
being
as
good
as
or
better
than
X
in
some
environ-
ment.
Then,
if
JN> 1,
meaningful
proteins
will
form
a
network,
and
evolution
by
natural
selection
is
possible.
In
estimating
Nit
is
necessary
to
distinguish
two
classes
of
.mutations:
(i)
substitutions
of
single
amino-acids,
and
additions
or
deletions
of
small
numbers
of
amino-acidR,
making
only
a
small
change
to
tho
protein;
and
(ii)
mutations
producing
a
major
change
in
amino-acid
sequence,
such
as
frame
shifts
and
intramolecular
inver-
sions.
NATURE
VOL.
225
FEBRUARY
7
1970
Mutations
of
the
former
type
are
much
more
likely
to
give
rise
to
meaningful
proteins
than
the
latter.
In
the
same
way,
a
single
random
letter
substitution
in
a
meaningful
word
is
more
likely
to
give
rise
to
a
meaningful
word
than
the
simultaneous
alteration
of
all
the
letters.
Although
frame
shift
mutations
are
known
to
occur,
it
is
not
clear
whether
they
have
ever
been
incorporated
in
evolution.
It
is
therefore
better
to
take
N
as
the
number
of
possible
substitutions
of
single
amino-acids.
If
all
substitutions
were
possible
in
a
single
mutational
stop,
N
for
a
protein
of
100
amino-acids
would
be
1,900.
In
practice
the
genetic
code
limits
X
to
approximately
10
3
•
Hence]
must
be
greater
than
1/1,000.
It
does
not
follow
that
the
fraction
of
all
possible
sequences
which
are
meaningful
need
be
as
high
as
1/1,000.
It
is
probably
much
lower.
There
is
almost
certainly
a
higher
probability
that
a
sequence
will
be
meaningful
if
it
is a
neighbour
of
an
existing
functional
protein
than
if
it
is
selected
at
random.
In
fact,
in
treating
X
as
the
number
of
amino-
acid
substitutions
rather
than
as
the
total
number
of
possible
mutational
steps,
it
was
in
effect
assumed
that
a
random
sequence
has
a
negligibly
small
probability
of
being
functional;
this
assumption
will
be
confirmed
if
it
turns
out
that
frame
shifts
are
rarely
or
never
incorporated
in
evolution.
Suppose
now
that
we
imagine
all
possible
amino-acid
sequences
to
be
arranged
in
a
"protein
space",
so
that
two
sequences
are
neighbours
if
one
can
be
converted
into
another
by
a
single
amino-acid
substitution.
Then
the
requirement
that
JN
> I
requires
that
the
"density''
of
functional
proteins
in
certain
n,gions
of
the
space
must
be
quite
high-perhaps
greater
than
1/1,000.
This
agrees
with
Salisbury's
conclusion
that
proteins,
and
hence
the
genes
that
determine
thorn,
cannot
be
as
unique
as
aJI
that.
As
a
convinced
Darwinist,
I
published•
the
con-
clusion
that
JN
> I
when
little
was
known
about
the
frequency
of
amino-acid
substitutions
in
evolution.
Since
then
evidence
has
accumulated
(for a
review,
see
King
and
Jukes
3
)
that
many
substitutions
are
either
selectively
neutral
or
at
least
make
comparatively
minor
changes
in
the
function
of
proteins.
If
JN
>
I,
no
quantitative
difficulty
arises
in
explaining
the
evolution
of
proteins
by
natural
selection.
A
difficulty
nevertheless
remains
in
explaining
the
origin
of
life-that
is,
in
explaining
the
origin
of
the
first
functional
proteins
together
with
the
genetic
mechanism
for
producing
them.
If
it
were
true
that
only
a
minute
fraction
of
possible
amino-acid
sequences
have
eYen
the
slightest
enzymatic
activity,
it
would
be
difficult
to
understand
how
the
first
proteins
arose.
I
do
not
want
to
discuss
the
problem
of
the
origin
of
life,
but
only
to
point
out
that
it
is a
quite
different
problem
from
that
of
the
mechanism
of
evolution.
Some
questions
about
molecular
evolution
can
be
formulated
more
clearly
in
terms
of
a
protein
space.
For
example:
(i)
Are
all
existing
proteins
part
of
the
same
continuous
network,
and
if
so,
have
they
all
been
reached
from
a
single
starting
point
?
Possible
alternatives
are
that
there
are
two
or
more
distinct
networks,
or
that
there
is
one
network
with
multiple
starting
points.
(ii)
How
often,
if
ever,
has
evolution
passed
through
a
non-functional
sequence
?
If
so,
has
this
been
achieved
by
the
random
walk
of
genes
rendered
redundant
by
duplication,
or
by
the
chance
concurrence
of
two
or
more
mutations?
(iii)
What
fraction
of
the
functional
net-
work
has
already
been
explored
in
evolution?
(iv)
vVhat
fraction
of
potentially
useful
proteins
are
inaccessible
?
JOHX
MAYNARD
SMfflI
School
of
Biological
Sciences,
Universit,y
of
Sussex
.
Received
November
7, 1969.
1
Salisbury,
F.
n.,
Nature,224, 342 (1060).
'Maynard
Smith,
J.,
in
Tlte Scientist Speculates
(edit.
by
Good,
I.
J.)
(Heine-
mann,
London,
1961).
3
King,
J.
L.,
and
,Tnkes,
T.
H.,
Science, 164, 788 (1060).
John Maynard Smith (1920-2004) was a British mathematical evolutionary biologist and geneticist.
Source: https://en.wikipedia.org/wiki/John_Maynard_Smith
Here is a great article that articulates the significance of 'Natural Selection and the Concept of a Protein Space' on its 50th anniversary: https://www.ncbi.nlm.nih.gov/pmc/articles/PMC7153927/
> "Natural selection and the concept of a protein space" has been described as among the most influential analogies ever proposed in evolutionary genetics.
Source: https://www.ncbi.nlm.nih.gov/pmc/articles/PMC7153927/
> Salisbury wrote in 1969 in "Natural Selection and the Complexity of the Gene", "Modern biology is faced with two ideas which seem to me to be quite incompatible with each other. One is the concept of evolution by natural selection of adaptive genes that are originally produced by random mutations. The other is the concept of the gene as part of a molecule of DNA, each gene being unique in the order of arrangement of its nucleotides. If life really depends on each gene being as unique as it appears to be, then it is too unique to come into being by chance mutations. There will be nothing for natural selection to act on. "
While it is difficult to estimate the overall potential protein-space, the amino acid vocabulary consists of 20 unique amino acids, and the longest known protein is Titin, which can be up to 35,000 amino acids long. While one can't extrapolate that the potential protein search space is therefore 20^35K or an even bigger number, it clearly is enormous...
Titin is a protein that is encoded by the TTN gene in humans, and has a length that ranges from ~27,000 to ~35,000 amino acids depending on the splice isoform. It is the third most abundant protein in muscle.
Titin background: https://en.wikipedia.org/wiki/Titin