►
Description
Review of "Periodicity in the Embryo" manuscript, Notetaking Strategies (Evergreen Method, Zettelkasten), and Papers from the Reading Queue on Connectome and Cell-type Dependent Morphogenesis. Attendees: Susan Crawford-Young, Richard Gordon, Bradly Alicea.
A
B
B
Yeah,
well
I
mean
the
time
change.
I
don't
know
what
happened,
but
if
you
yeah,
I
don't
know,
anyways
it'll
probably
be.
If
you
have
something
to
present.
That
would
be
fine.
There
might
be
some
other
people
coming,
but
I
don't
know
yet
I
don't
like
well,
I
can
start
off.
Do
you
have
something
you
want
to
present
today.
A
No
okay,
I'm
afraid
I
had
a
house
disaster.
I
realized
that
the
furnace
needed
to
run
because
it's
getting
colder
and
our
basement
flooded
in
the
spring
and
stayed
flooded
for
about
a
month
and
a
half,
and
so
basically,
everything
that
was
on
the
floor
had
to
leave
and
a
few
other
things
so
yeah.
So
far,
it's
three
truckloads
of
things.
B
A
A
B
A
B
B
B
All
right,
so
the
first
thing
is,
is
that
we
are
working
on
this
periodicity
in
the
embryo
paper,
and
I
know
that
has
been
asked
was
asking
about
it,
but
he's
unfortunately
in
quarantine.
Right
now
for
covent
19.,
his
father
got
covered
19,
unfortunately,
and
so
he's
been
suffering
with
that.
So
best
of
luck.
B
Yeah
yeah
yeah
yeah,
it's
there,
it's
pretty
rough
still
so
so
this
paper
is
the
periodicity
in
the
embryo,
emergence
of
order
and
space
diffusion
of
order
and
time
and
we've
talked
about
this
in
past
meetings
so
where
we
are
right
now
on
this
is
that
we
have
an
abstract.
It
can
be
revised.
I've
got
it
in
in
google
doc
form.
So
last
time
you
saw
it.
B
It
was
in
the
github
repository
as
a
markdown
file
again
getting
it
ready
for
heavier
editing
so
and
putting
it
into
the
into
a
google
doc,
and
so,
if
you'd
like
to
have
permissions
I'll
put
this
in
the
slack
channel
or
I'll,
send
it
to
people.
I
can
even
put
it
in
the
chat
right
now
for
susan.
If
you
want
to
look
at
it.
B
A
B
Yeah-
and
so
this
is
yeah-
this
is
it's
it's
about.
Eight
pages
right
now
needs
to
be
probably
about
at
least
twice
this
length,
and
some
of
it'll
be
like
filling
out
some
of
the
details
about
the
analysis
and
that,
but
some
of
it
is
going
to
be
like
you
know
the
introduction,
for
example,
so
we
have
a
nice
introduction
where
we
kind
of
talk
through
different
parts
of
the
paper.
B
You
know
what
what
are
we
talking
about
here?
Why
is
it
relevant
and
then
I
have
some
graphs,
so
I
have
some
graphs
here
which
are
probably
best
in
a
formal
results
section,
although
I
don't
really
have
that
distinguished
yet.
So
a
lot
of
this
is
just
kind
of
like
I
may
need
to
put
in
like
another
like
we
need
to
put
in
a
method
section
and
then
like
define
results,
and
then
this
is
a
well.
This
is
actually
c.
This
is
c
elegans.
B
B
A
B
A
B
B
I
don't
know
if
it's
in
here
but
anyways
and
then
this
is
something
we
call
information
isometry,
which
is
a
method
that
we
use
in
our
that
was
developed
in
a
paper
several
years
ago
by
the
group
where
we
look
at
taking
like
a
lineage
tree
and
flipping
the
nodes
internally
using
different
criterion.
So
you
give
it
give
the
cells
a
different
identity
and
you
flip
the
order
of
the
tree
and
the
sub
trees
within
it.
B
And
then
you,
based
on
the
difference
between
like
a
control
tree
and
like
the
tree
that
you
flipped.
What
is
the
amount
of
information
in
each
part
of
the
tree?
And
so
this
is
a
lineage
tree
kind
of
like
rooted
here,
and
then
the
cell
divisions
proceed
outward
like
this
and
you
can
see
the
this
is
all.
I
think
this
has
been
done
a
little
bit
differently,
so
I'll
have
to
like
explain
what's
going
on
in
this
graph.
B
B
B
So
it's
a
lot
like
what
we're
doing
in
this
graph
here
for
zebrafish,
but
we're
doing
it
down
here
for
like
a
synthetic
example,
and
so
we
can
start
with
a
uniform
set
of
divisions,
maybe
like
every
20
minutes,
there's
a
division
event
and
then
going
from
there.
We
can
like
distort
the
distribution
of
timing.
So,
instead
of
every
20
minutes,
we
might
say
well,
the
divisions
occur
an
unspecified
rate,
but
it
generally
happens.
B
You
know
within
a
certain
interval
of
that
20
minutes,
and
so
one
of
the
things
that
you
can
do
is
you
can
generate
these
trees
or
degenerate.
These
data
sets
using
a
sort
of
a
uniform
distribution,
but
you
can
also
generate
them
using
a
poisson
distribution
and
the
poisson
distribution
gives
you
a
little
bit
of
variability
in
terms
of
the
timing.
B
You
know
so
instead
of
every
20
minutes,
it'll
be
like
maybe
six
minutes,
eight
minutes,
15
minutes
and
so
forth,
and
you
can
generate
a
distribution
like
that
and
you
can
look
at
the
difference
between
those
two
division
regimes
and
see
what
they
look
like,
and
so
that's
what
we've
done
here.
I've
given
a
little
example
in
this
table,
so
a
small
sample
of
our
numeric
simulation.
B
B
B
B
B
You
know
with
a
broad
with
a
little
bit
broader
variability
than
the
than
the
standard
uniform
set
of
divisions,
and
so
we
find
is
that,
after
about
four
division
events,
you
start
to
get
more
division
events
earlier
in
developmental
time
on
average,
so
that
you
have
this.
This
poisson
distribute
division
time,
distribution
that
we've
created
here.
B
Everything
happens
a
little
bit
earlier
than
in
the
uniform
case,
and
so
that
that
mean
maybe
means
that
there's
some
other
type
of
distribution
that
it's
using
even
to
generate
events.
Earlier
I
mean
you
can
make
you
know
you
can
have
division
events.
I
guess
like
every
minute.
I
guess
that
wouldn't
be
that
surprising,
except
that
you
know
there
is
this
sort
of
you
know
there
are
limits
of
like
mitosis
and
things
like
that.
B
B
B
B
B
You
know:
are
there
like?
Are
there
tempos
and
modes
of
development
that
allow
you
to
yield?
You
know
to
really
explain
what's
going
on
in
some
of
these
data,
so
then
we
talked
a
little
bit
actually
about
something
called
the
quantum
mitosis
hypothesis
and
quantum
mitosis
is
something
that
I
guess
it's
a
theory
that
involves
rounds
of
cell
division
and
changes
in
gene
expression,
which
then
in
turn
changed.
B
Have
a
potential
to
sort
of
modify
the
fate
of
different
cells
in
the
embryo,
so
quantum
mitosis
involves
changes
in
gene
expression
every
time,
there's
a
cell
division,
there's
some
change
in
gene
expression
and
every
time
there's
a
change
in
gene
expression,
that's
potentially
enough
to
change
the
identity
of
the
cell
and
then,
ultimately,
the
observed
fate
of
the
cell.
So
you
know
you
have
a
lot
of
changes
in
gene
expression
that
change
the
identity
of
the
cell,
meaning
like
it's.
B
I
mean
we're
gonna,
add
more
to
the
discussion,
we'll
probably
talk
about
temperature
dependence
and
other
things
that
you
know,
maybe
things
that
we
haven't
accounted
for
here
or
you
know
things
to
look
at
and
others
you
know
in
the
future
and
then
our
references,
we
don't
have
a
lot
of
references.
We
have
about
15
references,
so
actually
that
can
be
rid
of
but
yeah.
So
it's
about
15
references
now
so
we're
we
need
more
references
in
this
paper,
but
so
that's
where
we
are.
B
A
B
You
yeah
thank
you
yeah,
and
so,
if
you're
watching
this-
and
you
say
I
want
to
be
involved
still,
then
you
know
we
have
other
things
you
can
do.
Definitely
literature
search
is
one,
and
maybe
you
know,
reading
through
and
editing
is
another
like
making
sure
things
make
sense.
Suggestions
for
like
graphs
and
visualizations
is
another,
so
we'll
walk
through
all
this.
You
know
before
it
gets
submitted,
and
hopefully
you
know
it
looks
pretty
good
by
the
time.
We're
done
and
looks
like
a
good
paper
but
yeah.
B
B
B
A
B
So
I
was
just
talking
about
the
periodicity
of
the
embryo
paper
that
was
that
we're
gonna
try
to
put
into
that
special
issue.
So
this
is,
I
mean
it's
not
really
that
organized.
Yet
it's
it's
sort
of
organized
trying
to
figure
out
how
to
put
everything
in
place,
but
I'm
just
you
know,
kind
of
walking
through
it
for
people
who
are
watching
this.
It's
like
15
references.
B
D
D
D
A
D
A
B
E
B
B
So
yeah-
I
guess
next
thing
we'll
do
in
the
meeting
here
is-
I
was
kind
of
hoping
jesse
would
show
up,
because
we
had
a
good
discussion
about
note-taking
on
saturday
at
her
other
meeting
and
he
has
a
method.
He
calls
the
twirly
gig
method
and
I
I
don't
know
like
I
guess
these
are
the
twirly
bird
method
like
there
are
these
things
that
these
seeds
that
spin
around
when
they
fall
off
the
trees.
B
B
A
B
It's
always
yeah.
It's
always
a
challenge
because,
like
there
are
different
methods
that
work
well
for
people-
and
I
I
don't
want
to
speak
to
like
say
that
you
know
everyone
has
this.
You
know
everyone
has
to
do
a
certain
method
for
note-taking,
because
it's
it's
and
that's
one
of
the
problems
that
people
have
with
note-taking
is
that
it's
you
know,
works
for
you.
Well,
it's
like
a
diet.
You
know
if
it
works
well
for
you,
then
that
works.
If
not,
then
forget
it,
and
so.
A
D
A
E
D
B
B
So
I
go
back
to
note
taking
so,
let's
assume
you
have
digital
notes,
but
the
issue,
of
course,
is
too.
If
you
have,
if
you
prefer
taking
notes
on
paper,
then
there's
no
question
of
digitizing
that,
but
if
you
want
to
take
digital
notes,
you
know
there
are
a
lot
of
ways.
You
can
do
this.
You
can
type
things
out
in
a
document.
They
have
now
pens
that
will
transcribe
things
into
like
from
your
writing
to
your
to
some
sort
of
searchable
text,
but
there
are
other
types
of
note
taking
systems
here.
B
B
So
this
is
the
evergreen
note
rating
system
and
this
is
created
as
a
way
to
sort
of
like
not
only
just
kind
of
improve
the
way
notes
are
taken
but
sort
of
organizing
them.
On
the
other
end,
you
know
how
do
you
sort
through
them
after
you've
taken
them
because
notes
aren't
really
any
good
if
you
just
like
write
them
down
and
just
put
them
away,
and
then
you
can't
really
access
them
later.
B
B
B
So
those
are
types
of
things
that
are
interested
here
and
then
that
this
led
to
this
development
of
this
evergreen
note
rating
system,
and
it
goes
at
a
fundamental
unit
of
knowledge
work,
which
means,
I
guess,
evergreen
note,
writing,
helps
insight
accumulate,
and
so
this
is
supposed
to
be
like
computer
supported
thinking
instead
of
computer
supported,
note
taking
so
that's
their
their
focus
on
this,
but
so
they've
presented
on
this.
This
is
a
rather
new
method.
B
This
is
a
couple
years
old,
maybe
where
they're
kind
of
building
this
note-taking
system,
that
includes
contacts,
context,
feedback
and
all
these
things.
That
will
be
helpful
in
interpreting
your
notes
as
well.
So
yeah
I
mean
another
thing
too
is
like
you
might
take
notes
and
they
might
not
be
useful
to
other
people.
So
if
you
take
notes
in
some
shorthand,
you
know,
can
you
understand
it
later?
B
D
B
A
D
A
B
C
B
You
don't
have,
and
you
have
you
can
also
do
you
know,
write
a
program
and
comment
on
it,
so
I
don't
have
a
example
of
that
to
pull
up
right
now.
But
basically,
if
this
you
know
this
window
were
filled
with
computer
code
and
we
had
comments
in
it.
You
know
we
could
do
you
know
we
could.
We
could
do
some
sort
of
commenting
and
maybe
another
file
in
the
directory.
B
B
Another
way
to
go
to-
and
you
know
it
makes
it
a
little
bit
more
like
at
least
we
have
the
version
control
aspect
of
it.
So
you
know
you
can
look
at
the
history
of
a
file
and
you
can
look
at
something
that
maybe
was
talked
about
earlier
and
see
how
the
comments
changed
or
people
have
addressed
the
comments
we.
B
Bit
with
some
of
the
writing
that
we
were
doing
in
another
group
of
mine
earlier
this
year,
we
were
writing
an
essay
and
we
wrote
and
we
would
have
like
comments
embedded
in
the
essay
and
then
you
know
we
could
address
the
comments
and
have
versions
of
it.
Where
the
comment
there
was
like
a
conversation
in
the
in
a
comment.
So
we'd
have
like
a
we'd.
Do
something
like
this.
B
We'd
have
like
four
bars
and
then
like
a
comment,
and
then,
if
you
commit
it,
you
can
see
that
it
makes
a
comment
like
this.
One
doesn't
work,
but
it's
it's.
I
can't
remember
if
it's
four
bars
or
five
bars
anyways
there's
a
way
to
make
a
comment
in
in
markdown,
where
it
sort
of
indents
it
and
makes
interns
color,
and
then
you
can
put
you
know,
notes
in
there
and
they're
kind
of
separate
from
the
rest
of
the
document.
B
D
B
C
D
Yeah
there
used
to
be
a
a
word
processor
that
made
that
extremely
easy.
It
was
called
mind
right,
and
I
actually
made
a
mixture
of
mind
right
and
pascal
so
that
I
could
take
the
hierarchical
structure
of
the
pascal
program
and
easily
incorporate
it
into
a
mind
right
and
go
back
and
forth
between
the.
E
B
B
B
B
You
saw
andy
matuchik's
notes,
and
this
is,
I
guess
this
is.
This
evergreen
is
an
example
of
the
zettocastin,
but
digi
doing
this
digitally,
and
so
this
article-
and
I
can
put
a
link
to
it
here
in
the
chat
if
you
want
to
read
more,
but
they
kind
of
go
through
implementing
this
on
their
own.
So
the
idea
here
is
that
you
know
your
people
talk
about
this
as
a
framework,
but
can
people
use
it
in
a
way?
B
B
B
B
Yeah,
so
I
mean
I
don't
know
if
I'll
go
into
that
too
much
more,
but
if
people
want
to
read
that
I'll
put
up
a
link
I'll
send
the
link
out
on
the
slack
as
well.
For
that,
then
there's
this
taxonomy
of
notice,
which
is
another.
This
is
another.
This
is
a
blog
post,
so
this
talks
about
taking
smart
notes,
it's
one
of
the
most
efficient
ways
to
increase
your
productivity
and
creativity.
D
B
B
There
are
probably
a
few
products-
oh
yeah,
I'm
sure
people
have
maybe
revisited
this
or
maybe
not
it'll,
be
interesting
to
see
so
that
I
put
a
link
to
the
taxonomy.
I
know
it's
in
here
and
then
yeah.
Thank
you
for
the
conversation
on
this.
I
think
maybe
we'll
follow
up
on
this
next
week,
or
so
maybe
jesse.
If
he's
here,
we'll
have
some
things
to
say
about
it,
but
I
think
it's
worth
talking
about
because
it's
it's.
I
think
it's
a
common
challenge
to
a
lot
of
people
and
it's
quite.
D
B
B
A
A
D
E
B
E
B
B
D
B
What
is
the
do?
You
know
what
the
book's
name
of
the
book
is
or
yeah
yeah
yeah
yeah
that'll
be
interesting,
so
yeah,
this
video
is
the
incf
put
it
out.
It
was
a
talk
and
then
this
is
about
them,
simulating
a
drosophila
brain,
I
think,
cell
by
cell
and
by
connections,
and
so
this
video
goes
through
a
lot
of
the
stuff
they
go
through.
D
D
B
Yeah
so
yeah
thanks
for
that,
so
this
this
video,
it's
it's
available
on
youtube.
They
talk
about.
You
know
the
entire
sort
of
drosophila
brain,
so
we
know
that
the
c
elegans
brain
we
have
the
full
connectome
and
they're
rapidly
finding
or
releasing
full
connectoms
in
different
parts
of
the
drosophila
brain.
So
I
think
they
have
a
a
published
connectome
of
one
part
of
the
drosophila
brain.
B
I
don't
think
it's
the
mushroom
bodies,
but
it's
something
else
and
so
they're
able
to
sort
of
give
us
some
of
these
they're
they're
using
that
data
as
the
basis
for
their
simulation
here
and
they're
able
to
do
so,
I
mean
I'm
gonna,
I'm
not
gonna,
go
through
the
video
that
much,
but
if
you
wanna
see
it
there
there,
it
is
a
couple
other
papers
here.
So
this
one
is
the
morphostatic
limit
for
a
model
of
skeletal
pattern
formation
in
the
vertebrate
limb.
B
This
is
an
interesting
mathematical
modeling
paper
from
2007.
I
ran
across
recently,
where
they
have
this
recently
proposed
mathematical
model
of
a
core
set
of
cellular
molecular
interactions
present
and
the
developing
vertebrate
limb
was
shown
to
exhibit
pattern
forming
instabilities
in
limb
skeleton-like
patterns
under
certain
restrictive
conditions,
suggesting
that
it
may
authentically
represent
the
underlying
embryonic
process,
and
so
they
do.
B
A
B
B
So
they
have
this
yeah,
so
this
is
a
then,
so
they
develop
a
mathematical
model
for
this,
and
so
this
might
be
an
interesting
one
if
you're
interested
in
some
of
these
issues
related
to
limb
development,
which
is
an
interesting
part
of
development.
We
don't
talk
about
as
much
in
the
group
as
we
usually
do,
because
it's
not
really
a
c
elegans
thing,
but
you
know.
Let
me
ask
you
a
stupid
question:
yeah
connectome.
B
B
B
We
kind
of
know
that,
like
if
you
look
at
it
like
neurons
synapsing
onto
other
neurons,
we
know
that
there
changes
over
time
and
some
of
those
in
some
cells,
but
not
others
with
respect
to
gap
junctions,
it's
more
conserved,
so
you
don't
see
a
lot
of
changes
in
in
development,
but
it's
you
know.
We
don't
really
know
that.
D
A
B
B
So
they
go
on
to
talk
about
this.
They
review
key
examples
and
proposes
similarities
in
morphogenesis,
as
well
as
associated
gene
expression.
Dynamics
may
reveal
an
evolutionarily
conserved
developmental
mode
as
well
as
provide
further
insights
into
the
role
of
external
or
extra
embryonic
cues
in
shaping
the
early
embryo,
so
embryo-like
systems
can
be
employed
to
inform
previously
uncharted
aspects
of
animal
body,
plan,
evolution
and
patterning
rules.
B
So
check
into
that,
so
that's
the
paper,
this
second
paper,
and
so
this
is
another
interesting
paper
which
we
have
a
lot
of
time
to
go
over,
but
this
they
give
a
nice
diagram
of
primary
axis
formation
during
gastrulase,
gastrulation,
metazoan
embryos
and
corresponding
artificial
systems,
so
they're
looking
across
phylogeny
here
of
of
metazoans
from
peripheral,
neidarians
and
then
into
arthropods
and
then
mollusks
and
then
invertebrates.
Finally,
and
so
you
can
see
some
of
these
changes
as
they
exist
in
embryos
across
phylogeny,
and
this
is
sort
of
the
idea
of
the
paper.
B
B
B
Real
quick
and
this
is
disentangling
scaling
arguments.
So
this
is
an
interesting
paper.
If
you
know,
if
you
think
about
scaling-
and
this
is
more
mathematical
than
developmental-
but
if
you
think
about
like
scaling
like
morphological
scaling
or
some
other
scaling
law
that
they
often
talk
about
like
in
network
science
or
something,
then
this
is
something
that
developed
in
the
field
of
physics.
B
You
know
they
talk
about
like
power,
loss,
scaling
and
things
like
that.
So
this
paper
kind
of
goes
over.
You
know
contemplating
what
that
means,
and
then
also
talking
about.
Maybe
you
know
where,
where
it
is
and
isn't
applicable,
so
it's
a
nice
kind
of
a
it
does
go
over
a
little
bit
of
the
history
and
it
goes
over
a
little
bit
of
the
mathematics
of
it,
and
so
I
mean,
if
you
know,
instead
of
when
you
read
about
power
laws
and
things
like
that.
B
B
So
I
think
we're
at
the
top
of
the
hour.
So
I
would
like
to
thank
everyone
for
joining
us
this
week
and
I
think
we
had
a
good
nice
discussion
about
the
note
taking
and
about
the
about
embryos
and
everything
else,
and
this
for
the
paper
that
I
showed
you
that's
an
ongoing
work
or
target,
like
I
said
we're
targeting
submission
at
the
end
of
the
year
for
that.
B
So,
if
you're
interested
in
participating,
if
you
wanna
well,
we'll
probably
send
out
drafts
when
we
get
closer
to
that
point,
but
that's
that's
something
everyone
can
help
with
but
yeah.
If
you
have
ideas
for
it
or
if
you
wanna
see
the
draft
in
its
current
state
I'll,
send
you
a
link
to
the
google
doc
and
we
maybe
we
can
discuss
it
in
more
next
week
too.