►
From YouTube: DevoWorm (2020, Meeting 15): update on 3-D modeling, Embryo Physics course, paper review.
Description
DevoWorm meeting: April 27, 2020. Attendees: Richard Gordon, Ujjwal Singh, Bradly Alicea, and Jesse Parent.
A
B
Guess
we
can
get
started,
yeah
I,
don't
know
any
other
people
will
show
up,
but
though
they
can
come
in.
So
welcome
to
the
meeting.
I
hope
you've
been
having
a
good
week
more
than
a
week
of
five
and
seen
you
since
Jesse
welcome
back
Jesse's
at
a
conference
today
for
machine
learning,
so
he's
doing
some
live,
tweeting
event
and
other
things,
and
then
dick
I
got
an
email
from
you
about.
Yesterday.
B
A
Asylum
and
said,
I
have
something
like
that
way.
This
shows
like
how
the
cells
are.
We
throw
in
a
set
rock,
so
I
was
looking
based
on
that
paper,
so
I
think
I
have
to
somehow
manage
the
cash
so
I
the
tailor,
Connecticut
and
usually
dates.
So
the
first
task
which
I
will
make
now
is
creating
the
animation
so
that
we
can
get
this
model
completely
I.
A
Inclusion/Exclusion
work
on
the
yes,
once
we
have
this
notation
in
any
layman
like
when
you
have
the
model
for
segmentation,
we
can
definitely
have
3d
segmentation,
and
we
can
also
say
that
I
am
also
working
on
some
piece
so
that
we
can
sell
these.
These
sales
can
be
set
apart
x-ray
entirely
so
that
we
can
focus
on
each
of
the
side
and
they
became
an
ammeter
either.
I
tell
me
they
also
work
on
cutting
down.
We
do
not
eat
in
this
of.
B
So
yes,
this
is
so
this
is
one
slice
of
an
embryo.
So
when
the
image
in
embryo
they
go
the
image
the
embryo
in
slices,
so
you
go
from
like
the
top
to
the
bottom
of
the
embryo
and
you
take
like
a
slice,
a
focal
plane,
slice
the
embryo.
So
this
is
like
the
middle
I
guess
of
the
embryos
this.
These
movies,
that
you
have
they
rather
old
movies.
B
So
they've
they're
not
like
the
highest
level
of
technology
available
today,
but
I
think
there's
still
pretty
good
videos
because
they
have
the
whole
sequence
and
it's
you
know
the
entire.
It's
sort
of
the
the
entire
embryos
all
the
cells
at
any
given
stage
so
I
think
good
place
to
do
this.
Yeah
I
think
that's!
You
can
extrude
from
this
image,
though,
so
you
know
we
can
have
like
that
one.
We
can
take
that
one
flat
focal
plane
and
we
can
stretch
it
out
into
cells.
A
C
B
That's
good
yeah.
This
looks
pretty
good.
Could
you
put
a
link
to
that
YouTube
video
in
the
chat
yeah,
so
this
is
the
three
copy
cell
3d
model
has
been
quite
elusive
to
the
group
over
the
years.
Cuz
I
visited
them
in
like
2015
and
I
haven't
been
able
to.
We
haven't
already
been
able
to
do
much
with
it.
B
Since
just
you
know,
I
take
it
there's
a
learning
curve
and
then
you
have
to
find
the
right
person
to
really
kind
of
dig
into
it
and
you
know
build
some
models,
but
the
models
are
kind
of
like
what
as
well
was
showing
in
in
the
video
they're
sort
of
agent-based
models.
They
have.
You
know
they
have
to.
You,
can
model
cells
and
you
have
this
field
of
cells
and
it's
you've
run
a
simulation.
You
give
the
cells
properties
and
you
can
run
simulations
of
cells
over
some
process.
B
You
know
they
have
a
lot
of
models
for
development,
not
necessarily
C
elegans
development,
but
like
chick
embryo
development,
and
there
are
a
couple
other
models
of
development
that
I'm
I
don't
know.
Maybe
they
have
it
on
the
YouTube
channel
there,
but
you
know
they
it's
a
pretty
versatile
program,
so
I
like
this,
so
this
is
this
is
good
good
progress
again,
I
think
the
neck.
You
know
I,
think
you
know
your
next
steps,
kind
of
you've
kind
of
mentioned
those.
B
So
you
said
that
you
were
going
to
sort
of
work
this
into
a
3d
model.
You
would
have
you
know
you
could
do
this
and
actually
to
do
this
template
for
any
number
of
videos.
So
this
is
just
one
example
there.
You
know
there
are
actually
there's
data
captured
where
people
have.
You
know
many
focal
planes
through
the
embryo
or
through
the
tissue
that
they're
working
with,
and
so
you
can
actually
do
the
same
sort
of
methodology
for
those
sorts
of
datasets
as
well.
B
Where
you
have
you
know,
images
at
different
focal
planes
and
you
can,
you
know,
put
them
in
a
model
like
this
and
then
extrude
them
out.
In
fact,
in
that
case,
you
could
use
information
from
each
slice
to
extrude
in
some
way.
In
some
more
educated
way,
I
mean
that
you
can
extrude
from
this
pretty
well,
but
they
don't
think
there's
a
lot
of
variation
on
the
on
the
on
the
dorsal
ventral
axis,
which
is
the
axis
where
you're
going
from
the
top
to
the
bottom
of
the
cell.
B
C
A
B
So
yeah
well
that
looks
good
and
then
you'll
be
giving
further
updates
like
in
coming
weeks
and
so
yeah.
Keep
us
posted
on
that.
Yes,
okay,
next
thing,
I
wanted
to
do
is
go
to
the
so
I
thought.
I
told
Dec
that
well
he
knows
about
that.
I've
been
working
on
getting
the
old
embryo
physics
course
into
a
new
format,
and
so
I
will
be
showing
that
now
so.
B
This
is
the
home
of
the
new
embryo
physics
course
open
course,
materials
based
on
the
embryo
physics
lecture
series.
Then
you
know
busted
2009
to
2014
in
silver
belong,
Second
Life.
So
for
the
people
who
weren't
there,
of
course,
which
is
Jesse
individual
dick
put
together
a
number
you
a
physics
course-
and
this
is
the
spirit,
a
number
of
topics
in
embryology
and
development
and
he
offered
he
brought
in
people
from
all
over.
You
know
people
brought
them
in
virtually
in
the
second
life
and
had
them
give
these
talks.
B
So
there's
a
lot
of
content
here.
There's
something
like
you
know:
probably
vote
15
talks
a
year,
so
that
was
over
45
years.
So
that's
a
lot
of
content.
That's
you
know,
and
it's
been
hosted
on
someone's
blog.
So
it's
it's
online
now,
but
we
wanted
a
little
bit
more
permanent
home
for
so
the
first
step
in
that,
of
course,
is
to
put
it
in
some
sort
of
archival
location
instead
of
someone's
personal
website.
So
for
this
right
now
we're
using
github
and
so
github
is
a
secure
server
and
it's
a
permanent
server.
B
Once
this
is
finished,
this
can
be
archived
to
something
like
zone
odo,
and
so
the
benefit
of
that
is
to
have,
like
you
know,
like
zip
files
that
people
can
download
and
it
would
have
like
a
DOI
on
it,
so
it
would
have
like
the
more
permanent
address
for
people
to
cite
it
or
things
like
that
in
papers,
and
so
the
way
this
archive
is
set
up
right
now
there
are
a
couple
folders
here
for
different.
This
is
media
images.
B
These
are
movies
related
to
the
lectures
the
presentations
which
are
the
PDFs
of
the
lectures
and
then
some
reference
lists
that
get
linked
in
the
main
document.
So
these
are
the
main
documents
here
are
the
main
sort
of
presentation
locations.
So
when
you
go
when
you
want
to
pick
a
certain
year,
so
you
want
to
find
out
about
lectures
from
2009.
B
B
So
way
it
was
set
up
was
that
you'd
go
in
and
here's
some
seating
for
the
avatars
you'd
go
in
a
second
life
and
choose
an
avatar.
So
this
is
my
avatar
at
the
time
and
you'd
go
in
as
location
and
Second
Life
and
you
your
avatars,
could
sit
around
this
campfire
and
then
here
are
the
boards.
So
these
boards
were
where
you
would
watch
the
presentation.
B
So
here
a
couple
will
the
presentations-
these
are
PowerPoint,
slides,
projected
onto
these
boards
and
then
you
would
watch
the
board.
So
you
could
start
this
presentation
here
at
the
start
button
and-
and
you
could
walk
through
the
presentation
with
these
arrows,
so
you
could
go
forward
and
you
can
go
backward.
So
anyone
could
look
at
some
of
these
presentations
that
are
put
up
on
these
boards.
B
You
know
they're
and
they're
kind
of
like
they're
for
visitors.
You
know
any
time
if
they
came
through
the
place,
but
then
when
there
was
actually
the
lecture
at
the
time
of
the
lecture
you
you
know
you
bring
up
that
week's
lecture
on
this
board
say
and
then
the
whole
group
could
sit
there
and
watch
it,
and
then
the
master
of
ceremonies
would
advance
the
slides
and
it
would
be,
you
know,
a
formal
lecture,
but
you
could
also
visit
you
know
in
the
off
hours
and
view
any
one
of
these
slideshows.
B
B
B
In
2009,
we
had
weekly
talks
starting
January
29th,
and
so
we
have
Stewart
a
Newman
from
New
York
Medical
College,
and
he
gave
a
talk,
a
pattern,
language
for
animal
form,
and
this
is
the
abstract
and
then
you
have
links
the
slides
into
related
blog
post,
so
the
slides
this
is
the
length
of
slides.
These
are
all
hosted
on
this
get
out
in
this
github
repository.
B
Think
it's
gonna
bring
up
the
slides
by
giving
them
download
this
once
it's
open
people,
click
on
the
link.
They
can
get
access
to
this
PDF
and
then
download
it,
and
then
you
know
view
it
on
their
own
machine
or
you
can
view
it
in
here.
I,
don't
know
if
it
advances
in
github,
but
in
any
case
you
have
ax
it's
it's
archived
in
a
in
a
static
location,
and
so
you
know
each
week,
we'd
have
different
speakers.
B
B
We
had.
We
have
some
talks
that
don't
have
abstracts,
so
some
of
them
don't
have
abstracts.
You
just
have
the
slides.
Most
of
them
do
and
again
their
links
off
site,
so
related
blog
posts
related
presentations.
Actually
these
are
related.
Presentations
are
talks
that
this
person
gave
in
another
year.
So
you
know
there's
sort
of
a
hyper
linkage
between
their
talks
from
different
years.
So
if
I
want
to
interested
in
this
talk,
I
can
see
other
talks
and
I
think
it
was
set
up
like
that.
B
In
the
old
archive,
but
I
brought
that
forward,
and
so
this
and
then
this
in
this
case
we
have
someone
who
was
presenting
something
that
was
very
movie
intensive.
So
the
talk
relied
a
lot
of
developmental
biology.
Lectures
will
rely
on
movies
because,
as
you've
seen,
that's
one
of
the
main
forms
of
data,
and
so
in
this
case
we
have
the
movies
and
they're
sort
of
in
this
area
where
the
abstract
normally
is.
B
So
we
just
have
the
links
to
the
movies
and
those
movies
are
actually
on
the
local
server
as
well
on
the
local
archive,
so
they're
all
sort
of
they
will
go
away
and
yeah.
So
that's
the
way
that's
set
up,
and
so
that's
that's
basically
I'm
not
finished
I,
don't
know
if
I'm
finished
with
this
year,
yet
I
think
I'm
finished
with
this
year.
But
there
are
a
couple
years:
I
still
have
to
go
on
this,
where
you
know
I
have
to
bring
over
the
abstracts
and
the
links
to
the
slides.
B
So
2013
is
another
example,
so
this
has
a
different
picture,
so
this
is
I
think
either
part
of
her
adjacent
to
the
silver
blog.
So
these
are
virtual
courses.
I
thought,
there's
a
nice
image.
I
actually
walked
around
at
the
time
and
I
took
it
made
screenshots.
Just
you
know
as
like.
A
travel
log
and
I
got
I
found
those
from
an
old
website
and
I
put
them
on
this
one.
So
that's
that
was
fortuitous
in
my
case.
Well,
we
have
again
we
have.
B
This
is
a
Richards
talk
on
january,
9th
of
2013,
and
this
case
he
has
a
reference
list,
so
the
reference
list
is
hosted
locally
as
well.
So
if
you
go
to
the
reference
list,
it's
just
like
you
know
references
of
academic
papers
that
are
noted
in
the
abstract,
with
these
brackets
1
2
3
4
5.
So
there
are
a
number
of
references
and
those
references
reference
lists.
Here
we
go
so
then
the
references
are
here.
Probably
we
need
more
work
on
like
linking
them
to
digital
versions.
B
You
know
like
different
processes
that
they
read
about
in
these
lectures.
I
mean
we
have
movies.
We
have
other
types
of
AIDS,
you
know
links
to
external
blog
posts,
but
it's
you
know,
maybe
missing
something
like,
and
you
know
something
you
can
run
in
your
browser.
It
doesn't
have
to
be
something
really
complicated.
B
Based
have
a
list
of
different
physics
models
that
I
have
found
and
like
back
when
they
had
flash
movies
and
flash
demos,
they
used
to
have
a
huge
list
of
flash
demos
for
different
physical
models
like
Avalanche
models,
and
things
like
that.
So
a
I
don't
know
if
they
have
those
as
much
anymore.
I'll
have
to
go
look,
but
there
might
be
some.
You
know
simple
models
that
people
can
run
on
their
browser,
like
that.
That
you
know
would
illustrate
some
of
the
concepts
walk
through.
B
B
B
B
B
During
the
course,
but
that
was
a
long
time
ago,
so
yeah
there's
a
lot
of
content
there.
It's
it's
revisiting.
It
I
was
reminded
of
a
lot
of
things
that
generate
an
unknown
list
of
the
talks
and
you're
done
yeah.
That
would
be
good.
I
think
that
would
be
good
to
have
like
a
reference
like
or
something
like
that,
where
you
have
a
like.
An
EndNote
list
is
like
a
formal
sort
of
set
of
citations
for
it.
B
B
B
B
Okay,
so
yeah
next
week,
alright,
so
next
week
we're
going
to
have
I'm
gonna,
give
okay,
which
will
says
I
will
have
to
go
through
the
repo
I'll.
Let
you
know
if
I
have
any
doubts
or
herslef
that's
good
and
then
okay
I'd,
give
an
update
about
the
conference
with
me
mean
more
so
next
week,
good,
that's
Jesse,
so
yeah
for
the
next
couple
of
weeks.
B
So
next
week,
I'm
going
to
give
a
practice
run
of
the
talk
I'm
going
to
give
to
the
virtual
worm
group,
and
so
this
is
a
group
that
was
born
of
like
this,
the
the
walk
down.
You
know
people
are
not
in
their
labs
in
there
at
home
and
bunch
of
C
elegans
people.
Okay,
I
could
talk
on
polygamy,
archaea
and
diatoms
yeah,
that's
good.
We
could
yeah.
We
can
do
this
next
week.
The
plague,
anarchy
and
diatom
stuff
I
forgot
about
that,
but
yeah
that
would
be
good
for
next
week.
B
B
It
can
present
on
the
yeah
percent
on
the
diatoms
and
then
Jesse
said
that
her
papers
I've
mentioned
yeah
in
the
future,
so
yeah
so
next
week,
then
we'll
it
will
do
dicks,
diatom
talk
and
then
we'll
do
this
virtual
worm
talk
and
that
was
born
from
people
who
were
affected
by
the
walk
down
there,
giving
virtual
toxin
zoom
it's
kind
of
a
private
group
and
each
week
like
they
have
one
or
two
people
giving
talks
and
different
aspects
of
C
elegans
biology.
So
that's
really
been
very
biologically
oriented.
B
You
know
there
are
a
lot
of
computational
people
in
the
group
or
a
lot
of
people
doing
different
things
with
C
elegans,
like
you
know,
just
basic
biology,
type
research.
So
you
know
C
elegans
is
a
model
organism,
and
so,
but
they
do
a
lot
of
basic
biology
on
C
elegans.
Looking
at
osmotic
stress-
and
you
know,
sensory
systems
and
other
types
of
things.
There
was
a
wonderful
talk
last
week
on
behavior
tracking
behavior,
but
and
on
the
6th
of
May.
B
There's
going
to
be
two
talks
and
I'm
gonna
give
one
it's
the
computational
week,
so
I'm
gonna
go
through
those
slides
next
week
and
that'll
be
available
afterwards
on
YouTube
and
then
the
following
week.
After
that
we
have
the
G
sock
students,
so
the
G
stuck
G
sock
selection
is
next
week.
May
I
think
May
4th
is
when
the
candidates
are.
The
successful
candidates
are
announced.
B
So
then,
the
week
after
that,
I
will
have
the
people
who
were
selected
give
a
talk
in
here
on
their
like
an
introductory
talk
on
on
their
proposals,
what
they
plan
to
do,
and
it's
not
it
means
I'm
gonna,
be
too
formal
because
they
only
have
a
week
to
prepare,
but
they'll
have.
Hopefully
we've
welcomed
them
into
the
group,
and
we
can
ask
some
questions
about
what
they
plan
to
do.
B
We
already
talked
about
the
proposals
in
this
group,
so
we
will,
we
will
see,
you
know
they'll
get
some
a
little
bit
of
interrogation
about
a
group,
so
there's
a
community
period
in
in
G
sock
where
people
have
to
kind
of
get
involved
in
the
community
as
well.
They
should,
and
in
previous
years
we've
done
it
separately
from
this
group.
So
when
I
kind
of
bring
it
together
at
this
group,
horror
all
right
so
yeah,
so
that's
good!
We
had
to
go
get
that
SAP
so
from
the
schedule.
B
B
So
the
major
tasks
again
like
we
finished
a
number
of
these
we've
got
actually
quite
an
impressive
list
of
finished
things
here
in
progress.
We
have
a
number
of
things
as
well.
Some
things
are
on
hold
and
then
to
do
there's
some
other
things
that
I
haven't
classified
I
just
wanted
to
go
through
the
in
progress
ones,
to
see
where
we
are
so
the
axolotl
embryo,
animations
and
segmentation.
That's
something
that
I
haven't
really
gotten
to
yet
I
was
I.
Did
the
animated
gifts
presented
those
a
couple
weeks
ago?
B
I
haven't
really
gotten
further
than
that
too
much
I'm
still
thinking
through.
However,
the
technical
details
of
that,
maybe
we
can
open
that
up
more
in
coming
weeks,
but
I
think
I
have
a
feel
for
the
data,
at
least
so
we
can
work
on
that
present
our
multi
cell
systems.
So
this
was
something
that
dick
when
he
talked
about
the
political
bacteria,
the
the
diatoms
and
plug
in
a
wife,
something
that
brought
to
mind
this
as
well.
B
But
this
is
something
that
I
can
do
the
next
few
weeks
baby
after
Dix
talk,
maybe
the
week
after
that,
along
with
the
G
Sox
students,
we
can
just
kind
of
quickly
go
over
that
I.
Wasn't
really
ready
for
that
today
create
a
dock
for
open
collaboration
of
papers.
So
this
is
actually
something
that
I
don't
know.
If
I
have
a
link
to
in
here,
they
don't
have
one
in
here
I'm,
creating
a
dock
for
people
to
open
collaborate
on
papers.
B
So
there's
a
number
of
papers
that
I
have
that
we've
kind
of
talked
about
like
abstracts,
and
things
like
that
that
we
don't
have
like
we,
it
can
kind
of
get
lost
in
the
shuffle.
If
we
just
mention
it
and
let
it
go
so
I'm
actually
creating
something.
I
get
help
and
I
can't
remember.
If
I
have
it
I
can't
remember
exactly
where
it
is
right
now,
but
I'll
find
it
I
think
it
may
actually
be
her
meetings.
B
So
maybe
we
can
go
to
that
after
this,
but
I've
created
a
document
that
has
kind
of
links
to
the
Google
Docs
for
these
abstracts
for
these
open
abstracts,
so
that
anyone
in
the
group
can
contribute,
and
of
course
you
have
to
ask
for
permissions
to
to
get
in
and
do
any
sort
of
editing.
But
you
know
once
you
have
the
permission,
then
you
can
contribute
in
some
way.
I
think
there
are
also
some
I
also
have
listed
some.
B
B
We
want
to
keep
that
a
little
bit.
You
have
some
securities
on
it,
but
yeah.
If
Jesse,
if
you're
interested
in
that,
we
can,
I
you
know,
I
can
when
I
get
find
the
list.
I
can
send
it
out
and
then
you
can
look
it
over
and
there
are
a
number
of
different
papers
that
are
sort
of
outstanding.
Can
that
pay.
B
Another
presentation
this
is
still
I'm
working
on
this,
make
google
Summer
of
Code
selections.
That's
gonna,
be
this
well.
Selections
have
already
been
made
and
I
can't
see
anything
about
it,
but
we'll
know
the
results
of
this
on
the
fourth.
So
next
Monday
we'll
know,
that's
the
results
and
I
talked
to
Vinay
about
this
and
we're
going
to
promote
this
on
social
media.
So
when
the
selections
are
made
will
you
know
will
issue
some
sort
of
mention
of
the
people
and
you
know
we'll
get
them
some.
You
know
with
an
open
wound.
B
Definitely
we're
going
to
get
them
some
exposure.
What
letting
people
know
these
are
new
students
for
GSR
and
then
maybe
go
over
their
presentation
like
in
the
following
week
and
we'll
talk
about
that.
So
I
want
to
be
able
to
like
give
them
some
exposure
to
the
broader
community
of
people
who
are
interested
in
this
stuff
and
then
so.
The
copy
cell
model
for
C
elegans,
that's
usual,
and
we
talked
about
that
today.
So
that's
continually
in
progress.
B
B
That
was
the
this
issue
here
versus
this
one
here,
Jake
any
glossed
over,
but
I'm
working
on
this
thing
with
Moyer
patterns
and
then
with
like
morphogenesis
and
perception,
it's
an
agent-based
model,
but
I'm
not
going
to
talk
about
today.
It's
kind
of
an
interesting
thing,
I'll
present
in
the
next
few
weeks,
but
thanks
for
I,
didn't
need
some
references
for
it.
That
was
actually
something
I
was
lacking
in
that
schedule
presentations.
So
we
just
did
that
I
Nick
volunteered
to
present
next
week.
B
The
bachelor
area,
non-neuronal
cognition,
that's
one
of
those
papers-
I
talked
about
that
were
open,
so
we'll
revisit
that
at
some
point
in
the
near
future.
The
embryo
physics
archive-
so
this
is
I-
just
showed
this
off.
This
is
in
progress,
definitely
and
then
reviewing
the
axolotl
data.
So
this
is
our,
of
course.
This
is
being
reviewed
so
we'll
I
guess
this
is
done,
but
I
need
to
make
another
issue
about
working
with
the
axolotl
data,
so
so
I
think
that's
all
for
the
in
progress
issues.
B
B
B
B
But
you
know,
none
of
them
are
very
developed
and
it's
just
you
know
people
are
interested
in
contributing
to
them.
You
can
go
through
and
look
at
the
document,
sometimes
they're,
very
rudimentary,
but
sometimes
they're.
Actually,
you
know
actual
outlines
like
for
this
one's
an
outline.
This
one
is
actually.
This
was
based
on
the
lecture
that
I
delivered
at
neuro
match,
but
it
might
have
some
relevance
to
this
group
and
I
put
a
github
repo
link
here.
B
So
if
you
want
to
contribute
to
the
github
repo,
this
is
the
github
repo
for
this
particular
idea,
and
so
there's
a
lot
of
stuff
in
here.
If
something
strikes
your
fancy,
you
can
contribute
to
it.
You
don't
have
to
issue
a
poor
quest.
You
can
just
email
me
and
say
this
is
something
that
relates
to
this
thing.
I
try
to
keep
this
open
as
much
as
possible
in
terms
of
multiple
channels,
because
we
have
some
people
were
very
proficient
at
github
and
other
people
who
don't
use
it.
B
B
Yeah
they're
pretty
technically
involved
so
I'm
just
gonna
go
through
them
very
quickly,
I.
Just
to
make
you
aware
that
they
exist,
you
don't
have
to
read
them
all
the
way
through.
If
you
don't
want
to.
This
is
something
that
Steve
McGrew
pointed
me
to
last
week,
sent
an
email
and
story
again.
Like
last
week,
I
said
that
sometimes
like
these
press
releases,
that
they
give
for
papers
are
particularly
misleading
or
they're
very
hyped.
And
then,
when
you
read
the
paper,
it's
it's
something
different,
but
it's
still
impressive.
B
This
one
falls
into
the
still
impressive
category
asses
more
physique,
so
this
is
where
they
took
a
chordate.
In
this
case
it
was
a
sea
squirt
and
they
looked
at
the
cells
in
the
early
embryo.
So
one
of
the
things
about
the
early
embryo
sea
squirts
is
that
they
have
this
very
orderly
division
process,
so
you
can
actually
have
been
able
to
very
exquisitely
characterize
the
phenotype.
Each
cell,
each
cell
divides
into
daughter
cells
and
those
daughter
cells
are
easily
identified
in
the
in
the
embryo.
You
can
track
them
and
they're
always
the
same.
B
Simple
left-right
symmetry
they
have
a
fourfold
symmetry,
so
they
actually
have
four
equivalent
hemispheres,
and
so
that
has
something
to
do
with
the
way
that
the
cells
divide
and
they
had
the
way
that
nomenclature
works
is
it's
like.
The
nomenclature
is
like
this
cells
divide
into
a
cells
and
B
cells,
and
then
there's
an
a
star
and
a
B
star,
and
that's
how
you
represent
that
fourfold
symmetry.
But
the
advantage
of
this
type
of
development
is
that
you
can
identify
cells
and
track
them
as
they
go
through
this
early
embryogenesis.
So
you
can
do.
B
Is
you
can
attach
gene
expression,
data
to
each
of
these
cells
and
that's
what
they
do
in
this
paper?
They
do.
This
thing
called
Morpho
seek,
which
is
single-cell
RNA
sequencing,
and
so
this
is
a
specific
type
of
RNA
sequencing
if
you're
familiar
with
what
they
call
next-gen
sequencing.
You
know
that
there
are
a
lot
of
different
methods
for
taking
RNA
and
sequencing
it,
but
this
one
is
based
on
sink.
You
know
recovering
RNA
from
a
single
cell,
amplifying
that
RNA
and
then
sync
with
sequencing
it
and
then
mapping
it
to
some
reference
genome.
B
They
have
these
data,
so
now
they
can
actually
trace
through
the
what
they
call
the
lineage
tree
and
identify
single
cells
by
their
own
a
profile,
and
so
they've
done
some
of
the
sort
of
C
elegans,
but
it
hasn't
been.
They
actually
haven't
done
it
in
development.
So
much
they've
done
it
in
adults
and
they
have
atlases
or
you
can
look
at
adult
cells
and
you
can
get
the
gene
expression
profile
for
adult
cells
for
development.
B
It's
been
a
little
bit
elusive,
and
so
they
describe
this
technique
here
and
so
what
they've
been
able,
but
the
additional
thing
that
they've
done
in
this
work-
and
this
is
an
example
of
how
the
cell
divides
in
this
fourfold
symmetry
right
and
then
eventually
it.
You
know
you
get
tissues
and
things
like
that
that
differentiate.
But
what
the
additional
thing
they've
been
able
to
do
in
this
paper
is
to
take
a
3d,
build
a
3d
model,
a
3d
computational
model
and
predict
the
cell
division
process.
B
So
I
don't
know
if
they
have
in
here
in
the
paper,
but
they
have
it
in
the
article
okay.
So
this
is
I
think
an
example
of
how
they've
done
this,
so
they
can
actually
map
these
gene
expression
profiles
to
a
virtual
model
of
the
embryo.
So
in
this
case
you
have
this
cluster
of
like
3d
fears
right
and
they've
been
able
to
actually
map
these
two
specific
cells
in
this
virtual
model.
B
So
this
is
just
a
model
of
what
you
observe
in
the
embryo
and
most
of
the
time
when
you
do
see
when
you
do
RNA
analysis,
you're,
maybe
able
to
localize
it
to
certain
parts
of
the
embryo
or
certain
cells.
Maybe
so
it's
very
you
know
it's
very
kind
of
approximate
in
this
case
they've
been
able
to
actually
map
them
to
single
cells,
so
they
can
define
single
cells
by
defining
their
RNA
expression
profile.
B
B
Of
the
of
the
virtual
embryo
that
they've
used
vegetal
pool
this
is
an
example,
the
vegetable
from
this
embryo,
and
they
have
different
cells
that
have
a
proto,
KT
or
an
expression.
So,
for
example,
this
is
where
these
this
is.
These
are
the
expression
patterns
for
that.
So
that's
a
pretty
interesting
paper.
B
Let
me
actually
give
you
a
link
to
this
folder
in
case
you
want
to
download
these
papers
and
read
them
yourself.
So
that's
the
paper
on
Morpho
seat
and
then
in
the
last
couple
minutes
we'll
talk
about
the
second
paper,
which
is
supposed
to
turn
tissue
pattern
formation.
So
this
is
something
so.
The
Turing
model,
of
course,
is
the
reaction
diffusion
model
that
we
know
and
love,
and
it
involves
you
know
it's
sort
of
a
chemical
morphogenesis
model
in
this
case,
they're
advocating
for
this
Meccano
chemistry
model
and
so
they're.
B
The
abstract
says
chemical
and
mechanical
pattern.
Formation
is
fundamental
during
embryogenesis
and
tissue
development
if
these
underlying
mechanisms
are
still
elusive.
Most
current
theories
assume
that
tissue
development
is
driven
by
chemical
processes,
either
as
a
sequence
of
chemical
patterns
each
depending
on
the
previous
one
or
by
a
pattern
spontaneously
arising
through
specific
interactions.
So
that's
your
turn.
Log
within
both
fairies
mechanical
patterns
are
usually
regarded
as
passive
byproducts
of
chemical
free
patterns.
B
However,
several
experiments
question
question
these
theories
and
an
increasing
number
show
them
tissue
mechanics
in
actively
influenced
chemical
patterns
during
development,
so
their
model
focuses
on
that
interplay
of
chemical
and
mechanical
patterns,
and
so
this
is,
let's
see
if
they
have
any
figures
in
here.
They
kind
of
talk
about
the
Turing
model
and
how
it's
inadequate
and
then
here's
a
here's,
a
figure
one
way
down
here.
Ok,
so
this
is
the
example
that
they
give
of
how
this
works
so
there's
a
feedback
loop
between
tissue,
mechanics
and
morphogen
introductions.
B
So
you
have
this
morphogen
production
going
on
here
of
the
surface
of
the
cell
and
it
emits
this
morphogen
this
you
know
morphogen
as
theoretical,
but
in
real
life
it's
some
sort
of
chemical
signal
that
tells
other
cells.
You
know
how
to
deform
along
with
the
cell.
That's
admitting
this
morphogen,
so
you
know
it's
a
collective
behavior
thing
among
cells,
but
then
there's
also
this
elastic
response.
B
So
when
you
have
say,
for
example,
a
bunch
of
cells
and
at
issue,
they
might
stretch
in
some
way
or
they
might
contract
in
some
way
and
that's
a
signal
as
well.
They're
well
known,
you
know
mechanical
transduction
pathways
and
cells
that
allow
them
to
respond,
and
so
they're
kind
of
fitting
this
into
one
theory.
B
B
So
they
I
don't
know
what
the
what
their
actual
beef
with
I
don't
think.
There's
a
beef
will
turn
necessarily
but
okay.
They
actually
do
distinguish
it
from
Turing
theory.
So
the
Train
theory
requires
highly
nonlinear
interactions
among
different
types
of
morphogens
in
order
to
produce
T
novo
patterns,
which
makes
the
underlying
assumptions
or
hurting
molecular
interactions
relatively
complex,
so
I
guess
their
argument
is
they're.
Making
they're
simplifying
this
relationship.
B
B
You
know
neural
system
and
we
were
talking
about
like
the
standard
model
of
looking
at
connections,
but
also
about
the
role
of
mechanobiology
and
things
like
that.
So
this
has
a
lot
of
you
know
the
sort
of
this
model.
You
know
as
type
of
model
we're
mixing
in
you
know
chemical
morphogenesis
and
mechanical
work
for
genesis.
It's
pretty
relevant
to
a
lot
of
different
areas,
not
just
embryos.
B
B
And
these
are
numerical
simulations
in
the
period
of
morphogen
concentration
across
the
sphere
that
they're
modeling
and
they
can
make
different
shapes
using
this
same
feedback
loop
in
this
case
they're,
going
at
something
apical
constriction,
so
they're,
looking
at
a
specific
type.
You
know
thing
that
happens
in
morphogenesis.
B
And
so
this
is
yeah.
This
is
an
interesting
paper.
I,
don't
know
how
much
problem
they
actually
break
in
this
paper,
but
it's
I
found
it
pretty
interesting.
I
thought
it
was
worth
bringing
the
group's
attention
to
again
Ike
I
said:
there's
a
lot
of
detail
in
here:
I'm
not
gonna,
go
through,
but
it's
something
that
you
can
read
on
your
own.
If
you're
interested
or
you
know,
if
you
have
further
questions
about,
we
can
talk
about
it.
B
B
Ok,
yeah
stay
safe
as
well
which
wall
we're
gonna
have
a
good
week.
Ok,
Jesse
said
I
might
ask
you
about
dry
papers
and
developmental
biology,
but
I'll
say
that
in
slack
mostly
key,
ok
yeah,
we
can
do
this
in
slack,
so
I,
you
know
talked
about
this
in
slack
or
by
email.
If
you
have
further
things
to
follow
up
on
it.
So
ok,
thanks
for
attending,
see
you
guys
next
week,
bye.