I’m going to start off by acknowledging
my colleagues Karen Rogers and Bruce
Watson in particular Karen and I gave a
red talk which is a Rensselaer version
of a TED talk last Friday at our capital
campaign kickoff and Homecoming weekend
and I decided to present a variant on
that talk so that you get an idea of
what we’re doing at Rensselaer and
before we do that I’m gonna keep you in
your seat by asking you to buckle your
seatbelt so now you don’t have any real
seatbelts but the reason I’m asking you
to do this is I’m going to take you
through 27 orders of magnitude in scale
and 4.5 billion years in 18 minutes
so just so get ready so here’s the Milky
Way it’s a spiral galaxy our earth or at
least may be an early version of our
earth is is located in in the corner of
one of those spiral arms this image
we’re going to come back to in a minute
it’s very very early Earth so it’s not a
real picture it’s an artist’s rendition
in those early systems especially in the
oceans on early Earth
there were hydrothermal systems which
had abundance we discovered had
abundance of life but when did that life
actually really begin begin to occur and
what happened to it afterwards and then
down at the very microscopic scale this
is a community of microorganisms
coexisting together and this is at the
scale of 10 to the minus 6 so in here we
have 27 orders of magnitude and the way
in which we listen to the earth and the
way in which we understand what it’s
trying to tell us is to move across each
of these scales and we do that in
laboratory settings experimental
settings as well as computational
settings as a result of looking across
the entire age of the planet 4.5 5
billion years from the very early Earth
to the current day where we can go and
study microbial systems using gene
sequencing and
and all of the omics techniques that are
available to us the volume of data is
substantially increased but our
challenge is to not just work with
today’s data today’s earth but to find
out things about the planet that have
could long long ago so here’s the early
Earth artist’s rendition what did it
really look like well you know if you
don’t you can’t go back and visit it you
have to resort to other means and one of
the very earliest means of asking the
planet what was doing was go into a
laboratory and sort of guess at what the
composition of the early Earth say exact
at Mysterio marine systems was composed
of this is a very famous picture it’s
probably in your biology textbook still
and secure experiment conducted by
Miller and Urey at the Scripps
Institution of Oceanography and what
they did if you’ve never heard of this
is they put ammonia and methane in in
this particular receptacle and zapped it
with static discharge so anyone know
what they produced they produced amino
acids amino acids are the fundamental
building blocks of proteins proteins
fundamentally related to the to the
formation of life and so for 60 years
almost
after that experiment which was in the
50s we thought that the early earth
atmosphere was about the same pressure
as it is today about the same density
but was composed comprised of primarily
methane and ammonia well that’s wrong
that’s completely wrong so far wrong and
it’s partly wrong because we went in and
we guessed and what we’ve been doing in
the last 15 20 years we’ve stopped
guessing and we started going out back
to other parts of the earth and asked
the earth by different means minerals
fossils and proteins what were you doing
at that time
now 4.5 billion years ago what was
happening well it turns out that there’s
in in Australia at the jack at Jack
River there are rocks that are three to
three-and-a-half
years old and we go and collect them and
in those three and a half billion year
old rocks there are these minerals you
if you polish them you call them
gemstones scientists call them minerals
those are 4.4 billion years old and they
still exist and we’ve had to find them
and my colleague Bruce Watson here has
been painstakingly examining these
zircons using relationships known
relationships between the element
titanium which is part of the zircon and
the temperature at the time and through
various analytic techniques we found out
that there was water on the earth from
the very earliest days back 4.4 billion
years ago the oceans are about 70
degrees C and the atmosphere was
actually comprised of carbon dioxide and
molecular nitrogen not methane not
ammonia and we even think there was
probably some reasonable amount of water
there so we just have fundamentally
changed by going and picking up these
rocks and bringing them back to the
laboratory and using very sophisticated
techniques to analyze them so that’s
good that’s early Earth we have the
zircons but the earth does evolve
through time and the earth has gone
through a series of movements in the
thinness at the system level the
continents have moved oceans have opened
and closed and as a result of that
things that we go and pick up today in
current earth environments are not where
they were billions of years ago millions
of years ago so we have to use even more
sophisticated techniques so here’s this
is so there’s the so-called
supercontinent cycle some of you may
have heard of God one a land and rodinia
and those things so we go we’re now
going back across each of those
supercontinent cycles and and looking at
things like when did the oxygen really
come into the atmosphere at the levels
it is today and it turns out there’s
been two oxidation events we think the
first one is called the great oxidation
event
because it was the first but there’s
been another one but the gray here
represents the tremenda and this is an
exponential log scale over here
tremendous amount of uncertainty and so
our job in listening to the planet is to
start to use our knowledge of evidence
of where the continents were and
composition of the atmosphere changes
over time and those those Clues lie in
minerals fossils and proteins so one
thing that we’ve done is we have an
extensive mineral record thanks to the
to the fascination that humans have with
collecting minerals have tremendous
crowd source databases MnDOT and
scientific databases and what’s been
very typical is that an individual
scientist will go and study a particular
mineral at a particular time in a
particular place the thing that’s
different now is Big Data
because we can now look at all of the
data and one thing we found out one of
the advanced and all that that xtext is
that minerals have a social life and a
social life many of you involved in
social networks is best explored through
network analyses so there this series of
images at the top without going into a
great deal of detail here at the ages 4
min 4 billion years 2 billion years 3/4
of billion years up to the current age
this is the the network of associations
of chromium minerals and it evolves over
time and it evolves in very interesting
ways in the way in which these networks
are laid out tell us a lot about the
evolution of those minerals the the
temperature and pressure conditions
under which they were formed as well as
trace traces of the composition of the
atmosphere another tool that we’re using
is looking at where minerals occur
together that should be
pretty boring right now you don’t see
that
there we go so this is the evolution of
minerals occurring together over time
this is a chord diagram and so I’m gonna
left here the silica silica based
minerals your guide and you’ll see the
complexity of the occurrence of minerals
occur where they occur together also
gives us clues as to the so the in a
comparison between the minerals because
minerals have different chemical
compositions as well as being fairly
cool to to look out we’re in addition
alright in addition we are able to now
look using visual analytics techniques
at all of the data that we have on
minerals and I’m not gonna show you all
of them but this is for four billion
years of history here’s the little
supercontinent cycle as you can see
across here and what you’re seeing are
the relative occurrences of minerals in
certain locations for each of the the
metal elements in the first row of the
periodic table so it’s called the first
row transition element so it’s cobalt
nickel chromium titanium zinc vanadium
manganese copper and iron and and it’s
animated because it’s a little bit hard
so it’s called a skyline plot and for
the first time mineralogists have been
able to look at all of this data at the
same time and draw correspondences
between where the supercontinent cycles
and the occurrence of minerals coincides
and doesn’t come inside and which
minerals show up in certainly
intercontinental cycles and don’t show
up in others but there’s one really
important thing that you should know
about this and that is minerals go
extinct we tend to think of living
things going extinct but minerals go
extinct and that extinction is another
really important thing that tells us
what the composition of the earth
because they go extinct under certain
chemical reaction conditions above
certain temperatures and pressures and
other environmental conditions
so the next thing that we we started to
do was take our for each of the
individual elemental elemental base
minerals so all minerals are basically
categorized by the primary element that
they are composed of this is the
manganese Network of all known minerals
and it has an extra set of data in there
whether actually has a lot of extra sets
of data and the colors represent
particular formation conditions for
those minerals and in a minute you will
go into it this is called a bipartite
Network bipartite network has two types
of nodes one is the mineral and the
other is its location and so very hard
to sort of tell what’s going on here but
you’ll see a basic structure you’ll see
a very condensed area at the lower part
of the network and you’ll see this more
isolated mostly red cluster up top and
this leads us by looking at all this is
all of the data on manganese it’s never
been looked at before we can now go and
say well what’s that cluster up there
and we can go in and explore it when and
we can go and do clustering tech
techniques and classification to find
other commonalities between the
manganese based crystals the other thing
is without going into too much detail
the separation between that upper part
of the network and the lower part of the
network actually gives us evidence on
extinction the fact that there is such a
large distance between those two
groupings tells us tremendous amount of
information about earth
these were set to autoplay so these are
these are some of the tools and
techniques that were able to sit
alongside mineralogists paleo biologists
and and biochemists and start to ask
questions about these networks and
you’ll see it’s very interactive you can
pick out particular minerals and the
gray nodes which here are a little bit
hard to see our mineral localities
and as soon as you let your mineralogist
friends take control of the mouse
there’s suing around zooming in zooming
out it’s very disorienting now because
we don’t have a virtual reality
projector here this is also available in
virtual reality form so you can actually
look at it on your VR enabled phone and
that is ridiculously cool here isn’t
here’s an example one of my favorite
elements I’m studying right now is
carbon this is the carbon bipartite
Network so the black dots are locations
the other colored dots are carbon
minerals the size of the dot is the
relative occurrence but there’s things
that we can extract out of this
particular diagram such as there’s a
time axis we think in this network
diagram that’s actually showing us the
fact that there are more of the red
co-occurring minerals of a very similar
type that have existed for a very long
time and all the blue new ones around
the end are very very recently formed so
here’s here’s the the VR rendering of
the of the carbon network again the gray
is the of the localities and we’re just
going to go in and take a look at this
it’s not playing
don’t have any control here so close
your eyes and imagine the same thing is
that you saw before we go in and we
examine clustering of locations and
you’ll notice that the larger
significantly a large larger number of
colors it’s because the the nodes are
colored using a different a different
piece of data it’s the actual oxidation
state the plus one plus plus two so this
is minerals so we’ve gone in and we’ve
started up to all known minerals we’ve
we’ve found out that as we construct
models of what these minerals have been
doing we’ve predicted that we haven’t
found around fifteen hundred minerals
there’s still 1,500 minerals that should
exist that haven’t been found and that’s
sort of interesting to ponder so because
people like minerals they’re off out
searching for them now I’m not going to
cover fossils fossils are really cool
but just to say colleagues that we’re
working with at Rutgers Jana Bromberg
has been doing the same thing for
proteins constructing network analysis
diagrams so this is a network of protein
evolution and the red is the is the iron
based proteins which we know is one of
the very earliest forming minerals for
proteins and them and the much later
ones a copper so there’s a time axis
going through this particular this
particular network as well so what do we
got as we go back in time our coverage
on earth is of course limited because
things have moved so we can only collect
things from where they were today we can
trace them in some cases back we can do
network analysis over time but let’s
come back a little bit to the
microorganisms the the settings that
that we started off with we’re
coexisting communities because there are
opportunities for substantial amounts of
data analysis in these environments
today so let’s take a look at the
microbiome so one of the challenges with
the with the microbiome and microbiome
is
Assembly of us of community of
microorganisms is that the conditions
that are representative earlier times on
earth higher pressures higher
temperatures different compositions
actually those environmental samples do
exist on the planet
there’s sites in volcano the sites in
Yellowstone National Park that actually
have compositional conditions and so
we’re about to undertake a project with
colleagues at RPI that’s going to go out
and sample all of these and you have
heads are cut off here but Karen Rogers
AG and Julius and Cynthia Collins and
what you’re seeing here is an
engineering approach to to examining the
environment and the reason why we need
to do this is in environmental science
in Earth history we have a sampling bias
because we can’t go back to all those
places we cannot create all the
temperature and pressure and salinity
and and and so on conditions but we can
do it in the lab but we have to be able
to transport the samples the actual real
physical samples so at the beginning I
showed you Miller you’re a we don’t want
to guess at what those microorganisms
are we don’t want to fake it we’re not
trying to build a medicine or something
like that we’re actually looking at
Earth so we go out we collect them and
we bring them back to the lab and then
in in at scale we analyze their
geochemistry the chemistry we do gene
sequencing and we expect to find out a
tremendous amount about what our planet
has been telling us so we started with
this very very sort of coarse view the
one where we don’t really know what the
planet looks like over time our
knowledge of what the planet has been
doing has has become clearer we’ve gone
down to smaller scales we’ve gone into
into conditions that are of order of the
original conditions on earth and now
we’re going down to the microbial level
and so we have fundamentally changed
just in the last 10 years the ways in
which we’re listening to the planet but
yet we still have me
more questions thank you very much
[Applause]
my colleagues Karen Rogers and Bruce
Watson in particular Karen and I gave a
red talk which is a Rensselaer version
of a TED talk last Friday at our capital
campaign kickoff and Homecoming weekend
and I decided to present a variant on
that talk so that you get an idea of
what we’re doing at Rensselaer and
before we do that I’m gonna keep you in
your seat by asking you to buckle your
seatbelt so now you don’t have any real
seatbelts but the reason I’m asking you
to do this is I’m going to take you
through 27 orders of magnitude in scale
and 4.5 billion years in 18 minutes
so just so get ready so here’s the Milky
Way it’s a spiral galaxy our earth or at
least may be an early version of our
earth is is located in in the corner of
one of those spiral arms this image
we’re going to come back to in a minute
it’s very very early Earth so it’s not a
real picture it’s an artist’s rendition
in those early systems especially in the
oceans on early Earth
there were hydrothermal systems which
had abundance we discovered had
abundance of life but when did that life
actually really begin begin to occur and
what happened to it afterwards and then
down at the very microscopic scale this
is a community of microorganisms
coexisting together and this is at the
scale of 10 to the minus 6 so in here we
have 27 orders of magnitude and the way
in which we listen to the earth and the
way in which we understand what it’s
trying to tell us is to move across each
of these scales and we do that in
laboratory settings experimental
settings as well as computational
settings as a result of looking across
the entire age of the planet 4.5 5
billion years from the very early Earth
to the current day where we can go and
study microbial systems using gene
sequencing and
and all of the omics techniques that are
available to us the volume of data is
substantially increased but our
challenge is to not just work with
today’s data today’s earth but to find
out things about the planet that have
could long long ago so here’s the early
Earth artist’s rendition what did it
really look like well you know if you
don’t you can’t go back and visit it you
have to resort to other means and one of
the very earliest means of asking the
planet what was doing was go into a
laboratory and sort of guess at what the
composition of the early Earth say exact
at Mysterio marine systems was composed
of this is a very famous picture it’s
probably in your biology textbook still
and secure experiment conducted by
Miller and Urey at the Scripps
Institution of Oceanography and what
they did if you’ve never heard of this
is they put ammonia and methane in in
this particular receptacle and zapped it
with static discharge so anyone know
what they produced they produced amino
acids amino acids are the fundamental
building blocks of proteins proteins
fundamentally related to the to the
formation of life and so for 60 years
almost
after that experiment which was in the
50s we thought that the early earth
atmosphere was about the same pressure
as it is today about the same density
but was composed comprised of primarily
methane and ammonia well that’s wrong
that’s completely wrong so far wrong and
it’s partly wrong because we went in and
we guessed and what we’ve been doing in
the last 15 20 years we’ve stopped
guessing and we started going out back
to other parts of the earth and asked
the earth by different means minerals
fossils and proteins what were you doing
at that time
now 4.5 billion years ago what was
happening well it turns out that there’s
in in Australia at the jack at Jack
River there are rocks that are three to
three-and-a-half
years old and we go and collect them and
in those three and a half billion year
old rocks there are these minerals you
if you polish them you call them
gemstones scientists call them minerals
those are 4.4 billion years old and they
still exist and we’ve had to find them
and my colleague Bruce Watson here has
been painstakingly examining these
zircons using relationships known
relationships between the element
titanium which is part of the zircon and
the temperature at the time and through
various analytic techniques we found out
that there was water on the earth from
the very earliest days back 4.4 billion
years ago the oceans are about 70
degrees C and the atmosphere was
actually comprised of carbon dioxide and
molecular nitrogen not methane not
ammonia and we even think there was
probably some reasonable amount of water
there so we just have fundamentally
changed by going and picking up these
rocks and bringing them back to the
laboratory and using very sophisticated
techniques to analyze them so that’s
good that’s early Earth we have the
zircons but the earth does evolve
through time and the earth has gone
through a series of movements in the
thinness at the system level the
continents have moved oceans have opened
and closed and as a result of that
things that we go and pick up today in
current earth environments are not where
they were billions of years ago millions
of years ago so we have to use even more
sophisticated techniques so here’s this
is so there’s the so-called
supercontinent cycle some of you may
have heard of God one a land and rodinia
and those things so we go we’re now
going back across each of those
supercontinent cycles and and looking at
things like when did the oxygen really
come into the atmosphere at the levels
it is today and it turns out there’s
been two oxidation events we think the
first one is called the great oxidation
event
because it was the first but there’s
been another one but the gray here
represents the tremenda and this is an
exponential log scale over here
tremendous amount of uncertainty and so
our job in listening to the planet is to
start to use our knowledge of evidence
of where the continents were and
composition of the atmosphere changes
over time and those those Clues lie in
minerals fossils and proteins so one
thing that we’ve done is we have an
extensive mineral record thanks to the
to the fascination that humans have with
collecting minerals have tremendous
crowd source databases MnDOT and
scientific databases and what’s been
very typical is that an individual
scientist will go and study a particular
mineral at a particular time in a
particular place the thing that’s
different now is Big Data
because we can now look at all of the
data and one thing we found out one of
the advanced and all that that xtext is
that minerals have a social life and a
social life many of you involved in
social networks is best explored through
network analyses so there this series of
images at the top without going into a
great deal of detail here at the ages 4
min 4 billion years 2 billion years 3/4
of billion years up to the current age
this is the the network of associations
of chromium minerals and it evolves over
time and it evolves in very interesting
ways in the way in which these networks
are laid out tell us a lot about the
evolution of those minerals the the
temperature and pressure conditions
under which they were formed as well as
trace traces of the composition of the
atmosphere another tool that we’re using
is looking at where minerals occur
together that should be
pretty boring right now you don’t see
that
there we go so this is the evolution of
minerals occurring together over time
this is a chord diagram and so I’m gonna
left here the silica silica based
minerals your guide and you’ll see the
complexity of the occurrence of minerals
occur where they occur together also
gives us clues as to the so the in a
comparison between the minerals because
minerals have different chemical
compositions as well as being fairly
cool to to look out we’re in addition
alright in addition we are able to now
look using visual analytics techniques
at all of the data that we have on
minerals and I’m not gonna show you all
of them but this is for four billion
years of history here’s the little
supercontinent cycle as you can see
across here and what you’re seeing are
the relative occurrences of minerals in
certain locations for each of the the
metal elements in the first row of the
periodic table so it’s called the first
row transition element so it’s cobalt
nickel chromium titanium zinc vanadium
manganese copper and iron and and it’s
animated because it’s a little bit hard
so it’s called a skyline plot and for
the first time mineralogists have been
able to look at all of this data at the
same time and draw correspondences
between where the supercontinent cycles
and the occurrence of minerals coincides
and doesn’t come inside and which
minerals show up in certainly
intercontinental cycles and don’t show
up in others but there’s one really
important thing that you should know
about this and that is minerals go
extinct we tend to think of living
things going extinct but minerals go
extinct and that extinction is another
really important thing that tells us
what the composition of the earth
because they go extinct under certain
chemical reaction conditions above
certain temperatures and pressures and
other environmental conditions
so the next thing that we we started to
do was take our for each of the
individual elemental elemental base
minerals so all minerals are basically
categorized by the primary element that
they are composed of this is the
manganese Network of all known minerals
and it has an extra set of data in there
whether actually has a lot of extra sets
of data and the colors represent
particular formation conditions for
those minerals and in a minute you will
go into it this is called a bipartite
Network bipartite network has two types
of nodes one is the mineral and the
other is its location and so very hard
to sort of tell what’s going on here but
you’ll see a basic structure you’ll see
a very condensed area at the lower part
of the network and you’ll see this more
isolated mostly red cluster up top and
this leads us by looking at all this is
all of the data on manganese it’s never
been looked at before we can now go and
say well what’s that cluster up there
and we can go in and explore it when and
we can go and do clustering tech
techniques and classification to find
other commonalities between the
manganese based crystals the other thing
is without going into too much detail
the separation between that upper part
of the network and the lower part of the
network actually gives us evidence on
extinction the fact that there is such a
large distance between those two
groupings tells us tremendous amount of
information about earth
these were set to autoplay so these are
these are some of the tools and
techniques that were able to sit
alongside mineralogists paleo biologists
and and biochemists and start to ask
questions about these networks and
you’ll see it’s very interactive you can
pick out particular minerals and the
gray nodes which here are a little bit
hard to see our mineral localities
and as soon as you let your mineralogist
friends take control of the mouse
there’s suing around zooming in zooming
out it’s very disorienting now because
we don’t have a virtual reality
projector here this is also available in
virtual reality form so you can actually
look at it on your VR enabled phone and
that is ridiculously cool here isn’t
here’s an example one of my favorite
elements I’m studying right now is
carbon this is the carbon bipartite
Network so the black dots are locations
the other colored dots are carbon
minerals the size of the dot is the
relative occurrence but there’s things
that we can extract out of this
particular diagram such as there’s a
time axis we think in this network
diagram that’s actually showing us the
fact that there are more of the red
co-occurring minerals of a very similar
type that have existed for a very long
time and all the blue new ones around
the end are very very recently formed so
here’s here’s the the VR rendering of
the of the carbon network again the gray
is the of the localities and we’re just
going to go in and take a look at this
it’s not playing
don’t have any control here so close
your eyes and imagine the same thing is
that you saw before we go in and we
examine clustering of locations and
you’ll notice that the larger
significantly a large larger number of
colors it’s because the the nodes are
colored using a different a different
piece of data it’s the actual oxidation
state the plus one plus plus two so this
is minerals so we’ve gone in and we’ve
started up to all known minerals we’ve
we’ve found out that as we construct
models of what these minerals have been
doing we’ve predicted that we haven’t
found around fifteen hundred minerals
there’s still 1,500 minerals that should
exist that haven’t been found and that’s
sort of interesting to ponder so because
people like minerals they’re off out
searching for them now I’m not going to
cover fossils fossils are really cool
but just to say colleagues that we’re
working with at Rutgers Jana Bromberg
has been doing the same thing for
proteins constructing network analysis
diagrams so this is a network of protein
evolution and the red is the is the iron
based proteins which we know is one of
the very earliest forming minerals for
proteins and them and the much later
ones a copper so there’s a time axis
going through this particular this
particular network as well so what do we
got as we go back in time our coverage
on earth is of course limited because
things have moved so we can only collect
things from where they were today we can
trace them in some cases back we can do
network analysis over time but let’s
come back a little bit to the
microorganisms the the settings that
that we started off with we’re
coexisting communities because there are
opportunities for substantial amounts of
data analysis in these environments
today so let’s take a look at the
microbiome so one of the challenges with
the with the microbiome and microbiome
is
Assembly of us of community of
microorganisms is that the conditions
that are representative earlier times on
earth higher pressures higher
temperatures different compositions
actually those environmental samples do
exist on the planet
there’s sites in volcano the sites in
Yellowstone National Park that actually
have compositional conditions and so
we’re about to undertake a project with
colleagues at RPI that’s going to go out
and sample all of these and you have
heads are cut off here but Karen Rogers
AG and Julius and Cynthia Collins and
what you’re seeing here is an
engineering approach to to examining the
environment and the reason why we need
to do this is in environmental science
in Earth history we have a sampling bias
because we can’t go back to all those
places we cannot create all the
temperature and pressure and salinity
and and and so on conditions but we can
do it in the lab but we have to be able
to transport the samples the actual real
physical samples so at the beginning I
showed you Miller you’re a we don’t want
to guess at what those microorganisms
are we don’t want to fake it we’re not
trying to build a medicine or something
like that we’re actually looking at
Earth so we go out we collect them and
we bring them back to the lab and then
in in at scale we analyze their
geochemistry the chemistry we do gene
sequencing and we expect to find out a
tremendous amount about what our planet
has been telling us so we started with
this very very sort of coarse view the
one where we don’t really know what the
planet looks like over time our
knowledge of what the planet has been
doing has has become clearer we’ve gone
down to smaller scales we’ve gone into
into conditions that are of order of the
original conditions on earth and now
we’re going down to the microbial level
and so we have fundamentally changed
just in the last 10 years the ways in
which we’re listening to the planet but
yet we still have me
more questions thank you very much
[Applause]
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