everything we know in science was
learned through experimentation and
research these form the foundation of
science despite this most students don’t
do any research until graduate school if
they go to graduate school I’ve been
helping my students perform real
research from the beginning even as they
are first learning the basic principles
of biology this can be challenging at a
community college faced with limited
funding and without expensive scientific
equipment today I will describe how my
beginning biology students have been
making real discoveries using advanced
technologies and sharing their findings
with the scientific community all
without spending any money one of these
students received support from NASA for
this work so I’ll begin by describing
how our research relates to space
exploration the Cassini spacecraft was
launched in 1997 and spent 13 years in
orbit around Saturn it made many
important discoveries during this time
but perhaps the most astonishing of
these concerned a small moon named and
selet us scientists observed what
appeared to be plumes of water erupting
from the southern pole suggesting there
might be oceans beneath the surface so
they sent a spacecraft back through to
do chemical analysis and they detected
water as well as methane and hydrogen
both of these are indicators of
hydrothermal activity in the oceans
below the surface where superheated
waters forcibly ejected through cracks
in the ice creating the plumes now this
got a lot of interest as deep sea
hydrothermal vents on Earth support an
array of life in some of the most unique
ecosystems on the
planet the life that lives at these
vents survives in an extremely hostile
environment the surrounding water is
nearly frozen and there at the bottom of
the ocean far from any sunlight as this
cold water though seeps into the
sediment and comes into contact with the
molten rock below it rear up s– as a
geyser of superheated water sometimes
these geysers bring with them energy
rich chemicals from the earth which
precipitate out as they hit the cold
water in what looks like black smoke now
this is key there are bacteria there are
microorganisms here that are able to
extract energy from these chemicals in a
process known as chemosynthesis this is
key to how life can exist at the bottom
of the ocean far from any sunlight and
without the photosynthesis of plants and
these chemosynthetic microorganisms form
the base of the food chain which
includes everything from shrimp and
mussels to tube worms greater than 6
feet in length and its seeming more and
more likely that if life exists
elsewhere in our solar system such as on
Enceladus it may resemble life at these
vents and be reliant on chemosynthesis
rather than photosynthesis my students
and I have been studying one of these
deep-sea chemosynthetic microorganisms
now it’s name is difficult diesel Fuhrer
bacterium thermo litho troffer which
from here on out I will just call desta
it was it’s a type of bacteria and it
was taken directly from one of these
vents and so it can withstand very high
temperatures and it feeds on hydrogen
spewing from the vent so it is performs
chemosynthesis critical for this
ecosystem now at this point you may be
wondering how at a community college we
can
study of bacteria from the bottom of the
ocean that lives in near boiling water
and feeds on hydrogen
well we didn’t send a student down to
the bottom of the ocean to look at it
actually not long after it was
discovered its genome was sequenced and
its genetic information was posted on an
online data bank for anyone to study so
we’ve just been studying the details of
its genetic instructions using the tools
of bioinformatics bioinformatics is an
interdisciplinary field where a biology
meets computer science it’s used when
the data from biology gets so large that
computers are required to make sense of
it as many applications in modern
biology including cancer therapy for
example many cancer patients are
unresponsive to drugs not because the
drugs are bad but merely because they
were an inappropriate treatment choice
for that particular tumor by analyzing
the specific genetic abnormalities of
that tumor doctors are able to select a
more appropriate chemotherapy and in
this way reduce the number of cancers
that don’t respond to treatment this
type of medicine will be commonplace one
day and it will require both doctors and
biologists knowledgeable in this field
of bioinformatics now another perhaps
better well-known example a big data and
biology is genomics a genome is the
complete set of instructions for an
organism these this information is
stored as DNA as a series of molecules
referred to as AC G and T so when a
genome is sequenced it means all the AC
G’s and T’s of that organism have been
determined the human genome was
sequenced in 2003 and since then many
many more species have had their genome
sequenced shown here are just
bacterial genomes that have been
sequenced by 2009 all of these were
placed into one of these online data
banks and many more have been added
since then including our destr a small
portion of one of these genomes looks
something like this
so even to a biologist this is
meaningless it’s as if you’re looking at
a book written in a language you don’t
understand or a string of ones and zeros
however after sequencing these genomes
are put through a process of automated
analysis where the new DNA sequence is
compared to ones that have already been
studied and in this way small regions of
the genome are determined to be genes
based on similarity to genes that have
already been characterized this process
is called genome annotation and it’s
almost a type of footnotes
to this sequence that’s generated by
computers here’s an overview of the
genome of dester the entire genome shown
as a circle and all these different
colored bands are the different genes
there’s about 1500 of them in dester if
we zoom into one portion you can see the
precise locations of these genes have
been identified and they’ve also been
assigned names and functions the problem
is these automated gene calls are wrong
or incomplete about 10% of the time for
example you can see here one gene that
was merely labeled as hypothetical there
are some things that computers are very
good at but there’s some things that
people can still do better and a pair of
human eyes looking at this can sometimes
catch and correct the mistakes that the
computers were unable to so this brings
this is where our community college
students can be helpful and brings me to
the details of our research project
students in my beginning biology class
are each assigned a gene from destr they
study it using a range of bioinformatics
tools and as they learn about their gene
most come to the conclusion that the
original gene call was correct however
occasionally a student finds a gene that
has mistakes or is incomplete these
genes of interest are funneled to
students willing to do more of this very
challenging work and these dedicated
students start to make corrections and
as they make corrections their notes are
posted back to this database for review
and in this way the initial mistake and
gene call can be corrected in an almost
Wikipedia style of editing for example
one student who worked on this project
researched several genes including the
one we saw labeled as hypothetical and
she supplied evidence that it was
actually a true gene and assigned it as
well as several others more appropriate
names these findings were presented at a
national meeting for undergraduate
community college research and another
student is currently working on the
genes involved in chemo synthesis and
will present these findings at
undergraduate meeting hosted by NASA a
very appreciative of these organizations
that support undergraduate research even
though it’s beginning research and is
often overlooked it’s very meaningful to
these students that work on it and I’m
most of all grateful to these students
who put so much effort into this project
it is very challenging work and without
them none of it would be possible and I
do believe undergraduate research is
important as it makes learning biology
more meaningful for students it shows
that science exists beyond the textbook
and is more than just memorizing a bunch
of facts and figures by doing this type
of on-the-job training students are
gaining real-life work skills
using cutting-edge technologies while
contributing to the collective
scientific knowledge all from the
beginning of their education thank you [Applause]
learned through experimentation and
research these form the foundation of
science despite this most students don’t
do any research until graduate school if
they go to graduate school I’ve been
helping my students perform real
research from the beginning even as they
are first learning the basic principles
of biology this can be challenging at a
community college faced with limited
funding and without expensive scientific
equipment today I will describe how my
beginning biology students have been
making real discoveries using advanced
technologies and sharing their findings
with the scientific community all
without spending any money one of these
students received support from NASA for
this work so I’ll begin by describing
how our research relates to space
exploration the Cassini spacecraft was
launched in 1997 and spent 13 years in
orbit around Saturn it made many
important discoveries during this time
but perhaps the most astonishing of
these concerned a small moon named and
selet us scientists observed what
appeared to be plumes of water erupting
from the southern pole suggesting there
might be oceans beneath the surface so
they sent a spacecraft back through to
do chemical analysis and they detected
water as well as methane and hydrogen
both of these are indicators of
hydrothermal activity in the oceans
below the surface where superheated
waters forcibly ejected through cracks
in the ice creating the plumes now this
got a lot of interest as deep sea
hydrothermal vents on Earth support an
array of life in some of the most unique
ecosystems on the
planet the life that lives at these
vents survives in an extremely hostile
environment the surrounding water is
nearly frozen and there at the bottom of
the ocean far from any sunlight as this
cold water though seeps into the
sediment and comes into contact with the
molten rock below it rear up s– as a
geyser of superheated water sometimes
these geysers bring with them energy
rich chemicals from the earth which
precipitate out as they hit the cold
water in what looks like black smoke now
this is key there are bacteria there are
microorganisms here that are able to
extract energy from these chemicals in a
process known as chemosynthesis this is
key to how life can exist at the bottom
of the ocean far from any sunlight and
without the photosynthesis of plants and
these chemosynthetic microorganisms form
the base of the food chain which
includes everything from shrimp and
mussels to tube worms greater than 6
feet in length and its seeming more and
more likely that if life exists
elsewhere in our solar system such as on
Enceladus it may resemble life at these
vents and be reliant on chemosynthesis
rather than photosynthesis my students
and I have been studying one of these
deep-sea chemosynthetic microorganisms
now it’s name is difficult diesel Fuhrer
bacterium thermo litho troffer which
from here on out I will just call desta
it was it’s a type of bacteria and it
was taken directly from one of these
vents and so it can withstand very high
temperatures and it feeds on hydrogen
spewing from the vent so it is performs
chemosynthesis critical for this
ecosystem now at this point you may be
wondering how at a community college we
can
study of bacteria from the bottom of the
ocean that lives in near boiling water
and feeds on hydrogen
well we didn’t send a student down to
the bottom of the ocean to look at it
actually not long after it was
discovered its genome was sequenced and
its genetic information was posted on an
online data bank for anyone to study so
we’ve just been studying the details of
its genetic instructions using the tools
of bioinformatics bioinformatics is an
interdisciplinary field where a biology
meets computer science it’s used when
the data from biology gets so large that
computers are required to make sense of
it as many applications in modern
biology including cancer therapy for
example many cancer patients are
unresponsive to drugs not because the
drugs are bad but merely because they
were an inappropriate treatment choice
for that particular tumor by analyzing
the specific genetic abnormalities of
that tumor doctors are able to select a
more appropriate chemotherapy and in
this way reduce the number of cancers
that don’t respond to treatment this
type of medicine will be commonplace one
day and it will require both doctors and
biologists knowledgeable in this field
of bioinformatics now another perhaps
better well-known example a big data and
biology is genomics a genome is the
complete set of instructions for an
organism these this information is
stored as DNA as a series of molecules
referred to as AC G and T so when a
genome is sequenced it means all the AC
G’s and T’s of that organism have been
determined the human genome was
sequenced in 2003 and since then many
many more species have had their genome
sequenced shown here are just
bacterial genomes that have been
sequenced by 2009 all of these were
placed into one of these online data
banks and many more have been added
since then including our destr a small
portion of one of these genomes looks
something like this
so even to a biologist this is
meaningless it’s as if you’re looking at
a book written in a language you don’t
understand or a string of ones and zeros
however after sequencing these genomes
are put through a process of automated
analysis where the new DNA sequence is
compared to ones that have already been
studied and in this way small regions of
the genome are determined to be genes
based on similarity to genes that have
already been characterized this process
is called genome annotation and it’s
almost a type of footnotes
to this sequence that’s generated by
computers here’s an overview of the
genome of dester the entire genome shown
as a circle and all these different
colored bands are the different genes
there’s about 1500 of them in dester if
we zoom into one portion you can see the
precise locations of these genes have
been identified and they’ve also been
assigned names and functions the problem
is these automated gene calls are wrong
or incomplete about 10% of the time for
example you can see here one gene that
was merely labeled as hypothetical there
are some things that computers are very
good at but there’s some things that
people can still do better and a pair of
human eyes looking at this can sometimes
catch and correct the mistakes that the
computers were unable to so this brings
this is where our community college
students can be helpful and brings me to
the details of our research project
students in my beginning biology class
are each assigned a gene from destr they
study it using a range of bioinformatics
tools and as they learn about their gene
most come to the conclusion that the
original gene call was correct however
occasionally a student finds a gene that
has mistakes or is incomplete these
genes of interest are funneled to
students willing to do more of this very
challenging work and these dedicated
students start to make corrections and
as they make corrections their notes are
posted back to this database for review
and in this way the initial mistake and
gene call can be corrected in an almost
Wikipedia style of editing for example
one student who worked on this project
researched several genes including the
one we saw labeled as hypothetical and
she supplied evidence that it was
actually a true gene and assigned it as
well as several others more appropriate
names these findings were presented at a
national meeting for undergraduate
community college research and another
student is currently working on the
genes involved in chemo synthesis and
will present these findings at
undergraduate meeting hosted by NASA a
very appreciative of these organizations
that support undergraduate research even
though it’s beginning research and is
often overlooked it’s very meaningful to
these students that work on it and I’m
most of all grateful to these students
who put so much effort into this project
it is very challenging work and without
them none of it would be possible and I
do believe undergraduate research is
important as it makes learning biology
more meaningful for students it shows
that science exists beyond the textbook
and is more than just memorizing a bunch
of facts and figures by doing this type
of on-the-job training students are
gaining real-life work skills
using cutting-edge technologies while
contributing to the collective
scientific knowledge all from the
beginning of their education thank you [Applause]
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