Data and Medicine
This is really a magic era for software. We can use computers now to
simulate so many different things. So every person has a DNA sequence that's 3 billion
letters long, that's a really long sequence! And in order for me to study it, I can't do
it by hand. I need to use computer programming in order to go through this code that's 3
billion letters long in order to figure out how your DNA code is associated with disease.
My interests are actually right at the interface between biology and computer science. There
is a huge database that contains all known organisms so humans, monkeys, mice, viruses,
bacteria. Usually now if a doctor is worried about you having an infection, based on your
age and where your symptoms are, if it's in your ear, your heart, or your brain, they
try to make a best guess as to what type of infection you have. Then they'll send off
tests specifically for those bugs. So if they think you have strep throat, they send off
the strep test. But the type of testing that we do, since we can essentially test for any
type of infection with a single test so we don't have to have a bias going into the testing
saying we think it's X, Y, or Z we just say let's see what's in there. A Cottage Grove
teenager now says he's taking one life one day at a time after being critically ill from
a mysterious illness. Mary Jolla has his story and details into new DNA sequencing that helped
solve a medical mystery. It's spring and like any other teenager, Joshua Osborn can't
be stuck indoors. Josh: "I feel wonderful today. It's 80 degrees." It's a welcome change
from last summer, here in the hospital and in a coma. His symptoms began last April with
fevers and headaches and he only got worse. Clark: "And he needed to be hospitalized."
Josh may not remember the hospital stay but his dad, Clark does. They tested for everything
that they knew. They tested for viruses and bacteria and ultimately he had a brain scan
and two or three spinal taps. He had all these crazy tubes. I remember that weekend when
they were doing it, it was so intense it was like he was going to die that week. We got
Josh's samples from his doctor, because his doctor was giving up. They had no idea. They
sunk millions of dollars into this kid and they have used hundreds of test. Hundreds--
sent to the CDC, sent to multiple labs, and they couldn't get an answer back. And they,
I mean so much money right, and they turned to us and they were like, "We need to know
what it is." So this is where we have the gene sequencers. We got a small amount of
Josh's cerebral spinal fluid which is the fluid that bathes the brain, with very powerful
computer algorithms we took out all the human sequences that were present in the data. And
then searched all the non-human sequences that we got against a giant database that
contains gene sequences of all known organisms. And very quickly we saw that the sequences
were all for a particular organism that Josh likely contracted when he visited Puerto Rico
about nine months before. And fortunately, that organism, it's a bacterium. And there
is a very straightforward treatment for it: penicillin. The doctor gave him the drugs
that same day and he was fine 24 hours later. All I can tell you is that, I'm happy to be
alive and I have dreams and I'm looking forward to accomplishing them. Data analysis is changing
all medicine. It's not just changing how diseases are diagnosed. Data is changing how we discover
cures to diseases. And even after a cure is known, data is used for delivering medicine
to patients, for example, to fight polio in Africa by distributing vaccines to everybody
who needs it. The magic of polio is finding all the kids and getting them to have the
vaccine three times. And so we're taking satellite photographs and using visual analysis to figure
out what the population is. And so we can look and see if we're giving out a certain
amount of vaccine are we really reaching all the kids? And amazingly what we found, on
the boundaries between political areas there are various settlements that one group thought
that the other group was taking care of. We also can take the phone that has the GPS tracking
and when they come back at the end of the day, plug it in, and see where they've been
every minute. And that's making all the difference because just getting coverage up from 80%
of kids to 90% of kids--that's the difference between success and failure. And literally
the software that lets us look at the movements of the teams, looks at the satellite maps,
gathers all the statistics together and tracks this thing, that's what's going to make this
the second disease we finally get rid of. So it's systems thinking, and the magic of
software are really at the center.