00:31:50.640You now have two copies of double-stranded DNA sequence of your choosing, having started
00:31:57.760with a single double-stranded parent, and then you repeat the process.
00:32:02.140each cycle doubles your DNA. After 30 cycles, you have turned one molecule into a billion copies.
00:32:12.420This technique is known as polymerase chain reaction, or PCR. But there was just one problem.
00:32:20.640The DNA polymerases people used at the time were derived from E. coli, and they fell apart when
00:32:27.640you heated them. So when every cycle of PCR required denaturing the DNA at near boiling
00:32:34.720temperatures, the polymerases could not survive the process, which meant you had to add fresh
00:32:41.200enzyme manually at every cycle. It worked, but it was tedious, expensive, error-prone,
00:32:49.020and basically not practical at any meaningful scale. The scientists at CETIS famously developed
00:32:56.520a robot to add fresh polymerase after each round of PCR in its thermocycler, dubbed Mr. Cycle.
00:33:05.400But this was still nowhere near a high-throughput, high-fidelity, cost-effective means for amplifying
00:33:12.240DNA. The team at Cetus needed a polymerase that could survive being heated to 95 degrees Celsius
00:33:20.320over and over without falling apart. They needed an enzyme that could survive in near
00:33:26.760boiling water. They turned to Thermus aquaticus. Polymerase is fundamentally necessary for life
00:33:34.640to continue. Every organism necessarily requires a means of copying their own DNA
00:33:40.500in order to pass that DNA onto new cells or new generations. Thermus aquaticus could apparently
00:33:47.340do this at temperatures of at least 88 degrees Celsius. In the mid-1970s, the Thermus aquaticus
00:33:54.660polymerase, commonly referred to as TAQ or TAC polymerase, had been isolated and partially
00:34:02.880characterized, in part because the species had been deposited in public culture collections
00:34:09.100after Brock's work. The CETIS team built on this, purified TAC polymerase in their lab,
00:34:14.900and plugged it into their PCR protocols. With this, the entire technique and all of biological
00:34:22.420sciences transformed. Now you could load the reaction, set the thermocycler, walk away,
00:34:29.240and come back to a billion copies of your sequence. We had a near endless supply of any
00:34:36.920DNA sequence we desired from any species we desired ready to go after a few hours of incubation
00:34:45.240on a cycling heating block. Mullis won the Nobel Prize in Chemistry in 1993 for inventing PCR,
00:34:54.180and deservedly so, but it was only possible because Brock and Freeze had asked decades earlier
00:35:00.960whether anything lived in extreme temperatures. They found life in an 88 degree Celsius hot
00:35:09.100spring. They found a way to collect and culture those species, and they shared that species with
00:35:15.140scientists everywhere to see, study, and utilize on their own. And I want us to think about what
00:35:22.160that unleashed. PCR is not a drug. PCR is something more fundamental than a drug. PCR is the enabling
00:35:30.060technology for essentially all of modern molecular biology. I'm sorry, this list is long. It's long
00:35:38.160enough to make the point, but it's not long enough to be nearly exhaustive. DNA is the code upon which
00:35:45.360all of life is programmed, and PCR is the tool we use to interact with that code. PCR is everywhere.
00:35:52.880It's the basis of genetic testing, forensic DNA analysis, cancer mutation panels, prenatal screening, vaccine development, ancestry testing, transgenic lab animals, fluorescent reporters like GFP, the cloning of any recombinant therapeutic protein, the entire field of genomics, the development of every gene therapy, and viral infection testing.
00:36:19.120All of it depends on PCR. So all of it depends on TAC polymerase. And all of it traces back
00:36:26.420to a microbiologist wondering whether anything could live in hot water. Without that 1969 paper,
00:36:33.760modern biology as it exists today simply could not exist. There's no plausible alternative history
00:36:40.040in which we get to where we are without somebody somewhere going to look in the boiling water for
00:36:46.560life. We just got lucky that that somebody was Tom Brock. And perhaps we got especially lucky
00:36:52.320that he got to do it in advance without anybody asking what disease he was trying to cure.
00:36:59.180And yet the discovery is so fundamental, so irrevocably intertwined with modern biology
00:37:05.320and medicine, that it's hard to imagine how any disease at all could have been cured in the last
00:37:11.52030 years without his work, his curiosity leading him to search for signs of microbial life
00:37:18.100inside of Yellowstone hot springs. This next story is, to me, a particularly exciting illustration
00:37:25.760of the principle because its ramifications were understood so recently that we are really in the
00:37:32.180midst of watching the timeline play out. The story begins in the late 1980s in the small
00:37:38.180Spanish coastal town of Santa Pola near Alicante on the Mediterranean. Santa Pola is famous for
00:37:45.460its salt flats, vast, shallow, evaporative ponds where seawater concentrates, creating dramatically
00:37:52.920saline pools of water. These salt ponds support a strange community of organisms, salt-tolerant
00:37:59.920or even salt-requiring microbes called halophiles, many of them archaea, that have adapted to thrive
00:38:07.500at salinity levels that would kill virtually anything else. A young Spanish microbiologist
00:38:14.520named Francesco Mojica was doing his PhD on one of these archaeas, Halophorex mediterinae,
00:38:23.000at the University of Alicante. His original project, in fact, was almost a different project
00:38:29.040entirely. He was studying how this organism responds to changes in salinity, but someone
00:38:34.680beat him to the punch and published it first. So along the way, he kept stumbling over a weird
00:38:39.820feature of its genome. There were these clusters of short, regularly spaced palindromic repeats,
00:38:47.840sequences of about 30 base pairs that repeated over and over, separated by unique, non-repeating
00:38:53.900spacer sequences of regular length. Now, just parenthetically, for those of you who might not
00:38:59.800be familiar with a palindrome. A palindrome is something that when read left to right and right
00:39:05.460to left is the same. So the word race car is a palindrome because regardless of which way you
00:39:10.920read it, it's the same way. And of course, my favorite palindrome, which I just learned of
00:39:15.500recently from one of our research analysts, is the phrase, go hang a salami, I'm a lasagna hog.
00:39:23.420I encourage you to prove to yourself that that is indeed a palindrome. Anyway, these were everywhere0.99
00:39:28.640in the genome, but he didn't know what they were. In fact, nobody knew what they were.
00:39:33.040He wasn't the first to see them, exactly. A Japanese group led by Yoshizumi Ishino had noted
00:39:38.720similar repeating patterns in E. coli in 1987, left as effectively a footnote in the discussion
00:39:46.640section of their paper. Mohika was the first to identify them explicitly as a feature to
00:39:53.380investigate. The function was a complete mystery, and most molecular biologists who came across
00:40:00.120these sequences shrugged and moved on. Mojica didn't move on. He spent the better part of a
00:40:06.880decade, the entire 1990s and into the early 2000s, trying to figure out what these repeats were
00:40:13.980doing. The breakthrough came in 2003. By that point, the genomics revolution was in full swing,
00:40:21.380and there were enough sequenced genomes in the public databases that Mojica could do something
00:40:27.120he couldn't do before. He could take the unique spacer sequences, the bits between the repeats,
00:40:33.900and ask the sequencing database, have you seen this sequence before? He sent it through the NIH
00:40:40.560database known as BLAST, and the answer came back, yes. Some of those spacer sequences exactly
00:40:48.220matched DNA from bacteriophages, viruses that infect bacteria and archaea. That was the key.
00:40:58.020Mojica realized that the repeats weren't random junk. They were a record. Each spacer was a
00:41:06.060snippet of DNA that the organism had captured from a past bacteriophage infection. The clusters
00:41:14.520of repeats were the index. Between the repeats were the codes for memories of past infections.
00:41:23.500This looked like an immune system, specifically an adaptive immune system. The bacterium,
00:41:30.720or archaean, was in effect vaccinating itself against viruses by holding onto fragments of
00:41:38.700the phage's genomes and using that information to recognize and destroy them on future encounters.
00:41:46.020This was a stunning insight. It implied that bacteria and archaea, the simplest organisms
00:41:52.720in biology, had a sophisticated adoptive immune system with memory. We now call that system
00:41:59.600CRISPR, clustered regularly interspaced short palindromic repeats, and the nearby proteins
00:42:08.540were deemed CAS, short for CRISPR-associated. Mojica wrote up the paper. He submitted it to
00:42:16.120Nature in 2003. It was rejected without external review. He sent that to the Proceedings of the
00:42:23.700National Academy of Science, rejected, lacking, quote, novelty and importance. He sent it to
00:42:30.880molecular microbiology, rejected. Nucleic acids research, rejected. Increasingly desperate and
00:42:38.980now afraid he was going to be scooped, he eventually submitted it to a smaller journal
00:42:45.000called the Journal of Molecular Evolution, which, after 12 months of review and revision,
00:42:51.340finally published it in February 2005. This is another place where we see that revolutionary
00:42:57.380science isn't simply underfunded. Once the revolutionary insight is seen and documented,
00:43:02.780even then, the field can still miss what it's looking at. The discovery that bacteria have an
00:43:08.920adaptive immune system, arguably one of the most important findings in molecular biology over the
00:43:13.400past 50 years, was rejected by four of the top journals in the field. The reviewers and editors
00:43:20.020did not see the significance of what they were looking at. Mojica was studying salt pond archaea.
00:43:25.760He was a Spanish microbiologist with a small lab, and his findings sounded like esoteric
00:43:31.040microbial biology. It took a lesser journal to publish what is, in retrospect, an absolute
00:43:37.120landmark paper. From there, the timeline is short. Labs around the world began to catch on,
00:43:44.780or discover other features on their own. Danisco, yeah, the yogurt company, provided direct
00:43:51.320experimental evidence that CRISPR really does work as an adaptive immune system in bacteria.
00:43:57.340Bacteria are necessary for dairy fermentation. Bacteria are susceptible to outbreaks
00:44:02.400of phage infections. This is an enormous practical problem for industrial dairy.
00:44:08.240Danisco's 2007 paper in the journal Science validated Mojica's hypothesis and identified
00:44:15.100Cas9 as the protein that recognizes CRISPR-encoded sequences to cut and destroy bacteriophage
01:00:12.880So I do think it's worth seeing biomedical science as existing on a continuum, with necessary time, attention, and resources devoted to each step in the chain.
01:00:24.040It is easy to look at recent medical advances and see something human-driven, human-designed, and intentional.
01:00:31.280Humans-made CAR T cells and checkpoint inhibitors for cancer therapy, monoclonal antibodies, kinase inhibitors, mRNA vaccines.
01:00:39.360What can be more difficult to see is that these products of human ingenuity would be impossible
01:00:44.900without scientists dissecting the natural world first. Chimeric T-cells cannot exist without
01:00:51.680understanding fundamental T-cell biology first. Checkpoint and kinase inhibitors can't be
01:00:57.860developed if we don't know the checkpoints and kinases worth inhibiting. Monoclonal antibodies
01:01:03.580make no sense without first understanding natural polyclonal antibody expression.
01:01:09.360and you get the point. While it's true that many of these basic questions begin in obviously
01:01:15.720disease-relevant systems, it still is in service of this thesis. The basic science,
01:01:22.280the foundational base of knowledge, is an irrevocably necessary part of the process
01:01:28.540of curing human disease. Someone, hundreds of thousands of someones really, had to be curious
01:01:35.400about how the natural world worked at its fundamental level.
01:01:40.040Only then, with the knowledge they gained,
01:01:42.360can we effectively supplement our labs and our bodies
01:01:46.320with designer molecules of our own creation.
01:01:49.720What I hope you'll leave with today is an appreciation for this idea.
01:01:53.540The drugs in your medicine cabinet did not just come from a clean idea in a lab.
01:01:59.100They started with a million small acts of curiosity about how the world works.
01:02:04.500And the lesson in humility here for me, the thing I genuinely take from all of this is that we should be much more generous as a culture and as a funding apparatus with the people who are out there asking those small, strange, sometimes apparently irrelevant questions because we are demonstrably terrible at predicting which one of them is going to change everything.
01:02:27.840We need people who translate curiosity into human outcomes, but I can't help but be struck by the
01:02:35.520fact that the apparently impractical question is sometimes the one that matters most.
01:02:42.860Thank you for listening to this week's episode of The Drive. Head over to peteratiamd.com
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