On the Right Taq

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I don’t know how you sit here and you call yourself cultured when you don’t know who Johnny Horton is. I don’t know who or what a Johnny Horton is. Is that some sort of Tim Hortons ripoff? No, not at all.

 

So, Johnny Horton is obviously a name. So, it’s Tim Hortons except they it’s a thing and they sell like coffee and donuts. Okay, I said who Johnny Horton is.

 

So, if you can like analyze basic sentences you would deduce that it was a person. Second, he was an American musician in like the 1950s. Super bomb.

 

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Okay, what songs did he have that were so super bomb? He sang North to Alaska, which has like a whole movie about it. Sink the Bismarck as well as the Battle of New Orleans. Okay, I have heard of that one.

 

Yeah, a lot of people have. It’s like a really common one. Yes, it was.

 

It’s something. It’s something. It’s fun.

 

You just have to like loosen up. I’m Dr. Dustin Edwards. And I’m Faith Cox.

 

Welcome to Demotics where we go to be from A in the most roundabout way. A mix of microbiology and history, in this series we connect different aspects of modern life and society to microbes through seemingly unconnected natural events, discoveries, and inventions. So how does the ballad by Johnny Horton, Sink the Bismarck, link to a tiny bacterium that revolutionized modern biology? Let’s find out.

 

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The Bismarck and her sister ship were the largest battleships ever built by Germany. It was a massive 800 feet long. I’ve only ever seen one battleship before in real life and that was the USS Texas that’s been moored underneath the San Jacinto Monument in Houston.

 

And it was about 575 feet long. The Bismarck then would have been about 40 percent bigger. And looking at it, seemingly unsinkable, armed with massive modern guns, and it was fast.

 

And it was one of the greatest warships ever built at that time. It was commissioned in 1940 near the beginning of World War II. And despite its capabilities, the Bismarck was sinking just eight months later.

 

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During its very first deployment, the Bismarck and a heavy cruiser, the Prince Eugen, encountered a Swedish ship that, although neutral, radioed in to its own home base that had encountered the battleship and the heavy cruiser. The Swedes then informed the British, who then sent ships to block its route. These ships included the battlecruiser, the HMS Hood, the largest battleship ever built by the UK.

 

It was an older ship, built about 20 years earlier towards the end of World War I and until the Bismarck was the dominant ship of the oceans. The battle group also included the battleship Prince of Wales. Upon encountering each other, the HMS Hood was no match for modern weaponry and was destroyed.

 

The Bismarck, though, did sustain a little bit of damage. Following orders by Winston Churchill, dozens of ships in the Royal Navy then relentlessly chased the Bismarck as it made its way towards occupied France for some repairs. The search, though, became frantic as the Allied ships began to run low on fuel and supplies.

 

The Bismarck, though, was eventually hit by obsolete biplane torpedo bombers, with one actually striking the steering mechanism, making direction change inoperable. It was further damaged by two British battleships and two heavy cruisers. The Bismarck was then scuttled by her own crew, sinking it.

 

Its wreckage was eventually found in water nearly three miles deep. I don’t know boat jargon. What does it mean to scuttle a ship? What they did was end up blowing some charges that would allow water to enter into the hull of the ship, sinking it so that it isn’t captured by the enemy.

 

Oh, okay. That makes sense. Its mission, though, was to disrupt shipping between the Allied powers of the US and Canada to the UK during the Battle of the Atlantic.

 

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So, as an island nation, the United Kingdom was highly dependent on imported goods. Britain required more than a million tons of imported material per week in order to be able to survive and fight. So, a strategy that Nazi Germany took was to force a quick surrender of the UK by starving out.

 

However, the Battle of the Atlantic turned into the longest continuous military campaign in World War II. The Battle of the Atlantic ran from September 3rd, 1939 to May 8th, 1945, lasting a total of five years, eight months, and five days. The Battle of the Atlantic was also known for large-scale submarine warfare.

 

After sighting a target, Axis German U-boats, which are submarines, would come together to attack, end masse, a single target, thereby overwhelming any escorting warships, very similar to wolf packs. The Battle of the Atlantic resulted in the deaths of over 72,000 Allied sailors and merchant seamen, the loss of 3,500 merchant ships, and 175 warships, while the Axis Kriegsmarine of Germany lost 30,000 sailors, 780 submarines, and about 50 warships, including the famed battleship Bismarck. One submarine that Germany lost to the British was the U-33.

 

On February 12th, 1940, the Royal Navy, which is the British just for reference, detected U-33 and dropped depth charges on the boat. Eventually, the submarine became so damaged that they had to surface for the crew to abandon the boat. On board the U-33 were parts to an encryption machine that the Allies had been trying to capture.

 

These parts were distributed among a few of the survivors who were instructed to release the rotors into the sea to avoid them being captured. They did not do this, however, and as a result, the British captured the parts, potentially changing the outcome of the war. So, the specific parts on board the U-33 belonged to the Enigma machine.

 

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The Enigma machine was an encryption device used in the early to mid-20th century, particularly by Nazi Germany. Germany used this to communicate and coordinate between all branches of their military. As such, the Allies aimed to understand the machine well enough to be able to decode the messages.

 

During the First World War, the British Army and Royal Navy merged their separate signals intelligence agencies into one called the Government Code and Cipher School, GCCS. During the Second World War, the agency was housed at Bletchley Park, primarily with the focus of decoding the Enigma machine. A particularly notable working at the GCCS was Alan Turing.

 

Alan Turing was a mathematician, computer scientist, and cryptanalyst who played a large role in World War II because of his work on decoding the Enigma machine. Before the war even began, Poland was deciphering messages from the Enigma machine by Nazi Germany. Poland shared the techniques they used to break the Enigma with Britain and France, establishing a strong cooperation to decode German messages.

 

Following security upgrades by Germany and invasion of both Poland and France, the British Government Code and Cipher School took over the bulk of the Enigma breaking efforts. At the British GCCS, Turing improved the British Bombay, which was a device used to predict the settings that the German Enigma machines were using to encrypt their messages, led Hutt 8, the specific branch of the GCCS responsible for decoding German naval messages, and developed techniques to help speed the decoding of German messages. His efforts and others combined to produce ULTRA.

 

ULTRA was the word used by the Allied Forces to refer to any information gained from Enigma messages decoding. After World War II the US continued using the word ULTRA to classify top-secret projects such as MKULTRA. MKULTRA was the cryptonym used to refer to a program of experiments on human subjects that were designed and performed by the United States Central Intelligence Agency.

 

The goal of these experiments was to identify and develop drugs and procedures that could be used in interrogations to weaken those being interrogated and extract knowledge and confessions through mind control. One particular drug that the CIA focused on was LSD. The CIA thought that they might be able to control drug Soviet spies with the drug and have them defect against their will.

 

The CIA would administer LSD to mental patients, prisoners, drug addicts, sex workers, CIA employees, military personnel, doctors, government agencies, and members of the general public, typically without the subject’s knowledge or consent. So, you’re saying there’s only like seven people left in the country that didn’t get dosed? Yeah, I read a joke that just like having random bad trips on acid just became like an occupational hazard of working at the CIA. It was actually a really bad thing.

 

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There were a lot of really bad outcomes and people who killed themselves as a result because they’d go on these horrible trips. So as such, the results of drugging people with LSD proved to be too unpredictable and the practice was abandoned by the CIA. How did they go about administering the drug? They just put it in people’s drinks sometimes.

 

But the people who like would consent, they’d often get subjected to like these wild experiments. Like there was this group of seven people that took acid every day for 77 consecutive days. It’s a lot.

 

There was one guy that he was like a higher up official. They drugged him and he didn’t know and so he was like going on a jog and he imagined there were dragons and all the cars running. Like as he was running, he thought all the cars driving by were dragons.

 

And I don’t know what happened. I just read about the dragon’s part. I don’t know if they had to go like capture him.

 

There was another guy that held up a bar at gunpoint because he was having a bad trip. And another guy that’s really notable and there’s actually like a documentary about it that he killed himself following his acid trip and jumped out of like a 13th story window. The privacy had to stop and it’s a good thing they did because they had a lot of these really bad experiences.

 

What happened next? Well, the CIA stopped using it but that didn’t mean like the general public stopped using it. So, LSD or lysergic acid diethylamide is a hallucinogenic drug that was first synthesized by Albert Hoffman in 1938. So, around the same time frame as like World War II.

 

Its hallucinogenic properties were first discovered in 1943 though after Hoffman accidentally ingested some of the compound. I guess he liked what he saw because after that the same year he started dosing himself to try to establish dosage. Just for like reference, apparently what a lot of people buy like off the street is between 20 to 80 like micrograms now.

 

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He started off with 250 micrograms. So, he was high as a kite. It’s even like said in his notes, he’s like, the effects were much stronger than I anticipated.

 

One of Albert Hoffman’s friends though was Carey Mullis who has admitted to dropping a lot of LSD. Mullis does a lot of things. He’s a climate change denier, an HIV and AIDS conspiracist, and a strong believer in science.

 

However, in the early 1980s, Mullis worked for a biotech company and his projects involved oligonucleotides. So, oligonucleotides are short segments of synthesized DNA or RNA. Driving on Route 101 in California at night with his girlfriend, trying to just get out of the lab for a while, the two of them were headed to a cabin and Mullis had this idea for amplifying DNA.

 

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As the story goes, he was high as a kite that day. So, he says in a video that he had to drink two bottles of wine to like come down off that high-is like stabilized thing, but he also notes that during his acceptance prize that we’ll talk about in a little bit. He used the oligos he was working with to replicate DNA millions of times from a single copy in a process called polymerase chain reaction or PCR for short.

 

PCR works by heating the double-stranded DNA to about 100 degrees Celsius, which is the same temperature that water boils at, in order to separate the two strands. Next you need the oligos, which act as primers that match up with the separated DNA. So, you now have this long piece of DNA that you want to duplicate, which we will call this the template strand, and two oligo primers that tell you where to start at.

 

And so, the primers will bind to either of the two separated strands. And so, this way the primers bracket either end of the section of DNA that you want to amplify. We then have to lower the temperature so that the long piece of DNA can bind to those shorter pieces of primer.

 

An additional component is an enzyme from E. coli called DNA polymerase, specifically the clonal fragment. That that’s the thing that’s all of the correct A’s and G’s and C’s and T’s that correspond to the DNA template. The clonal fragment and a single primer have been used before during early experiments with sequencing.

 

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However, what Mullis did was he was the first to use the two primers to try to bookend the DNA segment in order to amplify it. A problem with early PCR was that after one round of replicating DNA, in order to make more, the reaction would need to be brought back up to 100 degrees Celsius in order to separate the two DNA strands again. This would essentially cook the clonal fragment and it wouldn’t work anymore.

 

Heating up a protein is one way that you can denature it. And just for any listeners that don’t know, DNA polymerase is an enzyme and enzymes are made up by proteins. So, the problem is once you start to denature the proteins, the enzyme won’t work anymore.

 

So, this means that a person would have to reset the reaction by adding more polymerase each round. Amplifying this way was tedious and time consuming. But there was a solution to this problem a thousand miles away in Yellowstone National Park.

 

Yellowstone is famous for its large bison herds, geysers such as Old Faithful, and its hot springs. These pools of water have beautiful, colorful, concentric rings made up of algae and bacteria. So, when you’re looking at them and you see from the shore towards the center, there’s going to be greens and blues and reds and yellows.

 

So, these are made up of microorganisms. In the 1960s, scientists were studying what kinds of life could live in these extreme temperatures. One isolate was a rod-shaped bacterium that looked a lot like an earthworm named Thermus aquaticus, which means living in hot water.

 

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Thermus aquaticus was discovered by Thomas Brock at the Mushroom Spring about 10 years before Mullis even began his work with PCR. Because the bacteria were able to live in high temperature conditions, the bacteria’s DNA polymerase, TAC, which is short for Thermus aquaticus, was also thermostable. This means that we can increase the temperature of our reactions for PCR to separate the two DNA strands and TAC polymerase would not be denatured and would be ready for another round of application and another and another and another.

 

Mullis and company began experiments with this new thermostable polymerase and everything was going fairly well enough. However, we are still missing an important piece. The last component to make PCR both practical and revolutionary was the invention of a machine called a thermocycler.

 

This machine could be programmed to heat and cool the reactions on a time to schedule. The first thermocyclers were built to accommodate the clonal fragment-based PCR. These machines were a little bit more complex in that they were automated to be able to add new polymerase each round.

 

So, remember they could denature it every time they could heat it up. And because of that, the sample tubes actually had to be left open. After the inclusion of TAC polymerase in the reactions, a new simpler design was built.

 

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Kary Mullis goes on to win the Nobel Prize in Chemistry in 1993. He is perhaps the only Nobel laureate to have claimed to have talked to aliens. He also mentions acid in his Nobel Peace Prize and taking it with Hoffman.

 

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While all the components for PCR were known to science before he used them together, Mullis had the foresight, passion, and persistence to demonstrate their potential and to bring it to final product. There are tons of stories about him, including him getting into actual fistfights with other people in defense of his idea during those initial days developing PCR. Kary Mullis passed away a couple of weeks ago, but he has a TED talk that you can check out called Play, Experiment, Discover.

 

After watching and listening to him, I am just instantly reminded of John Malkovich and I hope that he plays him in a biography. In the 35 years since the invention of PCR, all of the components have been improved upon. There are faster and cheaper primer synthesis options, modifications in the TAC polymerase to be more stable and less error-prone at adding mutations, the discovery of other thermostable polymerases and other bacteria, and of course the thermocycler.

 

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Our science and society message today are about how a relatively small investment in basic science and research created this technology that has far-reaching implications in all of our daily lives. PCR has a large impact and can be used for all sorts of diagnostic tests and experiments by looking for gene amplification. Viral and bacterial infections can be determined by looking for genes specific to those viruses and bacteria.

 

You can also use PCR to amplify segments and determine which species it came from, or you can compare different samples in like a crime scene to determine maybe which suspected DNA fragment came from, and then genetic testing can also be performed to amplify genes that are associated with a disease indicating whether you have that disease or not. Segments can also be amplified in a manner they overlap a little bit and then the overlaps put together in sequence to determine the sequence of a genome like was done with SARS. Thank you for listening to episode two on the right TAC.

 

Show notes, transcripts, citations, and social media links are available on our website at germomics.com. Hey, remember the time I beat you in battleship for like six rounds straight? No. I do. I remember it perfectly.

 

So we were on our way back from a conference in DC and it had stormed like in Dallas on the way home and I remember thinking like man must suck to like be in a storm right now but I’m safe in my metal bird in the sky and I didn’t think about how the storm would like affect us because it wasn’t storming when like we were doing anything but turns out it’s like a butterfly effect so during the storm all the planes like before us couldn’t land so when they could all finally land all the loading docks were taken so it was our time to land we could like go on the ground but we couldn’t go into a loading dock and like settle and get off so we ended up being on our airplane about three hours longer than we were supposed to be so I actually remember someone sitting near us they um started a movie like as we were descending and I was like man how stupid it’s gonna like suck whenever you have to get off and then you have like an hour left this movie and I remember by the time we got off the plane they had actually like finished that movie and another one from beginning to end so we had this very long like wait just on our plane it was during that way that I beat you six times in battleship I think you cheated how do you cheat in battleship I think you’re looking at my screen the airplane screens are like set up in a manner that you can’t do that I would have I would have to physically move my face in front of yours to look at your screen I think you cheated I think you’re a sore loser I would play you in battleship right now and still beat you. Bet.

Written and performed by Dr. Dustin Edwards and Faith Cox

Music from
Opportunity Walks” by Kevin MacLeod; license CC BY 4.0

Images from
Yellowstone National Park, hot springs © Brian Schaller, CDC; license FAL
Thermus aquaticus © Diane Montpetit; public domain