ID 2.2 Lesson 2.5 Workbook - Tufts University
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91 Workbook Lesson 2.5 DEFINITIONS OF TERMS Esophagus — the tube that connects the mouth with the stomach. Duodenum — the first section of the small intestine located below the stomach. For a complete list of defined terms, see the Glossary . ______________________________ ______________________________ ______________________________ ______________________________ ______________________________ ______________________________ ______________________________ ______________________________ ______________________________ ______________________________ ______________________________ ______________________________ ______________________________ ______________________________ ______________________________ ______________________________ ______________________________ ______________________________ ______________________________ ______________________________ ______________________________ ______________________________ ______________________________ ______________________________ ______________________________ ______________________________ ______________________________ ______________________________ ______________________________ ______________________________ ______________________________ ______________________________ ______________________________ ______________________________ ______________________________ What is a stomach ulcer? A peptic ulcer is a persistent wound in the lining (epithelium) of the stomach, small intestine or the lower esophagus that does not heal. The epithelium in the stomach is normally resistant to the acid produced during a meal, but the ulcer exposes sensitive tissues. As a result, people with stomach ulcers experience pain, especially during a meal. Ulcers in the small intestines ( duodenal ulcer) are found where food exits from the stomach into the small intestines. In this case, the pain starts about 2–3 hours after a meal when the digested food enters the duodenum. Unlike stomach and LESSON 2.5 WORKBOOK Do bacteria cause stomach ulcers? Applying Koch's postulates This lesson continues to grapple with the problem of arriving at causation from correlation by looking at another infectious agent that presents challenges to fulfilling Koch’s postulates, Helicobacter pylori . H. pylori is thought to cause stomach ulcers, and its discovery revolutionized how we treat ulcers. However, Koch’s postulates have never been fully established for this infectious agent, begging the question — will the future reveal another 'cause' of stomach ulcers? Figure 1: Peptic ulcers are found in different regions of the gastrointestinal tract: the stomach, the duodenum, and occasionally, the lower esophagus.
Transcript of ID 2.2 Lesson 2.5 Workbook - Tufts University
W o r k b o o k Lesson 2.5
DEFINITIONS OF TERMS
stomach.
Duodenum — the first section of the small intestine located below
the stomach.
______________________________ ______________________________ ______________________________ ______________________________ ______________________________ ______________________________ ______________________________ ______________________________ ______________________________ ______________________________ ______________________________ ______________________________ ______________________________ ______________________________ ______________________________ ______________________________ ______________________________ ______________________________ ______________________________ ______________________________ ______________________________ ______________________________ ______________________________ ______________________________ ______________________________ ______________________________ ______________________________ ______________________________ ______________________________ ______________________________ ______________________________ ______________________________ ______________________________ ______________________________ ______________________________
What is a stomach ulcer?
A peptic ulcer is a persistent wound in the lining (epithelium) of the stomach, small intestine or the lower esophagus that does not heal. The epithelium in the stomach is normally resistant to the acid produced during a meal, but the ulcer exposes sensitive tissues. As a result, people with stomach ulcers experience pain, especially during a meal.
Ulcers in the small intestines (duodenal ulcer) are found where food exits from the stomach into the small intestines. In this case, the pain starts about 2–3 hours after a meal when the digested food enters the duodenum. Unlike stomach and
LESSON 2.5 WORKBOOK Do bacteria cause stomach ulcers? Applying Koch's postulates
This lesson continues to grapple with the problem of arriving at causation from correlation by looking at another infectious agent that presents challenges to fulfilling Koch’s postulates, Helicobacter pylori. H. pylori is thought to cause stomach ulcers, and its discovery revolutionized how we treat ulcers. However, Koch’s postulates have never been fully established for this infectious agent, begging the question — will the future reveal another 'cause' of stomach ulcers?
Figure 1: Peptic ulcers are found in different regions of the gastrointestinal tract: the stomach, the duodenum, and occasionally, the lower esophagus.
W o r k b o o k Lesson 2.5
DEFINITIONS OF TERMS
Peritonitis — inflammation of the peritoneum, the thin tissue that lines the inner wall of the
abdomen and covers most of the abdominal organs.
For a complete list of defined terms, see the Glossary.
1. A large study of biopsy samples from patients with ulcers conducted in the 1950s failed to observe H. pylori because
.a the scientists examined samples from healthy patients.
.b an inadequate staining technique was used leaving the bacteria ‘invisible’.
______________________________ ______________________________ ______________________________ ______________________________ ______________________________ ______________________________ ______________________________ ______________________________ ______________________________ ______________________________ ______________________________ ______________________________ ______________________________ ______________________________ ______________________________ ______________________________ ______________________________ ______________________________ ______________________________ ______________________________ ______________________________
duodenal ulcers, esophageal ulcers generally cause symptoms before meals or when a person is laying down. In all cases, symptoms may include vomiting and in extreme cases infection in the abdomen, which results from bacteria entering the sterile areas of the body through the ulcer. But even the less severe symptoms should be treated because ulcers may lead to the development of cancers. Up until 1982, genetics, stress and/or diet were thought to cause ulcers.
A crazy idea at the time — do bacteria cause stomach ulcers?
The hypothesis that ulcers are caused by bacteria, originated first in the 19th century. In 1875, German scientists found spiral-shaped bacteria in the lining of the human stomach but they were unable to culture them, and the results were eventually forgotten. A couple of decades later, Professor W. Jaworski, who worked at a University in Poland, investigated human stomach samples. He found bacteria with a spiral shape and was the first to suggest a possible role of the spiral bacteria in the pathogenesis of gastric diseases. But his work was published in a textbook written in Polish and went unnoticed. Later on, other studies also observed curved rods in the stomach of many patients with peptic ulcers and stomach cancer.
In 1954, a large study failed to observe the bacteria in 1,180 stomach biopsies. Unfortunately, this was the result of a technical limitation: the researchers used staining technique that was insufficient in visualizing the bacteria. A couple of decades later, a different staining technique allowed scientists to better visualize bacteria in samples from patients with gastric ulcers. Later, this bacterium was named Helicobacter pylori. At the time, conventional thinking was that no bacterium could live in the stomach given its acidity is similar to that of a car battery. The idea was that the strong acid destroys bacterial structures, specifically proteins, killing the bacteria. For this reason, most scientists and doctors were quite skeptical of the idea that the bacteria in the samples were more than contamination from poor technique.
Figure 2: H. pylori is a spiral shaped bacteria.
Figure 3: Microscopic images of H. pylori cells (dark brown spirals) on biopsy samples from an ulcer patient.
W o r k b o o k Lesson 2.5
DEFINITIONS OF TERMS
Bacterial colony — a cluster of billions of bacterial cells that originated from one single cell,
and are visible with a naked eye on the agar surface.
Endoscopy — a procedure used to examine a patient's
digestive tract. It is performed with an endoscope, a flexible tube equipped with a camera
and light to provide pictures of the digestive tract.
For a complete list of defined terms, see the Glossary.
2. Marshall and Warren had a hard time culturing H. pylori in the lab because
.a they did not know what was the optimal type of media to grow the microbes.
.b they did not know for how long to incubate them.
.c there was not enough information in the literature about H. pylori growth under lab conditions.
.d all of the above. ______________________________ ______________________________ ______________________________ ______________________________ ______________________________ ______________________________ ______________________________ ______________________________ ______________________________ ______________________________ ______________________________ ______________________________ ______________________________ ______________________________ ______________________________ ______________________________ ______________________________ ______________________________ ______________________________ ______________________________ ______________________________ ______________________________
Two of the doctors who observed bacteria in patients' samples, Robin Warren and Barry Marshall, contended that stomach ulcers were caused by infection with this bacterium rather than stress or spicy food, as had been assumed before. To test whether the bacterium was causing ulcers they sought to apply Koch's postulates.
Their first step was to look for an association between the H. pylori and ulcers. So they carefully studied biopsy samples from patients with ulcers, and over, and over again they could see the bacteria present in their biopsy samples. Years later, numerous research groups
confirmed their findings, and identified H. pylori in almost all patients with ulcers.
Their next step was attempting to isolate the bacteria from the patients’ samples as a pure culture. However, growing the bacteria under normal laboratory conditions proved very challenging — they tried numerous types of liquid medium and agar plates but nothing grew! With some luck, they unintentionally left their plates incubating for 5 days, instead of the usual 1–2 days, over one Easter weekend and returned to growing bacterial colonies.
Apparently these bacteria grow slower than most, but now that they could grow H. pylori, Warren and Marshall wanted to prove that it could cause a disease in healthy animals. But at this step Warren and Marshall ran into another problem, one that they could not solve: they could not find an animal model that was colonizable by H. pylori.
This left many scientists questioning how H. pylori might be related to ulcers. For example, was H. pylori causing or caused by gastric issues, or was it merely a bystander? So, to prove his theory Dr. Marshall did something no one should ever do — he drank a beaker of H. pylori culture. A few days later, he became ill with nausea and vomiting, and an endoscopy, performed about ten days later, revealed signs of irritation, and the presence of H. pylori. But before developing ulcers, he took antibiotics to clear the infection.
Figure 4: Barry Marshall (on the left) and Robin Warren (on the right) while working together in Perth in the 1980s.
Figure 5: Currently, the only organism H. pylori is known to infect are humans, which makes it hard to prove causation.
W o r k b o o k Lesson 2.5
DEFINITIONS OF TERMS
For a complete list of defined terms, see the Glossary.
3. When planning a scientific investigation, what factors play a role in the decision?
.a time
.d all of the above ______________________________ ______________________________ ______________________________ ______________________________ ______________________________ ______________________________ ______________________________ ______________________________ ______________________________ ______________________________ ______________________________ ______________________________ ______________________________ ______________________________ ______________________________ ______________________________ ______________________________ ______________________________ ______________________________ ______________________________ ______________________________ ______________________________ ______________________________ ______________________________ ______________________________ ______________________________ ______________________________ ______________________________ ______________________________
A few years later, the first therapy for the treatment of duodenal ulcers was invented, and with some modifications has been used ever since to treat ulcers. It is a cocktail of two antibiotics in combination with a drug that inhibits acid production. This was a major breakthrough because treating ulcers with acid lowering drugs alone did not permanently cure the disease, but using the antibiotics did! In 1994, the National Institutes of Health (NIH) published an opinion stating that most recurrent duodenal and stomach ulcers were caused by H. pylori and recommended that antibiotics be included in the treatment regimen.
Antibiotics are not bacteria specific, so we still can't exclude the possibility that the treatment works for reasons we are unaware of. This means that there is still no direct proof that H. pylori causes stomach ulcers, so ulcers join the list of diseases for which Koch's postulates could not be fulfilled.
Marshall and Warren rewrote the textbooks with reference to what causes gastritis and gastric ulcers. In recognition of their discovery, they were awarded the 2005 Nobel Prize in Physiology or Medicine.
The challenges of designing experiments to move from correlation to causation
When conducting research, scientists or doctors make observations that intrigue them or call what they know into question. After looking at what others have found out about a phenomenon, they can synthesize a hypothesis. Based on this hypothesis, experiments can be planned and performed to test its validity. Finally, the data is used to make conclusions, and update biological models.
There is no single correct experiment to address a question or a hypothesis: deciding what experiment to run is very challenging, and is based on many factors such as time, resources, importance of prompt discovery of a treatment or a vaccine, or whether or not we have the necessary equipment or methodology. As we will see, how the experiments are constructed limits the scope of our conclusions, a factor often missed by reports of scientific findings in the news. This brings us to an important point — if we don't know the used methodology we can't interpret results of an experiment! This is why, it is worth spending the time needed to understand how an experiment was done, so we can make our own conclusions.
Figure 6: Amoxicillin is one of the antibiotics in the triple therapy used to treat ulcers. Like most antibiotics, it inhibits the growth of other bacterial species.
W o r k b o o k Lesson 2.5
DEFINITIONS OF TERMS
Acid reflux — mucosal damage of the esophagus caused by stomach acid flowing into the
esophagus from the stomach.
For a complete list of defined terms, see the Glossary.
4. The following describe ulcers EXCEPT:
.a it’s a persistent wound in the epithelium of the stomach, small intestine or the lower esophagus that does not heal
.b stomach ulcers are painful because of the strong acid secreted into the stomach during a meal
.c duodenal ulcers are found in the large intestine below the stomach
.d none of the above ______________________________ ______________________________ ______________________________ ______________________________ ______________________________ ______________________________ ______________________________ ______________________________ ______________________________ ______________________________ ______________________________ ______________________________ ______________________________ ______________________________ ______________________________ ______________________________ ______________________________ ______________________________ ______________________________ ______________________________ ______________________________ ______________________________
Case study: Is excessive acid production causing ulcers?
“Dr. Annis was a gastroenterologist working in a busy clinic in the late 1960s. For the past two weeks, she had diagnosed five of her patients with stomach ulcers. She had treated all of them within the past few months, and they all complained of persistent acid reflux related to excess acid production. All five patients had previously refused to take antacids but instead were opting out for natural remedies such as change in diet, herbal teas, etc.
As she was going through their medical records, she wondered: did they get ulcers because of the higher than normal acid production? She did a literature search on the topic but she could not find any reports that supported or rejected her suspicions. She decided to call some of her colleagues across the country, and ask them whether they have had similar cases. All of her colleagues agreed to review their patients’ medical records and to discuss their findings with each other.
A few weeks later, all of the doctors reported such cases in their practices: in total there were 44 patients who suffered with severe acid reflux symptoms for months, used antacids only occasionally or never, and were eventually diagnosed with stomach ulcers.
The question that Dr. Annis asked earlier, came up again: did they get ulcers because of the excessive stomach acid production? All the doctors agreed that they needed to investigate this because it looked that there was correlation between long term exposure to high acid levels and ulcers. But was there causation? Did the acid really cause the ulcers?
Dr. Medina suggested that they went back and look through their records for another group of patients: the ones who took antacids regularly. Did they still get ulcers? This way, they could compare the two groups, and try to come up with some answers. Everyone agreed.
They all came back together a month later. This time the patients’ records were confusing. Most of the patients who were taking antacids followed their own regimen based on their personal preferences for dosage per day, type of antacid medication, etc. Some even took breaks from the medication for a few days or weeks. It was very difficult to sort through the data and come up with any conclusion.
But the doctors did not want to give up. What they needed was a better study. But whom would they include? Dr. Johnson proposed that they recruit new patients with severe acid reflux who have never gotten any treatment but do not have ulcers yet, and start all of them on consistent regimen with the same antacid. He also suggested that since there are other factors suspected to cause ulcers, such as stress, diet and weight, they should recruit people who have similar stress levels, diet, and weight range. Once
W o r k b o o k Lesson 2.5
DEFINITIONS OF TERMS
Control group — during an experiment, the subjects in a control group are treated
______________________________ ______________________________ ______________________________ ______________________________ ______________________________ ______________________________ ______________________________ ______________________________ ______________________________ ______________________________ ______________________________ ______________________________ ______________________________ ______________________________ ______________________________ ______________________________ ______________________________ ______________________________ ______________________________ ______________________________ ______________________________ ______________________________ ______________________________ ______________________________ ______________________________ ______________________________ ______________________________ ______________________________ ______________________________ ______________________________ ______________________________ ______________________________ ______________________________ ______________________________ ______________________________ ______________________________ ______________________________
they started treatment, they should do follow-ups every few months with endoscopies, to look directly at the stomach lining, and measure the number of stomach ulcers, if any. If most people did not develop ulcers or develop very few, then the excessive stomach acid production will be proven as the cause for ulcers.
However, Dr. Lu interjected that if they treated all patients with antacids, they would not be able to prove that the antacid made the difference because there could always be other factors. But if they prescribed medication to some people and not others, then they could draw better conclusions on the effect of antacids. She agreed with the plan Dr. Johnson proposed for selecting the patients, but she proposed changes in the experimental design. She suggested that the patients be randomly split into two groups: one experimental, which would get the antacid, and one control group, which would get sugar pills instead. The sugar pills would have no effect on acid neutralization. This way, if the experimental group developed less ulcers than the control group, the doctors would be more confident drawing the conclusion that excess stomach acid is a contributing factor in stomach ulcers. By giving the control group sugar pills, instead of nothing, they would not have to tell the patients in which group they were placed, eliminating any possible psychological factors. Then every few months, they would perform endoscopies on the patients from both groups and measure the number of ulcers per patient.
The rest of the doctors agreed with the proposed plan.
Dr. Annis reminded everyone that the outcome they hoped for, that people in the experimental group would have less ulcers if any compared to the people in the control group, was not the only possible one. In fact, there were three other possible outcomes. What do you think they might be?”
What people are you going to include in the study? There is no perfect group of people when it comes to studies. Do you select a wide age range? Do you include only people that have the condition? Do you include only people of one gender, age, and race? How many people do you include? Do you need to exclude people with other factors or diseases that might bias your results? Each of these choices has pros and cons — a narrow selection of people helps to control for unforeseen factors which may have an effect, while a wide selection might be better when you want to know if your findings are relevant to everyone.
Figure 7: Stomach endoscopy revealing typical stomach lining.
W o r k b o o k Lesson 2.5
DEFINITIONS OF TERMS
______________________________ ______________________________ ______________________________ ______________________________ ______________________________ ______________________________ ______________________________ ______________________________ ______________________________ ______________________________ ______________________________ ______________________________ ______________________________ ______________________________ ______________________________ ______________________________ ______________________________ ______________________________ ______________________________ ______________________________ ______________________________ ______________________________ ______________________________ ______________________________ ______________________________ ______________________________ ______________________________ ______________________________ ______________________________ ______________________________ ______________________________ ______________________________ ______________________________ ______________________________ ______________________________ ______________________________ ______________________________
How are you going to measure changes in the ulcers? It is critical that you 'look' for the ulcers, or any measure of disease, in a way that gives the most detail possible. Do you measure the number of ulcers by asking patients to report symptoms? Do you look at the stomach with an endoscope? Do you count the number of ulcers or the size? Each of these choices has pros and cons. For example, the less invasive a measurement is, the easier it will be for the patients, but it may not be accurate enough. Or, what if antacid treatment effectively gets rid of symptoms but does not promote healing of the ulcer?
How will the people be grouped and treated? This is not a straightforward decision and just like choosing participants there is no perfect way to group them. Do you assign groups to balance as many factors as you can (age, race, gender, height, weight, etc.), or do you assign the groups randomly? What if you miss a factor that matters? What if the randomly assigned groups are not evenly split? Each of these choices has pros and cons — controlling grouping can help when you know a lot about other contributing factors, while a wide selection might be better when the other factors are less well-known.
What will be your ‘control group’? To prove causation most experiments need a control because there is no way to know what a normal or untreated group should be unless you measure it. At its heart, this is the key ingredient for distinguishing causation from correlation — you need to be able to compare the results of an untreated (control) group with a group that is treated in order to conclude whether a treatment works or not. So, what will be the difference between your treatment (experimental) and your control group? Do you give the same drug to both groups but in different doses? Do you administer the treatment only once or over a period of time? Do you give the control group a placebo, like a sugar pill which will have no effect on the condition, so the control group thinks they are getting the treatment as well? Again, each of these choices has pros and cons, and the decision will be based on the current circumstances. For example, most often scientists or doctors prefer to give only placebo or no treatment at all to a control group. This will allow for a relative straightforward interpretation of the results. However, if the disease you want to treat is highly lethal or debilitating, withholding treatment from the control group may be considered unethical. In such a case, giving different low doses of a drug to the control group may be a better option.
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W o r k b o o k Lesson 2.5
TERM DEFINITION
Acid reflux Mucosal damage of the esophagus caused by stomach acid flowing into the esophagus from the stomach.
Bacterial colony A cluster of billions of bacterial cells that originated from one single cell, and are visible with a naked eye on the agar surface.
Control group During an experiment, the subjects in a control group are treated identically to the experimental group with the exception of the tested factor, e.g., a drug, a procedure or another factor.
Duodenum The first section of the small intestine located below the stomach.
Endoscopy A procedure used to examine a patient's digestive tract. It is performed with an endoscope, a flexible tube equipped with a camera and light to provide pictures of the digestive tract.
Esophagus The tube that connects the mouth with the stomach.
Hypothesis A testable explanation of a phenomenon.
Peritonitis Inflammation of the peritoneum, the thin tissue that lines the inner wall of the abdomen and covers most of the abdominal organs.
Placebo Medically ineffective treatment such as a sugar pill.
DEFINITIONS OF TERMS
stomach.
Duodenum — the first section of the small intestine located below
the stomach.
______________________________ ______________________________ ______________________________ ______________________________ ______________________________ ______________________________ ______________________________ ______________________________ ______________________________ ______________________________ ______________________________ ______________________________ ______________________________ ______________________________ ______________________________ ______________________________ ______________________________ ______________________________ ______________________________ ______________________________ ______________________________ ______________________________ ______________________________ ______________________________ ______________________________ ______________________________ ______________________________ ______________________________ ______________________________ ______________________________ ______________________________ ______________________________ ______________________________ ______________________________ ______________________________
What is a stomach ulcer?
A peptic ulcer is a persistent wound in the lining (epithelium) of the stomach, small intestine or the lower esophagus that does not heal. The epithelium in the stomach is normally resistant to the acid produced during a meal, but the ulcer exposes sensitive tissues. As a result, people with stomach ulcers experience pain, especially during a meal.
Ulcers in the small intestines (duodenal ulcer) are found where food exits from the stomach into the small intestines. In this case, the pain starts about 2–3 hours after a meal when the digested food enters the duodenum. Unlike stomach and
LESSON 2.5 WORKBOOK Do bacteria cause stomach ulcers? Applying Koch's postulates
This lesson continues to grapple with the problem of arriving at causation from correlation by looking at another infectious agent that presents challenges to fulfilling Koch’s postulates, Helicobacter pylori. H. pylori is thought to cause stomach ulcers, and its discovery revolutionized how we treat ulcers. However, Koch’s postulates have never been fully established for this infectious agent, begging the question — will the future reveal another 'cause' of stomach ulcers?
Figure 1: Peptic ulcers are found in different regions of the gastrointestinal tract: the stomach, the duodenum, and occasionally, the lower esophagus.
W o r k b o o k Lesson 2.5
DEFINITIONS OF TERMS
Peritonitis — inflammation of the peritoneum, the thin tissue that lines the inner wall of the
abdomen and covers most of the abdominal organs.
For a complete list of defined terms, see the Glossary.
1. A large study of biopsy samples from patients with ulcers conducted in the 1950s failed to observe H. pylori because
.a the scientists examined samples from healthy patients.
.b an inadequate staining technique was used leaving the bacteria ‘invisible’.
______________________________ ______________________________ ______________________________ ______________________________ ______________________________ ______________________________ ______________________________ ______________________________ ______________________________ ______________________________ ______________________________ ______________________________ ______________________________ ______________________________ ______________________________ ______________________________ ______________________________ ______________________________ ______________________________ ______________________________ ______________________________
duodenal ulcers, esophageal ulcers generally cause symptoms before meals or when a person is laying down. In all cases, symptoms may include vomiting and in extreme cases infection in the abdomen, which results from bacteria entering the sterile areas of the body through the ulcer. But even the less severe symptoms should be treated because ulcers may lead to the development of cancers. Up until 1982, genetics, stress and/or diet were thought to cause ulcers.
A crazy idea at the time — do bacteria cause stomach ulcers?
The hypothesis that ulcers are caused by bacteria, originated first in the 19th century. In 1875, German scientists found spiral-shaped bacteria in the lining of the human stomach but they were unable to culture them, and the results were eventually forgotten. A couple of decades later, Professor W. Jaworski, who worked at a University in Poland, investigated human stomach samples. He found bacteria with a spiral shape and was the first to suggest a possible role of the spiral bacteria in the pathogenesis of gastric diseases. But his work was published in a textbook written in Polish and went unnoticed. Later on, other studies also observed curved rods in the stomach of many patients with peptic ulcers and stomach cancer.
In 1954, a large study failed to observe the bacteria in 1,180 stomach biopsies. Unfortunately, this was the result of a technical limitation: the researchers used staining technique that was insufficient in visualizing the bacteria. A couple of decades later, a different staining technique allowed scientists to better visualize bacteria in samples from patients with gastric ulcers. Later, this bacterium was named Helicobacter pylori. At the time, conventional thinking was that no bacterium could live in the stomach given its acidity is similar to that of a car battery. The idea was that the strong acid destroys bacterial structures, specifically proteins, killing the bacteria. For this reason, most scientists and doctors were quite skeptical of the idea that the bacteria in the samples were more than contamination from poor technique.
Figure 2: H. pylori is a spiral shaped bacteria.
Figure 3: Microscopic images of H. pylori cells (dark brown spirals) on biopsy samples from an ulcer patient.
W o r k b o o k Lesson 2.5
DEFINITIONS OF TERMS
Bacterial colony — a cluster of billions of bacterial cells that originated from one single cell,
and are visible with a naked eye on the agar surface.
Endoscopy — a procedure used to examine a patient's
digestive tract. It is performed with an endoscope, a flexible tube equipped with a camera
and light to provide pictures of the digestive tract.
For a complete list of defined terms, see the Glossary.
2. Marshall and Warren had a hard time culturing H. pylori in the lab because
.a they did not know what was the optimal type of media to grow the microbes.
.b they did not know for how long to incubate them.
.c there was not enough information in the literature about H. pylori growth under lab conditions.
.d all of the above. ______________________________ ______________________________ ______________________________ ______________________________ ______________________________ ______________________________ ______________________________ ______________________________ ______________________________ ______________________________ ______________________________ ______________________________ ______________________________ ______________________________ ______________________________ ______________________________ ______________________________ ______________________________ ______________________________ ______________________________ ______________________________ ______________________________
Two of the doctors who observed bacteria in patients' samples, Robin Warren and Barry Marshall, contended that stomach ulcers were caused by infection with this bacterium rather than stress or spicy food, as had been assumed before. To test whether the bacterium was causing ulcers they sought to apply Koch's postulates.
Their first step was to look for an association between the H. pylori and ulcers. So they carefully studied biopsy samples from patients with ulcers, and over, and over again they could see the bacteria present in their biopsy samples. Years later, numerous research groups
confirmed their findings, and identified H. pylori in almost all patients with ulcers.
Their next step was attempting to isolate the bacteria from the patients’ samples as a pure culture. However, growing the bacteria under normal laboratory conditions proved very challenging — they tried numerous types of liquid medium and agar plates but nothing grew! With some luck, they unintentionally left their plates incubating for 5 days, instead of the usual 1–2 days, over one Easter weekend and returned to growing bacterial colonies.
Apparently these bacteria grow slower than most, but now that they could grow H. pylori, Warren and Marshall wanted to prove that it could cause a disease in healthy animals. But at this step Warren and Marshall ran into another problem, one that they could not solve: they could not find an animal model that was colonizable by H. pylori.
This left many scientists questioning how H. pylori might be related to ulcers. For example, was H. pylori causing or caused by gastric issues, or was it merely a bystander? So, to prove his theory Dr. Marshall did something no one should ever do — he drank a beaker of H. pylori culture. A few days later, he became ill with nausea and vomiting, and an endoscopy, performed about ten days later, revealed signs of irritation, and the presence of H. pylori. But before developing ulcers, he took antibiotics to clear the infection.
Figure 4: Barry Marshall (on the left) and Robin Warren (on the right) while working together in Perth in the 1980s.
Figure 5: Currently, the only organism H. pylori is known to infect are humans, which makes it hard to prove causation.
W o r k b o o k Lesson 2.5
DEFINITIONS OF TERMS
For a complete list of defined terms, see the Glossary.
3. When planning a scientific investigation, what factors play a role in the decision?
.a time
.d all of the above ______________________________ ______________________________ ______________________________ ______________________________ ______________________________ ______________________________ ______________________________ ______________________________ ______________________________ ______________________________ ______________________________ ______________________________ ______________________________ ______________________________ ______________________________ ______________________________ ______________________________ ______________________________ ______________________________ ______________________________ ______________________________ ______________________________ ______________________________ ______________________________ ______________________________ ______________________________ ______________________________ ______________________________ ______________________________
A few years later, the first therapy for the treatment of duodenal ulcers was invented, and with some modifications has been used ever since to treat ulcers. It is a cocktail of two antibiotics in combination with a drug that inhibits acid production. This was a major breakthrough because treating ulcers with acid lowering drugs alone did not permanently cure the disease, but using the antibiotics did! In 1994, the National Institutes of Health (NIH) published an opinion stating that most recurrent duodenal and stomach ulcers were caused by H. pylori and recommended that antibiotics be included in the treatment regimen.
Antibiotics are not bacteria specific, so we still can't exclude the possibility that the treatment works for reasons we are unaware of. This means that there is still no direct proof that H. pylori causes stomach ulcers, so ulcers join the list of diseases for which Koch's postulates could not be fulfilled.
Marshall and Warren rewrote the textbooks with reference to what causes gastritis and gastric ulcers. In recognition of their discovery, they were awarded the 2005 Nobel Prize in Physiology or Medicine.
The challenges of designing experiments to move from correlation to causation
When conducting research, scientists or doctors make observations that intrigue them or call what they know into question. After looking at what others have found out about a phenomenon, they can synthesize a hypothesis. Based on this hypothesis, experiments can be planned and performed to test its validity. Finally, the data is used to make conclusions, and update biological models.
There is no single correct experiment to address a question or a hypothesis: deciding what experiment to run is very challenging, and is based on many factors such as time, resources, importance of prompt discovery of a treatment or a vaccine, or whether or not we have the necessary equipment or methodology. As we will see, how the experiments are constructed limits the scope of our conclusions, a factor often missed by reports of scientific findings in the news. This brings us to an important point — if we don't know the used methodology we can't interpret results of an experiment! This is why, it is worth spending the time needed to understand how an experiment was done, so we can make our own conclusions.
Figure 6: Amoxicillin is one of the antibiotics in the triple therapy used to treat ulcers. Like most antibiotics, it inhibits the growth of other bacterial species.
W o r k b o o k Lesson 2.5
DEFINITIONS OF TERMS
Acid reflux — mucosal damage of the esophagus caused by stomach acid flowing into the
esophagus from the stomach.
For a complete list of defined terms, see the Glossary.
4. The following describe ulcers EXCEPT:
.a it’s a persistent wound in the epithelium of the stomach, small intestine or the lower esophagus that does not heal
.b stomach ulcers are painful because of the strong acid secreted into the stomach during a meal
.c duodenal ulcers are found in the large intestine below the stomach
.d none of the above ______________________________ ______________________________ ______________________________ ______________________________ ______________________________ ______________________________ ______________________________ ______________________________ ______________________________ ______________________________ ______________________________ ______________________________ ______________________________ ______________________________ ______________________________ ______________________________ ______________________________ ______________________________ ______________________________ ______________________________ ______________________________ ______________________________
Case study: Is excessive acid production causing ulcers?
“Dr. Annis was a gastroenterologist working in a busy clinic in the late 1960s. For the past two weeks, she had diagnosed five of her patients with stomach ulcers. She had treated all of them within the past few months, and they all complained of persistent acid reflux related to excess acid production. All five patients had previously refused to take antacids but instead were opting out for natural remedies such as change in diet, herbal teas, etc.
As she was going through their medical records, she wondered: did they get ulcers because of the higher than normal acid production? She did a literature search on the topic but she could not find any reports that supported or rejected her suspicions. She decided to call some of her colleagues across the country, and ask them whether they have had similar cases. All of her colleagues agreed to review their patients’ medical records and to discuss their findings with each other.
A few weeks later, all of the doctors reported such cases in their practices: in total there were 44 patients who suffered with severe acid reflux symptoms for months, used antacids only occasionally or never, and were eventually diagnosed with stomach ulcers.
The question that Dr. Annis asked earlier, came up again: did they get ulcers because of the excessive stomach acid production? All the doctors agreed that they needed to investigate this because it looked that there was correlation between long term exposure to high acid levels and ulcers. But was there causation? Did the acid really cause the ulcers?
Dr. Medina suggested that they went back and look through their records for another group of patients: the ones who took antacids regularly. Did they still get ulcers? This way, they could compare the two groups, and try to come up with some answers. Everyone agreed.
They all came back together a month later. This time the patients’ records were confusing. Most of the patients who were taking antacids followed their own regimen based on their personal preferences for dosage per day, type of antacid medication, etc. Some even took breaks from the medication for a few days or weeks. It was very difficult to sort through the data and come up with any conclusion.
But the doctors did not want to give up. What they needed was a better study. But whom would they include? Dr. Johnson proposed that they recruit new patients with severe acid reflux who have never gotten any treatment but do not have ulcers yet, and start all of them on consistent regimen with the same antacid. He also suggested that since there are other factors suspected to cause ulcers, such as stress, diet and weight, they should recruit people who have similar stress levels, diet, and weight range. Once
W o r k b o o k Lesson 2.5
DEFINITIONS OF TERMS
Control group — during an experiment, the subjects in a control group are treated
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they started treatment, they should do follow-ups every few months with endoscopies, to look directly at the stomach lining, and measure the number of stomach ulcers, if any. If most people did not develop ulcers or develop very few, then the excessive stomach acid production will be proven as the cause for ulcers.
However, Dr. Lu interjected that if they treated all patients with antacids, they would not be able to prove that the antacid made the difference because there could always be other factors. But if they prescribed medication to some people and not others, then they could draw better conclusions on the effect of antacids. She agreed with the plan Dr. Johnson proposed for selecting the patients, but she proposed changes in the experimental design. She suggested that the patients be randomly split into two groups: one experimental, which would get the antacid, and one control group, which would get sugar pills instead. The sugar pills would have no effect on acid neutralization. This way, if the experimental group developed less ulcers than the control group, the doctors would be more confident drawing the conclusion that excess stomach acid is a contributing factor in stomach ulcers. By giving the control group sugar pills, instead of nothing, they would not have to tell the patients in which group they were placed, eliminating any possible psychological factors. Then every few months, they would perform endoscopies on the patients from both groups and measure the number of ulcers per patient.
The rest of the doctors agreed with the proposed plan.
Dr. Annis reminded everyone that the outcome they hoped for, that people in the experimental group would have less ulcers if any compared to the people in the control group, was not the only possible one. In fact, there were three other possible outcomes. What do you think they might be?”
What people are you going to include in the study? There is no perfect group of people when it comes to studies. Do you select a wide age range? Do you include only people that have the condition? Do you include only people of one gender, age, and race? How many people do you include? Do you need to exclude people with other factors or diseases that might bias your results? Each of these choices has pros and cons — a narrow selection of people helps to control for unforeseen factors which may have an effect, while a wide selection might be better when you want to know if your findings are relevant to everyone.
Figure 7: Stomach endoscopy revealing typical stomach lining.
W o r k b o o k Lesson 2.5
DEFINITIONS OF TERMS
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How are you going to measure changes in the ulcers? It is critical that you 'look' for the ulcers, or any measure of disease, in a way that gives the most detail possible. Do you measure the number of ulcers by asking patients to report symptoms? Do you look at the stomach with an endoscope? Do you count the number of ulcers or the size? Each of these choices has pros and cons. For example, the less invasive a measurement is, the easier it will be for the patients, but it may not be accurate enough. Or, what if antacid treatment effectively gets rid of symptoms but does not promote healing of the ulcer?
How will the people be grouped and treated? This is not a straightforward decision and just like choosing participants there is no perfect way to group them. Do you assign groups to balance as many factors as you can (age, race, gender, height, weight, etc.), or do you assign the groups randomly? What if you miss a factor that matters? What if the randomly assigned groups are not evenly split? Each of these choices has pros and cons — controlling grouping can help when you know a lot about other contributing factors, while a wide selection might be better when the other factors are less well-known.
What will be your ‘control group’? To prove causation most experiments need a control because there is no way to know what a normal or untreated group should be unless you measure it. At its heart, this is the key ingredient for distinguishing causation from correlation — you need to be able to compare the results of an untreated (control) group with a group that is treated in order to conclude whether a treatment works or not. So, what will be the difference between your treatment (experimental) and your control group? Do you give the same drug to both groups but in different doses? Do you administer the treatment only once or over a period of time? Do you give the control group a placebo, like a sugar pill which will have no effect on the condition, so the control group thinks they are getting the treatment as well? Again, each of these choices has pros and cons, and the decision will be based on the current circumstances. For example, most often scientists or doctors prefer to give only placebo or no treatment at all to a control group. This will allow for a relative straightforward interpretation of the results. However, if the disease you want to treat is highly lethal or debilitating, withholding treatment from the control group may be considered unethical. In such a case, giving different low doses of a drug to the control group may be a better option.
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W o r k b o o k Lesson 2.5
TERM DEFINITION
Acid reflux Mucosal damage of the esophagus caused by stomach acid flowing into the esophagus from the stomach.
Bacterial colony A cluster of billions of bacterial cells that originated from one single cell, and are visible with a naked eye on the agar surface.
Control group During an experiment, the subjects in a control group are treated identically to the experimental group with the exception of the tested factor, e.g., a drug, a procedure or another factor.
Duodenum The first section of the small intestine located below the stomach.
Endoscopy A procedure used to examine a patient's digestive tract. It is performed with an endoscope, a flexible tube equipped with a camera and light to provide pictures of the digestive tract.
Esophagus The tube that connects the mouth with the stomach.
Hypothesis A testable explanation of a phenomenon.
Peritonitis Inflammation of the peritoneum, the thin tissue that lines the inner wall of the abdomen and covers most of the abdominal organs.
Placebo Medically ineffective treatment such as a sugar pill.
