Philosopher Paul Thagard has written a couple of very interesting and insightful articles outlining the various dynamics involved in the discovery of H. pylori as the causative agent behind ulcers [1,2]. These articles help us to appreciate what is involved in bringing about a change of view in science.

Thagard introduces his subject as follows:

In 1983, Dr. J. Robin Warren and Dr. Barry Marshall reported finding a new kind of bacteria in the stomachs of people with gastritis. Warren and Marshall were soon led to the hypothesis that peptic ulcers are generally caused, not by excess acidity or stress, but by a bacterial infection. Initially, this hypothesis was viewed as preposterous, and it is still somewhat controversial. In 1994, however, a U. S. National Institutes of Health Consensus Development Panel concluded that infection appears to play an important contributory role in the pathogenesis of peptic ulcers, and recommended that antibiotics be used in their treatment...This paper is the first of two that discuss the development and reception of the bacterial theory of ulcers from a combination of historical, methodological, psychological, and social perspectives. It examines the nature of the discoveries made by Marshall and Warren, including the new bacteria now known as Helicobacter pylori, the hypothesis that peptic ulcers are often the result of bacterial infection, and the hypothesis that peptic ulcers can be cured by treatment with antibiotics. This paper also describes the kinds of conceptual change that attended the adoption of the new hypotheses. It then examines the reasons for the initial rejection of the bacterial theory of ulcers as well as the reasons for its increasing acceptance. It discusses how causal hypotheses can be established in medical research and analyzes the acceptance and rejection of the bacterial theory of ulcers in terms of explanatory coherence. The perspective in this paper is cognitive, considering the mental operations that produced the discovery and acceptance of the bacterial theory of ulcers. The sequel (Thagard, forthcoming-b), looks at the same case from physical and social perspectives. The development of the bacterial theory of ulcers depended on the physical use of instruments such as microscopes and endoscopes, and on the devising of experiments to test the association of Helicobacter pylori and gastric problems. It also had important social dimensions, including: the collaborative work of Marshall, Warren, and their associates; the processes of communication by which the new concepts and hypotheses spread; and the processes of negotiation by which consensus began to form, for example on the NIH panel. This paper shows how social explanations of scientific development can complement psychological and methodological explanations. The two Ulcers and Bacteria papers together give a broad, integrated, naturalistic explanation of a recent episode in medical science, treating science as a complex system of interacting cognitive, physical, and social processes. - emphasis added

There is no need to retell the story, especially since Thagard does such an outstanding job. Nevertheless, allow me to highlight some of the interesting cognitive dynamics behind this discovery.

From 1979-1981, Robin Warren, a pathologist, had observed spiral bacteria contained in biopsy specimens from individuals with gastritis. In 1981, Barry Marshall began to work with Warren, further investigating these bacteria as part of his training program in internal medicine. Marshall then did a study looking for a correlation between the presence of these bacteria and individuals with stomach problems (gastritis and ulcers). Marshall found a statistically significant correlation and as Thagard notes, he "submitted a report for the meeting of the Australian Gastroenterology Society contending that the bacteria may be responsible for ulcers. Although 59 out of 67 submissions for this meeting were accepted, Marshall's was not." Nevertheless, Warren and Marshall published their findings in Lancet. The scientific community initially reacted by viewing their thesis as preposterous [3]. Over the next decade, Marshall, with the help of key collaborators, was able to reverse this tide of skepticism to the point where it is now widely accepted that bacteria are the causative agent behind ulcers.

The factors involved in turning this tide are worth exploring. First, there is serendipity. Naïve views of science downplay or overlook this important factor, but often times, such things as luck, just happening to have the right contacts, and being in the right place at the right time, have been crucial ingredients in many scientific breakthroughs. Thagard explains the role of serendipity as follows:

Warren's initial noticing of the spiral gastric bacteria can best be described as serendipitous. He was not seeking an explanation of gastritis or ulcers, and he just happened to examine gastric specimens with sufficient microscope magnification to make bacteria visible. Warren was not consciously following up on the research of others who had observed similar bacteria (e.g. Steer and Colin-Jones, 1975; Fung, Papadimitriou, and Matz, 1979). Rather, he independently and accidentally discovered the bacteria in the course of his everyday work. Persistent in the face of colleagues who were skeptical about the bacteria, he pursued a more systematic observation of the bacteria. Serendipity also played a role in the efforts to culture the bacteria. During the 1970s, techniques for culturing Campylobacter had been developed, but thirty attempts in late 1981 to use these techniques to culture the gastric bacteria failed, partly, it was later discovered, because of faulty incubators. Agar plates on which the bacteria were supposed to grow had been discarded after forty-eight hours with no growth visible. Then in April, 1982, because of a four-day Easter weekend and other demands on the microbiology laboratory, the culture was left in the incubator for five days, long enough for bacterial colonies to become visible (Marshall, 1989, p. 14). This is an example of pseudoserendipity, since the investigators certainly had the goal of culturing the bacteria, but incubating for five days was not a method that they had been considering.

Second, there is Barry Marshall himself. Marshall was convinced very early on that these bacteria caused ulcers, even though his data uncovered only a correlation (which is not the same as cause). This type of conviction could flourish because Marshall was not trained to think otherwise. Thagard explains this nicely:

Barry Marshall (1989, p. 19) was convinced that the new bacterium was the primary cause of peptic ulcer disease by 1983, after an experiment involving 100 patients tested for presence of the bacterium and presence of stomach disease. All 13 patients with duodenal ulcer had the bacterium, and the association between gastric ulcers and the bacterium was also statistically significant (Marshall and Warren, 1984). Marshall was relatively new to gastroenterology, having only begun specialized training in the field in 1981. Accordingly, his adoption of the new hypotheses did not require abandonment of a set of well entrenched beliefs that conflicted with the new ideas. In contrast, other more established medical researchers and practitioners had beliefs about the nature and treatment of ulcers that clashed with the new hypotheses and led them to reject them summarily.

Three conceptual obstacles stood in Marshall's way. First, most physicians believed the stomach was a sterile environment, being too acidic for any microorganisms to exist. Secondly, most physicians thought that excess acid was the cause of ulcers. Thirdly, most physicians found that ulcers could be effectively treated with various antacids. So in a way, Marshall was perceived as proposing a silly explanation for a non-problem. Or as Thagard explains it, "Hence Marshall, a young, unknown Australian who put forward his new hypotheses with confidence amounting to brashness, was viewed as crazy."

Thagard also notes that hindsight allows us to see this reaction differently. For example, no one knew why the stomach produced excess acid, although many attributed it to stress and genetics. Also, while antacids did treat ulcers, they did not cure them. These unsolved problems allow enough room for Marshall to develop and eventually establish his hypothesis.

Another area where Marshall's personality played an important role in this discovery is evident in the extreme measures he took to prove his point. If these bacteria cause ulcers, then the best way to show this would be to infect a disease-free animal. If the animal develops ulcers, the hypothesis has been greatly strengthened. Initial attempts to infect pigs failed, so Marshall decided to infect himself. He "swallowed a flourishing three-day culture of the bacteria." After a week, he began to vomit and a biopsy of his stomach showed the bacteria had established themselves. Of course, if bacteria cause stomach problems, and antibiotics kill bacteria, antibiotics should cure stomach problems. Over the following years, studies were done to demonstrate this. Marshall's hypothesis would soon win in the end.

Thagard's papers are truly enlightening, as he explores the interacting cognitive, physical, and social processes involved in scientific discovery. From the dynamic I have chosen to highlight above, we gain an interesting insight. Novel and radical hypotheses are likely to be received with extreme incredulity and require a stubborn person with strong convictions to nurture, maintain, and eventually establish the hypothesis. I think it very significant that Marshall was convinced of his hypothesis very early on, yet he did not have the sufficient evidence to warrant such a strong opinion. Yet without this strong conviction, one wonders if the hypothesis would have been nurtured and pushed so that today we all recognize the role of H. pylori as a cause of ulcers. Without such conviction, would Marshall have really infected himself after the animal studies had failed? In fact, Marshall himself seemed discouraged at some point, as Thagard notes, "Initially, Marshall thought that his hypothesis about a bacterial cause for ulcers would gain quick acceptance. Discouraged by the negative reception, he came to believe that only the development of a new generation of gastroenterologists would bring acceptance of the new ideas."

Clearly, the notion that the original life forms on this planet were the products of advanced bioengineering rather than the emergent results of geochemistry is a hypothesis that is viewed to be far more preposterous than Marshall's views on ulcers. So preposterous, in fact, that apart from some brief speculations from Francis Crick, no one in the scientific community has taken it serious enough to speculate about, even though the heuristic value of such an approach seems obvious. However, as we can see from the Marshall story, such reactions are not an indicator of the true merit of a hypothesis. This ID hypothesis could simply be like Marshall's original hypothesis, namely, something that conflicts with established wisdom.

The lesson then is not to expect to come up with something, in the beginning, that will suddenly convince all the skeptics. Marshall had only a simple correlation study, a few observations, and (I suspect), a deep gut-feeling (no pun intended). Put simply, Marshall had to convince himself first to acquire the necessary drive to carry through with his hypothesis in the face of so much ridicule. ID theorists can do likewise. Are there data patterns that strongly suggest an intelligent cause behind life's origins. If so, then contemplate ways to build on these in a gradual and progressive fashion. And the encouraging thing is this: the problems associated with concepts of a non-teleological origin of life are far more severe than those associated with the traditional views of ulcers. Nevertheless, ID theorists face tremendous obstacles.

The problem is that science is a complex system of interacting cognitive, physical, and social processes. I think Thagard's papers important because a rather naïve view of science often serves as the foundation for debates about Intelligent Design and the Origin of Life. This naïve view would have us think that the issue is merely about "the evidence" that is derived from a study of nature. This then leads to a common argument employed against ID that often takes the following form: Since science does not recognize or employ Intelligent Design in the living world, there is no evidence for Intelligent Design in the living world. After all, if there were such evidence, science would recognize and employ it.

Yet Thagard's review clearly highlights that science does not work according to such a simplistic model. The world, and its data, are not the only factors that influence scientific opinion. Thagard summarizes as follows:

Although it has been convenient to organize this paper and its companion in terms of mind, nature, and society, we must not forget the interactions among these elements. Mind affects nature through the mental processes crucial to the use of instruments and the design of experiments, at the same time as nature affects mind by producing observations and experimental results which may or may not conform with expectations. Society affects mind through the goals and interests that motivate scientists and through the organizations and social networks that make modern science possible, at the same time as mind affects society when organizations are affected by the discoveries of individuals (8). Society affects nature through the contributions of needs, organizations, and networks to experimental research, at the same time as nature affects society when scientific organizations contribute to new discoveries arising from interactions with the world.

In accord with figure [5], my account of the emergence in the past decade and a half of major new views about the causes of ulcers has described science as a complex system. The system is simultaneously: psychological (involving individual scientists' cognitive processes for discovery and acceptance), physical (requiring scientists to interact with the natural world using instruments and experiments), and social (involving the interaction of scientists with each other). Only by attending to all these aspects of the growth of knowledge can we fully explain scientific change.

One can view the psychological and social factors involved in scientific discovery as a two-edged sword. On one hand, cognitive and social dynamics can encourage the emergence of a new theory, yet on the other hand, they can work against its development. In the case of Marshall, for example, the social factors, along with the psychological dynamics of other scientists, were discouraging. What turned the tide were the data derived from nature, dependent on instrumentation and even serendipity. At some point, the physical dynamics reached a threshold were the social and psychological factors were transformed into encouraging dynamics. Thagard attributes this shift to coherence (one should read section 10 of his first paper).

Clearly, the psychological and social factors in modern science work as strong discouraging dynamics for any ID hypothesis. In the future, we will explore both sets of factors to see why. However, unlike Marshall, it is not clear how Nature can come to the rescue. In Marshall's case, he was working with something that could be both observed and manipulated and the demonstration of his hypothesis would be rather straight forward - associate bacteria with ulcers: correlate, infect non-diseased organisms and cure diseased organisms. But with the OOL and ID, there is no intelligent designer to observe and manipulate and there are no original life forms to observe and manipulate. We instead must rely on great amounts of speculation and very indirect methods of testing. But could this ever be sufficient physical data to overcome the negative psychological and social factors behind ID's rejection?

When scientists face the question of a teleological origin of life, many view this as an extraordinary claim in need of extraordinary evidence. Yet what exactly is extraordinary evidence? Marshall's claims were perceived as being rather extraordinary (enough to label them crazy), yet it's difficult to see in what way his accumulated evidence were "extraordinary." More problematic is that while a teleological origin of life may be considered an extraordinary event, there is no reason whatsoever to think extraordinary evidence would follow from this event. Put simply, the evidence for ID behind the OOL may be subtle. And if that is the case, can subtle, indirect evidence for X ever overcome the social and psychological dynamics that oppose X?

Figure 5 in Thagard's second paper is most illuminating. It helps us to visualize that scientific belief is an interplay of physical, social, and psychological factors. Normally, the input from Nature prevents this web of dynamics from becoming purely an interplay of psychological and social factors. Or better yet, it is normally the case the Nature eventually asserts itself as the referee and leading guide (if only because sooner or later, a person with the right psychology in the right place at the right time comes along to hear Nature). But if we are dealing with an extraordinary event X, and the data that exist because of X present themselves in a subtle and indirect fashion, might the referee's hands be tied? Might this be a situation where the social and psychological factors no longer exist in a give and take relationship with Nature, but instead exist as dominant factors that mold Nature to their ends?

A teleological cause behind the OOL is today considered an extraordinary claim and there may very well be no extraordinary evidence of its occurrence. What can an ID theorist do? Apart from learning from Marshall's personal drive and motivation, following the rest Marshall's example will not help. The is nothing to directly observe and manipulate to bring about a widespread change in view over the next decade. Instead, we might want to follow Charles Darwin's example. Today, non-teleological mechanisms behind evolution are widely accepted not because teleological mechanisms have been refuted. They are accepted because such mechanisms have been formulated and a track record of success has followed. Teleologists, in turn, have retreated into the realm of religious apologetics and typically offer nothing but criticisms of non-teleological explanations, along with various attempts to erect walls that a non-teleological cause supposedly cannot surmount.

Instead, teleologists should begin to think more positively about an intelligent cause behind life's origin and what this implies about the living world. Tests should then be done to determine if such implications bear out. Successful tests can then develop into a track record. Of course, the trick is in determining what the implications of ID are......

To be cont.

3. Early reactions to Marshall's hypothesis included such statements as ""the most preposterous thing I'd ever heard; I thought, This guy is a madman." and a "totally crazy hypothesis."