Wednesday, January 30, 2013

A Scientist's Conclusion, Part 4

As the time for Sung's comprehensive exam drew near, Carl still doubted that Sung was, in fact, prepared, that he could ever be prepared to stand that examination and do it justice. Even in their weekly sessions, Sung hesitated to complete answers and usually refused to pursue a line of reasoning without receiving a nod of affirmation, or an authoritative "Go ahead." from Carl. Carl mused to himself, half­ seriously, that he might be able to nod Sung through some of the more difficult questions on the oral exam if the student could only get himself off to a correct start.
The week of comprehensives came and Sung passed the general written exam—not brilliantly but adequately. His specialty written exam was uneven; he had badly botched one of the three questions on that exam. Because of his performance, he had been given a borderline pass. Thus, the issue of whether he passed or failed, and, hence, whether or not he could continue his pursuit of the Ph.D. degree, hung upon the oral exam. His committee was composed of four individuals in addition to Carl: Drs. James Karesh and Otto Munster from the Biochemistry Department, Dr. Harris Stillwell from Pathology, and Dr. Anando Vanadian from Immunology. Carl was very proud of having gathered this committee for his first graduate student; they were among the best minds and greatest reputations at the institution. Their willingness to serve on this committee was taken by Carl, perhaps with some justification, as an indication that he was accorded a certain esteem as a scientist, despite the fact that he had not yet achieved national recognition.
The format of the oral exam was structured so that the student first gave an overview of his thesis project, including highlights of any preliminary data he might have obtained. Then the committee members were free to question the student on any material to which he could reasonably be expected to have been exposed during his course work and his literature search pertaining to the thesis topic. In practice, the examination usually began with questions centering around the candidate's thesis project, then ranged farther afield as answers to questions suggested new questions to the examiners. A successful exam was usually fairly brief, perhaps an hour and a half, whereas less successful exams often went on for three or four hours.
Carl had rehearsed Sung twice on his presentation and, after each rehearsal, had asked Sung several questions of the type that might logically relate to the presenta­tion. Carl had also scheduled the examination for the afternoon at 2:00 P.M., for two reasons. First, he hoped that the committee would be in a pleasant, ruminative mood after lunch, and secondly, he hoped that, since the exam was to begin fairly late in the day, it might not last for more than two or three hours and Sung might be spared some of the more probing and esoteric questions that often come at the end of a long examination.
The afternoon of the examination, two others were present in the seminar room in addition to Sung's committee: the departmental graduate advisor, Dr. William Bock, and the department chairman, Dr. Henry Davidson. Carl was not entirely surprised, since it was quite within accepted procedure for any member of the department to be present at the oral examination of any departmental student. Nonetheless, their presence made Carl uneasy.

The next installment is  here .

Wednesday, January 23, 2013

A Scientist's Conclusion, Part 3

The first two installments of this story are  here/ and here.

The next day, Carl announced to Sung that he would have to postpone taking his comprehensive exams until the following spring.

"But I already make one delay already," objected Sung.

"I'm sorry, but I can't have you taking the comprehensives as poorly prepared as I'm afraid you are. We'll get together and go over background material for a few hours every week until I feel you're in control of it." Carl thought he was doing Sung a real favor by mentoring him in the only fashion he knew how, by helping him to think and understand as a true scientist. 

Sung had already postponed taking his comprehensives once, because Carl insisted that he take an English course and an additional methodology course before standing for such a demanding examination.

The retraining began once more in earnest, that first Tuesday afternoon. Carl began, slowly and patiently, trying to lead Sung to understand for himself the processes of logic: the differences between induction and deduction and the types of traps and fallacies inherent in each.  He tried to teach Sung to see that it was important to ask "Why?" of everything, that there were no final answers, only answers that led to new questions.

And above all, Carl urged Sung to question published orthodoxy. This was the most difficult task of all, since Sung clung stubbornly, almost fanatically, to belief in the authority of the printed word--not only the truth of the data, but also the validity of interpretations drawn from them.

In order to make Sung more at ease in the question-answer period, Carl initially asked questions centering around assigned topics. As the sessions progressed, Carl deviated from the topic at hand in an effort to force Sung's mind to range more broadly, to synthesize information from several subjects into a coherent whole, to approach a given question from more than one perspective.

Throughout this protracted process, Sung became increasingly demoralized. The year before this, his wife, Kai-Hi, had come over from Korea after nearly two years of separation, because they had thought he would be finished in another year—or two at the most. Now the task seemed endless. Sung had taught high school for six years in Korea before coming to the U.S.; he and his wife had postponed having children so that Sung could obtain the prestigious Ph.D. degree from an American university. The money that they saved so carefully and painfully during those years was gone, and Sung's wife had taken a job as a waitress in Philadelphia's Chinatown. Everything in America was so expensive that Sung's brother-in-law had also recently come to Philadelphia to provide another family wage and was working as a cook in the same restaurant as Kai-Hi .  That made two others whose lives were intertwined with his, here, in this indifferent country among incomprehensible people, three whose visas were temporary and for whom there was not enough money for passage back to Korea.  The dream of a prestigious American degree was becoming a frightening nightmare.

The next installment is here

Wednesday, January 16, 2013

A Scientist's Conclusion, Part 2

(continued from part-1.html)

It was with the realization that Sung Lee did not, in fact, understand the importance (or even the purpose) of controls that Carl came to appreciate the enormity of the undertaking to which he had committed himself. That realization came about after Carl's suggestion that a drug effect on Sung's tumor-cell line might have been caused by increased cell membrane permeability or by increased levels of a calcium-binding protein in the cells as a consequence of the drug treatment.

Sung Lee thereupon went to the library to find methods to assay those parameters. After more than three weeks of hard work and experimentation, Sung came triumphantly into Carl's office with the announcement that Carl had been right on both accounts. Carl asked the obvious questions concerning the time-course and dose-dependence of the effect, and it was clear that Sung had either not considered these questions, or else he did not have the courage to say: "These are just preliminary data." It was as if Sung expected Carl to be so pleased at being told that his ideas were correct that the methodology would not be questioned. Then Carl, in what he thought was an inquisitive (not inquisitorial) tone, asked Sung:

"Why do you think your data show increased calcium-binding protein in the cells rather than increased binding of calcium to the protein that's already there?"

"No, calcium-bind protein increase," said Sung emphatically.

"How could you determine that it was increased protein rather than increased affinity?"

"Everybody say so.  Anderson do same experiment on amoebae and say calcium partition coefficient directly proportional to amount of calcium-bind protein."

"Yes, but that's in a non-permuted system. Let me see your data."

Sung hesitantly gave him some graphs and Carl asked for the counter tapes. He noticed that, on the first tape he looked at, the counts were all quite similar.

"What counts are these?"  Carl asked.

"They calcium counts from drug-treated cells," said Sung proudly.

"Where are the controls?" asked Carl.

"Controls in other experiment," explained Sung.       

"What do you mean, other experiment?" Carl's voice rose through incredulity to anger. "You don't know a God-damned thing if you don't run controls with every single experiment! For Christ's sake, what do you think a control is for, anyway? Do you have any idea?"

Sung was mute--stunned.  There was nothing in his background, nothing in his training, nothing in his cultural heritage that had prepared him for this outraged outburst by one who was supposed to be his guide and protector.

"Well...I asked you, what do you think a control is for?" demanded Carl, impatiently.

Confused, ashamed, and unable to understand why such an apparently trivial matter assumed such importance for his mentor, Sung answered, "I don't know."

"Oh, for God's sake. Come back to my office at two o'clock tomorrow afternoon and we'll talk about controls." Carl didn't have the mental energy to deal with the subject at that moment, and he also knew that Sung had become so alarmed and defensive that any further discussion of the matter at the time would be futile.

In the interim, Carl confided to some colleagues that he had serious doubts about Sung's ability to do the work necessary for a Ph.D. degree and, more importantly, he wondered whether or not Sung had the mind to be a scientist at all. One of the colleagues in whom Carl confided was the departmental graduate advisor, Dr. William Bock. Dr. Bock suggested that Carl postpone Sung's comprehensives until the next scheduled exam, which was six months hence.

The next installment of this story is here.

Sunday, January 6, 2013

A Scientist's Conclusion, Part 1

I'm reactivating this fiction blog. I've run out of fairly short and simple stories, or stories that have already been published, and I've decided to serialize a longer, unpublished short story.

A little background. For most of my professional life, I taught and did research in the biomedical sciences. In the beginning, I was extremely idealistic, believing that the practice of science was the pursuit of truth, and that scientists were acolytes in that almost sacred activity. It did not take many years for me to realize that this was a hopelessly idealistic notion, and that scientists are as flawed, emotionally and morally, as any other individuals. Many of the stories I wrote reflect this disenchantment, so they are not happily-ever-after stories. And because I was still practicing science, I chose a pseudonym for these literary efforts, some of which were published. I'm now retired, and anonymity doesn't matter anymore, but I'll still keep the pseudonym for fiction.

A Scientist's Conclusion, Part 1

Carl Sawyer's one-time research collaborator, George Ganon, had been an enthusiastic, imaginative man, although by Carl's standards, not a very thorough scientist. The two of them made a good team; George was full of ideas, and Carl tempered them with his thorough, analytical mind and tested them with rigorously designed experiments. But George and his enthusiasms had left the University of P... for a job in Texas, where free-flowing oil money promised better equipment and more ample funds for salary and supplies. Carl was left with the remnants of their shared equipment and with Sung Lee Park, a Korean graduate student who had been working on a Ph.D. degree in George's lab.

George had also been enthusiastic about Sung Lee--saw him as a diligent and willing pair of hands at a bargain price that could grind out answers to problems. Sung Lee didn't  want to go to Texas because his family had just settled in Philadelphia. So Carl inherited a student who was essentially finished with course work and already working on a thesis project. Carl saw Sung Lee differently than George did. Carl saw him as a moderately well-trained technician who needed to be turned into a scientist. Carl was willing to assume the responsibility for this transformation, but not without misgivings.

Carl thought both he and Sung Lee were at a disadvantage, having inherited one another. It was like taking on a half-sculpted piece of marble; the previous artist's vision can seldom be realized in another man's hands, and one who completes another's creation is rarely satisfied with the result. Carl realized the enormity of the task involved in turning a pleasant, uncritical Asian into a competent and confident scientist in the Western mold. Moreover, even if Sung did develop into a genuinely skilled scientist, it might still be difficult for him to find a good position. Carl did not have the network of colleagues and connections that a more self-consciously political scientist would have generated.

Carl took on the training of Sung Lee with the same thoroughness and objectivity that he used to tackle scientific problems. Carl began by asking Sung Lee, during their first few discussions together, to repeat in his own words what had just been said to him, instead of simply saying "Oh, yes." or "Yes, Sir." This was intended to determine whether or not Sung understood what Carl had said and could transform it into an alternative, comprehensible form of English.

During this time, Carl also asked Sung Lee questions about the research problem he was working on, which had begun under George's tutelage, and he examined the data Sung had already generated. Carl often challenged Sung's answers and data with questions like "How else could you interpret those results?" or "What could you do to verify that?"

When discussing the scientific literature relating to Sung's work, Carl often asked, "Was their methodology adequate to allow them to draw that conclusion?" or "What was wrong with the way those experiments were designed?" This line of questioning sometimes threw Sung Lee into confusion and Carl noticed that, when they were speaking together, Sung's mouth occasionally twitched visibly, which he tried to hide by drawing his hand to his face.

The next installment of this story is  here.