Dr. Stuart Reichler Bio 325

Sample Exam Questions: Some organisms have much more DNA than humans do. Does this mean that they can make a greater diversity of proteins than humans can? Why or why not?

Sample Exam Questions: Some organisms have much more DNA than humans do. Does this mean that they can make a greater diversity of proteins than humans can? Why or why not? Not necessarily. They may have more non- coding DNA.

Sample Exam Questions: If a transposon was inserted into an intron, would the gene product still be properly produced? Why or why not?

Sample Exam Questions: If a transposon was inserted into an intron, would the gene product still be properly produced? Why or why not? Either: Yes, the intron will be spliced out along with the transposon thereby having no effect on the final mRNA. No, the transposon will disrupt proper splicing of the intron thereby causing the mRNA to have additional and improper sequence.

Sample Exam Questions: What is a major weakness of the data obtained via microarray analysis?

Sample Exam Questions: What is a major weakness of the data obtained via microarray analysis? Microarrays show differences in mRNA levels, but that does not necessarily correlate to changes in protein levels.

Studying Biology: Start with a question. –For example: How? Why? When? Where? Etc? How do we get answers? –Strong Inference presents one method (article on webpage)

Cause of Peptic Ulcers: Overabundance of stomach acid due to Stress Diet Anxiety

Cause of Peptic Ulcers: Overabundance of stomach acid due to Stress Diet Anxiety Treatment: Antiacid U.S. bought $4.4 billion in 1992 Tranquilizers

Dr. Barry Marshall

The real cause of 80% of ulcers… H. pylori

Strong Inference Knowledge is gained by eliminating incorrect ideas. Disproof is more reliable than proof.

Where does the matter come from for plants to grow? Matter can not normally be created or destroyed, only moved from one place to another.

Aristotle (~2,300 y.a.) : Plants gain mass by taking it from the soil. Supporting Evidence: Plants need soil to grow. If roots are removed, plants die. After several years of cultivation, soil loses its ability to support plant growth.

Johann Baptista van Helmont did a simple experiment in the early 1600’s

Johann Baptista van Helmont in 1600’s Supporting Evidence: Plants need soil to grow. If roots are removed, plants die. After several years of cultivation, soil loses its ability to support plant growth. Aristotle (~2,300 y.a.): Plants gain mass by taking it from the soil… What is the major difference between these two approaches to science?

The Rules of Strong Inference: Strong Inference is a method for looking at scientific problems by trying to disprove hypotheses and accepting the hypotheses that can not be disproved. Using Strong Inference entails following these rules (from an article by John Platt, 1964): 1. Devise multiple hypotheses.

The Rules of Strong Inference: Strong Inference is a method for looking at scientific problems by trying to disprove hypotheses and accepting the hypotheses that can not be disproved. Using Strong Inference entails following these rules (from an article by John Platt, 1964): 1. Devise multiple hypotheses. 2. Design experiment(s) to eliminate one or more of the hypotheses.

The Rules of Strong Inference: Strong Inference is a method for looking at scientific problems by trying to disprove hypotheses and accepting the hypotheses that can not be disproved. Using Strong Inference entails following these rules (from an article by John Platt, 1964): 1. Devise multiple hypotheses. 2. Design experiment(s) to eliminate one or more of the hypotheses. 3. Carry out the experiments in a manner that gives a clean result.

The Rules of Strong Inference: Strong Inference is a method for looking at scientific problems by trying to disprove hypotheses and accepting the hypotheses that can not be disproved. Using Strong Inference entails following these rules (from an article by John Platt, 1964): 1. Devise multiple hypotheses. 2. Design experiment(s) to eliminate one or more of the hypotheses. 3. Carry out the experiments in a manner that gives a clean result. 4. Repeat. Refine hypotheses.

The Rules of Strong Inference: Strong Inference is a method for looking at scientific problems by trying to disprove hypotheses and accepting the hypotheses that can not be disproved. Using Strong Inference entails following these rules (from an article by John Platt, 1964): 1. Devise multiple hypotheses. 2. Design experiment(s) to eliminate one or more of the hypotheses. 3. Carry out the experiments in a manner that gives a clean result. 4. Repeat. Refine hypotheses.

The Question: Can your hypothesis be disproved? What experiment(s) can disprove your hypothesis?

The Rules of Strong Inference: Strong Inference is a method for looking at scientific problems by trying to disprove hypotheses and accepting the hypotheses that can not be disproved. Using Strong Inference entails following these rules (from an article by John Platt, 1964): 1. Devise multiple hypotheses. 2. Design experiment(s) to eliminate one or more of the hypotheses. 3. Carry out the experiments in a manner that gives a clean result. 4. Repeat. Refine hypotheses.

What causes Mad Cow Disease (aka BSE)?

Brain tissue from cow with BSE. Scrapie in sheep, CJD or Kuru in humans looks similar.

How could you test for the infectious agent?

Dr. Stanley Prusiner was awarded the Nobel Prize in 1997 for the discovery of prions… infectious proteins.

normally folded proteins Prion (abnormally folded protein) Interaction between prion and normal protein causes normal protein to misfold… … which leads to increasing numbers of prions Prion Propogation

Scientists communicate by publishing their findings in journals…

What is in a journal article?

Basic info: who, what, where, when

The abstract is a summary of the rationale and results.

The introduction has background information.

What is this?

References are how scientists cite other people’s ideas or data. (Castrogiovanni et al., 1998) Castrogiovanni P, Iapichino S, Pacchierotti C, Pieraccini F Season of birth in psychiatry: a review. Neuropsychobiology 37:175–181.

(Castrogiovanni et al., 1998) Using other’s ideas or data is fine, but not citing where the information came from is plagiarism. Castrogiovanni P, Iapichino S, Pacchierotti C, Pieraccini F Season of birth in psychiatry: a review. Neuropsychobiology 37:175–181.

SUBJECTS AND METHODS To investigate the influence of birth season on examination marks, we used the (anonymous) examination results from 1995–2001 of undergraduate students at the University of Vienna, together with their dates of birth……. Materials and methods or other synonymous sections detail how the experiments were done.

RESULTS The distribution of scores attained by male and female students is associated with their birth season (see data in Table 1)……… The results section details the outcomes of the experiments.

RESULTS The distribution of scores attained by male and female students is associated with their birth season (see data in Table 1)……… The results section details the outcomes of the experiments, and refers to the tables and figures in the paper.

Figures are graphical representations of data.

Sometimes tables are used.

DISCUSSION We find that examination scores are related to season of birth in both female and male students, indicating that there could be some biologically significant underlying ontogenetic or early life- history mechanism……… The discussion is where the results are explained and related to other research. (sometimes it is combined with the results)

What is in a journal article?