Advanced GeneticsBIOL597R; spring2011; HazenBiology Department, University of Massachusetts Amherst

I would appreciate input on improving the course. Please provide input on the following issues and any others you might have. This post will not be discussed in lecture.

Species. Do you care what species are used as examples of various topics? Would you prefer to hear more or less about the various possibilities: peas, maize, Arabidopsis, tomato, petunia, fly, worm, e coli, yeast, human, mouse, others?

YouTube. One approach towards teaching is to lecture for no more than 12 minutes at a time and break the class up into smaller groups. My experience is that students don't like the group thing. Do you? What do you think of having one or two movie clips on the techniques, history, etc.. of the relevant areas that may or may not lead to discussion? Does it seems like the gym teacher that always shows movies in health class or is it a worth while break and a good way to learn?

Textbook. I will stick with the primary literature open book format next spring. Should I continue NOT to recommend a textbook? Is the supplemental reading useful?

Papers. Last year I required two papers based on a selection from the primary literature of the students liking. While you did not experience this format for this class in particular, you are certainly familiar with writing papers. Do you think this would add to the course?

Work load. Is the time required for three exams, twelve blogs, and no final consistent with your other courses?

Course level. Since this is a 500 level course I had/have high expectations. The class is comprised of juniors, seniors, and graduate students. Incidentally, as a whole juniors seem no less prepared to handle the course than seniors. Do you pay much attention to course number? Is it meaningful? Would you like to see the university offer more genetics course like Epigenetics, Quantitative genetics, Animal and Plant Breeding, or Human Genetics.

Topics. Are there any topics you would have likes to explore more or less?

Watch the documentary film "The New Biology".
http://www.pacificbiosciences.com/aboutus/video-gallery?videoImage=The%2...

Propose to address a question with a systems biology approach and be prepared to discuss this further.

Read this pair of duelling essays published in Nature.
http://www.nature.com/nature/journal/v457/n7231/full/457786a.html

The topic is whether there is any justification for scientific exploration of associations between gender or race and intelligence; Stephen Ceci and Wendy M. Williams from Cornell argue the affirmative, while Steven Rose takes up the opposing case.

What are your thoughts?

Several companies were formed in the 1990s with the purpose of sequencing portions of the human genome and using this information to devise new drugs. These companies sought to patent each bit of DNA sequence that they decoded even if they did not know wether it encoded a gene product. Their justification was to ensure that any use of the sequence would yield payback for their research. This strategy failed as shown by the failure of most of these companies. Do you think patents should be granted for each gene sequence that has been determined? Do you think patents should be granted for entire genome sequences even if we do not know what the gene does? What criteria do you think are compatible with facilitating private-industry drug development, encouraging research, and protecting intellectual property? See this recent story in the New York Times describing the invalidation of patents for testing the BRCA genes we discussed in an earlier post. Judge Invalidates Human Gene Patent http://www.nytimes.com/2010/03/30/business/30gene.html

In 1902, a German medical journal reported an astonishing experiment. A physician had attached the blood vessels of a patient dying of kidney failure to a pig’s kidney set up by her bedside. The patient’s immune system rejected the attachment almost immediately.

Nearly a century later, in 1997, a similar experiment took place. A 19-year old suffering from acute liver failure survived for six hours with his blood circulating outside of his body through a living liver removed from a 15-week-old, 118-pound pig. The pig had been genetically modified and bred so that her cells displayed a human protein that controlled rejection of tissue transplanted from another species. Because of this slight but key bit of added humanity, plus immunosuppressant drugs, the boy tolerated the pig liver until a human liver became available.

Pig parts as transplants may become necessary due to the shortage of human organs. Discuss (1) the morality of raising animals to use their organs as transplants, (2) the danger of xenotransplants transferring viruses from animal to humans, (3) the morality of raising human clones to supply the cloned human organs (a la “The Island” starring Ewan McGregor and Scarlett Johansson).

Vaccine-autism claims, "Frankenfood" bans, the herbal cure craze: All point to the public's growing fear (and, often, outright denial) of science and reason, says Michael Specter. He warns the trend spells disaster for human progress.
http://www.ted.com/talks/michael_specter_the_danger_of_science_denial.html
Comment on something you like or don't like about this talk.

Many scientists who are employed as professors at universities have become involved in biotechnology ventures outside the university. Companies often set up their laboratories near universities to take advantage of the intellectual resources there. Industries that develop near universities employ nonscientists in the community as well as scientists and are generally looked upon as an asset to the community. The president of a major state university is encouraging faculty members to become active in the development of associated industries, viewing their mission as academics to include community-related activities. But legislators and the public, whose tax dollars fund the university, believe that the professors should concentrate on teaching. Should faculty be encouraged to participate in outside ventures because it is a service to the community and potentially to humankind through development of new biotechnology, or should they be held more strictly to a solely academic, teaching mission?

Thousands of years ago, people living in the Middle East discovered that when they added a tiny quantity of extract from the inner lining of the fourth stomach of a freshly killed calf to cows milk, the milk turned to cheese. In the twentieth century, biochemists isolated and characterized the responsible agent: an enzyme named chymosin. The enzyme is encoded by a single gene that is expressed only in animals that chew their cud and only before weaning. Until just two decades ago, cheese makers had to use this animal product as an essential component of the cheese-making process. Then, using the tools or recombinant DNA technology, biotechnologists cloned the cow chymosin gene in a bacterial expression vector, making it possible to produce fully functional chymosin in a culture of cloned bacteria. In 1990, chymosin produced in this way became the first approved product of recombinant DNA technology to enter the US food market. Unlike calf chymosin, recombinant cow chymosin can be standardized; it can also be inexpensively produced, and it doesn't require the killing of any animals. Purified calf chymosin and bacterially produced chymosin are indistinguishable in their structure and enzymatic activities. By 2004, over 90% of the cheese on supermarket shelves in the US, Europe, and most other countries around the globe were produced using recombinant chymosin.

Chr. Hansen, the Danish company that produces recombinant chymosin under the trademark of ChyMax, claims in their promotional literature that it is "nature's own enzyme for clotting milk and a natural ingredient for the food industry." What is the definition of the term natural? Is it appropriate for a company to use this term to describe a protein made from a mammalian-specific gene inside bacterial cells? Does it matter that the purified chymosin proteins from the calf's stomach and from cloned bacteria are structurally and functionally identical? How important is the process relative to the product in assessing something's naturalness?

Antoine and Naomi's first child has cystic firbrosis. They would like to have a second child but want to make sure the child does not have cystic fibrosis. After in vitro fertilization, seven embryos are screened for the presence of the disease. Of the seven, two are determined to have the disease. Prior to preimplantation, Antoine and Naomi asked the doctor to screen the remaining "healthy" five embryos for gender as they want to have only one more child, and they want that child to be a boy to carry on the family name. What would you tell the couple if you were the doctor? Is there a difference, in your opinion, between screening for a genetic disease and gender? If a genetic test for a phenotype exists, should the screening be available (e.g., if Antoine and Naomi asked to select an embryo carrying the genes to express blue eyes and blond hair should they be able to do so)? What are some potential implications of selecting for alleles that do not have an impact on survival? What types of genetic screening, if any, should be available?

In 1992, the biotechnology company Calgene applied for approval of their rot-resistant tomato, the Flavr Savr tomato. They had engineered the tomato plant by introducing a copy of the gene encoding a softening enzyme downstream of, and in reverse orientation to, a strong promoter active in the fruit. When the engineered gene is transcribed, an "antisense RNA," complementary in sequence to the softening enzyme mRNA, is produced. The antisense RNA binds to the normal RNA and blocks translation of the softening enzyme so the tomatoes stay ripe longer. The FDA approved the sale of the tomato without any additional labeling because the DNA that had been introduced into the tomato was tomato DNA. (The FDA's policy on bioengineered foods is to label food as genetically engineered only when a new substance has been introduced that could cause an allergy or when there has been a change to the foods nutritional value.) Several consumer groups were upset by the FDA's action and wanted to see labeling about genetic modification appear on the tomatoes in the stores. Their protest significantly stalled the sale of these tomatoes. Were the consumer groups' actions, which blocked an advance that people might have wanted, warranted? Are these groups important watchdogs of everyone's well-being, or are they hindering progress?