Thoughts after the first session

There are many levels on which to think about the first session. How was it technically? Good- we had one glitch with the graphics, but pointing the camera at the screen solved that. As someone who likes to make videos, I am going to use the remote next time and actively record Venkat as he speaks and switch to the audience for the questions. Let me compliment Madras- I think you had the most dynamic coverage! How was the content? There is no doubt the material is interesting. For my part, I know I rushed the next-generation sequencing and need to cover some of it again. I will do that- a recap that will fit well with the next topics anyway. Mike thanks for bringing the Scope and starting the STR analysis. I will be down to film you on Monday as you process the samples! Venkat, you have thrown down the gauntlet- I see this is a genomics versus proteomics competition. It is interesting how many 'omics' must be considered. Your point is well taken, as was an audience point that it is in fact the activity of factors (proteins, RNAs, and other molecules, comments on these anyone?) that really represent the phenotype of the cell. I look forward to the next installment!

After the session we adjourned to the room next door and ate pizza and Ruth's delicious homemade chocolate cake! We talked. Two main subjects: how did it go and what topics would be good for the student presentations? The students thought that more interaction during the session would be good. Together we came up with the idea of pairing students between the sites- so that we can learn more about each other. Probably most of this will go on behind the scenes. Venkat reminded us that this course is an experiment and that we could write it up as a paper for a science education journal. So I encourage you to do what I am doing now- write down your thoughts privately or publicly. Then we will have data.

Topics for student presentations. 1) The $1000 genome was the first idea and I have already blogged about it. 2) Functional genomics and/or genetic engineering. These topics are rife with Nobel prizes, science, technology and ethical issues. We struggled with a third equally interesting idea. Then Sathiya suggested: 3) Biology and law. A wonderful idea- how do findings in science get made into products? And if they do what happens next ? -an interesting mix of patents, generic drugs, money, egos and more!

Next generation sequencing- the movie

I met with Jeff and Tim who gave me a tour of the SOLiD system in the Department of Human Cancer Genetics. To tell the story I made this movie. Thanks, to you both. 

My interest in next and next-next generation sequencing is increasing the more I learn. Venkat and I discussed student projects and agreed that the quest for the $1000 genome (personal genomics) would be a very interesting topic. It could combine a Nobel prize (Sanger), technology (single molecule sequencing) and ethics (what are the implications?).

my first lecture

The history of genetics starts a long way back with the male- and blood-centric views of the ancient Greeks. Mendel the father of genetics changed everything with an experimental and quantitative approach that led to his two laws. He published his famous paper in 1866, but it lay dormant until its rediscovery in 1900. In 1983, Barbara McClintock received a Nobel prize for her work on transposons. Just as Mendel was ahead of his time- so was McClintock. She stopped publishing her results for a long period because of the skepticism of other scientists. The Nobel prize came some 40 years after her initial findings. The prize was a vindication for her and a landmark for women, as she was the first female scientist to win the "physiology" Nobel outright.

My first lecture is about some of this history and then goes on to genome projects and technology. I have been very struck by so-called next generation sequencing. It is amazing creative technology and quite simply mind blowing. It is all heading towards the $1000 genome. Imagine what that can mean for medicine and more. Perhaps Dr. Farrell who will be giving the ethics component of this class will have some comments.

Finalization of my lecture plan

I am now quite excited by the outline of my lectures and how they relate to the three timelines- landmarks in genetics, technology developments, and Nobel prizes. The connections are interesting of course. I talked to colleagues and asked them what I had missed. Depending on their own expertise they suggested certain things. For example, Boveri from a cell biologist and 'one gene one enzyme' from a Neurospora expert. My yeast colleague and I were talking and I will add the genome-wide yeast knockout strain library- that's genomics and reverse genetics!

Jeff, who runs the microarray core in the Cancer Center has agreed to star in a movie I will make about the 'Solid' sequencer he operates. This is one of the next generation seqencers. They use it to sequence microRNAs so it will connect to the content on several levels. The students I teach in another class toured his facilty and were very impressed with the million dollar machine!

The use of genomics in forensics will be another thing I discuss. Mike who runs the sequencing center in my building has a kit, which is the same one that the FBI use, so he can profile people for alleles at 13 loci. I have asked him if he will come to class to profile some of our students. I'm waiting to hear back from him.

Planning the course

Venkat and I visited the Learning Collaboration Studio, where the videoconferences will be held. It is a really nice room in many ways. There is of course all the technology, which was surprisingly easy to use (we think). Venkat said we were 'Luddites' but Meghan, who runs the facility, assured us that we weren't. In fact I like it very much and am excited at the prospect of this new way (for me) to teach and learn. We called into a test conference and talked to a guy in Philadelphia, who was preparing for a conference later that day. It was a chance to practice with the cameras, sound etc. The podium computer has 'Smart' technology, which means you can turn your mouse into a pen and write on the PowerPoint slides. We practised writing neatly and I drew some Drosophila (fruit flies).

I am finalizing my lectures. The overarching title is Genetics and Genomics in the Analysis of Biological Problems. Three timelines (landmarks in genetics, techniques, and Nobel prizes) will set the backbone. Certain topics in the timeline will be expanded and I will discuss three 'case studies' in detail.