CS200: Computer Science, Spring 2004
Notes: Friday 23 April 2004
- Monday, 26 April (last day of class): PS8
- Friday, 30 April, 4:55pm: Final Exam (handed out 26 April)
Project PresentationsIf your team will be presenting your web site, before 10:55am Monday you must submit a zip file of all your code (by email to firstname.lastname@example.org; put "CS200 PS8: Team n" in the subject line where n is your team number to make sure I don't miss it).
If you want to use a few PowerPoint slides in your presentation, you may submit those also. You will not be able to use slides unless you send them to me before 10:55am Monday.
If your team has one or 2 members, you have up to 3 minutes for your presentation. If your team has 3 or more members, you have up to 5 minutes. If you have a reason why you need more time, you may be able to negotiate for it by explaining why to me before Monday.
You only have 3 or 5 minutes so use them wisely:
- Figure out beforehand what you will do
- Recommended format: one team member drive web browser, one (or two) talk
- Focus on what visitors should know about your website, not about how you built it (unless there is something especially interesting)
NotesCentral Dogma of BiologyDNA is transcribed into RNAGenomes Four Nucleotides: adenine (A), guanine (G), cytosine (C), and thymine (T)
RNA is translated into Protein (chains of amino acids)
A group of 3 nucleotides is a codon. A codon encodes one of 20 amino acids or the stop marker.
Smallest known genome: Nanoarchaeum equitans, 490855 bases
Human gemone: 3 Billion bases (but > 95% of it is probably unused junk)
Two randomly selected humans differ by only 2.1 million bases!
Molecular structure of Nucleic Acids, James Watson and Francis Crick. Nature, 25 April 1953. [ PDF] National Human Genume Research Institute (Director: Francis Collins) James Shreeve, The Genome War: How Craig Venter Tried to Capture the Code of Life and Save the World, 2004. White House Announcement, June 26, 2000.
Francis S. Collins
University of Virginia
May 20, 2001
President Casteen, Professor Ackerly, distinguished faculty of this great University, graduating students of the Class of 2001 and especially parents, families, spouses and significant others who have sweated, slaved and sacrificed to make this day possible... Congratulations to all of you.
Remember, parents: the best revenge is to live long enough to become a problem to your children.
It is a great honor to be your commencement speaker today. As you have heard, I sat in your seat thirty-one years ago today, here on the Lawn. I experienced a remarkable depth and breadth of an education here at Mr. Jefferson's university. I first learned to love scientific research a few hundred yards from here under the able and patient mentorship of Professor Carl Trindle, now of your Brown College. Glad to hear that you are represented here. That is great.
This is also a family event for me as it is for many of you because, as you heard, I grew up not far from here in Staunton. My parents still live there. My mother is here today as are my three brothers. And two of my three brothers are UVA alumni. And the third was, for a time, on the faculty. Perhaps most importantly, my niece, Ruth Collins, is in the graduating class today. Yeah, Ruth!
So, Class of 2001, you enter a distinguished cadre of UVA alumni today: senators, governors, writers, scientists, business leaders, artists, and athletes. Here at UVA you have learned the truth of William Butler Yeats' words, 'Education is not the filling of a pail, it is the lighting of a fire.' And I suspect, later on today, your fires will all be well lit.
But who are you, class of 2001? Well, I have spoken to your senior class president, Drew Davis. And he tells me that you care profoundly about your university, your country, and your future. That you have high ideals, but that you know how to have fun. That you have been actually sobered by the recent revelations of honor code violations, but proud of the honor system and confident in the integrity it represents, as am I.
I have read about the 'goings on' around the University in the Cavalier Daily. The concerns about graduate student health care, the athletic triumphs and heartbreaks, the Dave Matthews concert. I sort of wondered should he be your speaker. He seems to be a pretty popular fellow around here. But, I am glad I had the chance instead. And I even read about the UVA law student who played tempter on Temptation Island, my goodness.
A lot has changed since I was a student here going to eight o'clock in the morning classes on Saturday wearing a coat and tie. Which is what we did in 1966. But, yet so much is still the same. Which reminds me of the famous observation from Clark Kurt, 'The problems of the university are universal and timeless: sex for the students, athletics for the alumni, and parking for the faculty.'
So, recognizing that so-called wisdom imparted in commencement addresses tends to have a half-life measured in milliseconds, what can I say to you this morning that will matter? And how can I, a scientist and professor, do this without slides or Power Points, overheads or handouts? Well, I have actually tried to remember the dozen or so commencement addresses that I have sat through. And I regret to say that only one of them leaves the faintest memory of what was said. But that one, which was actually my high school graduation, still stays with me to this day. So, with gratitude and apologies to the Presbyterian minister who delivered it, I am going to adopt his theme.
So, this speech consists of an exhortation, supported by a focus on four decisions that I would like you to think about.
The exhortation: Seek a balanced life. Sounds good, but what does that mean? I suggest that this could perhaps be achieved by arriving at satisfactory conclusions to four life decisions. You can think of these as the four food groups of a balanced life, if you wish.
Decision number one: What will be your life's work? Put another way, what will you contribute? What will you leave behind? It has been said that the purpose of life is a life of purpose. What will be yours?
Here on graduation day, many of you already have a clear picture of this. Many of you don't. That is okay. Some of you think you do. And five years from now, you will have completely revised it.
Sitting in your seat thirty-one years ago, I was sure I knew what I wanted to do. I wanted to be a physical scientist working in quantum mechanics. And I went off to get a graduate degree in physical chemistry at Yale. But along the way I discovered molecular biology. Something that I wasn't that aware of because it was just beginning to spring out of the research and biology of the previous few years. And discovering that it was headed for a genuine revolution that would have profound consequences for our understanding of ourselves, I changed fields. I went to medical school and found my passion in medical genetics. A field which as I was here as an undergraduate, I didn't even know existed. So, keep loose. You can't be confident that your plans will be quite as linear as perhaps they seem today. But that is a wonderful privilege to have the chance to make those changes when they come along.
I now have this remarkable job of standing at the helm of the Human Genome Project. This effort, an international effort, to map and sequence all of the letters of our own DNA code, to read our own instruction book. And what an instruction book it is. Inside each cell of your body you have 3.1 billion letters of this DNA code. If I decided because it would make a nice commencement speech to read them for you, and I would read at an average pace of 'a, c, g, g, t, a, c, c, g, t, a, c, c...' and asked you to stay here because it is such an important day and this is such an important reading, while I hope you would have brought along a little refreshment because we would be here for thirty-two years. And you have all that information inside each cell of your body. And guess what, ninety-five percent of that is now on the Internet for you to go and look at, and try to help us figure out what it means. Because just in the space of the last year, we have crossed a threshold that is of historic significance in our history as to human race. We now have read our own instruction book.
And that was done by a cohort of sixteen centers in six countries that I have had the privilege to lead. And it has been an extremely exhilarating experience. In no small part because it involved physics, chemistry, biology, ethics, and theology and a whole host of other disciplines. So, would I have predicted that when I sat in your seat? No, and the same will happen to you.
I also find I spend a lot of my time worrying about the ethical implications of this. Will, for instance, if you decide to find out what you are at risk for (because we can now read your DNA sequence) will that information be used to take away your health care or your jobs? That is unjust. That is something that we should put a stop to, but that requires the legislative process to kick in.
So, when I go to Congress to talk about that, I find myself quoting Thomas Jefferson who said, 'Our laws and institutions must go hand in hand with the progress of the human mind.' Yet rapid advances in medical technology of this sort must not be allowed to displace the human touch of medicine. Albert Schweitzer said, 'Our technology must never exceed our humanity.' And we must not forget in these exhilarating days where so many unknowns become knowns, that the way we touch lives is one at a time. I tend to forget that sometimes. I get carried away with the excitement of the moment.
And it always helps me to go back to a day about ten years ago when I spent three weeks working in a missionary hospital in West Africa. If you have not been to the Third World, I strongly encourage you to do so. It will change your life.
I went there with my medical student daughter. And I had grand ideals about how in those three weeks, I was going to change the course of health care in Nigeria and those 93 million people who live there would never be the same because I had been there for my three weeks. And I got there working in this very crowded little hospital, surrounded by people with terrible illnesses. And I began to feel pretty discouraged. Because while I could help one or two of them, I knew they would go back out to the same environment. And the same conditions that caused them to be ill would still be there.
So, I was feeling pretty low about this and wondering, 'Why am I here?' And on rounds one morning, a young farmer who had been admitted almost dead the night before with fluid around his heart from tuberculosis that we were able to draw off and bring him back to at least temporary health. He stopped me and said, 'You know, you are different. I have the sense that you haven't been around here very much. And I have a sense that you are wondering why you are here at all.' I was a little taken aback. I didn't know it was quite that obvious. And he said, 'I want to tell you something. You came here for one reason. You came here for me.'
And that occurred to me that that is all it ever is about. To reach out to one person, to make a difference in one life, that is really what we are here for. So, have your grand dreams. Have your great plans for what your professional life will be, but don't forget that it is one person at a time where we really leave a legacy.
Decision number two: Well, this is the one that makes people squirm. What are you going to do about faith? Uh oh, not that one. But can there be any more important questions than these: How did we all get here? What is the meaning of life? How is it that we know deep-down inside what is right and wrong and yet rarely succeed in doing what is right for more than about thirty minutes? What happens to us after we die?
Surely these are among the most critical questions in life. And ones which a university should carefully consider. But how much time have you spent on them? Perhaps you, like I, grew up in a home where faith played a significant role, but you never made it your own. Or you concluded it was a fuzzy area that made you uncomfortable. Or even concluded that it was all superstition, like Mark Twain's schoolboy, who when requested to define faith said, 'It is believing what you know ain't so.' Or perhaps you simply assumed that as you grew in knowledge of science that faith was incompatible with a rigorous intellect and that God was irrelevant and obsolete. Well, I am here to tell you that this is not so.
All of those half-truths against the possibility of God have holes in them big enough to drive a truck through, as I learned by reading C.S. Lewis. In my view, there is no conflict between being a 'rigorous, show me the data' physician-scientist and a person who believes in a God who takes a personal interest in each one of us and whose domain is in the spiritual world. A domain not possible to explore by the tools and language and science, but with the heart, the mind and the soul.
Yet, it is remarkable how many of us fail to consider those questions of eternal significance until some personal crisis or advancing age forces us to face our own spiritual impoverishment. Don't make that mistake.
Decision number three: What are you going to do about love? Well, first love for another. Listen to Jefferson's words, 'Nature implanted in our breasts a love of others. A sense of duty to them. A moral instinct, in short, which prompts us irresistibly to feel and suffer their distresses. The creator would indeed have been a bungling artist had he intended man for a social animal without planting in him social dispositions.' Listen to those dispositions. Act on them, to all your brothers and sisters.
Sadly, prejudice still abounds in our society. Though genetics is teaching us that there is no scientific basis for drawing sharp boundaries around ethnic or racial groups, we still focus on physical differences of skin color, facial features, and hair texture. As if they meant something biologically profound. They do not. At the DNA level, we are all 99.9% the same. All of us.
And what of romantic love? That enduring, glowing fire! I don't agree with the wag who wrote, 'The trouble with loving is that pets don't last long enough and people last too long.' Yet our fast-paced and material world places romantic love at risk all too often. So, whether you have found your life's partner or still looking, make this a priority of the highest order.
So, these three decisions so far: work, faith and love. What of the fourth one? Well, maybe it doesn't quite belong on the same plane, but I think it is important too.
Decision number four: How will you keep fun in your life? Yes, fun. Seems to be resonant chord here this morning. Life is full of enough sobering and tragic moments, don't forget to exercise your sense of humor, you are going to need it. Listen to Winston Churchill, 'You cannot deal with the most serious things in the world unless you also understand the most amusing.'
Now, I admit, fun is a difficult subject to lecture on. So, with apologies to President Casteen for springing this on him, I would like to conclude with a tongue-in-cheek exhibit. A song actually about the university experience, adapted from a little noticed group from the 1980s, Bright Morning Star. The first two verses of this song are for you, the last is mine. Instrument please.
So, congratulations and Godspeed, Class of 2001. We'll send you off with a little music:I came, I bought the books, I stayed in the dorms, followed directions.
I worked, I studied hard, made lots of friends that had connections.
I crammed, they gave me grades, and may I say, not in a fair way.
But, I am a good Wahoo, I did it their way.
I learned so many things, although I know I'll never use them.
The courses that I took were all required. I didn't choose them.
You'll find that to survive, it is best to play the doctrinaire way.
And so, I knuckled down, and did it their way.
Well, yes there were times I wondered why
I had to cringe when I could fly
I had my doubts, but after all,
I clipped my wings and learned to crawl.
I learned to bend and in the end, I did it their way.
Now, this is my verse:
And now, my fine young friends,
Now that I am a full professor, where once I was oppressed,
I have become the cruel oppressor.
With me, I hope you will see the double he-lix
Is a highway and yes, you will learn it is best
To do it my way.
Well, wait, wait, wait...
Well, I am just a man, what can I do.
Open your books, read chapter two.
And if it seems a bit routine,
Don't talk to me, go see the Dean.
Just start today, dear UVA
And do it my way.
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