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“我的家庭从1911年就居住在Oregon西部的牧场,我进入大学是为了逃离我认为是枯燥无味的在牧场养家畜的生活。我的目标是在我期盼找工作的时候能有一个稳定的收入的工作,这样我就能够不做那些牧场运营和砍伐木头的工作,而这些工作是我在大学暑假一直做的工作。研究和教学看起来对我是不可能的,想也不敢想,我考上博士的工作,只是因为我想要的工作没有出现。
“在Michigan州的研究院,我发现了一个非常好的导师——John Kinney, 他是我学习遍历和信息论的老师。John给了我一个数论分支来作为我研究的博士论文题。我们在它成为一时流行的焦点前,我们研究了那些确定性函数迭代的统计特性。我开始用计算机来研究这些迭代,这使我的某些教授们感到困惑,他们认为我浪费了可以用来证明定理的时间。在研究生毕业之后,我在Iduho的规模很小的学校中找到了一个非研究类的工作,我在对函数迭代的工作导致了我能在暑假期间对Los Alamas国家实验室的访问。而后在1971年,我认识了Temple Smith, 开始进行生物学问题的研究。正如后来在我的新墨西哥短文中我写到的:
‘直到1974年夏天,我还是一个无知的数学家,从那时以后,我认识了Temple Ferris Smith, 在Los Alamas国家实验室与他在一个办公室工作了两个月。这个经历改变了我的研究方式,我的生活,甚至我的头脑。我们见面后不久,他拿出一个小黑板,开始给我讲生物学:什么是生物学?为什么它重要?将来它会怎样?有些地方也暗示了我们将要做什么,而事实上他也不知道那是什么。对这些,我非常困惑:氨基酸,核酸,β折叠......它们是什么?这里数学在哪?’
“我根本不知道现代生物学,但是研究联配和进化非常地吸引了我。最大的有趣之处是来构想问题。按照我的观点在我们这个学科中这一点仍然是最重要的:Temple和我化了几天甚至是几个星期来弄清我们要做的是什么。一个在刚开始的人类基因组计划中重要的生物学家Charles Delisi, 当时正在实验室的T10研究室(理论生物学),当他看到我们在联配问题中的进展,就来找我说有一个其它的题目可能使我感兴趣:RNA折叠问题,这个没有接触过的问题。Tinoco已经发表了一些用序列碱基配对矩阵的想法来处理这个问题。在1974年的秋天,我看到了联配和折叠问题之间很好的联系,在接下来的暑假里,我写了一个长的手稿来定义这个研究问题,确定了它们的一些性质,阐明了折叠的基本问题(包含了所有结构单元的自由能),最终给出了解决问题的算法。我以前也构想这是一个怎样的发现,而它是非常令人满意的。但是整个的过程象是探索而不是象我预期的那样是创造来的巨大成功。事实上,我总是想当一个探索者,很遗憾美国有边界;在这个新的RNA的地图上的漫游非常令人振奋,正是象我的想象一样,作为一个孩童通过白日梦的方式走出自己的家园,而到新的、未开垦的土地上的一次探险。”
原文:
Michael Waterman (born 1942 in Oregon)
currently holds an Endowed Associates Chair at the University of Southern
California. His BS in Mathematics is from Oregon State University, and his PhD
in Statistics and Probability is from Michigan State University. He was named a
Guggenheim Fellow in 1995 andwas elected to the NationalAcademy of Sciences in
2001. In 2002 he received a Gairdner Foundation Award. He is one of the
founding fathers of bioinformatics whose fundamental contributions to the area
go back to the 1970s when he worked at Los Alamos National Laboratories.
Waterman
says:
I went to
college to escape what I considered to be a dull and dreary existence of
raising livestock on pasture land in western Oregon where my family has lived
since 1911. My goal was to find an occupation with a steady income where I
could look forward to going to work; this eliminated ranching and logging
(which was how I spent my college summers). Research and teaching didn’t seem
possible or even desirable, but I went on for a PhD because such a job did not
appear.
In
graduate school at Michigan State I found a wonderful advisor in John Kinney
from whom I learned ergodic and information theory. John aimed me at a branch of number theory for a thesis. We
were doing statistical properties of the iteration of deterministic functions
long before that became a fad. I began using computers to explore iteration,
something which puzzled certain of my professors who felt I was wasting time I
could be spending proving theorems. After graduation and taking a nonresearch
job at a small school in Idaho, my work in iteration led to my first summer
visit to Los Alamos National labs.
Later I met Temple Smith there in 1973 and was drawn into problems from
biology. Later I wrote in my book of New Mexico essays Skiing the Sun (107):
I was an innocent
mathematician until the summer of 1974. It was then than I met Temple Ferris
Smith and for two months was cooped up with him in an office at Los Alamos
National Laboratories. That experience transformed my research, my life, and
perhaps my sanity. Soon after we met, he pulled out a little blackboard and
started lecturing me about biology: what it was, what was important, what was
going on. Somewhere in there by implication was what we should work on, but the
truth be told he didn’t know what that was either. I was totally confused:
amino acids, nucleosides, beta sheets. What were these things? Where was the mathematics?
I knew
no modern biology, but studying alignment and evolution was quite attractive to
me. The most fun was formulating problems, and in my opinion that remains the
most important aspect of our subject.
Temple and I spent days and weeks trying to puzzle out what we should be
working on. Charles DeLisi, a biophysicist who went on to play a key role in
jump-starting the Human Genome Project, was in T-10 (theoretical biology) at
the lab. When he saw the progress we had made on alignment problems, he came to
me and said there was another problem which should interest me. This was the
RNA folding problem which was almost untouched. Tinoco had published the idea
of making a base-pairmatrix for a sequence and that was it. By the fall of 1974
I had seen the neat connection between alignment and folding, and the following
summer I wrote a long manuscript that defined the objects of study, established
some of their properties, explicitly stated the basic problemof folding (which
included free energies for all structural components), and finally gave
algorithms for its solution. I had previously wondered what such a discovery
might feel like, and it was wonderfully satisfying. However it felt entirely
like exploration and not a grand triumph of creation as I had expected. In fact
I had always wanted to be an explorer and regretted the end of the American
frontier; wandering about this new RNA landscape was a great joy, just as I had
thought when I was a child trying to transport myself by daydreams out of my
family’s fields into some new and unsettled country.
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