Multiple ad hoc studies in computer assisted sequence research have been based on the assumption that the DNA genome is a text carrying many messages written in many languages. Although this linguistic analogy was originally meant to be just a metaphor, it was taken quite literally. An arbitrarily defined pattern in a nucleotide sequence has often been promoted to the rank of a "word" in an alleged "language" responsible for an alleged (but often unknown) "function." The sequence analysis papers published to date are full of "signals," "codes", "languages", "texts", "information" and similar names that do not refer to any precise concept or phenomenon. As a result, most of the scientific conclusions of the ad hoc period were based on speculation and inference from premature evidence. This unpleasant situation created a real need for computational biologists to carefully formulate the very foundations of their field. The Telluride workshops are planned as a systematic forum for the exchange of ideas and results pertinent to this effort. The 1991 workshop was entirely devoted to the general foundations of biolinguistics. While discussions on this theme will continue and it is expected that several of the collaborations from last summer will be completed during the1992 workshop, the main focus in 1992 will be the concepts of function and (functional) specificity.
The problem of defining function is based on an analogy between the living cell and a complicated machine. When we are faced with a part of the cell (for example a genome fragment) we can naturally ask what role this part plays in the alleged machine. The answer to such question very much depends on our representation of the alleged machine. Each element of the cell can be thought of as data to be processed by other elements, as software for processing other elements or as hardware that actually does processing of other elements. This shows us that the construction of a "correct" machine metaphor is essential for the definition of function. The primary focus of effort during the 1992 workshop will be aimed at the following topics concerning a correspondence between structure and function of genome fragments:
1) Segmenting a given genome region into putative functional domains according to a model of "fragment expression".
2) Measuring the degree of correspondence between putative functional domains and "textual" domains in a genome fragment (represented as a string of symbols).
3) Creating a database of correspondences between functional and
"textual" domains in the genomes from several species.
4) Creating a database of "genome expression" pathways.
The following, more general, topics will also be discussed:
5) Procedures for choosing the best metaphor based on the available knowledge of the system.
6) Methods of choosing the non-obvious elements of the system such that function could be defined.
7) Methods to determine potential functionality of the obvious elements of the system without defining the function.
Discussions between scientists representing opposite approaches to the above questions are planned. The most obvious "clash" can be expected between reductionist molecular biologists and developmental biologists. Such discussions are expected to be as constructive for both sides as they had proved to be during the 1991 workshop. It is expected that the 1992 workshop will shed some light on the definition of function at the molecular level. It is also expected that the discussions will lead to a consensus definition of functional domains in a genome.
Paticipants:
George Bell
Richard Blake
Jonathan Blake
Douglas Brutlag
John Mich Claverie
J.D. Dautricourt
James Fickett
Michael Gribskov
Martin Huyens
Dannielle Konnigs
Andrezj Konopka
Hugo Martinez
George Michaels
Steve Modena
Pavel Pevzner
Murry Smigel
Richard Stamm
Willy Taylor
John Wootton
Kathy Wu
TENTATIVE AGENDA OF THE WORKSHOP
Monday, July 20
10:15 - 10:30 ............... A.K.Konopka, Opening remarks (pg. 1)
10:30 - 11:00 ............... M. Gribskov (pg. 3)
11:00 - 12:30 .............. Discussion
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21:00 - 22:00 .................... General discussion
Tuesday, July 21
10:00 - 10:30 ............... A. Kolaskar (pg. 10)
10:30 - 12:00 ................ Discussion
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21:00 - 22:00 ..................... General discussion
Wednesday, July 22
10:00 - 10:30 ............... C. Wu (pg. 13)
10:30 - 12:00 ................ Discussion
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21:00 - 21:30 ................. J. Murtagh (pg. 21)
21:30 - 23:00 ................. Discussion
Thursday, July 23
10:00 - 10:30 ................. W. Taylor (pg. 23)
10:30 - 12:00 ................. Discussion
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21:00 - 22:30 ......................General discussion
Friday, July 24
10:00 - 10:30 ................. G. Bell (pg. 31)
10:30 - 12:00 ................. Discussion
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21:00 - 22:30 ..................... General discussion
Saturday, July 25
10:00 - 10:30 ................. A. Konopka (pg. 35)
10:30 - 12:00 ................. Discussion
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21:00 - 22:30 ..................... General discussion
Sunday, July 26
10:00 - 10:30 ................ M. Borodovsky (pg. 42)
10:30 - 12:00 ................ Discussion
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21:00 - 22:30 ..................... General discussion
Monday, July 27
10:00 - 10:30 ................. J-M. Claverie (pg. 46)
10:30 - 12:00 ................. Discussion
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21:00 - 22:30 ..................... General discussion
Tuesday, July 28
10:00 - 10:30 ................. R. Blake and J. Blake (pg. 48)
10:30 - 12:00 ................. Discussion
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21:00 - 21:30 ................. G. Michaels (pg. 59)
21:30 - 22:00 ................. Discussion
Wednesday, July 29
10:00 - 10:30 .................J-P. Dautricourt and R. Stamm (pg. 60)
10:30 - 12:00 ................ Discussion
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21:00 - 22:30 .................... General discussion
Thursday, July 30
10:00 - 10:30 ................ D. Brutlag (pg. 69)
10:30 - 12:00 ................ Discussion
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21:00 - 22:30 .................... General discussion
Friday, July 31
10:00 - 10:30 ................ J. Fickett (pg. 75)
10:30 - 12:00 ................ Discussion
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21:00 - 22:30 .................... General discussion
Saturday, August 1
10:00 - 10:30 ................ J. Wootton (pg. 77)
10:30 - 12:00 ................ Discussion
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20:30 - 21:00 ................ P. Salamon (pg. 82)
21:00 - 22:30 ................ Discussion
Sunday, August 2
10:00 - 11:30 .................... General discussion
Telluride School