Synbio 2007 From OpenWetWare General Info Spring 2007 Instructor: Jay Keasling (keasling@berkeley.edu) GSI: Jeffrey Dietrich (jadietrich@gmail.com) Logistics: Lecture/Discussion: 2 hours, 10-12 AM Friday Grading: Literature Review 30% Group Project 60% Class Participation 10% Office hours: contact Jeffrey Dietrich to arrange a meeting Announcements ASSIGNMENT (Due 2/16): email Jeff with your three top choices for topics to lead in literature review group discussion. Tentative Schedule 1/19 Introduction, Basis for Synthetic Biology - Jay Keasling 1/26 Modeling and Design of Synthetic Systems - Adam Arkin Genetic models, stochastic and continuous simulations, adaption of circuit methods to SB. 2/2 Drugs from Bugs-Jay Keasling 2/9 Design of Tumor-Killing Bacteria - J. Literature Review Assignment Every student will be required to lead one class discussion over selected readings/topics assigned for that week. Group Project Ideas Group projects from 2007 (Presentations and References) a. b. c. d. Policy Approach
An Ecological Approach to Cognitive Science{1} John T. Sanders Polish Academy of Sciences [1] Cognitive science is ready for a major reconceptualization.(1) This is not at all because efforts by its practitioners have failed, but rather because so much progress has been made. [2] These bonds are extremely hard to break. [3] The straightjacket I am thinking about, of course, is the vague picture of the human situation that imagines centralized, internal minds in control of bodily machines. [4] In what follows, I shall try to offer an approach which on the one hand capitalizes on the excellent progress that has been made in cognitive science in the last few decades, and which on the other hand offers a general approach that may help at some level in the attempt to shake "Cartesian" bonds. The Ecological Approach [5] The "ecological approach" to this-and-that follows a pattern that was probably first recommended for evolutionary biology. [6] The perceptual psychologist J. Materialism Why, Then? [25] What is that sense?
Free ebooks - Download 20,000 free ebooks at the eBook Directory. Laboratory Fundamentals of Synthetic Biology From OpenWetWare Syllabus Class Format The Class will meet twice a week, one 2 hour classroom session, and one 3 hour lab session. Problem sets will be assigned weekly for the first eight weeks. A midterm exam will cover the classroom material and the first several weeks of lab instruction. Grades The final grade will be as follows: 20% Problem Sets 30% Midterm Exam 20% Lab Evaluations 30% Final Project Schedule Introduction - Synthetic Biology: History, current applications and future directions Powerpoint (w/content from Drew Endy) Assignments: Endy Article and Comic Strip The Biology (4 sessions) Cells, DNA, RNA and Protein DNA - information encoding, structure, sequencing and synthesis RNA - encoding, structure, function (RNA Enzymes, RNA Aptamers) Proteins - Crystallography, functions, scaffolds Introductory packet about DNA, RNA, Protein. Create a biobrick out of a sequence (force them to re-optimize a coding region into e. coli and remove a biobrick incompatibility). Reading List
Cognitive Science: The Effects of Writing on Language, Mind and Consciousness - John Searle The following interview with Dr. John Searle was conducted at his office on the campus of U.C. Berkeley in California. The following transcript has not been edited for journal or magazine publication (see 'Interview Notes' for more details). Bold is used to emphasize our [Children of the Code] sense of the importance of what is being said and does not necessarily reflect gestures or tones of emphasis that occurred during the interview. David Boulton: We want to talk about writing and its effect on civilization, its effect on consciousness, and then go where language, intelligence and writing meet. Human Spoken Language: Dr. Animals can signal danger or sexual desire or a few things like that, but they cannot get this articulated form of precise representation that we get in human languages. Human languages have also involved this remarkable ability of commitment; humans commit themselves to doing something when they make a promise. Written Language: Dr. Dr. Dr. David Boulton: Excellent.
Fallacies Dr. Michael C. Labossiere, the author of a Macintosh tutorial named Fallacy Tutorial Pro 3.0, has kindly agreed to allow the text of his work to appear on the Nizkor site, as a Nizkor Feature. It remains © Copyright 1995 Michael C. Other sites that list and explain fallacies include: Constructing a Logical Argument Description of Fallacies In order to understand what a fallacy is, one must understand what an argument is. There are two main types of arguments: deductive and inductive. A fallacy is, very generally, an error in reasoning.
Introduction to Neural Networks CS-449: Neural Networks Fall 99 Instructor: Genevieve Orr Willamette University Lecture Notes prepared by Genevieve Orr, Nici Schraudolph, and Fred Cummins [Content][Links] Course content Summary Our goal is to introduce students to a powerful class of model, the Neural Network. We then introduce one kind of network in detail: the feedforward network trained by backpropagation of error. Lecture 1: Introduction Lecture 2: Classification Lecture 3: Optimizing Linear Networks Lecture 4: The Backprop Toolbox Lecture 5: Unsupervised Learning Lecture 6: Reinforcement Learning Lecture 7: Advanced Topics [Top] Review for Midterm: Links Tutorials: The Nervous System - a very nice introduction, many pictures Neural Java - a neural network tutorial with Java applets Web Sim - A Java neural network simulator. a book chapter describing the Backpropagation Algorithm (Postscript) A short set of pages showing how a simple backprop net learns to recognize the digits 0-9, with C code Reinforcement Learning - A Tutorial
CogSpace - Collective Mind Map of Cognition and Consciousness Research Intro to debate The Mystery Behind Anesthesia Going under: Emery Brown’s quest to understand how anesthesia affects the brain could provide crucial clues about what goes wrong in certain disorders. A video screen shows a man in his late 60s lying awake on an operating table. Just outside the camera’s view, a doctor is moving his finger in front of the man’s face, instructing him to follow it back and forth with his eyes. As an anesthesiologist at Massachusetts General Hospital (MGH), Brown is constant witness to one of the most profound and mysterious feats of modern medicine. But though doctors have been putting people under for more than 150 years, what happens in the brain during general anesthesia is a mystery. Brown, who is also a neuroscientist and professor at MIT, aims to transform anesthesia from a solely clinical tool into a powerful instrument for studying the most basic questions about the brain. Brown, however, has a different perspective from most anesthesiologists; he’s also a statistician.
Supplementing Textbooks with Student Constructed Knowledge Bases Originally posted on iPads in Education Ning network site Authored by Sam Gliksman, Twitter: @samgliksman We’re just a few weeks removed from a major Apple announcement regarding the release of a new eTextbooks initiative. I’m keenly aware of the significance of the move to eBooks, especially as I have a 13 year old that carries 20 pounds in his backpack to school every day. However important the move from paper to digital textbooks, I’m still left with a taste for more. I have been critical of the ways most schools still rely on text as the primary, almost solitary, medium for exchanging information. The “real world” trades information using an amalgam of different media that includes video, audio, images … and text. iBooks could have included aspects of social reading so “friends” could exchange questions and notes right within the pages of the book. Instead we could prioritize “content construction”. Organizing Content Social Bookmarking