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?
150 Free Textbooks: A Meta Collection Free textbooks (aka open textbooks) written by knowledgable scholars are a relatively new phenomenon. Below, find a meta list of 200 Free Textbooks, and check back often for new additions. Also see our online collection, 1,700 Free Online Courses from Top Universities. Art History A Textbook of the History of Painting by John Charles Van Dyke, Rutgers Biology Anatomy and Physiology – Edited by various profs at OpenStaxBiology – Edited by various profs at OpenStaxBiology Pages, John W. Business and Management Business Ethics by Jose A. Chemistry Chemistry, Grades 10-12, Created by the FHSST Project (Free High School Science Texts)Chemistry Virtual Textbooks by Stephen Lower, Simon Fraser UniversityCK-12 Chemistry (Grades 9-12) by multiple authors. Classics Computer Science & Information Systems Earth Science CK-12 Earth Science for Middle School by multiple authors.Earth Systems, an Earth Science Course (Grades 9-10). Economics & Finance Education Electrical Engineering Engineering History Languages
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.
Free Online Classes through Harvard's Open Learning Initiative At Harvard Extension School, free and open learning is hardly a new concept. In fact, the Extension School was founded with this mission in mind: to create an affordable way for any motivated student to take courses at Harvard. We stay true to this mission today, offering several free courses and nearly 800 for-credit courses at reasonable tuition rates. Explore our series of free or low-cost courses below. Video accessibility. Abstract Algebra In these free videotaped lectures, Professor Gross presents an array of algebraic concepts. The Ancient Greek Hero A long-time offering at Harvard College and Harvard Extension School, Gregory Nagy's popular exploration of the hero motif in classic literature is offered as a course for credit at Harvard Extension School, as a course on edX, and as a series of free video lectures. American Poetry from the Mayflower through Emerson Discover how the United States developed its own national literature with Elisa New, Powell M. Bits China Terms of Use
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 Stanford School of Engineering - Stanford Engineering Everywhere 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.
Cognitive Science - News - Optogenetics Karl Deisseroth uses a combination of green algae, blue lasers, gene therapy and fiber optics to map neural circuits deep inside the brain. The technique is called optogenetics. The technique begins with the placing of light-sensitive proteins from green algae inside specific types of brain cells. The cells can then be turned on or off with pulses of blue and yellow light. According to Deisseroth: "Optogenetics is the combination of genetics and optics to control well-defined events within specific cells of living tissue. It includes the discovery and insertion into cells of genes that confer light responsiveness; it also includes the associated technologies for delivering light deep into organisms as complex as freely moving mammals, for targeting light-sensitivity to cells of interest, and for assessing specific readouts, or effects, of this optical control." You can find a number of videos on the internet. Read more at: